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Sample

October 2016

DNA Sequencing Markets: Global Analysis and Opportunity Evaluation 2016 to 2020

DNA Sequencing Markets

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Data Files

Purchasers of the ‘report and data’ package of this report also receive the full raw data collected during the conduct of these two global sequencing studies. This includes details of participating organisations. These raw data files allow the analysis of specific market sectors or segments of interest, as well as relationships between different areas of these markets, specific to your own strategic interests.

File Description This files (in excel.xlxs format) consist of rows (corresponding to the number of participants) and columns (corresponding to the study questions and data). Data contained within this excel file can be analysed using the filters already set up. Identifying Opportunities The raw data spreadsheet can be analysed in many different ways, including the identification of market opportunities. To give a few examples, it is possible to analyse data sets where the highest rates of growth are expected by end-users, relationships between techniques and applications, costs and throughput, as well as by suppliers into specific areas of the market. Where there are sufficient numbers of participants, these data can also be analysed by country, region and in other ways.

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1.1. This Chapter Laboratory Markets Limited has carried out two comprehensive market studies of nucleotide sequencing. These studies involved the participation of 526 experienced end-users and profiled current practices, developments, trends and plans over the next three years, as well as growth and opportunities across key sectors of these markets. Its findings provide a wealth of market information on the current and evolving use of nucleotide sequencing. 1.2. Background The last decade has seen remarkable innovation and development in the nucleotide sequencing field. Today, a number of powerful high–throughput sequencing technologies are available and are being used to address an increasingly diverse range of biological problems. The quantitative scale and efficiencies of next-generation sequencing platforms are also seeing unprecedented progress and growth in many areas of fundamental research. Dramatic reductions in the associated costs and the operational complexities of these techniques are also being seen and are opening up applications in areas that would have been unimaginable just a decade ago. This report presents the findings of two global studies of nucleotide sequencing, which profiled the use of these techniques from the end-users' perspectives. These studies which evaluated end-users' current sequencing practices and three-year plans, investigated market growth; the competitive positions of global sequencing suppliers, sequencing techniques and applications, polynucleotide types, advantages and disadvantages of techniques, sequencing costs versus genetic code lengths, use of specialist software, disease areas, sample types and sample preparation, sectors, disease biomarkers and other areas. These studies involved the participation of 526 end-users across 60 countries and profiled current practices, developments, trends and future plans over the next three years, as well as growth and opportunities across key sectors of these markets. Laboratory Markets' specialised market studies are designed to assist suppliers and developers to profile current and evolving market opportunities. All of our studies are carried out through specialist groups of experienced researchers and clinicians, and therefore findings are based on 'real world' primary market data. By providing new insights and a better understanding of end-user practices, needs and future plans, our studies assist suppliers to sell into these markets and also support innovation and strategic planning.

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1.3. Market Questions 2016 Study (217 Participants) Trends and Growth: Based on recent trends in the number of sequencing studies carried out in their laboratories, end-users' estimates of by how much (% increase or % decrease) their laboratory use of sequencing has changed over the last three years. Also, based on current trends in the number of sequencing studies carried out in their laboratories, end-users' estimates of by how much (% increase or % decrease) they anticipate their laboratory use of sequencing will change over the next three years. Sequencing Techniques: Sequencers’ main use of specific sequencing techniques, both currently and anticipated in three years from now, where the techniques considered were 454 Pyrosequencing (Roche), Chain Termination Method (Sanger Sequencing), DArT Seq (Diversity Array Technology), DNA Nanoball Sequencing (Complete Genomics), DNA Nanopore Sequencing (Oxford Nanopore Technologies), Electron Microscopy-Based Sequencing (ZS Genetics), Gene Electronic Nano-Integrated Ultra-Sensitive Technology (Geneapsys), Ion Torrent (Thermo Fisher), Massively Parallel Signature Sequencing (Illumina), Microfluidic Sequencing (GnuBIO), Nanowire Biosensor Sequencing Technology (Quantumdx), RAD Sequencing (University Oregon/Floragenex), Sequencing by Hybridization (Affymetrix), Sequencing by Hybridization-Assisted Pore-Based sequencing (NABsys), Sequencing by mass spectrometry, Sequencing by Reversible-Hybridization (Complete Genomics), Sequencing by Synthesis (Illumina/Solexa), Shotgun Sequencing/Chain Termination (Sanger), Single Molecule Nanopore Sequencing (Noblegen Biosciences), Single Molecule Real-Time Sequencing (Pacific Biosciences), Single-molecule Semiconductor-Based Sequencing (Genia/Roche), SOLiD Sequencing (Applied Biosystems), Tunnelling Current DNA sequencing and others. Sequencing Instruments: Sequencers’ main use of specific sequencing techniques, both currently and anticipated in three years from now, where the techniques considered were 454/Roche: GS Junior+ System, 454/Roche: GS Junior System, 454/Roche: GS FLX+ System, Applied Biosystems: 3730xl DNA Analyzer, Applied Biosystems: 3730 DNA Analyzer, Applied Biosystems: 3500xL Genetic Analyzer, Applied Biosystems: 3500 Genetic Analyzer, Applied Biosystems: 3130XL Genetic Analyzer, Applied Biosystems: 3130 Genetic Analyzer, Applied Biosystems: 310 Genetic Analyzer, Applied Biosystems: SOLiD Next-Generation System, BGI: BGISEQ-500 NGS System, Diversity Array Technology: Scanner (DArT Seq), Geneapsys: GENIUS, GnuBio: GnuBIO instrument, Illumina: MiniSeq, Illumina: MiSeq, Illumina: MiSeqDx, Illumina: MiSeq FGx, Illumina: NextSeq 500, Illumina: HiSeq 2500, Illumina: HiSeq 3000/HiSeq 4000, Illumina: HiSeq X Five, Illumina: HiSeq X Ten, Oxford Nanopore: MinION, Oxford Nanopore: PromethION, Oxford Nanopore: GridION System, Pacific Biosciences: Sequel System, Pacific

