2020 RESOURCE GUIDE - Lab Manager€¦ · three emerging diagnostic tools in microbiology on page...

2020 | Resource Guide

2020RESOURCE GUIDE

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4 Clinical Lab Manager 2020 Resource Guide ClinicalLabManager.com

ClinicalLabManager.com

CONTENTS 06 16

20

25

34

FEATURES

survey06 Cost Reduction Is Key

Erica Tennenhouse, PhD

08 Biobanking: Current State and Fu-ture Prospects Julia Jenkins, PhD

10 How to Detect Tampered Drug Tests Raeesa Gupte, PhD

16 The Latest Tools for Proteogenomics Nimita Limaye, PhD

20 Detecting Rare Cell Events: Flow Cytometry Versus Microscopy Raeesa Gupte, PhD

25 How Informatics Can Improve Health Care Shalaka Samant, PhD

28 Experiences in Clinical Lab Automation Laura M. Bolt, PhD

34 Trends in Clinical Microbiology Diagnostic Methods Michelle Dotzert, PhD

36 Trends in Point-of-Care Testing Neeta Ratanghayra, M.Pharm

40 How Whole Slide Imaging Is Changing the Role of the Pathologist Catherine Crawford-Brown

infographic 50 Endometriosis: The Invisible Illness

Michelle Dotzert, PhD

CATEGORIES

08 Biobanking10 Clinical Chemistry 16 Genomics & Proteomics20 Imaging 25 Informatics28 Laboratory Automation34 Microbiology36 Molecular Diagnostics40 Pathology46 Services48 Supplies & Consumables

2020 Resource Guide

52020 Resource Guide Clinical Lab Manager

editor’s note

In the issue, we take a break from our regular format, but our mis-sion remains the same: to help leaders of clinical laboratories become better managers.

One key aspect of being a top manager is keeping on top of the trends, technologies, and tools in one’s field. That’s exactly where our 2020 Resource Guide can help. We’ve broken this issue into sec-tions based on the clinical fields

in which our readers work. Each of these sections contains insightful editorial that is required reading for any clinical laboratory leader.

We also wanted to learn more about how our readers make purchasing decisions for their labs, so we surveyed 100 clinical laboratory leaders. The results, which can be found on page 6 of this issue, point to price as the most critical factor influencing purchasing decisions. Given the financial challenges that clinical laboratories face these days—low reimbursement rates and increasing competition—it’s no surprise that price figures so prominently in the minds of our readers.

When it comes to trying to save money in the lab, knowledge is power. Once again, the resource guide can help. To find out how other clinical laboratory leaders are saving money, turn to page 28 to read about how one laboratory leader’s efforts to automate previously manual laboratory processes at the University of Ala-bama Birmingham’s medical center have paid off with increased efficiency and reduced labor costs.

Another key to cutting costs is becoming more knowledgeable about what tools you do and don’t need for your lab. Explore the pros and cons of fluorescence microscopy and flow cytometry for rare cell imaging on page 20. Compare the advantages and limitations of three emerging diagnostic tools in microbiology on page 34.

The resource guide discusses plenty of other key trends for clinical laboratory leaders to follow. For example, learn about how whole-slide imaging is changing the face of histopathology (page 40), what tools are available to detect adulterated drug test samples (page 10), and how biobanking is evolving to meet the growing needs of the clinical lab (page 8). On the research side, read about how proteogenomics is helping scientists interpret genotype-phenotype correlations (page 16).

Our hope with this issue is that our readers will head into next year feeling informed and optimistic about the future of their labs.

Here’s to a successful 2020.

Erica Tennenhouse, PhD, Managing Editor

looking ahead managing editor Erica Tennenhouse, PhD [email protected]

editorial director Trevor Henderson, PhD [email protected]

managing editor, Lab Manager Lauren Everett [email protected]

associate editor, Lab Manager Rachel Muenz [email protected]

art director Danielle Gibbons [email protected]

contributors Julia Jenkins, PhD Raeesa Gupte, PhD Nimita Limaye, PhD Laura M. Bolt, PhD Shalaka Samant, PhD Neeta Ratanghayra, M.Pharm

business coordinator Andrea Cole [email protected]

eMarketing coordinator Laura Quevedo [email protected]

scientific technical editor Michelle Dotzert, PhD [email protected]

editor, laboratory design MaryBeth DiDonna [email protected]

digital media coordinator Catherine Crawford-Brown [email protected]

audience development specialist Matthew Gale [email protected]

publisher / sales Edward Neeb [email protected] 203.448.0728

Published by LabX Media Group president Bob Kafato [email protected]

managing partner Mario Di Ubaldi [email protected]

general manager Ken Piech [email protected]

production manager Greg Brewer [email protected]

custom article reprints The YGS Group [email protected] 800.290.5460 717.505.9701 x100

subscription customer service [email protected]

478 Bay Street, Suite A213 Midland, Ontario, Canada, L4R 1K9 888.781.0328

Erica Tennenhouse

Cost Reduction Is KeyPURCHASING TRENDS SURVEY FINDS PRICE MATTERS MOST TO CLINICAL LABORATORY LEADERS by Erica Tennenhouse, PhD

C linical Lab Manager recently surveyed over 100 leaders of clinical laboratories to learn about how they purchase equipment and supplies.

Nearly 80 percent of the respondents identified them-selves as the laboratory manager, director, or supervisor.

While only around 15 percent of labs noted that they are planning to increase their budgets for products and services next year, just 10 percent are decreasing their bud-gets. Indeed, the majority of labs surveyed are planning to maintain the status quo in terms of budget into 2020.

Cost reduction in the laboratory remains a significant concern for all respondents. It is therefore unsurprising that the top feature that influences the purchase of new products and services is price. The importance of cost savings may explain why 32 percent of clinical labs either currently purchase or are considering purchasing pre-owned equipment.

Among those clinical labs that are planning to pur-chase new equipment in the next year, some of the most common reasons include an expiring contract or lease agreement, an increase in test volume or an expanded test menu, the need to replace aging equipment, the availability of a new product, and starting a new project.

survey


The top five features that influence respondents’ main considerations when making decisions on purchasing products and services:

Price/value of vendor’s products 84%

After-sale support, maintenance, and warranty 78%

Long-term efficiency and operating costs 77%

Compatibility of vendor’s products with current systems 73%

Vendor reputation and brand awareness 69%

Yes 32%

No 52%

Don't know 16%

survey

The lab manager or lab leader makes a request/proposal. 73%

A lab member identifies a problem or opportunity. 43%

A department makes a request/proposal. 33%

Corporate or administrative management makes a request/proposal. 24%

An individual outside the team (e.g., IT, facilities team, purchasing agent) makes a request/proposal. 10%

Strongly agree

Somewhat agree Disagree

Our laboratory is among the most innovative compared to other labs of the same type.

31% 52% 17%

Our lab prefers to source products from as few brands or manufacturers as possible.

26% 55% 19%

We tend to find products that best serve our needs regardless of brand.

49% 43% 7%

Cost reduction is a significant concern when purchasing products for our lab.

59% 41% 0%

Our lab is among the first to adopt new technologies. 25% 48% 26%

Our lab is in expansion or growth mode. 33% 41% 27%

Respondents were asked if their labs currently purchase or are considering purchasing pre-owned equipment:

Major reasons for respondents purchasing new equipment in the next year include: • Expiring contract or lease agreement • Increased test volume and/or expanded test menu• Replacement of aging equipment• Availability of a new product • Start of new projects

Erica Tennenhouse, PhD, is the managing editor of Clinical Lab Manager.

Concerning laboratory operations, here’s what respondents had to say:

Here’s how respondents say new technology purchases in their labs are initiated:

370+520+9 260+390+110340+550+8 230+460+8 330+470+130 250+440+8 290+480+8 250+600+8 260+550+9 130+560+14 310+560+7Consumable

productsNew lab Education Funding for new

research projectsHiring staff Investing in existing

research projectsInvesting in lab

technologyStaff compensation

/benefitsModernizing existing

lab facilityOutsourcing

servicesRaw

materials

60%

50%

40%

30%

20%

10%

0%

Increase / Stay the same / DecreaseLab Budget Changes Over the Next Year

Over the next year, respondents’ laboratory budgets are changing in the following ways:


T he advent of large-scale, high-throughput technologies has transformed medical research by ushering in “omic” science

(e.g., genomics, transcriptomics, proteomics, metabolomics). Information technology has evolved in parallel, leading to the curation of large electronic databases that store big data. The availability of extensive collections of well-annotated patient samples and clinical information is fundamental to the success of personalized medicine and biomarker discovery. Modern biobanks are expanding their scope and size to support innovations that will advance our understanding of health and disease.

Types of biobanksBiobanks are repositories that receive,

document, process, and store biomedical specimens for research. Historically, these specimens were limited to genetic material, cells, fresh and paraffin-embedded tissue, and fluids such as blood, saliva, and urine. Re-cently, biobanks have expanded their scope to include digital holdings, such as MRI scans.

Biobanks have many different forms. The most common types collect disease-specific specimens used for clinical trials or basic research. These are

typically collected by research units at universi-ties and teaching hospitals. Disease-oriented biobanks may focus on a single tissue type, for example, brain, or multiple tissue types, such as breast, liver, pancreatic, and colon specimens held in a cancer biobank. Population-based biobanks are designed to link biomarkers with medical his-tory and lifestyle information and hold multiple specimen types such as blood or isolated DNA.

Sample acquisition, handling, storage, and labeling

The acquisition of a biobank specimen must start with informed consent. Ideally, the consent is wide and enduring enough to allow the sample to be used in multiple studies with different aims throughout its lifetime.

Care must be taken to handle the sample appro-priately, and rapid harvesting is needed for friable analytes such as RNA. Samples may need to be tak-en in sterile conditions or placed into relevant me-dia or stabilizing solutions, depending on end use. To ensure sample integrity, shipping and transport should be under controlled and monitored condi-tions (e.g., maximum transport time, maximum and minimum temperature monitoring) and the chain of custody documented. Upon receipt, the sample

Biobanking: Current State and Future ProspectsTHE FUTURE OF BIOBANKING IS INTIMATELY TIED TO THE NEW AND RAPIDLY EXPANDING ERA OF PERSONALIZED MEDICINE by Julia Jenkins, PhD

Bio

bank

ing


biobanking

should be anonymized and assigned a unique identifier.One component of a proper identification system is

labeling. One of the pressing problems with storing and retrieving biological samples at low temperatures is the difficulty of reliably reading the unique identifier that links each storage tube with the database containing sample details. Advancements in technology have provid-ed numerous solutions, including bar codes that may be one- or two-dimensional or laser-etched, radio-frequency identification (RFID) labeling,1 and light-activated micro-transponders, known as p-Chips, which may be especially useful for smaller tubes.2 The capability to rapidly access specimens in cold storage is paramount to prevent thaw-ing; therefore, it is crucial that the identification system selected is compatible with the IT system used.

Consideration must also be given to container selec-tion (e.g., certain types of polypropylene tubes may de-crease protein yield following extraction).3 Preparation of samples should be optimized when possible to the end use of the samples, and multiple aliquots should be prepared to limit freeze-thawing cycles. Robotic pipet-ting may be used to standardize sample preparation.

Good laboratory practiceGood laboratory practice, which includes training, docu-

mentation, and SOPs, is crucial to ensuring the success of a biobank and will ensure that the concept of zero sample loss is upheld, which is paramount because any compromise

would deprive the community of a valuable specimen.Biobanks have rich data sets derived from a large num-

ber of participants. The biobanks provide critical informa-tion and a framework that supports research. The number and diversity of available specimens and images will continue to drive future medical research and discovery.

References1. Paskal, Wiktor, et al. "Aspects of modern biobank activity–compre-

hensive review." Pathology & Oncology Research 24.4 (2018): 771-785.

