Implementing Next Generation Seqqg()uencing (NGS) as a ...€¦ · NGS Survey of CAP PT...

2013 Laboratory Accreditation Program Audioconferences and gWebinars Implementing Next Generation Sequencing (NGS) as a Clinical q g ( )Tool in the Laboratory

Nazneen Aziz, PhD,

Director, Molecular MedicineTransformation Program Office

February 20, 2013

TopicsTopics

• Next Generation Sequencingo Technology overview o Rapidly evolving field o Factors driving adoption of NGS in diagnostic

medicine o CAP/CLIA standards developed for NGSo CAP/CLIA standards developed for NGS o NGS methods based PT in development

© 2013 College of American Pathologists. All rights reserved. 2

Introduction to Next Generation SequencingOverview: History

Human genome Project led the path to genomic medicine

Overview: History

(1990–2003) Now

Human Genome Project Genomic medicineHuman Genome Project

13 years | $3 billion

Genomic medicine

Sequence Compare Report


Research Applications Predict and diagnose diseases

Sanger Sequencing: Autoradiography ChromatogramsSanger Sequencing: Autoradiography Chromatograms


The Human Genome Project (first reference sequence) was done using Sanger sequencing.

Sanger vs Next Generation SequencingSanger vs Next Generation Sequencing

Sanger Next Generation


Sequencing

Sanger vs Next Generation SequencingSanger vs Next Generation Sequencing


Illumina Genome Analyzer

A

Compiled Image

A

C

T

C

G

Flow Cell Clusters

Qualitative and Quantitative InformationQualitative and Quantitative Information

G>Illumina

Ref SeqG>A

Coverageor number of reads

8

Next Generation Sequencing BioinformaticsNext Generation Sequencing Bioinformatics

Variant IdentificationImage Capture Identification

Annotation

Giga-Terabyte

Conversion to Bases

Image ProcessingSequence Read

FilesBase Quality Scores

Signal to Noise


Rapid Evolution of Next Generation SequencersFirst Wave Second Wave

454/Roche“2005” Illumina Life

Tech Helicos Pacific Biosciences

GS FLX GenomeAnalyzer SOLiD HeliScope SMRT

Third Wave

GS Junior

SOLiD 5500 SOLiD 5500xl

GAIIxGAIIe

Ion TorrentJunior GAIIe

HiScanSQHiSeq

PGSIon Proton

miSeqo oto

Proton

Sequencing Chemistries and Signals are VariedSequencing Chemistries and Signals are Varied

Pyrosequencing454

Sequencing by LigationSOLiD

Reversible Dye TerminatorsIllumina Ion Torrent

Generation of Luminescent or Fluorescent Images gor chemical signals


Conversion to Sequence

Illumina HiSeq 2000Illumina HiSeq 2000

2 Independent Flow Cells8 Lanes per Flow Cell

Multiple Samples per Lane

2 G Fl C ll2- 3 Exome(s) per Lane


2 Genomes per Flow Cell7 days/genome

New PlatformsL th h t f t t d tiLower throughput - faster turn around time

Ion Torrent PGMIllumina miSeq

Reversible Dye Monitors H+


Reversible Dye Terminators

Monitors H+ Release

Ion Proton DNA SequencerIon Proton DNA Sequencer

• Semiconductor chips form the heart of the pmachine.

• CMOS chips detect chemical changes instead of lightinstead of light.

• The Ion Proton I chip has 165 million sensors Mid-2012.

• The Ion Proton II Chip has 660 million sensors.

• Late 2012.

• Significant increase in speed and reduction f th t f l l i

14© 2013 College of American Pathologists. All rights reserved.

of the cost of genome-level sequencing.