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Biosciences: PacBio RS II, Thermo Fisher: Ion PGM System Ion PGM System, Thermo Fisher: Ion Proton System for NGS, Thermo Fisher: 3500 Genetic Analyser (Sanger), Other, None and Other (please specify). Laboratory Location: The location of the laboratory or laboratories where end-users’ nucleotide sequencing activities are carried out, both now and anticipated in three years, where the locations considered were Own Laboratory, External Laboratory and Both Own Laboratory and External Laboratory. Instrument Suppliers: End-users' current main suppliers of nucleotide sequencing instruments, products or consumables to their laboratory, now and anticipated in three years, where the companies considered were 5-Prime, Abbott, Affymetrix, Agencourt (Beckman Coulter), Agilent, AGRF, Ambion (Lifetech), Anatech, Answer Choices, AppliChem, Applied Biosystems, BD, Beckman, BGI, Bioline, Biomérieux, Biometra, BioNanomatrix, Bioneer, Bionobile, Bionobile, Bio-Rad, Celera, Chemagen (PE), Complete Genomics, DNA Technologies, Eppendorf, Eurofins, EURx, Exiqon, Fermentas, Fisher Scientific, Fluidigm, FugiFilm, GE, GenDx, Halcyon Molecular, Illumina, In-House, Inqaba Biotechnology, Integrated DNA Technologies (IDT), Intelligent BioSystems, Invitek, Invitrogen (Lifetech), Ion Torrent (LifeTech), Kapa Biosystems, Labgene, LGC Genomics, Li-Cor, Life technologies, Lucigen, Macherey-Nagel, Macrogen, Mallinckrodt Baker, Millennium Bioscience, MO BIO, Molecular Research Center, MP Biomedical, MWG Operon, NABsys, New England Biolabs, Nexttec, Nippon Gene, Nugen, Orion Genomics, Other, Oxford Nanopore, Pacific Biosciences, Panomics, Perkin Elmer, Phoenix (Microarray), Primm Biotech, Promega, Qiagen, r-Biopharm, Roche, Roche (454), Roche Diagnostics, Roth, Sangon Biotech, Seegene, SeqLL, Sequenom, Sequiserve, Siemens, Sigma-Aldrich, Solis BioDyne, Stab Vida, Takara/Clontech, Tecan, Thermo Scientific, USB Corp, Vivantis, Zymo Research and any others. Applications: End-users' current main applications of sequencing as well as the applications they anticipate using in three years from now, where the applications considered were Allele size detection, Aneuploidy and CNV analysis, Antibacterial resistance analysis, Antiviral resistance analysis, Bacterial typing, ChIP-Seq, Cloning, Complex populations, De Novo Sequencing, Detection, identification of bacteria, Detection, identification of viruses, Diverse gene polymorphisms, DNA barcoding, species identifications, DNA quantification, Epigenome characterization, Exome sequencing, Fragment analysis for epidemiological analysis, Full 16S sequencing for identification and phylogeny, Gene expression (mRNA), Gene mutations or alterations, Gene variants in disease, Genetic mapping, Genome Resequencing, Genotyping by Sequencing, Genotyping of microorganisms, Haplotypes, Immune diversity, Metagenomics, Methylation Sequencing, Microbial Sequencing, MicroRNA Studies, Microsatellites, Phylodynamic analyses, Rapid Diagnostic – Genetic Markers,