2. Mandecki, Wlodek, et al. "Tagging of test tubes with electronic p-Chips for use in biorepositories." Biopreservation and Biobank-ing 15.4 (2017): 293-304.

3. Kofanova, Olga A., Kathleen Mommaerts, and Fay Betsou. "Tube polypropylene: a neglected critical parameter for protein adsorption during biospecimen storage." Biopreservation and biobanking 13.4 (2015): 296-298.

Dr. Jenkins is a biochemist with special expertise in wound heal-ing, muscle regeneration, vascular biology, and gene transfer tech-niques. Her PhD research focused on viral gene transfer methods, and she spent eight years working as senior postdoctoral research fellow at King’s British Heart Foundation Centre of Excellence. At the University of Singapore, she collaborated with bio-engineers to model mechanical damage, using bio-artificial muscle in a novel lab-on-chip device. Dr. Jenkins has published 42 papers in peer-reviewed journals and has co-authored several scientific book chapters. She now works as a specialist technical writer.

DIRECTORY OF MANUFACTURERS

SAMPLE COLLECTION

Brooks Life Sciences www.brookslifesciences.com

Cardinal Health www.cardinalhealth.com

Centogene www.centogene.com

GenTegra www.gentegra.com

Greiner Bio-One www.gbo.com

Heathrow Scientific www.heathrowscientific.com

Helmer Scientific www.helmerinc.com

Indivumed www.indivumed.com

ProMedDx www.promeddx.com

Thermo Fisher Scientific www.thermofisher.com

SAMPLE PREP






SAMPLE TRANSPORT / STORAGE

Abbott www.abbottdiagnostics.com

Agilent www.agilent.com

Angelantoni www.angelantoni.it

Archiva BioLogistics www.archivabio.com

Autoscribe www.autoscribeinformatics.com


Bruker www.bruker.com

Cryopal www.cryopal.com

DNA Genotek www.dnagenotek.com

GenTegra www.gentegra.com

Hamilton www.hamiltoncompany.com



LiCONiC US www.liconic.com



TTP LabTech www.ttplabtech.com


The Drug-Free Workplace Act, passed in the US in 1988, prohibits federal employees, contractors, and grantees as well as those

in federally regulated industries or safety- and security-related industries from possessing or using controlled substances. Although not mandated, several private employers have also adopted a drug-free workplace policy. Outside of the workplace, drug testing is regularly em-ployed in health care, sports, and forensics.

People cheat on drug tests for a variety of reasons—to retain their jobs, keep their medals, avoid going to prison, and maintain their spotless reputations. In fact, cheating on drug tests has essentially become an industry in its own right.

Types of drug testsDrug tests commonly follow a two-step process.

First, immunoassays provide a qualitative “yes” or “no” answer to whether the drugs being tested for are present in the biological sample. Immunoas-says use antibodies to detect the presence of spe-cific drugs and/or their metabolites. If drug con-centrations in the sample are below the designated threshold value, it indicates a negative result. If the initial screen yields a positive result, samples are processed for further confirmation and quan-tification. In the second confirmatory step, gas

chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), or LC tandem mass spectrometry (LC-MS/MS) is performed on the samples. These tech-niques separate the compounds in the samples, which are then identified based on their unique molecular fingerprints and quantified.

Drug testing can be performed on several types of biological samples, each with their own pros and cons.

How long do drugs stay in the body?

Workplace drug testing is based on the Substance Abuse and Mental Health Services Administration’s five-panel immunoassay, commonly referred to as SAMHSA-5. This panel traditionally tests five categories of drugs: amphetamines, marijuana, cocaine, opi-ates, and phencyclidine (PCP).

Most commercially available drug screens also test for alcohol, barbiturates, benzodiaze-pines, MDMA (ecstasy), and synthetic opioids (oxycodone, hydrocodone, buprenorphine, and methadone) in addition to the SAMH-SA-5 panel. Table 1 shows the average dura-tion over which these drugs can be detected in various biological matrices.2

How to Detect Tampered Drug TestsAS DRUG TEST ADULTERATION BECOMES MORE SOPHISTICATED, SO DO DETECTION METHODS by Raeesa Gupte, PhD

Clin

ical

Che

mis

try


clinical chemistry

Ways to beat a drug testOwing to privacy concerns, urine collection is often

performed unobserved. Therefore, urine samples are most amenable to manipulation in the following ways:3

1. SubstitutionTo avoid a positive result, test takers substitute a

synthetic urine or drug-free urine from another person or from an animal.

2. DilutionDilution of urine samples takes many forms. Water

or other liquids may be added to the collected sample to dilute it. Alternatively, test takers may drink lots of water or consume products marketed as “detox” drinks, which claim to rid the body of drugs, anywhere from a few hours to a few days prior to sample collection. The mechanisms of action of these products are often

unknown but likely involve dilution of urine in order to lower the concentration of drug(s) below detection lim-its.4 The side effects may vary from changing urine color to causing intestinal issues and nausea. Some so-called detoxifiers also claim to render a negative result on hair tests following varying periods of abstinence.

3. AdulterationIn vitro adulteration involves addition of substances to

urine after sample collection that will interfere with the test results. A slew of adulterants, including household substances (vinegar, detergent, bleach, iodine, isopropyl alcohol, and eye drops), food items (lemon juice and soda), and commercially available chemicals (nitrite, glutaraldehyde, and pyridinium chlorochromate), are regularly used to cheat a drug test. These substances may interfere with the detection of some but not all drugs on the test panel. For instance, pyridinium chlorochromate (PCC) may reduce detection of morphine and marijua-na5 but increase sensitivity to amphetamines without af-fecting the detection of PCP. Depending on the concen-tration used, glutaraldehyde may produce false-negative results for marijuana, amphetamine, methadone, ben-zodiazepine, and cocaine metabolites.6 The mechanism by which adulterants produce false-negative results may

“Cheating on drug tests has essentially become an industry in its own right.”

SUBSTANCE URINE HAIR SALIVA/ORAL FLUID BLOOD SWEAT

Alcohol 10-12 hours Up to 90 days Up to 24 hours Up to 6 hours N/A

Amphetamines 2-4 days Up to 90 days 1-48 hours Up to 48 hours 7-14 days

Methamphetamine 2-5 days Up to 90 days 1-48 hours Up to 48 hours 7-14 days

Barbiturates Up to 7 days Up to 90 days N/A Up to 48 hours N/A

Benzodiazepines Up to 7 days Up to 90 days N/A Varies N/A

Marijuana 1-30 days Up to 90 days Up to 24 hours Up to 36 hours 7-14 days

Cocaine 1-3 days Up to 90 days 1-36 hours Up to 48 hours 7-14 days

Codeine 2-4 days Up to 90 days 1-36 hours N/A 7-14 days

Morphine 2-5 days Up to 90 days 1-36 hours Up to 20 hours 7-14 days

Heroin 2-3 days Up to 90 days 1-36 hours Up to 20 hours 7-14 days

Oxycodone 2-4 days N/A N/A N/A N/A

Hydromorphone 2-4 days N/A N/A N/A N/A

Methadone 3 days N/A N/A N/A N/A

Propoxyphene 6-48 hours N/A N/A N/A N/A

Phencyclidine (PCP) 5-6 days Up to 90 days N/A Up to 24 hours 7-14 days

MDMA (ecstasy) Up to 48 hours N/A Up to 24 hours Up to 24 hours N/A

Table 1. Average durations over which different drugs can be detected in various biological matrices

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EMDMillipore.com/biomedical

The life science business of Merck KGaA, Darmstadt, Germany operates as MilliporeSigma in the U.S. and Canada.

© 2019 Merck KGaA, Darmstadt, Germany and/or its affi liates. All Rights Reserved. MilliporeSigma, the vibrant M, Milli-Q, Elix and E.R.A. are trademarks of Merck KGaA, Darmstadt, Germany or its affi liates. All other trademarks are the property of their respective owners. Detailed information on trademarks is available via publicly accessible resources.

2019-23207-Milli-Q_CLX_7000_Milli-Q_Connect_Print_AD_MSIG.indd 1 6/13/19 3:14 PM

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clinical chemistry

vary. Nitrites, peroxides, and chromates may hamper the detection of drugs and their metabolites by oxidizing them, for example, whereas glutaraldehyde may interfere with the enzymes used in certain assays.

How to detect a tampered drug test

1. Physicochemical characteristicsChanges in the appearance and odor are usually the

first indications of sample manipulation. Dilution of urine by drinking excessive water may produce a clear, almost water-like appearance. In contrast, urine detoxi-fiers may produce unnaturally colored urine. However, some detoxifiers contain niacin that imparts a natural yellow color and is not flagged as an adulterant. Adulter-ation with vinegar, bleach, or alcohol can be detected by the distinctive odors they produce. Turbidity or exces-sive frothing indicates addition of detergents. Because human urine has several known physiochemical values—temperature between 32 degrees Celsius and 38 degrees Celsius (when freshly collected), specific gravity between 1.002 and 1.02, creatinine concentrations above 20 mg/dL, and pH of 4.5-9—deviations from these ranges are indicative of dilution or substitution.

2. Spot testing for adulterantsSeveral colorimetric reactions can be used to detect the

presence of specific adulterants such as nitrite, PCC, and glutaraldehyde. For instance, hydrogen peroxide turns urine adulterated with PCC brown, and potassium per-manganate added to urine adulterated with nitrite turns from pink to colorless upon addition of hydrochloric acid.

3. Adulteration test stripsSeveral on-site adulteration detection strips and

devices are commercially available. Certain urinalysis tests contain individual strips that can detect pH, creati-nine, glutaraldehyde, nitrites, PCC, and other oxidants.

The changing landscape of drug test cheating

Positive results on workplace drug testing continue to rise in certain sectors such as transportation and construc-tion. The widening chasm between legalization of marijua-na in several states and federal drug-free workplace policies may further spur cheating on drug tests. As the sale of drug-free urine is being banned in some states, and several states have pending legislation that would ban the use and sale of synthetic urine, ways to obfuscate drug tests get ever more creative (e.g., powdered urine kits and home remedies such as washing hair three to four times a day with vinegar and salicylic acid). As such, detection methods ultimately end up playing catch-up with the deviousness of drug test cheats.

References1. Boscolo-Berto, Rafael, et al. “Sensitivity and specificity of

EtG in hair as a marker of chronic excessive drinking: pooled analysis of raw data and meta-analysis of diagnostic accuracy studies.” Therapeutic Drug Monitoring 36.5 (2014): 560-575.

2. Hadland, Scott E., and Sharon Levy. “Objective testing: urine and other drug tests.” Child and Adolescent Psychiatric Clinics 25.3 (2016): 549-565.

3. Jaffee, William B., et al. “Is this urine really negative? A system-atic review of tampering methods in urine drug screening and testing.” Journal of Substance Abuse Treatment 33.1 (2007): 33-42.

4. Cone, Edward J., Robert Lange, and William D. Darwin. “In vivo adulteration: excess fluid ingestion causes false-negative marijuana and cocaine urine test results.” Journal of Analytical Toxicology 22.6 (1998): 460-473.

5. Wu, Alan HB, et al. “Adulteration of urine by ‘Urine Luck.’” Clinical Chemistry 45.7 (1999): 1051-1057.

6. George, S., and R. A. Braithwaite. “The effect of glutaraldehyde adulteration of urine specimens on Syva EMIT II drugs-of-abuse assays.” Journal of Analytical Toxicology 20.3 (1996): 195-196.