Oxford Nanopore: Single Molecule Sequencing Oxford Nanopore: Single Molecule Sequencing


Alignment SoftwareAcademic Software

Alignment Software

maq assemble [-sp] [-m maxmis] [-Q maxerr] [-r hetrate] [-t coef] [-q minQ] [-N nHap] out.cns in.ref.bfa in.aln.map2> out.cns.log

• In-house built

• Free

• Genome community supportGenome community support

• Feature rich user interface

Commercial Software

• $$$

• Company support


AgendaAgenda

• Next Generation Sequencingo Technology overview o Rapidly evolving field

F t d i i d ti f NGS i di ti di io Factors driving adoption of NGS in diagnostic medicine o Standards developed for laboratory accreditation at CAP o NGS methods based PT in developmentp


Growth in Sequencing Revenues: Genetic TestingGrowth in Sequencing Revenues: Genetic Testing

Estimated to reachEstimated to reach $5 billion : 2015


The Cost of Genome Sequencing is Decreasing Rapidly and Driving Clinical Adoption of Genomic Analysis g p y

Cost per Genome Data Generation, Sep 2001 – Oct 2011$100 000 000

$10,000,000

$100,000,000

$100,000

$1,000,000

$1,000

$10,000

$1,000

Oct

-01

Apr

-02

Oct

-02

Apr

-03

Oct

-03

Apr

-04

Oct

-04

Apr

-05

Oct

-05

Apr

-06

Oct

-06

Apr

-07

Oct

-07

Apr

-08

Oct

-08

Apr

-09

Oct

-09

Apr

-10

Oct

-10

Apr

-11

Oct

-11

© 2013 College of American Pathologists. All rights reserved. 19Source: National Human Genome Research Institute

Cost for genome sequence data generation today is <$3,000

Decline in Sequencing Costs Likely to ContinueDecline in Sequencing Costs Likely to Continue


Genomic Analysis by Next Gen Sequencing Currently UsedCurrently Used

Past and Continuing Molecular Pathology Tests Genomic Analysis: Most

commonly used

Genomic Analysis:Growing and perhaps

common in the near future

Si l G /P th

Single/Few Mutations Gene Panels

E T i t

Genome

Single Gene/Pathogen

Few Genes

Exome Transcriptome

Genomic Analysis by Next Gen Sequencing


NGS Survey of CAP PT CustomersNGS Survey of CAP PT Customers

• 19% current users• 55% plan to begin NGS

• 20% within 6 months20% within 6 months• 14% within 12 months• 21% within 1 – 3 years

• 19% do not plan to begin using NGS technology 176 d gy

• Of those using NGS technology, 61% perform less than 10 tests per month

176 responders


per month

Disease Area NGS TestsDisease Area NGS Tests


NGS Tests Offered: Panel Exome GenomeNGS Tests Offered: Panel, Exome, Genome


Expansion Plans of NGS Test OfferedExpansion Plans of NGS Test Offered


Confirmation Using Alternate TechnologiesConfirmation Using Alternate Technologies

• 41% always use Sanger or other technologies to confirm pathogenic variants prior to

tireporting

• 22% use it only for specific cases/assayscases/assays

26© 2013 College of American Pathologists. All rights reserved.

Bioinformatics SupportBioinformatics Support

30% require out-sourced bioinformatics support


Clinical Genomic Analysis ProcessClinical Genomic Analysis Process

Pre-AnalyticalPre-Analytical

Sequence Data GenerationSequence Data Generation

Sequence Data Interpretationq p

Reporting & Billing

Clinical Consultation


Pre-Analyticale a yt ca

D t i if t ti i li i ll f l• Determine if testing is clinically useful

• Determine appropriate test, specimen, and laboratorypp p , p , y

• Obtain sample and patient consent


Sequence Data Generation

Data QA & Sequence AlignmentSequencing Process

• DNA extraction • Quality assessment of sequence data (d th f i t f

• DNA fragmentation

• Fragment selection

(depth of coverage, variant frequency, etc.)

• Align sequence data to reference • Fragment selection

• Adapter ligation

g qsequence

• Identify variants based on reference sequence• Clonal amplification

• Sequencing

sequence

• 6 Billion bases (maternal and paternal)


• 4 Million variants (10% complex variants: indels, SV, CNVs…)

Sequence Data Interpretation

Cli i l I t t tiV i t A t Clinical Interpretation Variant Assessment

• Compare variants to databases • Integration of potentially Compare variants to databases (OMIM, COSMIC, dbSNP, 1000 Genomes, ENCODE, etc.)

V i t i t l i ( l ti

teg at o o pote t a ysignificant variants with clinical phenotype of the patient, family, and literature

• Variant impact analysis (evolutionary conservancy analysis, protein structural analysis, pathway analysis, etc.)