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Regulatory elements, Ribosomal DNA (rRNA) Studies, RNA Sequencing, Short Tandem Repeat Analysis, Single Nucleotide Polymorphisms, Single-Strand Conformation Polymorphism, Small insertions or deletions, Small Interfering RNA (siRNA) Studies, Small Nuclear RNA (snRNA) Studies, Small RNA and miRNA Sequencing, Targeted DNA sequencing, Targeted Resequencing, Tissue typing, Total RNA Sequencing (Transcriptome), Transfer RNA (tRNA) Studies, Ultra-Low-Input/Single-Cell RNA-Seq, Viral Typing, Whole-Genome Sequencing and any others. Diseases: End-users’ current sequencing activities and those sequencing activities they anticipate in three years from now, relating to specific disease areas, where the diseases considered were Antimicrobial resistance, Arthritis, Asthma and allergy, Autoimmune Diseases, Bone Metabolism, Cancer, Cardiovascular, Central Nervous System, Dentistry, Dermatology, Endocrine, Gastrointestinal, Genetic diseases, Genito-Urinary System, Haematology, Hearing Loss, Immunodeficiency, Infections, Infertility, Inflammation, Liver disease, Metabolic Disorders, Musculoskeletal Disorders, Nutrition, Obstetrics and Gynaecology, Ophthalmology, Pain, Phytopathology, Psychiatry, Rare diseases, Reproduction, Respiratory, Sexually transmitted infections, Skin, Stem cells, Transplantation medicine, Vector borne disease, Virus diseases, None, or any others. Nucleotide Types: Main nucleic acid types currently sequenced, as well as those anticipated to be sequenced in three years from now, where the nucleic acids considered were Archaeal DNA, Bacterial DNA, Bacterial PCR amplicons, Bisulfite-converted DNA, cDNA, cell free miRNA, fungal DNA, Genomic DNA, ITS region, Metagenomic DNA, MicroRNA, Mitochondrial DNA, mRNA, Noncoding RNA, Nuclear DNA genes, Pathogen RNA/DNA, piRNA, Plant viral RNA or DNA, Plasma Cell Free DNA, Plasmid DNA, Prokaryotic small RNA, Protist DNA, Ribosomal RNA (rRNA), Small interfering RNA (siRNA), Small nuclear RNA (snRNA), Total RNA, Transfer RNA (tRNA), Tumour Cell DNA, Viral DNA, Viral PCR amplicons, Viral RNA and any others. Software: Sequencers main software programs used for their nucleotide sequencing activities, where the software considered were (A – M) ABA (Raphaelet al.), ABySS (Simpson et al.), ACANA (Huang et al.), ACT (Sanger), Alamut (Interactive Biosoftware), ALE (Blandy et al.), AlignMe (Stamm et al.), ALLPATHS (Broad Institute), Alta-cyclic (Omictools), AMAP (Schwartz et al.), AnnHyb (MyBiosoftware), Annovar (Open Bioinformatics), anon. (Powell et al.), Artemis (Sanger), Augustus (Göttingen), AVID (Vista), BAliBASE (Thompson et al.), Bali-Phy (Redelings et al.), BarraCUDA (GPL), Base-By-Base (Brodie et al.), BBMap (Source Forge), Beast (Drummond et al.), Belvu (Sanger), BFAST (GPL), BigBWA (Omictools), Bioconductor (Aboyoun et al.), BioEdit (Ibis), BioLinux (EON), Biomart (Ensembl), BioNumerics (Applied Maths), BioPerl dpAlign (Chan et al.), Biopieces (Biostars), BisMark (Babraham), BLAST (Altschul et al.), BLASTN (NCBI), BLASTZ,LASTZ (Schwartz et

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al.), BLAT (Non-Commercial Academic), BLOCKS (Molbio-Tools), Bowtie (Artistic License), BS-Seq (UCLA), Bustard (Illumina), BWA (GPL), BWA-PSSM (Bio-BWA), Cap3 (Genome), Casava (Illumina), CASHX (Non-Commercial Academic), CEQ (Beckman et al.), CHAOS/DIALIGN (Brudno et al.), ChIP-Seq (DNASTar), Chromas (Technelysium), Clarity (Genologics), CLC Genomic Workbench (CLCBio), Clone Manager (CLCBio), Cloudburst (Artistic License), ClustalW (Thompson et al.), CNVnator (Omictools), CNV-Seq (Chao et al.), CodonCode Aligner (Richterich et al.), Compass (Sadreyev, et al.), Contig Express (Contig), CS-BLAST (Angermueller et al.), CUDA-EC (Omictools), CUDAlign (Source Forge), CUDA-MEME (MyBiosoftware), CUDASW++ (Liu et al.), Cufflinks (Cole-trapnell), CUSHAW (GPL), CUSHAW2 (GPL), CUSHAW2-GPU (GPL), CUSHAW3 (Source Forge), Custom Designed (In-House), Dalliance (Omictools), dbSNP (Open Source), DECIPHER (DecipherProject), DESeq (Bioconductor), DIALIGN-TX and DIALIGN-T (Subramanian et al.), DIAMOND (GitHub), DNA Alignment (Roehl et al.), DNA Baser Sequence Assembler (Heracle BioSoft), DNADot (Bowen et al.), DNAsp (UBEdu), DNASTAR (DNAStar), DOTLET (Pagni et al.), dpAlign (BioPerl), drFAST (BSD), EagleView (Boston College), Edena (Hernandez ), EDNA (Salama et al.), ELAND (Illumina), EMBL-EBI (EBI Ac), eMOTIF (Stanford), Ensemble (Ensembl), ERANGE (Wold Lab), ERNE (GPL), EULER-SR (Chaisson ), Excel (Open Source), Exonerate (Guy St C Slater et al.), ExpressionSuite (Thermo Fisher), FASTA (Faster Biotech), Fastpcr (PrimerDigital), FastQC (Babraham), fastseq (Helical), fastx-tools (Hannon), FEAST (Hudek et al.), FindPeaks (Bainbridge et al.), FMM (Open Source), FreeBayes (Omictools), FSA (Bradley et al.), Galaxy (Galaxy), GapMis (Frousios et al.), GASSST (Omictools), GATK (Broad Institute), GEM (Non-Commercial Academic), GenAlex (BiologyAssets), Genalice MAP (Genalice), GenDB (Open Source), Gene Construction Kit (Textco), Gene Mapper (ABI), Gene tex (Genetex), GeneInsight (Geneinsight), Geneious (Drummond et al.), Geneious Assembler (Geneious), GeneMapper® Software (ABI), Genologics (Illumina), Genomatix (Genomatix), Genome Browser (UCSC), Genome Compiler (Genome Compiler), GenomeMapper (1001 Genomes project), GenomeStudio Software (Illumina), Genomics Workbench (CLCBio), Genoogle (Genoogle), Genotyper (ABI), GenSearch (Phenosystems), GensearchNGS (Omictools), Geospiza (Geospiza et al.), GGSEARCH, GLSEARCH (Pearson et al.), Gibbs motif sampler (Omictools), Glimmer (CBCD), GLProbs (Omictools), GMAP and GSNAP (Non-Commercial Academic), G-Mo.R-Se (CNS, France), GNUMAP (Omictools), G-PAS (Frohmberg et al.), GS Amplicon Variant Analyzer (Roche), HapCompass (Omictools), HGMD (Biobase), HHpred / HHsearch (Söding et al.), HiSeq Software (Illumina), HIVE-hexagon (Hive), HMMER (Durbin et al.), HMMTOP (SACS), HOMSTRAD (Mizuguchi et al.), Htseq (Huber et al.), HyPhy (Hyphy et al.), Ibis (Ibis), IDF (CSUni), IGV (Broad Institute), IMEX (Omictools), IMGT (IMGT), Infernal (Eddy), Ingenuity (Ingenuity), In-House (In-House), Ion Reporter (Thermo Fisher), Ion torrent (Thermo Fisher), iSAAC (Non-Commercial Academic), I-sites (Open Source), JAligner (Moustafa et al.), Jalview (Jalview), JCoils