Raeesa Gupte, PhD, is a freelance science writer and editor specializing in evidence-based medicine, neurological disorders, and translational diagnostics.


clinical chemistry


CHEMISTRY ANALYZERS


Beckman Coulter www.beckmancoulter.com

DRG International www.drg-international.com

EKF Diagnostics www.ekfdiagnostics.com

ELITechGroup www.elitechgroup.com

HORIBA www.horiba.com/medical

Mindray www.mindray.com

Randox Laboratories www.randox.com

Roche Dignostics www.diagnostics.roche.com

Siemens Healthineers www.siemens-healthineers.com


COAGULATION



Diagnostica Stago www.stago-us.com

Diapharma www.diapharma.com




Helena Laboratories www.helena.com


Instrumentation Laboratory www.instrumentationlaboratory.com

MilliporeSigma www.sigmaaldrich.com



Sarstedt www.sarstedt.com



DRUG MONITORING



Bio-Rad Laboratories www.bio-rad.com

Eagle Biosciences www.eaglebio.com




Streck www.streck.com


HEMATOLOGY


ALCOR Scientific www.alcorscientific.com


bioMérieux www.biomerieux-usa.com

Cellavision www.cellavision.com

Corning www.corning.com

Drucker Diagnostics www.druckerdiagnostics.com

DWK Life Sciences www.dwk.com



Globe Scientific www.globescientific.com

Hacker Instruments & Industries www.hackerinstruments.com

Hardy Diagnostics www.hardydiagnostics.com


Leica Biosystems www.leicabiosystems.com


Mindray www.mindray.com

Modulus Data Systems www.modulusdatasystems.com

ORFLO www.orflo.com

Polymedco www.polymedco.com




Sysmex America www.sysmex.com/us


Ward's Science www.wardsci.com

TOXICOLOGY



Diapharma www.diapharma.com




URINALYSIS











Precision medicine is defined by the Preci-sion Medicine Initiative—a nationwide initiative launched by President Barack

Obama in 2015—as “an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person.”1

To be able to drill down to the fine level of precision that precision medicine de-mands, it’s helpful to step back and see the bigger picture. Proteogenomics can provide a systems perspective that can help scientists interpret genotypic-phenotypic correlations. This type of integrated, holistic view—span-ning genome sequences, RNA transcription, protein synthesis, and post-translational modifications—has helped answer ques-tions like why only 30 percent of changes in mRNA translate into corresponding changes in protein structure.

Proteogenomics provides a holistic ap-proach to help scientists envision what may be happening within the human body. Not only does proteogenomics help in the prevention, diagnosis, and treatment of disease, but it can also be leveraged to identify biomarkers to

understand disease mechanisms, support drug discovery, and enable patient stratification for precision medicine.

High-sensitivity, high-performance liquid chromatography tandem-mass spectrometry is the method of choice for protein identification in proteogenomics, as it allows for faster and easier analysis of a larger number of analytes than the more conventional gas chromatogra-phy mass spectrometry.2 Alternatively, matrix-assisted laser desorption ionization (MALDI-MS), involving the use of a laser beam that vaporizes and ionizes the sample, can be used to identify proteins. MALDI-MS is a bottoms-up approach for protein identification that uses peptide-map fingerprinting and is used mainly in the identification of microbes. Signature peptides of potential protein biomarkers can be identified using multiple reaction monitor-ing or selected reaction monitoring.

While MS is a powerful tool used in prote-ogenomics for the relative quantification of changes in a cell’s protein content, a tar-geted proteomics approach, using synthetic proteotypic peptides (PTPs), can enable the quantification of selected proteins of

The Latest Tools for Proteogenomics HOW MASS SPECTROMETRY, NEXT-GENERATION SEQUENCING, AND BIOINFORMATICS TOOLS ARE REVOLUTIONIZING PERSONALIZED MEDICINE by Nimita Limaye, PhD

Gen

omic

s & P

rote

omic

s

http://www.aircleansystems.com


genomics & proteomics

interest. Targeted proteomics can also provide quanti-tative information to support the specific and sensitive simulation of biochemical systemic perturbation. PTPs mimic peptides produced by the proteolytic cleavage of target analyte proteins. Deep learning algorithms have been developed for peptide detectability prediction. These algorithms can interrogate deep neural networks that have learned from vast protein databases and use tools such as SVMLight, RankNet, or LambdaMART to solve peptide ranking problems.3 This methodology is complemented by next-generation sequencing (NGS), or massively parallel sequencing (MPS), which enables the sequencing of millions of fragments of DNA per run.

Proteogenomics establishes the correlation between mRNA and protein pairs in samples, showing mutations, post-translational modifications, and signaling path-ways. The analysis of a direct association between these markers of genetic variation and gene expression levels, typically measured in tens or hundreds of individuals, can be performed using techniques such as expression quantitative trait loci (eQTL) analysis, microRNAs (miRNAs), and copy number aberrations.4 eQTLs are genomic loci that explain all or a fraction of variation in expression levels of mRNAs. miRNAs are small, non-coding RNA molecules found in plants, animals, and some viruses. The miRNAs pair with complementary sequences within mRNA molecules to affect their action and silence gene expression. Single nucleotide poly-morphisms (SNPs) and translocations in DNA can be identified using NGS. These SNPs can be translated into proteoforms and added to vast protein databases, which can be used to interpret MS data. Similarly, RNA-seq, which uses high-precision, deep-sequencing technol-ogy to convert RNA to cDNA and then amplify and sequence it in a high-throughput manner, can be used to analyze and quantify the ever-evolving transcriptome.5 The sequenced DNA can be integrated with proteomic

data to identify novel peptides and derive meaningful insights into the mechanism of action of drugs.

The use of bioinformatic software systems and seam-less data integration is crucial to enable an effective, real-time analysis of the continuous feedback loop be-tween genomic, proteomic, and transcriptomic data. The proteogenomic suite of bioinformatics solutions includes Ingenuity Pathway Analysis, parallel reaction monitor-ing, Progenesis, Library of Integrated Network-Based Cellular Signatures, Skyline, DESeq, limma, edgeR, R, MStats, and PGTools, some of which are open source.

Proteogenomic data is voluminous and spans multiple genomic and proteomic platforms. Information-rich, AI-driven data visualizations leverage mixed reality to inte-grate physicochemical properties and predictive models. They have the potential to span multiple genomic/proteomic platforms and provide unprecedented insights into the molecular mechanism of the action of drugs.

One of the key therapeutic areas where proteoge-nomics is being utilized is oncology, where the discov-ery of biomarkers is leading the path for innovation. The National Cancer Institute, in collaboration with the National Human Genome Research Institute, has led major initiatives driving the growth of PM in on-cology. For example, the launch of the Cancer Genome Atlas (https://cancergenome.nih.gov) in 2006 resulted in the approval or addition of new indications to 47 drugs or biologics for oncology by the FDA in 2018, and 20 by mid-2019. However, while extensive research has been done in the genomics space, genomics alone has been inadequate to establish firm linkages between tumor biology and patient outcomes. Research has also shown that there may be not one but rather multiple mutations causing phenotypic changes and that, owing to protein modifications and configurational changes, genotypic changes may not necessarily result in cor-responding phenotypic changes. This realization has resulted in a heightened understanding of the signifi-cance of proteogenomics and the launches of the Clinical Proteomic Tumor Analysis Consortium in 2006 and the International Cancer Proteogenome Consortium in 2016.6

Proteogenomics is an integrative approach that leverages genomic, transcriptomic, and proteomic data and computational power to analyze and interpret the molecular basis of disease. It continues to revolutionize precision medicine by providing a robust, interconnected framework to the earlier disconnected omics fabric.

“To be able to drill down to the fine level of precision that precision medicine demands, it’s helpful to step back and see the bigger picture.”


References1. Ferryman, Kadija, Mikaela Pitcan. “What is precision medicine?

Contemporary issues and concerns primer.” Data & Society (2018).

2. Loo, A. J. “The tools of proteogenomics.” Advances in Protein Chemistry 65 (2003): 25-56.

3. Zimmer, David, et al. “Artificial intelligence understands pep-tide observability and assists with absolute protein quantifica-tion.” Frontiers in Plant Science 9 (2018): 1559.

4. Ruggles, Kelly V., et al. “Methods, tools and current perspectives in proteogenomics.” Molecular & Cellular Proteomics 16.6 (2017): 959-981.

5. Wang, Zhong, Mark Gerstein, and Michael Snyder. “RNA-Seq: A revolutionary tool for transcriptomics.” Nature Reviews Genet-ics 10.1 (2009): 57.

6. Rodriguez, Henry, and Stephen R. Pennington. “Revolution-izing precision oncology through collaborative proteogenomics and data sharing.” Cell 173.3 (2018): 535-539.

Dr. Nimita Limaye has a PhD in biotechnology and has been working in drug development for over 20 years across the pharma, CRO industry.


CAPILLARY ELECTROPHORESIS

BiOptic www.bioptic.com.tw

GE Healthcare Life Sciences www.gelifesciences.com

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MicroSolv Technology mtc-usa.com

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MASS SPECTROMETERS


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Applied Microarrays www.appliedmicroarrays.com

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Illumina www.illumina.com

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NEXT GENERATION SEQUENCING (NGS)


Epigentek www.epigentek.com



Integrated DNA Technologies www.idtdna.com

QIAGEN www.qiagen.com

Takara Bio USA www.takarabio.com


Vela Diagnostics www.veladx.com

SEQUENCERS


BGI www.bgi.com

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Macrogen www.macrogen.com

Oxford Nanopore Technologies www.nanoporetech.com

Pacific Biosciences of California (PacBio) www.pacb.com





genomics & proteomics

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Rare cell events may serve as diagnostic, prognostic, and predictive biomarkers of disease. For instance, tumor cells may be

shed into peripheral blood long before clini-cal symptoms develop, metastasis occurs, or cancer recurs.1 Similarly, circulating endo-thelial cells may be used as markers of tumor angiogenesis, vascular injury, and cardiovascu-lar disease.2 Quantification of residual cancer cells may also be used to predict disease remission following treatment.

Challenges in detecting rare cell events

In all of the above cases, the circulating cells or residual cells are extremely rare events, often representing anywhere between 0.01 and 0.0001 percent of the total sample.2 Given their low frequency, it may be necessary to parse millions of events to obtain a statistically and clinically relevant result. Therefore, important consider-ations when choosing a technique for rare cell detection include enrichment strategies, speed of detection, and accuracy of detection.

Flow cytometry and fluorescence micros-copy have been extensively used to detect rare

cell events in blood, bone marrow, and solid tu-mors. But is one more suitable than the other?

Flow cytometryMulticolor flow cytometry offers the advan-

tage of detecting up to 20 fluorescently labeled antibodies, allowing for in-depth analysis of cell types. Furthermore, samples do not necessar-ily have to be enriched because flow cytometers can efficiently quantify single cells. Most flow cytometers can detect thousands of cells per second. Rare cells can also be sorted and collected for further analysis. However, to reduce the time spent analyzing a large volume of a single sample, enrichment of target cells is often performed.

Positive enrichment involves labeling the sample with tumor cell antigens such as epithelial cell adhesion molecule (EpCAM). During negative enrichment, samples are labeled with hematopoietic cell antigens, such as CD45 for leukocytes. Labeled cells are then separated from the rest using mag-netic beads. Alternatively, samples may be enriched using density gradients or microflu-idic devices that separate cells based on their physical properties.3 To ensure that cells

Detecting Rare Cell Events: Flow Cytometry Versus MicroscopyTECHNICAL SOLUTIONS TO THE UNIQUE CHALLENGES OF RARE CELL DETECTION by Raeesa Gupte, PhD

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recovered after flow cytometry can be used for other types of analyses, enrichment protocols need to be chosen such that they do not compromise cell viability.