• Interpretive report generation)

• Literature reviews


Reporting & Billing

• Report in LIS, EHR., and PHR

• Code and bill for testing & interpretationCode and bill for testing & interpretation

© 20123College of American Pathologists. All rights reserved. 32


Ph i i lt• Physician consults

• Clinical conferences

• Patient consultations with physician and genetic counselorscounselors


Clinical Genomic Analysis Process Sequence Data Generation

Data QA & Sequence AlignmentSequencing ProcessPre-Analytical

• DNA extraction • Quality assessment of sequence data (depth • Determine if testing DNA extraction• DNA fragmentation• Fragment selection• Adapter ligation• Clonal amplification

Sequencing

Quality assessment of sequence data (depth of coverage, variant frequency, etc.)

• Align sequence data to reference sequence• Identify variants based on reference

sequence6 Billion bases (maternal and paternal)

Determine if testing is clinically useful

• Determine appropriate test, specimen, and laboratory

Sequence Data Interpretation

• Sequencing • 6 Billion bases (maternal and paternal)• 4 Million variants (10% complex variants:

indels, SV, CNVs…)

laboratory• Obtain/document

patient consent

Integration of Report in LIS • Individual • Compare variants to databases


Reporting & Billing

Clinical Interpretation Variant Assessment

• Integration of potentiallysignificant variants with clinical, family, and literature

• Report in LIS, EHR and PHR

• Code and bill for testing & interpretation

• Individual physician consults

• Clinical Conferences

• Compare variants to databases (OMIM, COSMIC, dbSNP, 1000 Genomes, ENCODE, etc.)

• Variant impact analysis (evolutionary conservancy

• Write interpretive report

• Patient consultations

analysis, protein structural analysis, pathway analysis, etc.)

• Literature reviews© 2013 College of American Pathologists. All rights reserved. 34

CAP/CLIA Steps in Clinical Genomic Testing Process

Work FlowWork Flow

CAP/CLIA Steps in Clinical Genomic Testing Process

Physician Genome CLIA lab Deliver data PatientPhysician orders IGS for patient

Genome Sequencing

and QC

CLIA lab delivers

results to physician

Deliver data to patient

Patient Understands Implications

CAP’s standards in accreditation, PT services, reporting of NGS labs

AgendaAgenda

• Next Generation Sequencingo Technology overview

R idl l i fi ldo Rapidly evolving field o Factors driving adoption of NGS in diagnostic medicine o Standards developed for laboratory accreditation at CAPo Standards developed for laboratory accreditation at CAP o NGS methods based PT in development


Why do we need to have standards for NGS clinical tests?Why do we need to have standards for NGS clinical tests?

3 3 53- 3.5 Million variants/genome

Dramatically increased complexity

Test results need to capture not only the unique genetic differences but also the

tt f diff© 2013 College of American Pathologists. All rights reserved.

patterns of differences37

NGS Work Group Charter

Id tif R fi d R d L b t A dit tiIdentify, Refine, and Recommend Laboratory Accreditation Standards for the Analytical and Bioinformatics Workflow for Clinical Tests Using NGS

1

Recommend Proficiency Testing Protocols, Reference Materials and Product Development2 Materials, and Product Development

Other Goals: Adapt to Meet Growing Questions/NeedsRaised by Next Generation Sequencing3


Process We Follow

• Employ Existing “Applicable” RequirementsEmploy Existing Applicable Requirements

• Introduce New Requirements Where Needed

• Find the Right Balance


Next Generation Sequencing: Steps in WorkflowNext Generation Sequencing: Steps in Workflow

Analytical Wet Bench Process: sample handling librarysample handling, library preparation, sequence generation

Bioinformatics process:Alignment, variant calling, and variant annotation


Clinical Interpretation

NGS Accreditation Checklist Themes:

Documentation Documentation

Test Validation

Quality control and quality assurance

Traceability of test results reported (instrument, chemistry, versions)

Test Validation

Quality control and quality assurance

Traceability of test results reported (instrument, chemistry, versions)Traceability of test results reported (instrument, chemistry, versions)

Exceptional log - test samples

Confirmatory testing using an alternate method during validation

Traceability of test results reported (instrument, chemistry, versions)