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(CHEmbnet), K*Sync (Chivian et al.), Kalign (Lassmann et al.), KLAST (CLCBio), Kodon (Applied Maths), LALIGN (Pearson et al.), Lasergene (DNAStar), LAST (GPL), LASTZ (NCBI), LookSeq (Sanger), MACS (Zhang et al. ), MacVector (MacVector), MAFFT (Katoh et al.), Mage Platform (Genoscope), mAlign (Powell et al. ), Manattee (Manattee), MapNext (Sun-Yat Sen Univ), MapView (Sun-Yat Sen Univ), MAQ (GPL), MARNA (Siebert et al.), Matcher (Longden et al.), Mauve (Darlinglab), MAVID (Bray et al.), MCALIGN2 (Wang et al.), MEGA (Megasoft), MEME/MAST (Meme) and (M to Z) MERCI (Bioinfo), Metacore (Omictools), MG RAST (Metagenomics), MGA (Omictools), Mira (Omictools), MIRA2 – MIRA (Source Forge), MirCheck (Mybiosoftware), Mirdeep2 (MDC Berlin), miREvo (Omictools), MiSeq (Illumina), MiSeq Software (Illumina), MOM (CS.CMU), MOSAIK (Strömberg et al. ), MPscan (Omictools), MrBayes (MrBayes), mrFAST and mrsFAST (BSD), MSA (Lipman et al.), MSAProbs (Liu et al.), MSeqDR (Open Source), Mulan (Mulan), MULTALIN (Corpet et al.), Multi-LAGAN (Brudno et al.), Multiz (Mybiosoftware), MUMmer (Kurtz et al.), MUSCLE (Edgar et al.), Mutation Surveyor (Softgenetics), Mothur (Mothur), mVista (Genome), MyRAST (Mybiosoftware), NCBI (Open Source), Needle (Bleasby et al.), NETGLYC (CBS), NetPrimer (PremierBiosoft), Newbler (Roche), NextGENe (Softgenetics), NextGenMap (Omictools), Ngila (Cartwright et al.), NISC (NIH), Novoalign & NovoalignCS (Non-Commercial Academic), NW-align (Zhang et al.), Omixon (Omixon), Opal (Wheeler et al.), Oxbench (Raghava et al.), PAL_finder (Source Forge), PALMapper (GPL), Pandaseq (Github), Panther (Omictools), Parasail (BMC), Partek (Partek), Pasa (Pasa), PASS (CRIBI), Path (Gîrdea et al.), PathSeq (Broad Institute), PatternHunter (Ma et al.), PAUP (Evolution), PeakSeq (Rozowsk et al.), Pecan (Paten et al.), PerM (GPL), PFAM (Sanger), PHI-Blast (NCBI), Phylo (McGill Bioinformatics), Phylogeny (Evolution), Phyloscan (NCBI), phyML (ATGC), Picard (Broad Institute), PicXAA (Omictools), PLAST-ncRNA (NCBI), PMS (Open Source), POA (Lee et al.), PolyBayesShort (Boston College), Polyphen (Harvard), Praline (Heringa et al.), PRATT (EBI Ac), PREFAB (Edgar et al.), Primer 3 (PremierBiosoft), PRIMEX (Open Source), Prism (ABI), ProbA (also propA) (Mückstein et al), Probalign (Roshan et al.), ProbCons (Do et al.), Prodigal (Omictools), PROMALS3D (Pei et al.), Proseq (Biosoft), PRRN/PRRP (Totoki et al), PSAlign (Sze et al.), PSI-BLAST (Altschul et al. ), PSI-Search (Li et al.), PyMOL (DeLano et al.), PyroBayes (Boston College), Python (DigitalBiol), QIIME (QIIME), Qpalma (De Bona et al. ), QuEST (Stanford), R (Open Source), RAST (Molbiotools), Ray (Denovo), RazerS (LGPL), RDP (NCBI), REAL, cREAL (GPL), REPuter (Kurtz et al.), RevTrans (Wernersson et al.), RMAP (GPL), rNA (GPL), RNASAT (Stanford), Rolexa (Bioconductor), RTG Investigator (Non-Commercial Academic), SABERTOOTH (Teichert et al.), SABmark (Van Walle et al.), SAGA (Notredame et al.), SAM (Krogh et al.), Satsuma (Grabherr et al.), ScalaBLAST (Oehmen et al.), ScanProsite (Prosite), Se-Al (Rambaut et al.), Seaview (Mybiosoftware), Segemehl (Non-Commercial Academic), SEQALN (Waterman et al.), SEQAN (Rausch et al.), SeqMan (DNAStar), SeqMap (Jiang et al.), SeqScape