One of the greatest limitations of flow cytometry is its low resolution, which fails to provide an adequate analy-sis of cell morphology and therefore visual confirmation of cell identity. Therefore, flow rates and gating strate-gies may need to be extensively optimized to ensure high target cell specificity to minimize the occurrence of false positives and false negatives.4

MicroscopyImmunocytochemistry is widely used clinically to

enumerate and characterize circulating tumor cells. Fol-lowing EpCAM enrichment, cells are immunostained with a nuclear dye, leukocyte-specific antibodies, and epithelial-specific antibodies. Semiautomated fluores-cence microscopes or scanning fluorescence microscopes are then used to identify possible rare cell events based on cell surface marker expression. The system presents computer-generated cellular images to an operator for final review. Therefore, it offers the ability to study cell morphology, viability, and protein co-localization.

However, fluorescence microscopy is limited by the number of fluorophores that can be used to characterize a rare cell population. Imaging is usually restricted to three or four fluorophores at a time. In addition, manual identification of morphological features makes this a subjective and time-consuming process.

The best of both worldsWhat if rare cell events could be detected with the

speed of a flow cytometer and the spatial resolution of a fluorescence microscope? This can be accomplished with the use of imaging flow cytometry. With the exception of cell sorting, imaging flow cytometry offers all the advantages of regular flow cytometry and provides the added benefit of visualizing morphology at a single-cell level. It is a useful tool in the enumeration of rare cells and their phenotypic characterization because it allows morphological and fluorescent data to be analyzed at both a single-cell and population level.5

Innovations in microscopy and flow cytometry

Traditional flow cytometry and microscopy continue to be updated in order to develop better methods for rare cell detection. One such approach is acoustic focusing cytometry

that accelerates event acquisition without compromising data quality. In vivo flow cytometry6 and in vivo confocal micros-copy7 have also been developed to noninvasively quantify and characterize circulating cells within blood vessels. These approaches are yet to be reliably applied in a clinical setting.

ConclusionThe decision to use flow cytometry or microscopy

for detection of rare cell events usually depends on the downstream applications. Overall, flow cytometry en-ables rapid quantification of rare cells without providing morphological insights. Conversely, microscopy has low throughput but provides better characterization. Cur-rently, most common approaches rely on epithelial cell markers for enrichment or capture of circulating rare cells using immunomagnetic beads or flow cytometry, followed by fluorescence microscopy or nucleic acid sequencing for further characterization. Emerging evidence suggests that rare cell populations such as circulating tumor cells and circulating endothelial cells have heterogeneous pheno-types. Therefore, methods that allow both enumeration and better characterization of these cells are needed.

References1. Marrinucci, Dena, et al. “Fluid biopsy in patients with metastatic

prostate, pancreatic and breast cancers.” Physical Biology (2012).

2. Khan, Sameena S., Michael A. Solomon, and J. Philip McCoy Jr. “Detection of circulating endothelial cells and endothelial progenitor cells by flow cytometry.” Cytometry Part B: Clinical Cytometry (2005): 1-8.

3. Ferreira, Meghaan M., Vishnu C. Ramani, and Stefanie S. Jef-frey. “Circulating tumor cell technologies.” Molecular Oncology (2016): 374-394.

4. Hedley BD and Keeney M. “Technical issues: flow cytometry and rare event analysis.” International Journal of Laboratory Hematology (2013): 344-350.

5. Samsel, L and McCoy Jr. JP Samsel, Leigh, and J. Philip McCoy. “Detection and characterization of rare circulating endothelial cells by imaging flow cytometry.” Methods in Molecular Biology (2016): 249-264.

6. Tan, Xuefei, et al. "In Vivo Flow Cytometry of Extremely Rare Circulating Cells." Scientific Reports 9.1 (2019): 3366.

7. Hu, Yuhao, et al. "Monitoring circulating tumor cells in vivo by a confocal microscopy system." Cytometry Part A 95.6 (2019): 657-663.

Raeesa Gupte, PhD, is a freelance science writer and editor specializing in evidence-based medicine, neurological disorders, and translational diagnostics.

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It is not uncommon these days for a patient with an abnormal heart rhythm to have a remote-monitored pacemaker device. Digi-

tal data from the device is relayed via a por-table transmitter to a receiving station. The station faxes alerts of irregularities in cardiac rhythm to the patient’s local cardiologist in a matter of minutes, making a quick medical intervention possible if necessary.

Due to its pervasive nature, information tech-nology (IT) has become integral to transforming health care. The application of IT in health care goes by many names—health informatics, clinical informatics, biomedical informatics, and health information systems. Conventionally, when “informatics” is used in conjunction with the name of any discipline, it denotes the ap-plication of computer science and information science to assist in the management and pro-cessing of information in that discipline. Simi-larly, health informatics (HI) uses information technology to maintain, organize, and analyze health records in order to improve health care outcomes. The aim of HI is to apply technology and data analytics to health care data with the goal of improving patient care.

HI has tremendous potential to improve clini-cal workflow by enhancing and expanding the

clinician’s ability to work with patient data and information. For example, handheld scanners are used to read electronic medication records in the form of bar codes to submit and fill pre-scriptions. The scanners transmit information, such as medication dosage, medication type, and refill history, to a central workstation via Bluetooth technology. This enables doctors and pharmacists to make prescription and dispens-ing decisions based on knowledge of previous prescriptions, current medication regimens, and previous medication reactions. These e-records also significantly reduce prescription errors and allow the patients to actively participate in their medication management. Having electronic access to their own health history and recom-mendations empowers patients to adopt a more responsible role in their own well-being. A valuable extension of the electronic medica-tion record is a comprehensive e-health record, which stores and shares all information, such as treatment and tests undertaken, from all provid-ers involved in a patient’s care.

Problems of legibility, access, and transport-ability of paper-based, handwritten health care information are frequently reported. HI ensures that high-quality and reliable data are available when needed, and that those data can be easily

How Informatics Can Improve Health CareHEALTH INFORMATICS HAS A ROLE TO PLAY AT ALL STAGES OF PATIENT CARE by Shalaka Samant, PhD

Informatics


shared among the dozens of caregivers that a patient typi-cally encounters during one hospital stay. Pharmaceutical concerns, nutrition, blood chemistry, physical therapy, scans, and discharge instructions are just a few of the areas of in-teraction between patients and caregivers. In the absence of coordinated sharing of relevant conversations, information, and instructions, patient care might suffer. HI provides the way forward as it simplifies this necessary coordination.

Wasteful health care practices, such as repeat proce-dures and delays or errors in care, can often be attributed to use of traditional methods of sharing information. HI improves communication by bringing lab results to clinicians sooner and avoiding transcription errors. This improves patient care and reduces the cost of treatment. Another key issue is that paper-based patient files and data are more easily lost or misplaced. HI addresses this effectively, as computer-based records are more secure than paper-based ones, and access to such records can be controlled and monitored.

HI has the potential to greatly improve patient safety. The rapid changes in health care norms and practices make it impossible for the clinician to carry around all the relevant information available about disease type, medica-tion, and dosage in order to make an informed decision. Electronic decision support is an HI tool that can assist by providing access to guidelines and pathways, built-in alerts, prompts for care, continued patient monitoring, drug indi-ces, links to current health information, and journals of in-terest. Quick access to a detailed log of a patient’s medical history could be lifesaving, especially in a hospital setting.

A strong criticism of HI is that it increasingly leads to

impersonalization of health care delivery. The situation is now shifting from one in which the caregiver or clinician knows more about the patient to one in which the data-base or algorithm is more knowledgeable. However, on the upside, the ability of HI to make the patients more knowl-edgeable helps them become active participants in their own health care decisions. A more engaged and informed patient is likely to make better health care decisions.

Health information systems are in a phase of rapid de-velopment with several questions still unresolved in terms of architecture, functionality, and management; there is a significant amount of research going on in HI to address these questions. However, the instrumental role of HI in ensuring the efficient flow of information at all stages of patient care should not be underestimated.

Shalaka Samant is the founder and chief scientific consultant at Biombrella, a life science consulting firm. Her areas of interest are probiotic research, green chemistry research, and microbial bio-technology. Prior to starting Biombrella, Shalaka obtained her PhD in pharmaceutical biotechnology from the University of Illinois at Chicago in 2008 and completed postdoctoral training in micro-bial pathogenesis at Yale University and University of Texas at Houston. For the past nine years she has been a senior manager in the Discovery Research department of Anthem Biosciences Pvt. Ltd., a contract research organization in Bangalore, India.


DATA MANAGEMENT

Abbott Informatics www.informatics.abbott



Elemental Machines www.elementalmachines.io

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Sherry Polhill, MBA, is associate vice president for hospital labs, respiratory care, and pulmonary function services

at the University of Alabama Birmingham (UAB), UAB Medicine. Polhill has worked in high levels of hospital administration for more than 30 years. From 2003 to 2017, Polhill was the administrative director for hospital labs and respiratory care for UAB Medicine Health System, and from 1988 to 2003, Sherry was the division director of operations administrator for Children’s Hos-pital of Alabama.

Q: What was the initial motivation behind lab automation at UAB? How did the automation process happen?A: UAB is a large academic medical center, so we wanted to make UAB a more progressive institution that offered increased lab efficiency and data quality. We realized automating a lab would be a long process. The idea for the lab was first mentioned in 2007, and serious discussion started in the years following. It took several years to implement the bar code system for lab samples, which was a necessary precur-sor to automation. The process took time, but we were very pleased with the results.

Q: Your automated lab at UAB has now been running for three years. How has the performance of the automated equipment compared to your expectations?A: We knew that automation would ramp up the hospital lab’s processing capability, but it has exceeded expectations. Samples rapidly process with automation and without the hu-man factor. Using bar codes largely minimizes human error, with the barcodes directing how samples are processed and then directed toward the instrumentation. The lab allows us to provide safe care for many more patients than we could have prior to automation.

Q: With automation, how does the lab’s processing schedule work? How much human input is necessary?A: The lab now runs 24/7. The equipment was installed with a minimum of duplication devices in the areas of automation, so when analyzers are taken down for maintenance, samples continue to run seamlessly. However, automation still requires labor. For example, employees working during the morning shift perform the equipment maintenance, and lab technicians take samples out of the pneumatic

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tubes and load specimens in the pre-analytical trays. Medical technologists monitor the automated processes at the central command station and troubleshoot issues dur-ing the testing process. The automation system programs reference testing and other nonautomated testing to go to the outlet station for manual pickup when needed.

Q: How has the UAB hospital lab’s use of personnel changed since the automated lab started running? A: We were able to repurpose eight staff members from automation to other business lines. Three other businesses were created in which labor from automa-tion was added. The molecular diagnostics lab received labor. We added a mass spectrometry confirmation lab for drugs with application to pain management, with the

intention to bring in new revenue. This new lab is not operable quite yet but will be in the near future. Labo-ratory medicine added a customer service department, with lab technicians and a medical lab technician lead available within the call center for 12 hours daily each weekday. This customer service department has received incredible reviews from physicians and clinicians within the health system. Everyone in the health system now receives care more efficiently as a result.

Q: What was the total cost of automating your lab? How will UAB recoup the costs associated with installing automation? A: The total cost of automation was $9.8–$10 million. The actual automation line and equipment cost ap-proximately $7 million, while the renovations needed to provide the supporting infrastructure (e.g., new heating system, reinforced floors, new water system) cost another $2.8–$3 million. The biggest financial savings so far has been on the wages for the lab employees. Labor costs usually estimate around 65 percent of total operating costs. By creating other business opportunities, we were

able to save on labor with the talented labor pool we had available. The total cost of automating the lab will take a long time to recoup, but you cannot put a price tag on the other benefits that automation provides. Automa-tion causes increased efficiency and data quality, which in turn means a higher quality of care for many more patients. You cannot place a financial value when giving higher quality and safer results. In essence, we were able to create a high-reliability organization (or an HRO) after implementing the automation project.