Exceptional log - test samples

Confirmatory testing using an alternate method during validation

Monitoring and implementing- upgrades to the chemistry or bioinformatics

software

D t t d d t t f l d ti d HIPAA

Monitoring and implementing- upgrades to the chemistry or bioinformatics

software

D t t d d t t f l d ti d HIPAA Data storage and data transfer – cloud computing and HIPAA

Clinical interpretation of variants - using professional guidelines

Reporting of unexpected and significant findings (incidental findings)

Data storage and data transfer – cloud computing and HIPAA

Clinical interpretation of variants - using professional guidelines

Reporting of unexpected and significant findings (incidental findings)


p g p g g ( g )p g p g g ( g )

MOL.XXX02The laboratory validates the analytical wet bench process and revalidates after changes or upgrades to any components used to generate next generation sequencing dataor upgrades to any components used to generate next-generation sequencing data.

NOTE: Validation of the analytical wet bench process can be method-based or analyte-specific and must describe required performance characteristics of the entire analytical process and individual process steps. Revalidation may cover all or a subset of steps in the process depending on the extent of the modification. Acceptance criteria for analytical runs must be established.

•Validations must include information on the analytical target (examples: exons, genes, exomes, genomes, transcriptomes). The ability of the analytical process to sequence the target (e.g., percentage of target adequately sequenced) must be describedadequately sequenced) must be described.

•Validations must determine and document analytical sensitivity, specificity, reproducibility, repeatability and precision for the types of variants assayed (e.g., single nucleotide variants, insertions and deletions, homopolymer or repetitive sequences).

•Interference by clinically relevant pseudogenes and other sequences highly homologous to the target must be determined and documented.

•Sequencing error rates (i.e., false positives and false negatives) for variants assayed must be determinedSequencing error rates (i.e., false positives and false negatives) for variants assayed must be determined and documented using an alternative method which may include an alternate NGS chemistry.

•Indexing (bar coding) and sample pooling methods must be validated to ensure that individual sample identity is maintained throughout the analytical wet bench process.


Evidence of compliance:•Records of validation and revalidation studies

MOL 34936: Validation Wet Bench AnalyticalMOL.34936: Validation - Wet Bench Analytical The laboratory validates the analytical wet bench process and revalidates after changes or upgrades to any components used torevalidates after changes or upgrades to any components used to generate next generation sequencing data

•Validations must determine and document analytical sensitivity, specificity, reproducibility repeatability and precision for the types of variants assayedreproducibility, repeatability and precision for the types of variants assayed (e.g. single nucleotide variants, insertions and deletions, homopolymer or repetitive sequences).

•Interference by clinically relevant pseudogenes and other sequences highly homologous to the target must be determined and documented.

•Sequencing error rates (i.e. false positives and false negatives) for variantsSequencing error rates (i.e. false positives and false negatives) for variants assayed must be determined and documented using an alternative method which may include an alternate NGS chemistry.

I d i (b di ) d l li th d t b lid t d t

43

•Indexing (barcoding) and sample pooling methods must be validated to ensure that individual sample identity is maintained throughout the analytical wet bench process.

MOL 34940 C fi t T tiMOL.34940: Confirmatory Testing

The laboratory has a policy for when confirmatory testing of id tifi d t d i t ill b d t i d bidentified or reported variants will be determined by an alternative method.

The laboratory maintains an ongoing record of the sensitivity, specificity, false positives, false negatives, reproducibility and repeatability of results and compares these with datarepeatability of results and compares these with data obtained during the validation process.

Evidence of Compliance:Policy or procedure that describes the indications for confirmatory testing.


y g

MOL 34944 P ti t R tMOL.34944: Patient Reports

The specific methods, instrument(s) and reagents are t bl f h ti t ttraceable for each patient report.


MOL 34948 M it i f U dMOL.34948: Monitoring of Upgrades

The laboratory has a policy for monitoring andThe laboratory has a policy for monitoring and implementing upgrades to instruments, sequencing chemistries, and reagents or kits used to generate next

ti d tgeneration sequence data.