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(Thermo Fisher), Sequence Scanner Software (ABI), Sequences Studio (Meskauskas et al.), Sequencher (Gene Codes Corp), Sequencing Analysis Software (ABI), Sequencing Analysis Viewer (Illumina), Sequerome (Bioinformatics.org), Sequilab (Lifescisoft), Serial Cloner (SerialBasics), SHARCGS (Dohm et al.), SHORE (1001 Genomes project), Shrec (Omictools), SHRiMP (Brudno et al.), Shuffle-LAGAN (Stanford), SIBsim4 / Sim4 (NEBC), SIM, GAP, NAP, LAP (Huang et al.), SISSRs (Jothi et al.), Slider (BCGSC), SlimSearch (EdwardsLab), SMART (Letunic et al.), SOAP, SOAP2, SOAP3 and SOAP3-dp (GPL), SOCS (Ondov et al.), SOLiD™ Software (ABI), SPA (Shen et al), SPAdes (Open Source), Splign (Open Source), SSAHA and SSAHA2 (Non-Commercial Academic), SSAKE (Omictools), SSEARCH (Pearson et al.), Staden (Source Forge), Stampy (Non-Commercial Academic), StatAlign (Novak et al.), Stemloc (Holmes et al.), SToRM (Omictools), stretcher (Longden et al.), Subread and Subjunc (GPL), SureCall (Agilent), SWAPHI (Open Source), SWAPHI-LS (Open Source), SWIFT suit (Rasmussen et al.), SWIPE (GNU), SXOligoSearch (Synamatix), Syngene (GeneTools), Tablet (Omictools), Taipan (Non-Commercial Academic), T-Coffee (Notredame et al.), TEIRESIAS (IBM), TopHat (Univ's Maryland/California ), Torrent (Thermo Fisher), tranalign (Williams et al.), Trinity (Strozzi et al.), UCHIME (Mothur), UCLUST (NEBC), UGENE (GPL), USEARCH (Drive5), VarScan (Source Forge), VCAKE (Omictools), Vector NTI (Thermo Fisher), VectorFriends (BioFriends team), VelociMapper (Omictools), Velvet (Zerbino et al), Vmatch (VMatch ), water (Bleasby et al.), wordmatch (Longden et al.), XMatchView (Warren et al. ), XpressAlign (Non-Commercial Academic), YASS (Noe et al), Zenbu (Omictools), ZOOM (Omictools) and any others. Fields: End-users' fields in which they use sequencing, where the fields considered were Bacteriology, Bioinformatics, Blood groups, Blood products, Cell research, Clinical research, Clinical trials, Conservation Genetics, Diagnostic screening, Diagnostics, Diagnostics research, Disease biomarkers, Disease research, Drug R&D, Drug targets, Environmental microbiology, Environmental tests, Evolutionary biology, Food monitoring, Forensics Genetics, Fundamental research, Genomics, Histology, HLA-Typing for transplantation, Immunology, Laboratory surveillance, Metagenomics, Microbiology, Mitochondrial DNA, Molecular Ecology, Molecular epidemiology, Molecular Systematics, Natural products, Parasitology, Paternity Testing, Phylogenetics, Plant Breeding, Plant Evolution, Plant Sciences, Population genetics, Preclinical research, Proteomics, Soil ecology, Taxonomy, Treatment monitoring, Virology and any others. Clonal Amplification: End-users’ current methods used for clonal amplification, and those they anticipate using in three years, where the methods considered were Bridge PCR Amplification, Emulsion PCR Amplification, Rolling Circle Amplification, None (e.g. Single Molecule Sequencing) and any others.