Q: Do you have plans to increase automation levels for this clinical laboratory or to apply automation to any other processes at UAB? A: We have already upgraded the sample loader. We noticed the sample loader was running at capacity after two years of automation. Looking ahead to the future, we wanted to upgrade the loader to be able to receive an additional 40–45 percent capacity for future work. We also want to implement automation in the microbiology department. The proposed system will plate microor-ganism samples more efficiently and will increase safety for personnel. Right now, all medical technologists have to identify microorganisms by placing plates containing infectious agents in close proximity to their faces. With automation, technologists will be able to process plates with an additional barrier between themselves and the infectious agents. This will minimize hands-on lab work with pathogens and make the work environment safer. The growth time for the microorganisms with automa-tion is also more rapid than the traditional methods of batching the current work volume, meaning that work will also be more efficient.

Q: Have there been any unanticipated benefits to installing automation at UAB? A: One benefit I did not think about prior to automa-tion was the close relationships we would establish among the different key stakeholders from the automa-tion project. All of us worked on and shared strategic values over a long period of time to make automation happen. Our experiences together led to rewarding continuing relationships throughout various hospital departments. Another benefit from automation was the HRO we created. Through automation, the customer service department, and giving clinicians rapid, ac-curate, and value-added information, we successfully created and sustained an HRO.

“Automation causes increased efficiency and data quality, which in turn means a higher quality of care for many more patients.”

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Q: What advice would you give to other fa-cilities that are considering implementing an automated hospital lab? A: My advice would be to consult with someone who has been through the automation process before you begin. Do not try to do things on your own; consult someone experienced. You need to benefit from the strategic thinking, guidance, and insights gained by those who have already navigated automation effec-tively. Ask your vendor for a list of at least five custom-ers who implemented automation, including those sites

where the process went well and those where it went poorly. You can learn from the users from both experi-ences. Also, be realistic about your expectations for how long the automation process will take. Automation does not happen overnight but will be worth it in terms of adding quality. Laura M. Bolt, PhD, is a writer, researcher, and university-level educator based in Toronto, Canada. She holds degrees from the University of Cambridge (UK), the University of Toronto, and Queen’s University (Canada).


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D iagnosis of microbial infections requires specimen collection, sample preparation, and analysis. New meth-

ods are emerging that allow for faster, more cost-effective, and more accurate microbial identification. Quicker diagnosis allows for fast treatment and prevents the overuse of antibiotics, which can lead to resistance.

Standard procedure for confirming an infec-tious disease requires specimen collection and test selection. Routine diagnostic tests include microscopic examination, culture and biochemi-cal tests, serological tests including agglutination and ELISA, and genetic tests. More advanced diagnostic methods are emerging, focused on speed, accuracy, and cost effectiveness.

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS)

MALDI-TOF-MS has been approved by the FDA for microbial identification. The Clinical and Laboratory Standards Institute Guideline M58 published in 2017 provides information for sample preparation and

analysis, result interpretation and reporting, and troubleshooting.

MALDI-TOF-MS is a nonfragmenting, or soft ionization, technique. The analyte is em-bedded in an acidic matrix material on a metal plate, and nitrogen laser excitation is used to catalyze the charge transfer from the matrix to the analyte for desorption. Ions are separated based on their m/z, and a mass analyzer is used for detection and creation of a spectral profile.

Future directions for MALDI-TOF-MS include antimicrobial susceptibility testing, microbial virulence, and glycans.

Trends in Clinical Microbiology Diagnostic MethodsEMERGING METHODS FOCUS ON SPEED, ACCURACY, AND COST EFFECTIVENESS by Michelle Dotzert, PhD

Mic

robi

olog

y

Advantages Limitations

• It is suitable for high-throughput testing and may be completely automated.

• IVD-compliant systems are available.

• This technique does not require pre-analytic separation steps.

• It necessitates microor-ganism culture to obtain whole-cell or extracted protein specimens with a minimum number of CFUs.

• It is not able to separate multiple spectra collected simultaneously, which may occur with polymicrobial cultures.


microbiology

Next-Generation Sequencing (NGS)The NGS workflow begins with pathogen culturing

and isolation, followed by DNA extraction and library preparation. Images or signals are converted into base calls during primary analysis. Further data processing in secondary analysis includes trimming and filtering, and sequence reads are assigned to a reference sequence or assembled with de novo assembly. The identification of clinically significant findings in tertiary analysis is used to generate a final report.

Automated Polymerase Chain Reaction (PCR)

Multiplex PCR is especially useful for specimens from patients presenting with nonspecific symptoms, which may result from any number of different pathogens.

A sample-to-result automated PCR system enables the addition of a clinical specimen directly to the device. The sample is treated with multiple reagents for nucleic acid extraction followed by amplification and detection of a target sequence. Platforms range in classification from high-complexity molecular assays to FDA-cleared moderate-complexity IVD tests.

Michelle Dotzert obtained her PhD in kinesiology from the University of Western Ontario. Her research examined the effects of exercise training on skeletal muscle lipid metabolism and insulin resistance in the context of type 1 diabetes.


• NGS may be used for whole genome sequencing on bacterial isolates from a single patient or from multiple patients.

• It offers rapid bacterial identification and has the capacity to differentiate between clones.

• The technique is becoming increasingly automated, and the cost continues to decrease.

• NGS generates complex data that necessitates interpretation by a clinical microbiologist to ensure the report is designed to help the physician select an appropriate treatment.

Sensitivity and specificity of individual platforms cannot be compared directly.


• Automating PCR limits specimen handling to reduce the risk of contamination.

• Automated multiplex instruments are suitable for rapid detection of a greater number of targets than detected by traditional PCR.

• Cost per test is reduced when multiple specimens are processed together.

• Patient care decisions sometimes require rapid testing, and auto-mated on-demand testing is more costly than batch testing.


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P oint-of-care testing (POCT), or on-site testing, is rapidly emerging as a potential alternative to conventional

laboratory-based diagnostic testing. By pro-viding actionable information at the time and location of care, POCT allows diseases to be diagnosed at an early stage. Emerging POCT trends include the development of less invasive and more continuous testing, growth of miniaturized technologies, and the use of telemedicine for remote monitoring.

BiosensorsThe biosensor is the most critical com-

ponent of point-of-care diagnostics.1 The integration of biosensor systems into POC systems can improve patient care through real-time and remote health monitoring.

Label-based techniques are laborious and time-consuming as they require the attach-ment or “labeling” of target molecules with labels such as fluorescent dyes, radioisotopes, or epitope tags. This drawback makes label-based techniques impractical for use in POC appli-cations. In contrast to label-based techniques, label-free detection methods depend on the measurement of an inherent property of the

query itself, such as molecular weight (e.g. mass spectroscopy) or refractive index (e.g., surface plasmon resonance), to monitor molecular presence or activity. Label-free detection avoids interference due to tagging molecules, which aids in the rapid evaluation of biomolecular interactions in real time. By offering label-free assays with immediate results and employ-ing small and user-friendly devices, biosensor platforms can overcome challenges faced by conventional diagnosis techniques. Addition-ally, the use of label-free optical sensors for point-of-care applications enables direct and multiplex analysis due to the lack of strong interference from the sample matrix (a major limitation of electrochemical sensors).

Innovative technology platforms that inte-grate biosensors into POC systems are cur-rently being explored. Label-free biosensors employing impedance spectroscopy, SPR, and white light reflectance spectroscopy are being studied for the development of a more efficient and less time-consuming POCT.

Impedance biosensors Impedance biosensors are electrical biosen-

sors that help quantify biological molecules

Trends in Point-of-Care TestingPOINT-OF-CARE TECHNOLOGIES HOLD TREMENDOUS POTENTIAL TO IMPROVE HEALTH CARE DELIVERY by Neeta Ratanghayra, M.Pharm

Mol

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iagn

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s


molecular diagnostics

in a sample by measuring the changes in the capacitance or resistance caused by the binding of analytes (tar-get molecule) to an immobilized probe. The binding causes a change in the device impedance, which can be measured to quantify the corresponding analyte. Impedance biosensors may be integrated into on-chip systems and require a smaller volume of sample for the measurements compared to laboratory-based platforms. Interdigitated electrode (IDE) arrays are widely used in impedance biosensors. IDE sensors are highly sensitive and have been explored to detect DNA2 and antigen-antibody interactions.3

White light reflectance spectroscopy-based sensing platforms

White light reflectance spectroscopy (WLRS)-based sensing platforms are being explored for the detection of high or low molecular weight analytes.4 These platforms use the reflection of a broadband light beam from an en-gineered surface to produce an interference fringe in the visible spectrum. WLRS biosensors consist of a reflec-tion probe and a sensing element. The reflection probe is composed of six fibers at the periphery that deliver the light to the surface, and a central fiber that collects the specular reflected light. The sensing element consists of a single layer or stack of films (made from transparent materials with different refractive indices) over a silicon substrate (with moderate reflectance). The emitted light is guided by the reflection probe vertically to the sensing element, where it is reflected by the silicon surface and by the transparent material layers of different refractive indices. The result is an interference spectrum that is collected by the central fiber of the reflection probe and passed on to the spectrometer, where it is continuously recorded. The spectra obtained can be monitored and correlated to respective analyte concentrations.

WLRS is an optical label-free method devoid of any moving optical parts and alignment needs. The non-disposable instrumentation, and the ability to work with complex matrices, make WLRS a cost-effective option. The addition of conventional microelectronic processes to WLRS, along with advanced algorithms, could be ben-eficial in multi-analyte determinations.

Surface plasmon resonance biosensorSurface plasmon resonance (SPR) is a surface-sensitive

spectroscopic method to probe changes in the refractive index of biosensing material at surfaces of metals. SPR is

a label-free, sensitive technique to examine bio-molecular interactions. SPR has been explored for the detection of stroke biomarkers,5 monitoring of tumor antigen-serum antibody interactions, and detection of neurotoxins.

Mobile health care technologiesSmartphone-based imaging and sensing platforms are

emerging as promising alternatives to complex diagnos-tic procedures. The portability, cost-effectiveness, and connectivity of these platforms offer several opportuni-ties for POCT integration.

The computational power of smartphones can be useful for process control and data analysis. The optical sensing capabilities of complementary metal-oxide-semiconductor (CMOS) cameras in smartphones can also be used in imaging-based or spectrometry-based analysis.6 Imaging-based applications include flow cytometry, colorimetry, photoluminescence, and fluo-rophores. Spectrometry-based smartphone-integrated platforms can be used to probe reactions or changes of molecules. Another important aspect of the integra-tion of POCT with smartphones is that it makes patient data available on a cloud-based server for telemedicine. Telemedicine provides secure access to medical records to both clinicians and patients from anywhere around the globe, which saves time for both the health care organi-zations and the patients.

Wearable and implantable devicesWearable and implantable devices enable continuous,

longitudinal health monitoring outside the hospital or health care facility. Wearable and implantable technolo-gies sense various disease parameters and can either transfer data to a remote center or automatically perform a function based on what the sensors are reading. This latter feature is especially beneficial for chronic disease and wellness monitoring. The most significant advances in wearable and implantable devices are in the field of diabetes, with a number of devices being developed or commercialized for continuous glucose monitoring (CGM). Besides CGMs, wearables and implantables to monitor cardiac parameters are also available. For example, mobile cardiac outpatient telemetry (MCOT) monitors cardiac patients in real time during normal daily activities, using built-in detection algorithms and cellular technology. The system also helps to detect and capture significant arrhythmic events, even when no symptoms are experienced.