MOL 34952 Sequence Variants: Interpretation/ReportingMOL. 34952 Sequence Variants: Interpretation/Reporting

Interpretation and reporting of sequence variants takesInterpretation and reporting of sequence variants takes into consideration professional organizations' recommendations and guidelines.

•The laboratory should have a decision making process for classifying and interpreting pathogenic variants, potential pathogenic variants, benign variants, and variants of unknown clinical significance.


MOL 34954 Cli i ll Si ifi t G ti Fi diMOL.34954: Clinically Significant Genetic Findings

The laboratory has a policy regarding reporting ofThe laboratory has a policy regarding reporting of clinically significant genetic findings unrelated to the clinical purpose for testing.

• Gene panel(s), exome, transcriptome, and genome sequencing may yield unexpected (or incidental) clinically q g y y p ( ) ysignificant genetic findings unrelated to the disorder for which the patient is undergoing testing.


MOL 34958 P /Pi li D t tiMOL.34958: Process/Pipeline DocumentationThe laboratory documents the bioinformatics process or pipeline(s) used to support the analysis, interpretation, and reporting of next generation sequencing based results.

• A bioinformatics process or pipeline includes all algorithms, software, scripts, database packages, reference sequences, and databases whether in-house developed, vendor-developed and/or supported or open source. Flow diagrams may be helpful in providing a graphical overview of processes.

Documentation used to support clinical operations must include:• The individual applications used, with versions and appropriate command line flags or other

configuration items that deviate from the standard, baseline installation

• Additional scripts or steps used to connect discrete applications

• Description of input and output data files or information in each process step

• Metrics and QC parameters for optimal performance


• Criteria for variant calling

MOL 34968 V i T bilitMOL.34968: Version Traceability

The specific version(s) of the bioinformatics process or pipeline(s) d t t t ti i d t t bl fused to generate next generation sequencing data are traceable for

each patient report.

• Details of the version of the bioinformatics process or pipeline used to generate each patient report may utilize a laboratory-specific system that refers to the entire process or pipeline, as well as changes to the versions of the individual components within the process or pipeline.


MOL 34972 D t T f C fid ti lit P liMOL.34972: Data Transfer Confidentiality PolicyThere are procedures in place to ensure that internal and external storage and transfer of sequencing data provides reasonablestorage and transfer of sequencing data provides reasonable confidentiality and security, and conforms to patient confidentiality requirements.

• It is recognized that laboratories may transfer data to external laboratories and other service providers for storage and analysis. This may include data storage and analysis through cloud-based computing.

• Procedures to ensure confidentiality might include message security, system and user authentication activity logs encryption and accesssystem and user authentication, activity logs, encryption, and access restrictions.


AgendaAgenda

• Next Generation Sequencingo Technology overview

R idl l i fi ldo Rapidly evolving field o Factors driving adoption of NGS in diagnostic medicine o Standards developed for laboratory accreditation at CAPo Standards developed for laboratory accreditation at CAP o NGS methods based PT in development


Plans for Proficiency Testing in NGS Plans for Proficiency Testing in NGS

• Offer a pilot product in 2013

• Learn from this offering:Technology platforms usedWGS Exome gene panels usedWGS, Exome, gene panels used

• Troubleshoot

• Full fledged PT offering by 2014 – 2015


Types of Next Generation Sequencing PTTypes of Next Generation Sequencing PT

Analytical Wet Bench Process: sample handling library Wet challengesample handling, library preparation, sequence generation Total

g

Total challenge

Bioinformatics process:Alignment, variant calling, and variant annotation

Dry challenge

54

Clinical Interpretation© 2013 College of American Pathologists. All rights reserved.

Relevant White PapersRelevant White Papers

• Opportunities and Challenges Associated with Clinical Diagnostic Genome Sequencing. A Report of the Association for Molecular Pathology. The Journal of Molecular Diagnostics. Vol. 14, No. 6, November 2012.

• Assuring the quality of next-generation sequencing in clinical laboratory practice. Nature Biotechnology. Vol. 30, No. 11, November 20122012.


AcknowledgementsAcknowledgements

• Karl Voelkerding for some slides on NGS methods

• NGS Work Group at CAP for development of the NGS checklistNGS checklist

• The Case-for-Change M4 Team at CAP for some slidesslides

© 2013College of American Pathologists. All rights reserved. 56

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