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Read Lengths: End-users were asked to indicated the read length (bp) that they typically achieve in their sequencing work. Accuracy: End-users were asked to indicate the sequencing accuracy (%, single read, not consensus) they believe they typically achieve in their sequencing work. Reads Per Run: End-users were asked to indicate the reads per run (in millions of bases e.g. 1 million bases, 50 million bases) that they typically achieve in their sequencing work. Run Time: End-users were asked to indicate the typical time per run (indicated in minutes, hours, days, weeks or months) in their sequencing work. Sequencing Costs: End-users were asked to indicate the sequencing costs of their sequencing activities in terms of USD$ per 1 million bases. Advantages: End-users were asked to indicate the main advantages of their most commonly used nucleotide sequencing method. Disadvantages: End-users were asked to indicate the main disadvantages of their most commonly used nucleotide sequencing method. Samples: End-users were asked to indicate the main study samples that they use in their nucleotide sequencing activities in the laboratory, where the samples considered were Algal, Animal tissues, Archaeal cultures, Bacterial cultures, Bone, Cell isolates, Cells, Cerebrospinal fluid, Dried blood, Embryos, Environmental samples, Faeces/Stools, Fermented foods, Foodstuffs, Fungal material, Genetic material, Human tissues, Insect material, In-vitro solutions, Isolated viruses, Marine, Marine invertebrates, Paraffin embedded tissue, Phage material, Plant material, Plasma, Protozoa, Cultures, Respiratory fluids, Saliva, Semen, Serum, Soil, Swabs, Teeth, Urine, Venom, Water, Whole blood and any others. Sample Preparation: End-users were asked to indicate the main sample preparation method(s) they use in their nucleotide sequencing activities, where the options considered were Solution-Phase Methods, Automated Solution-Phase Methods, Solid-Phase Methods, Automated Solid-Phase Methods and any others. Kits: End-users were asked to indicate whether they use kit-based sample preparation products in their nucleotide sequencing activities. Here, the options were either Yes or No. End-users using kits were also asked to indicate their preferred suppliers.

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Disease Biomarkers: End-users were asked to indicate whether they research, discover or measure disease biomarkers using nucleotide sequencing, where the options were Yes or No. Disease Biomarker Types: End-users were asked to indicate which disease biomarker types they study or measure in their nucleotide sequencing work, where the options were Absolute DNA quantification, Alternative spliced variants, Bacteria detection, DNA methylation, Gene copy number, Gene expression, Gene mutations/polymorphisms, Haplotypes, microRNA, Protein mRNA quantification, Single nucleotide polymorphisms (SNPs), Small interfering RNA, Small nuclear RNA, SSRs or TRs, Tissue typing, Virus detection and any others. Numbers of Samples Analysed: End-users were asked to indicate the number of study samples that they sequence in their laboratory each month. Here, the the options were <1, 1, 1 to 2, 2 to 3, 3 to 4, 4 to 5, 5 to 7, 7 to 10, 10 to 15, 15 to 25, 25 to 40, 40 to 60, 60 to 100, 100 to 150, 150 to 200, 200 to 250, > 250 and Not applicable. Role: End-users’ main role relating to their use of nucleotide sequencing, where the options were Laboratory Scientist, Physician or Clinician, Laboratory or Clinical Manager, Veterinarian and Other. Organisation Type: End-users’ organisation type, where the options were Clinic, Government Organisation, Hospital, Large International Company, Medium Sized Company, Research Institute, Small Company, Teaching Hospital, University, Veterinary Organisation or other. If purchased, organisation names are included in the raw data Excel file. Experience: End-users' years of experience using nucleotide sequencing. Job Title: End-users’ job titles. Countries and Regions: End-users' countries and global regions; Asia, North America, South America, Africa (Sub-Saharan), Central America/Caribbean, Australia, New Zealand and Oceania and Middle East/North Africa/and Greater Arabia. 2015 Study (309 Participants) Trends and Growth: Based on recent trends in the numbers of sequencing studies carried out in their laboratories, end-users' estimates of by how much (% increase or % decrease) their laboratory use of sequencing has changed over the last three years. Also, based on current trends in the numbers of sequencing studies carried out in their