Non-invasive POCTNon-invasive diagnostic techniques have long been de-

sired for several reasons. Invasive methods are not suitable for continuous monitoring. The pain and risk of infection with invasive techniques act as potential barriers to its use. Moreover, invasive methods are time-consuming and pose the risk of needle stick injuries. Non-invasive techniques offer real-time painless measurements of disease-related parameters without the risk of infection. Near-infrared scanning and volatolomics are two innovative examples of non-invasive POCT. Near-infrared spectroscopy is a non-ionizing, inexpensive monitoring and imaging technique that uses near-infrared light to probe tissue optical prop-erties. A portable brain scanner (Infrascanner) is a well-known application of near-infrared to detect traumatic brain injury with intracranial bleeding. The device helps screen individuals who need immediate referral for a CT scan and neurosurgical intervention.

Volatolomics is the study of chemical processes involving volatile organic compounds (VOCs)—me-tabolites produced as a result of disease processes that alter the normal physiological and metabolic pathways occurring within the disease-affected tissues. Several complex chemical-detection technologies that employ metabolomic approaches to disease diagnostics, with complex instruments such as gas chromatography-mass spectroscopy (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy, have been used to identify disease-associated VOC-metabolites.

The measurement of VOCs by an electronic nose (or e-nose) is an innovative example of volatolomics. Electronic noses are portable sensor systems made up of chemical cross-reactive sensor arrays. The sensors help in characterizing patterns of breath volatile compounds and have algorithms for breath print classification. E-noses provide real-time data and, in conjunction with NMR-based metabolomics of exhaled breath con-densate, can identify patients with respiratory diseases such as asthma, chronic obstructive pulmonary disease (COPD), and lung cancer.

Challenges of POCTPoint-of-care technologies are valuable tools for popu-

lation health, precision medicine, disease prevention, and chronic disease management. However, POCT still faces these potential hurdles:• POCT errors can be a major source of error com-

pared to other laboratory errors. In a traditional

laboratory, issues related to hemolyzed specimens, insufficient specimen, or incorrect specimen can be easily detected; however, the same issues are difficult to detect in POC settings due to nonadherence to standard procedures and use of uncontrolled reagents.

• POCT is generally undertaken by non-laboratory clinical staff, who are primarily involved in delivery of patient care. If incorrectly performed, POCT may present a risk to patient care and its inappropriate use may lead to substantial cost of patient care.

• Rural regions often lack access to the requisite tech-nology for smooth implementation of POCT. There is also often a lack of trained staff to perform the tests and carry out the subsequent diagnoses in rural areas.

• There are security concerns over privacy of personal data with mobile health care technologies. The re-quirement of international cloud computing standards and the management of big data can also be daunting.

References1. Vashist, Sandeep. "Point-of-care diagnostics: Recent advances

and trends." Biosensors (2017): 62.

2. Berdat, Daniel, et al. "Label-free detection of DNA with in-terdigitated micro-electrodes in a fluidic cell." Lab on a Chip 8.2 (2008): 302-308.

3. Taylor, Richard F., Ingrid G. Marenchic, and Richard H. Spen-cer. "Antibody-and receptor-based biosensors for detection and process control." Analytica Chimica Acta 249.1 (1991): 67-70.

4. Koukouvinos, Georgios, et al. "Development and bioanalytical applications of a white light reflectance spectroscopy label-free sensing platform." Biosensors 7.4 (2017): 46.

5. Harpaz, Dorin, et al. "Point-of-care surface plasmon resonance biosensor for stroke biomarkers NT-proBNP and S100β using a functionalized gold chip with specific antibody." Sensors 19.11 (2019): 2533.

6. Geng, Zhaoxin, et al. "Recent progress in optical biosensors based on smartphone platforms." Sensors 17.11 (2017): 2449.

Neeta Ratanghayra, M.Pharm, is a freelance medical writer who creates content for pharmaceutical and health care industry. She has a background in academic and clinical research.




ASSAY / IMMUNOASSAY

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H istopathology, which involves the microscopic examination of patient tissues for the identification of tissue

abnormalities, is a largely manual process. It requires slide preparation by fixing, followed by staining for specific cell and tissue markers, and finally, visual inspection by a pathologist.

As technologies continue to evolve, vendors are looking to develop solutions to automate this intensive and time-consuming process. Automation can help move the largely qualitative field of pathology to a quantitative assessment that avoids human bias and enables the precise and reproduc-ible extraction of data from slides. The digi-tization of pathology slides through whole slide imaging (WSI) represents a major step toward this automation.

In WSI, slides are prepared and stained in the same way as in conventional microscopy, but instead of examining the slide with a mi-croscope, the slide is scanned and visualized on a computer screen.1 The user can navigate the tissue and annotate any findings using software.

While this technology has been used for slide archiving, remote consultations, and education, among other applications, the use of WSI for diagnosis in the clinical lab is still in its infancy.

Uses of whole slide imagingSlide archives

Environmental factors can degrade tissue mounted on slides over time. Slides are also prone to breakage, misplacement, or mislabel-ing, and they take up physical space. Digital slide archives maintain the quality of the slide image over time and provide long-term storage solutions so that only tissue blocks need to be physically stored.1

Remote consultationThe digitization of histology slides allows

them to be accessed anywhere by anyone.2 Specialists around the world can be sent digital slides in minutes and examine the entire slide instead of relying on the sender to choose a representative section.

How Whole Slide Imaging Is Changing the Role of the PathologistTHE USE OF WHOLE SLIDE IMAGING IS STILL IN ITS INFANCY, BUT IT HAS THE POTENTIAL TO REVOLUTIONIZE THE FIELD OF PATHOLOGY by Catherine Crawford-Brown, MSc

Path

olog

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pathology

EducationDeveloping and maintaining tissue sets of histol-

ogy slides is challenging. First, instructors need to find high-quality specimens that are free of artifacts and produce enough representative sections. When slides are digitized, an entire class can have access to the same tissue set anywhere.2 Only a single tissue section needs to be scanned, and slide-to-slide variation is eliminated. Digitization also promotes sharing and distribution of histopathologic specimens so that resources across train-ing programs are broader and more homogenous.

FDA approval—a major step forward for the clinical lab

In 2017, the United States Food and Drug Administration (FDA) approved the first WSI scanner for primary diagnosis in surgical pathology.3 The scanners are defined as Class III medical devices, and the FDA regulates these instruments to help ensure that images being analyzed for clinical use are safe and effective for their defined purpose.4

Before approval was conferred, the whole slide imager was thoroughly validated to show that it produced results comparable to conventional microscopy. Many studies have investigated whether there is a difference in diagno-sis when pathologists use conventional microscopy ver-sus WSI.5 These studies have shown high concordance rates among these two imaging types; however, study participants found that WSI was too slow for routine use when examining slides and that digital images were more difficult to evaluate than were glass slides.6,7

ChallengesIt has been shown that WSI performs just as well as

does conventional microscopy. However, there are sev-eral challenges that are discouraging clinical labs from adopting this technology.

Standardization and data managementVendors of WSI platforms use proprietary formats to

store image data and metadata, which makes it challeng-ing to organize images acquired from a different scan-ner. As a result, labs are limited to using a single type of scanner when performing WSI, which can impact interoperability and scalability. One solution is Digital Imaging and Communications in Medicine, which is an international set of standard file formats and com-munication protocols that provide a vendor-neutral and universal language for medical imaging.1

Another major issue is the amount of data created when WSI is used. If the average image is between 200 MB and 1 GB, and the average number of slides per surgical case is 12.2, then anywhere from 2.4 to 19.5 GB of stor-age will be required for each case.8 The costs can add up when storing this much data, but discarding images can be almost as costly, especially if the glass slides aren’t being retained. One solution might be to have pathologists flag images that contain information important for diagnostics and discard the remaining slides from each case.8

ReproducibilityThere are many factors that can impact image quality

when performing WSI. Pre-analytical variables during slide preparation, such as tissue procurement, fixation time, fixa-tion type, and antigen retrieval protocol, all need to be stan-dardized to ensure consistency.2 A single slide scanner can also produce different quality of images of a single slide, depending on external factors such as temperature and me-chanical shifts.7 Finally, slide scanners aren’t standardized, so image quality from one scanner to the next could differ, making the images obtained incomparable.2

Future directionsAs technology advances, there is potential for WSI to

be used for more detailed and complex analysis using fully automated processes.

3D reconstruction/stereologyWSI remains a 2D imaging technique, and because of

this, it leaves a gap between recorded slide observations and the original state of the tissue.1 Stereology is the study of 3D representations generated from a random sampling of 2D images.9

3D imaging would allow for the evaluation of entire tissues rather than single representative samples.2 These images could also be compared with other diagnostic im-ages such as those from magnetic resonance imaging and conventional computer tomography to identify diagnos-tic patterns.1 However, stereology requires a significant amount of time and tissue as well as a skilled stereologist and a specially trained histologist to correctly prepare the samples. For this reason, pathologists continue to argue about whether the benefits are worth the effort.2

Image analysisTools are being developed to extract information from

tissue slides to avoid the error-prone and repetitive

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pathology

nature of manual assessment. The basic principle in-volves a mathematical algorithm that can process images and segment picture elements into regions of interest based on color, texture, and context.2

Commercial software for image analysis differs in the amount of supervision required or allowed.2 Unsuper-vised software is pre-built and easy to use right out of the box, whereas supervised software allows the user to program specific algorithms to develop unique analyses and requires extensive training. Either way, a pathologist needs to be involved to design the study, determine what the biological end point will be, define the regions of interest, and evaluate whether the software is correctly measuring that end point.

As pathologists know, abnormalities exist on a spec-trum rather than in discrete groups. The advantage of image analysis compared with manual analysis is that it can measure variables as continuous rather than ordinal, and these values can then be analyzed using statistics.2 This evaluation can help decrease observer variability and increase reproducibility.

Artificial intelligence and machine learningThe use of artificial intelligence (AI) and machine

learning in the evaluation of digitized slide images is still far from reality. In theory, artificial intelligence will allow for the discovery of patterns in tissue images that can be used to derive insights and make predictions. One day, this technology might be used for computer-aided diagnosis.1

On a more basic level, AI could relieve pathologists of mundane tasks and simplify more complex tasks. It could also analyze individual pixels of images more deeply, un-locking diagnostic information that might not be available when slides are visually inspected with a microscope.10

While there are clear opportunities for AI in pathol-ogy, there are many challenges that must be overcome before this technology can be implemented.10 For example, pathologists still need to be heavily involved in manually delineating the region of interest in images before automated analysis is conducted. The variability found in tissue can also challenge AI because the number of patterns that the software would need to identify in tissue could be nearly infinite.10

ConclusionWSI has the potential to revolutionize the field of pa-

thology, but it will in no way eliminate pathologists. These experts will continue to play an important role in slide and

image quality assurance, labeling slides and selecting regions of interest, and evaluating algorithm performance. None-theless, use of this technology could transform pathology from a largely qualitative field to one that is data-driven and relies on quantitative rather than qualitative analysis.

References1. Zarella, Mark D., et al. "A practical guide to whole slide imag-

ing: a white paper from the digital pathology association." Ar-chives of Pathology & Laboratory Medicine 143.2 (2018): 222-234.

2. Webster, J. D., and R. W. Dunstan. "Whole-slide imaging and au-tomated image analysis: considerations and opportunities in the practice of pathology." Veterinary Pathology 51.1 (2014): 211-223.

3. Evans, Andrew J., et al. "US Food and Drug Administration approval of whole slide imaging for primary diagnosis: A key milestone is reached and new questions are raised." Archives of Pathology & Laboratory Medicine 142.11 (2018): 1383-1387.

4. FDA. "Technical Performance Assessment of Digital Pathol-ogy Whole Slide Imaging Devices." (2016) https://www.fda.gov/regulatory-information/search-fda-guidance-documents/technical-performance-assessment-digital-pathology-whole-slide-imaging-devices.

5. Goacher, Edward, et al. "The diagnostic concordance of whole slide imaging and light microscopy: a systematic review." Ar-chives of Pathology & Laboratory Medicine 141.1 (2016): 151-161.

6. Onega, Tracy, et al. "Use of digital whole slide imaging in der-matopathology." Journal of Digital Imaging 29.2 (2016): 243-253.

7. Jayakumar, Rajeswari, et al. "Can whole slide imaging replace conventional microscopic evaluation? A comparative study over a spectrum of cases." Journal of Applied Clinical Pathology (2018): 4.

8. Balis, Ulysses G. J., et al. "Whole-slide imaging: thinking twice before hitting the delete key." AJSP: Reviews & Reports 23.6 (2018): 249-250.

9. Aeffner, Famke, et al. "Introduction to digital image analysis in whole-slide imaging: A white paper from the Digital Pathol-ogy Association." Journal of Pathology Informatics 10 (2019).

10. Tizhoosh, Hamid Reza, and Liron Pantanowitz. "Artificial intelligence and digital pathology: Challenges and opportuni-ties." Journal of Pathology Informatics 9 (2018):38.

Catherine Crawford-Brown has an MSc in pathology and molecular medicine from Queen's University where she re-searched circulating biomarkers for breast cancer. She also holds an MSComm from Laurentian University.


pathology


AUTOPSY

CSI-Jewett www.csi-jewett.com

EXAKT Technologies www.exaktusa.com


Hygeco www.hygecogroup.com

Milestone Medical www.milestonemed.com

Mopec www.mopec.com

Mortech Manufacturing Company www.mortechmfg.com


CYTOLOGY

Applied Spectral Imaging www.spectral-imaging.com

Azer Scientific www.azerscientific.com



Biocare Medical www.biocare.net

Biomedical Polymers www.biomedicalpolymers.com

Bio Plas www.bioplas.com


CellPath www.cellpath.com

Centurion Scientific www.centurionscientificglobal.com

CONMED www.conmed.com


G-Biosciences www.gbiosciences.com


Hettich www.hettweb.com


McKesson Medical-Surgical www.mckesson.com

Milestone Medical www.milestonemedsrl.com


Motic www.motic.com

Polysciences www.polysciences.com

Puritan Medical Products www.puritanmedproducts.com

RICCA Chemical Company www.riccachemical.com


Rovers Medical Devices www.roversmedicaldevices.com

Sakura Finetek USA www.sakuraus.com

Sanderson MacLeod www.sandersonmacleod.com


Simport Scientific www.simport.com



HISTOLOGY

Biocare Medical www.biocare.net

Bio Plas www.bioplas.com



Definiens www.definiens.com

G-Biosciences www.gbiosciences.com





Kartell Labware www.kartelllabware.com


Milestone Medical www.milestonemedsrl.com

Mopec www.mopec.com

Polysciences www.polysciences.com

Sakura Finetek USA www.sakuraus.com

Spectrum Chemical Manufacturing www.spectrumchemical.com

Starplex Scientific www.starplexscientific.com



MICROSCOPY

AFMWorkshop www.afmworkshop.com

Asylum Research afm.oxinst.com



Carl Zeiss Microscopy www.zeiss.com

CRAIC www.microspectra.com


EUROIMMUN US www.euroimmun.us

Hamamatsu www.hamamatsu.com

Hitachi High Technologies America www.hitachi-hta.com


Keyence www.keyence.com

Kramer Scientific www.kramerscientific.com


LW Scientific www.lwscientific.com

Meiji Techno America www.meijitechno.com

Motic www.motic.com


Ocean Optics www.oceanoptics.com


Park Systems www.parksystems.com


Prior Scientific www.prior.com

Rigaku Americas www.rigaku.com




WITec www.witec.de

http://afm.oxinst.com


services


CALIBRATION

Accurate Calibration Industrial www.accuratecalibrationind.com


Artel www.artel-usa.com


Fluke Biomedical www.flukebiomedical.com

MATsolutions www.matsolutions.com

Mayfield Medical Services www.mayfieldmedical.com


Micro Quality Calibration www.microqualitycalibration.com

Pace Analytical www.pacelabs.com



SiteCal www.sitecal.com


Thomas Scientific www.thomassci.com

Troemner www.troemner.com

CONSULTANTS


American Elements www.americanelements.com

American Laboratory Consultant www.starturlab.com

Baron Analytical Laboratories www.baronlabsct.com

Beyond Lab Consulting www.beyondlabconsulting.com

Biobank Resource Centre www.biobanking.org

C&C Clinical Laboratory Consulting www.cclabconsult.com

Chi Solutions www.chisolutionsinc.com

Clinical Lab Consultants www.clinicallabconsultants.com

Clinical Lab Consulting www.clinicallabconsulting.com

Clinical Laboratory Consultants www.clinicallaboratoryconsultants.com

COLA Resources (LabUniversity) www.labuniversity.org


Discovery Life Sciences www.dls.com

Genedata www.genedata.com

IHRC www.ihrc.com

LabMetrics Consulting www.labmetrics.com

Laboratory Consulting Services www.laboratoryconsultingservices.com

LANDAUER www.landauer.com

Lighthouse Lab Services www.lighthouselabservices.com


Nichols Management Group www.nicholsmanagementgroup.com

ProCore Lab Consulting www.procorelabconsulting.com




South Shore Laboratory Consultants www.sslabconsultants.com



Xeno Diagnostics www.xenodiagnostics.com

CONTRACT LABS

Alfa Chemistry www.alfa-chemistry.com

Altasciences www.altasciences.com


American Preclinical Services www.americanpreclinical.com

Arcinova www.arcinova.com

Cellular Technology Limited www.immunospot.com

ChRi Laboratories www.chrilabs.com

Cicadea Biotech www.cicadeabiotech.com

Clinical Research Laboratories (Eurofins) www.crlresearchlabs.com

Covance www.covance.com

Criterium www.criteriuminc.com

Flow Contract Site Laboratory www.fcslaboratory.comSe

rvic

es


services

Frontage Clinical Services www.frontagelab.com

Indivumed www.indivumed.com

iuvo BioScience www.iuvobioscience.com

Metis Laboratories www.metislabs.com

NEOMED-LABS www.neomedlabs.com

Olon Ricerca Bioscience www.ricerca.com

Pine Lake Laboratories www.pinelakelabs.com


SGS www.sgs.com

Xeno Diagnostics www.xenodiagnostics.com

Zymetrix www.zymetrix.com

MULTIVENDOR SERVICES

Avantor www.avantorsciences.com


GE Healthcare www.gehealthcare.com

Medecon Healthcare www.medecon.co.uk


Philips www.usa.philips.com

Shimadzu Scientific www.shimadzu.com



PROFICIENCY TESTING

AAB Proficiency Testing Service www.aab-pts.org

American College of Physicians www.acponline.org/mle

American Academy of Family Physicians www.aafp.org

American Proficiency Institute www.api-pt.com

Bio-Rad Laboratories (QC-Net) www.qcnet.com

Boston Clinical Laboratories www.bostonclinicallab.com

CEQAL www.ceqal.com

Clinical Microbiology Proficiency Testing www.cmpt.ca

College of American Pathologists www.cap.org

ECAT Foundation www.ecat.nl

Institute for Quality Management in Healthcare www.iqmh.org

LGC www.lgcgroup.com

Oneworld Accuracy www.oneworldaccuracy.com

Pennsylvania Department of Health www.health.pa.gov

Quality Control for Molecular Diagnostics www.qcmd.org


Wisconsin State Laboratory of Hygiene www.slh.wisc.edu

Weqas www.weqas.com

REFERENCE LABS

ARUP Laboratories www.aruplab.com

Aurora Diagnostics www.auroradx.com

BioReference Laboratories www.bioreference.com

Boston Clinical Laboratories www.bostonclinicallab.com

Clinical Reference Laboratories Of America www.crlamerica.com


LabCorp www.labcorp.com

Mayo Clinic Laboratories www.mayocliniclabs.com


Sonic Reference Laboratory www.sonichealthcareusa.com

STAFFING

Adecco www.adecco.com

Aerotek www.aerotek.com

AMN Healthcare www.amnhealthcare.com

Anders Group www.andersgroup.org

B2B Staffing Services www.b2bstaffingservices.com

Commonwealth Sciences www.cwsciences.com

CompHealth www.comphealth.com

HCN HealthCare Recruiting www.hcnhealthcare.com

HealthCare Connections Inc. www.labcareer.com

Julia Edmunds Associates www.juliaedmunds.com

K.A. Recruiting www.ka-recruiting.com

Kinetica www.kinetica.co.uk

LabMetrics Consulting www.labmetrics.com

LabMinds Staffing & Recruiting www.labmindstaffing.com

Lighthouse Lab Services www.lighthouselabservices.com

MAS Medical Staffing www.masmedicalstaffing.com

Medical Staffing Network www.msnhealth.com

MedPro Healthcare Staffing www.medprostaffing.com

Micann Services www.micann.com

NuWest Group www.nuwestgroup.com

PassportUSA www.passportusa.com

Rapid Temps www.rapidtemps.com

Seltek Consultants www.seltekconsultants.co.uk


supplies & consumables


GLASSWARE

Ace Glass www.aceglass.com

AMSBIO www.amsbio.com

Bel-Art Products www.belart.com

Boekel Scientific www.boekelsci.com


Chemglass Life Sciences www.chemglass.com

Corning Life Sciences www.corning.com


Flinn Scientific www.flinnsci.com


Kemtech America www.kemtech-america.com


United Scientific Supplies www.unitedsci.com

Wilmad-LabGlass www.wilmad-labglass.com

KITS, CHEMICALS, & REAGENTS


Abbiotec www.abbiotec.com

Abbott Molecular www.molecular.abbott

Active Motif www.activemotif.com



ATCC www.atcc.org

AUDIT MicroControls www.auditmicro.com


Bio Basic www.biobasic.com

Biochain www.biochain.com

Bioline Reagants www.bioline.com


BioSupply www.elisakits.co.uk

Bio-Synthesis www.biosyn.com

Biotium www.biotium.com

Cambio www.cambio.co.uk


Cayman Chemical www.caymanchem.com

Cedarlane www.cedarlanelabs.com

Creative Diagnostics www.creative-diagnostics.com


Elabscience www.elabscience.com

Empirical Bioscience www.empiricalbioscience.com


Expedeon www.expedeon.com

GFS Chemicals www.gfschemicals.com

Integrated DNA www.idtdna.com

Lucigen www.lucigen.com


MilliporeSigma www.emdmillipore.com


New England Biolabs www.neb.com

PBL Assay Science www.pblassaysci.com


Promega www.promega.comSu

pplie

s & C

onsu

mab

les


supplies & consumables


Quansys Biosciences www.quansysbio.com

Roche Molecular Systems www.lifescience.roche.com

Rockland Immunochemicals www.rockland-inc.com

Santa Cruz Biotechnology www.scbt.com




PLASTICWARE

Agela Technologies www.agela.com


Bel-Art Products www.belart.com



Chemglass Life Sciences www.chemglass.com

Corning Life Sciences www.corning.com


Dynalon Labware www.dynalon.com


ExtraGene www.extragene-web.com




Micronic www.micronic.com

Pall Corporation www.pall.com


Porvair Sciences www.porvair-sciences.com


Simport www.simport.com

SSI www.ssibio.com

Tecan www.tecan.com


United Scientific Supplies www.unitedsci.com

VistaLab Technologies www.vistalab.com

PPE

3M Science www.3m.com

AliMed www.alimed.com

Alpha Pro Tech www.alphaprotech.com

Ansell www.ansell.com

Associated Bag www.associatedbag.com

Bulwark Protection www.bulwark.com


Denline Uniforms www.denlineuniforms.com

DuPont www.dupont.com

Dynarex www.dynarex.com

Encon Safety Products www.enconsafety.com

Fashion Seal Healthcare www.fashionsealhealthcare.com

Halyard www.halyardhealth.com


Keystone Safety www.keystonesafety.com

Kimberly-Clark Professional

www.kcprofessional.com

McKesson Medical-Surgical

www.mckesson.com

Medicom

www.medicom.com

Medline Industries

www.medline.com

PlatinumCode

www.platinumcode.us

Pro Advantage

www.proadvantagebyndc.com

Protective Industrial Products

www.us.pipglobal.com

Sempermed

www.sempermedusa.com

Tech Optics International

www.techopticsinternational.com

Tempshield Cryo-Protection

www.tempshield.com

Thermo Fisher Scientific

www.thermofisher.com

The Safety Zone

www.safety-zone.com

Tronex International

www.tronexcompany.com

VWR International

www.vwr.com

ENDOMETRIOSIS

EMERGING TREATMENTS + CLINICAL TRIALS

Ectopic Endometrial

Tissue

Endometriosis is a condition characterized by ectopic endometrial tissue growth, resulting in inflammation, infertility, and severe, chronic pain. Symptoms include dysmenorrhea, pain with intercourse, pain with bowel movements or urination, excessive bleeding or intermenstrual bleeding, and infertility.