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laboratories, end-users' estimates of by how much (% increase or % decrease) they anticipate their laboratory use of sequencing will change over the next three years. Sequencing Techniques: Sequencers’ main use of specific sequencing techniques, both currently and anticipated in three years from now, where the techniques considered were DNA Nanoball Sequencing (Complete Genomics); Gene Electronic Nano-Integrated Ultra-Sensitive Technology (Genapsys); In-Vitro Virus High-Throughput Sequencing; Ion Torrent Sequencing (Life Technologies); Lightning Terminator Sequencing Technology (Lasergen); Massively Parallel Single-Molecule DNA Sequencing (Genia, Roche); Microfluidic Sanger sequencing; Microfluidics based next-generation sequencing platform (Gnubio); Nanopore DNA Sequencing (Oxford Nanopore Technologies); Nanowire Biosensor Sequencing Technology (Quantumdx); Optical Nanopore Sequencing Technology (Noblegen); Pyrosequencing 454 (Roche); RNAP Sequencing; Sanger Sequencing; Sequencing by Hybridization; Sequencing with Mass Spectrometry; Single-Molecule Real-Time (Pacific Bio); Solexa sequencing (Illumina); SOLiD Sequencing (Applied Biosystems); Transmission Electron Microscopy DNA Sequencing; Tunnelling Currents DNA Sequencing or others. Instrument Suppliers: End-users' current main suppliers of sequencing instruments, products or consumables, as well as those companies they anticipate will be supplying these products to their laboratories in three years from now, where 79 companies are considered, namely, 5-Prime, Abbott, Affymetrix, Agilent, Ambion (Lifetech), Anatech, AppliChem, Applied Biosystems, BD, Beckman, Bio Linx, Bioline, Biomérieux, BioNanomatrix, Bioneer, Bionobile, Bio-Rad, Celera, Chemagen (PE), Complete Genomics, DNA Technologies, Eppendorf, Eurofins, EURx, Exiqon, Fermentas, Fisher Scientific, Fluidigm, FugiFilm, GE, Halcyon Molecular, Illumina, In-House, Inqaba Biotechnology, Intelligent BioSystems, Invitek, Invitrogen (Lifetech), IonTorrent (LifeTech), Knome, Lasdex, LGC Genomics, Licor, Life technologies, Macherey-Nagel, Macrogen, Mallinckrodt Baker, MO BIO, Molecular Research Center, MP Biomedical, MWG Operon, NABsys, New England Biolabs, Nexttec, Nionobile, Nippon Gene, Orion Genomics, Oxford Nanopore, Pacific Biosciences, Panomics, Perkin Elmer, Primm, Promega, Qiagen, r-Biopharm, Roche, Roche (454), Roche Diagnostics, Roth, Sangon, Seegene, Sequenom, Siemens, Sigma-Aldrich, StabVida, Takara/Clontech, Tecan, Thermo Scientific, USB Corp, Zymo Research and others. Applications: End-users' current main applications of sequencing as well as the applications they anticipate using in three years from now, where the applications considered were 16S/18S environmental analysis, Allele size detection, Antibacterial resistance analysis, Antiviral resistance analysis, Cloning, Detection, identification of bacteria, Detection, identification of viruses, Diverse gene polymorphisms, DNA barcoding, species identifications, DNA quantification, DNA-protein interactions (ChIP-sequencing), Epigenome characterization, Exome sequencing, Fragment analysis for

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epidemiological analysis, Full 16S sequencing for identification and phylogeny, Gene expression (mRNA), Gene mutations or alterations, Gene variants in disease, Generating genetic probes, Genetic mapping, Genome resequencing, Genome sequencing, Genotyping of microorganisms, Haplotypes, Immune diversity, Metagenome, MicroRNA Studies, Microsatellites, Pathogen sequences, Phylodynamic analyses, Regulatory elements, Ribosomal DNA (rRNA) Studies, RNA-sequencing, Short Tandem Repeat Analysis, Single Nucleotide Polymorphisms, Single-Strand Conformation Polymorphism, Small insertions or deletions, Small Interfering RNA (siRNA) Studies, Small Nuclear RNA (snRNA) Studies, Tag sequencing, Tissue typing, Transcriptome (RNA) sequencing, Transfer RNA (tRNA) Studies and others. Diseases: End-users’ current sequencing activities, and those sequencing activities they anticipate in three years from now, relating to specific disease areas, including Arthritis, Autoimmune Diseases, Bone Metabolism, Cancer, Cardiovascular, Central Nervous System, Dentistry, Dermatology, Endocrine, Gastrointestinal, Genito-urinary System, Haematology, Infections, Inflammation, Metabolic Disorders, Musculoskeletal Disorders, Nutrition, Obstetrics and Gynaecology, Ophthalmology, Pain, Psychiatry, Respiratory, Skin or others. Nucleotide Types: Main nucleic acid types currently sequenced, as well as those anticipated to be sequenced in three years from now, where the nucleic acids considered were Bacterial DNA, cDNA, Genomic DNA, Metagenomic DNA, MicroRNA, Mitochondrial DNA, mRNA, Noncoding RNA, Pathogen RNA/DNA, piRNA, Plant viral RNA or DNA, Plasma Cell Free DNA, Plasmid DNA, Prokaryotic small RNA, Ribosomal RNA (rRNA), Small interfering RNA (siRNA), Small nuclear RNA (snRNA), Total RNA, Transfer RNA (tRNA),Tumour Cell DNA, Viral DNA, Viral RNA or others. Software: Sequencers main software programs used for their nucleotide sequencing activities. Costs of sequencing: Sequencers estimates of the costs of nucleotide sequencing for a typical study sample in their laboratory, where the cost options were <$1,000; $1,000 to $2,000; $2,000 to $3,000; $3,000 to $4,000; $4,000 to $5,000; $5,000 to $7,000; $7,000 to $10,000; $10,000 to $15,000; $15,000 to $25,000; $25,000 to $40,000; $40,000 to $60,000; $60,000 to $100,000; $100,000 to $150,000; $150,000 to $200,000; $200,000 to $250,000; $250,000 to $500,000; $500,000 to $1,000,000; > $1,000,000. Numbers of Samples: Sequencers estimates of the number of study samples they sequence in their laboratory, where the options were <1; 1; 1 to 2; 2 to 3; 3 to 4; 4 to 5; 5 to 7; 7 to 10; 10 to 15; 15 to 25; 25 to 40; 40 to 60; 60 to 100; 100 to 150; 150 to 200; 200 to 250 or 250.