It is estimated that endometriosis a�ects approximately 1 in 10 women of reproductive age, with a mean latency of 6.7 years from the onset of symptoms to diagnosis. It is also considered an invisible illness contributing to an increased risk of depression.

Symptoms, history, and physical examination

indicate endometriosis

Add-back regimen: progestins,progestins plus bisphophonates,low-dose progestins, or estrogens

Oral contraceptives, progestogens, NSAIDs

No improvement

No improvement

Preserve fertility:Laparoscopy and surgicalremoval of

lesions

Do not wish topreserve fertility:

Hysterectomy with bilateral

salpingo-oophorectomy

Gonadotropin-releasing hormone (GnRH) agonists

No improvement

There is no single, e�ective treatment strategy for endometriosis, and several clinical trials will begin to examine the e�ects of novel treatment strategies. Dichloroacetate (DCA), for example, has been shown to stop the growth and survival of endometriosis cells and reduce lactate production in a laboratory setting and its e�ects on endometriosis-associated pain will be examined in a clinical trial. Low-dose Naltrexone combined with hormonal suppression (standard of care) will also be evaluated for its e�ects on endometriosis pain.

Endometriosis is also associated with poor reproductive outcomes in the context of in vitro fertilization, and embryo transfer. Elagolix (Orilissa) is a new generation orally active GnRHR antagonist FDA approved for the treatment of endometriosis and pelvic pain. In a randomized controlled trial, the medicine will be compared to oral contraceptives for suppression of endometriosis prior to embryo transfer.

Other studies will examine hormonal suppression in combination with novel treatments. Interleukin-1 (IL-1) receptor antagonist Anakinra, is a subcutaneous injectable drug FDA approved for rheumatoid arthritis, and its e�ects in combination with hormonal suppression will be examined for pelvic pain. Similarly, a study will examine the e�ects of GnRHa combined with autologous natural killer (NK) cell therapy.

TREATMENT

Superficial peritoneal lesions are usually located on pelvic organs or the pelvic peritoneum. Classic lesions are bluish or blue-black and resemble the endometrium, whereas non-classic lesions include clear, red, and white lesions. Ovarian endometriomas consist of a dense, brown fluid, and deep infiltrating endometriosis (DIE) is a blend of fibromuscular tissue and adenomyosis, primarily found in the uterosacral ligaments or cul-de-sac.

Visual inspection by laparoscopy is the gold standard for the diagnosis of endometriosis, and may be combined with biopsy for histological confirmation. Two or more histologic features must be present for diagnosis: endometrial epithelium, endometrial glands, endometrial stroma, or hemosiderin-laden macrophages.

Non-invasive techniques include ultrasound and MRI. Transvaginal ultrasound may be useful to diagnose endometriomas, bladder lesions, and deep nodules. MRI may be used to guide surgical approaches for deep infiltrating endometriosis.

Diagnosis also relies on symptom evaluation, patient history review, and physical examination to identify nodules, retroverted uterus, masses, or external endometriomas.

Endometriosis remains poorly understood, and several theories for its pathogenesis have been proposed

PATHOGENESIS THEORIES

Coelomic Metaplasia Theorypostulates endometriosis results from extrauterine cells in the mesothelial lining of the visceral and abdominal peritoneum that abnormally di�erentiate into endometrial cells. Hormonal and immunological factors are thought to stimulate di�erentiation.

Embryonic Rest Theoryproposes that specific stimuli to cells present in the peritoneal cavity, originating from the müllerian duct system, may induce them to form endometrial tissue. This theory may account for the presence of rectovaginal endometriosis.

Retrograde Menstruationis an early theory, proposing that endometriosis is the result of retrograde flow of cells and debris into the pelvic cavity via fallopian tubes during menstruation. Shed cells attach to the peritoneum, proliferate, di�erentiate, and invade the underlying tissue.

Lymphatic & Vascular Metastasisthis theory proposes that endometrial tissue is present at ectopic sites, including the brain, lungs, lymph nodes, and abdominal wall, resulting from lymphatic and hematogenous spread.

ENDOMETRIOSIS

MEDICAL RECORD

DIAGNOSIS

IMPROVEMENT

IMPROVEMENT

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refractory metals

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isotopes

epitaxial crystal growth

photovoltaics

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quantum dots

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InAs wafers

platinum ink

perovskite crystals

CIGS

rare earth metals

spintronics

thin �lm

osmium

buckyballs

zeolites

Nd:YAG

yttrium stabilized zirconia

dielectrics

deposition slugs

organometallics

optical glass

gold nanocubes

mesoporus silica

chalcogenides

laser crystalsOLED lighting

graphene oxide

solar energy

�exible electronics

carbon nanotubes metallocenes

CVD precursors

pyrolitic graphite

silver nanoparticles

MOFs

palladium catalysts nickel foam

III-IV semiconductors

gallium lump

ITO

scandium powder

nanoribbons

nanogels surface functionalized nanoparticles

mischmetal

ultralight aerospace alloys

rhodium sponge

nanodispersions

Ti-6Al-4V

li-ion battery electrolytes

h-BN

MOCVD

Invar

InGaAs

GDC

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ferro�uid

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140.116Cerium

58 28

181992Ce

140.90765Praseodymium

59 28

182182Pr

144.242Neodymium

60 28

182282Nd

(145)Promethium

61 28

182382Pm

150.36Samarium

62 28

182482Sm

151.964Europium

63 28

182582Eu

157.25Gadolinium

64 28

182592Gd

158.92535Terbium

65 28

182782Tb

162.5Dysprosium

66 28

182882Dy

164.93032Holmium

67 28

182982Ho

167.259Erbium

68 28

183082Er

168.93421Thulium

69 28

183182Tm

173.054Ytterbium

70 28

183282Yb

174.9668Lutetium

71 28

183292Lu

232.03806Thorium

90 28

183218102

Th231.03588

Protactinium

91 28

18322092

Pa238.02891Uranium

92 28

18322192

U(237)

Neptunium

93 28

18322292

Np(244)

Plutonium

94 28

18322482

Pu(243)

Americium

95 28

18322582

Am(247)

Curium

96 28

18322592

Cm(247)

Berkelium

97 28

18322782

Bk(251)

Californium

98 28

18322882

Cf(252)

Einsteinium

99 28

18322982

Es(257)

Fermium

100 28

18323082

Fm(258)

Mendelevium

101 28

18323182

Md(259)

Nobelium

102 28

18323282

No(262)

Lawrencium

103 28

18323283

Lr

1.00794Hydrogen

1 1

H

6.941Lithium

3 21

Li9.012182

Beryllium

4 22

Be

22.98976928Sodium

11 281Na

24.305Magnesium

12 282Mg

39.0983Potassium

19 2881K

40.078Calcium

20 2882Ca

85.4678Rubidium

37 28

1881Rb

87.62Strontium

38 28

1882Sr

132.9054Cesium

55 28

181881Cs

137.327Barium

56 28

181882Ba

(223)Francium

87 28

18321881

Fr(226)

Radium

88 28

18321882

Ra

44.955912Scandium

21 2892Sc

47.867Titanium

22 28

102Ti

50.9415Vanadium

23 28

112V

51.9961Chromium

24 28

131Cr

54.938045Manganese

25 28

132Mn

55.845Iron

26 28

142Fe

58.933195Cobalt

27 28

152Co

58.6934Nickel

28 28

162Ni

63.546Copper

29 28

181Cu

65.38Zinc

30 28

182Zn

88.90585Yttrium

39 28

1892Y

91.224Zirconium

40 28

18102Zr

92.90638Niobium

41 28

18121Nb

95.96Molybdenum

42 28

18131Mo

(98.0)Technetium

43 28

18132Tc

101.07Ruthenium

44 28

18151Ru

102.9055Rhodium

45 28

18161Rh

106.42Palladium

46 28

1818Pd

107.8682Silver

47 28

18181Ag

112.411Cadmium

48 28

18182Cd

138.90547Lanthanum

57 28

181892La

178.48Hafnium

72 28

1832102Hf

180.9488Tantalum

73 28

1832112Ta

183.84Tungsten

74 28

1832122W

186.207Rhenium

75 28

1832132Re

190.23Osmium

76 28

1832142Os

192.217Iridium

77 28

1832152Ir

195.084Platinum

78 28

1832171Pt

196.966569Gold

79 28

1832181Au

200.59Mercury

80 28

1832182Hg

(227)Actinium

89 28

18321892

Ac(267)

Rutherfordium

104 28

183232102

Rf(268)

Dubnium

105 28

183232112

Db(271)

Seaborgium

106 28

183232122

Sg(272)

Bohrium

107 28

183232132

Bh(270)

Hassium

108 28

183232142

Hs(276)

Meitnerium

109 28

183232152

Mt(281)

Darmstadtium

110 28

183232171

Ds(280)

Roentgenium

111 28

183232181

Rg(285)

Copernicium

112 28

183232182

Cn

4.002602Helium

2 2

He

10.811Boron

5 23

B12.0107Carbon

6 24

C14.0067

Nitrogen

7 25

N15.9994Oxygen

8 26

O18.9984032Fluorine

9 27

F20.1797Neon

10 28

Ne

26.9815386Aluminum

13 283Al

28.0855Silicon

14 284Si

30.973762Phosphorus

15 285P

32.065Sulfur

16 286S

35.453Chlorine

17 287Cl

39.948Argon

18 288Ar

69.723Gallium

31 28

183Ga

72.64Germanium

32 28

184Ge

74.9216Arsenic

33 28

185As

78.96Selenium

34 28

186Se

79.904Bromine

35 28

187Br

83.798Krypton

36 28

188Kr

114.818Indium

49 28

18183In

118.71Tin

50 28

18184Sn

121.76Antimony

51 28

18185Sb

127.6Tellurium

52 28

18186Te

126.90447Iodine

53 28

18187I

131.293Xenon

54 28

18188Xe

204.3833Thallium

81 28

1832183Tl

207.2Lead

82 28

1832184Pb

208.9804Bismuth

83 28

1832185Bi

(209)Polonium

84 28

1832186Po

(210)Astatine

85 28

1832187At

(222)Radon

86 28

1832188Rn

(284)Nihonium

113 28

183232183

(289)Flerovium

114 28

183232184

Fl(288)

Moscovium

115 28

183232185

(293)Livermorium

116 28

183232186

Lv(294)

Tennessine

117 28

183232187

(294)Oganesson

118 28

183232188

Nh McCn Ts Og

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