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Disease Biomarkers: Sequencers were asked if they use sequencing to research, discover or measure disease biomarkers, where the options were yes or no. Those who answered yes to this question were asked to indicate which disease biomarkers they study in their sequencing work. These included Absolute DNA quantification; Alternative spliced variants; Bacteria detection; DNA methylation; Gene copy number; Gene expression; Gene mutations/polymorphisms; Haplotypes; microRNA; Protein mRNA quantification; Single nucleotide polymorphisms (SNPs); Small interfering RNA; Small nuclear RNA; SSRs or TRs; Tissue typing; Virus detection or others. Study samples: Sequencers were asked to indicate the main study samples in their sequencing activities where the options were algal; Animal tissues; Bacterial cultures; Bone; Cell isolates; Cells; Cerebrospinal fluid; Dried blood; Environmental samples; Faeces; Foodstuffs; Fungal material; Genetic material; Human tissues; Insect material; In-vitro solutions; Isolated viruses; Marine; Paraffin embedded tissue; Phage material; Plant material; Plasma; Respiratory fluids; Saliva; Semen; Serum; Soil; Swabs; Teeth; Urine; Venom; Water; Whole blood or other. Sample Preparation: Sequencers were asked to indicate the main sample preparation method(s) that they use in their sequencing activities, where the methods considered were solution-Phase Methods; Automated Solution-Phase Methods; Solid-Phase Methods; Automated Solid-Phase Methods or others. Sequencers were also asked to indicate if they used kit-based sample preparation products in your nucleotide sequencing activities. Those who did were invited to indicate their preferred suppliers. Advantages and Disadvantages: Sequencers were asked to indicate that they considered to be the main advantages and disadvantages of their most commonly used nucleotide sequencing techniques. Fields: End-users' field or sector relating to their use of sequencing, including Biology, Biotechnology, Chemicals, Clinical, Defence, Diagnostics, Ecology, Energy, Environmental, Food and Drink, Forensics, Geology, Government, Healthcare, Hospital, Marine, Medicine, Natural Products, Paternity, Pharmaceuticals, Research, Institute, Security, University, Veterinary or others. Purpose: End-users' purposes or reasons for their sequencing activities, including cell research, Preclinical research, Clinical research, Clinical trials, Diagnostic screening, Diagnostics research, Routine diagnostics, Treatment monitoring, Disease biomarkers, Disease research, Drug R&D, Drug targets, Environmental tests, Food monitoring, Fundamental biological research, Genomics, Histology, Microbiology, Proteomics, Screening blood products, Toxicology, Virology or others.

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Role: End-users’ main role relating to their use of nucleotide sequencing, where the options were Laboratory Scientist, Physician or Clinician, Laboratory or Clinical Manager, Veterinarian and Other. Organisation Type: End-users’ organisation type, where the options were Clinic, Government Organisation, Hospital, Large International Company, Medium Sized Company, Research Institute, Small Company, Teaching Hospital, University, Veterinary Organisation or other. Experience: End-users' years of experience using nucleotide sequencing. Job Title: End-users’ job title. Countries and Regions: End-users' countries and global regions; Asia, North America, South America, Africa (Sub-Saharan), Central America/Caribbean, Australia, New Zealand and Oceania and Middle East/North Africa/and Greater Arabia. Participants: Names, organisation name and business email address [not included in this report].

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2.1. This Chapter This chapter presents background information relating to the DNA sequencers (end-users) who took part in the 2015 (hereafter referred to as SEQ 2015) and 2016 (hereafter referred to as SEQ 2016) studies. Participants were selected for participation in this study, based on the fact that they are authors or co-authors of one or more publications that describe the use of DNA sequencing techniques. 2.2 Global Regions 2016 Study

Figure 2.3. Global regions of participants in SEQ 2016

Table 2.3. Global regions of participants in SEQ 2016

Global Region %

Europe 51.6

North America 25.3

Asia 6.5

South America 5.1

Australia, New Zealand and Oceania 4.6

Middle East / North Africa / and Greater Arabia 4.1

Africa (Sub-Saharan) 2.8

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2015 Study Figure 2.1. Global regions of participants in SEQ 2015

Table 2.1. Global regions of participants in SEQ2015

Global Region %

Europe 50.6

North America 17.8

Asia 17.2

South America 4.1

Australia, New Zealand and Oceania 3.5

Middle East / North Africa / and Greater Arabia 2.9

Africa (Sub-Saharan) 2.5

Central America / Caribbean 1.3

Findings on the global regions of participants in the 2016 study show that Europe (the largest region at around 52%) and North America (25%) account for around 77% of participants. Findings on the global regions of participants in the 2015 study show that Europe (the largest region at 51%) and North America (18%) account for around 69% of participants. Market findings in this study therefore relate in particular to Europe and North America.

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2.3. Countries 2016 Study

Figure 2.4. Top ten countries of participants in SEQ 2016

Table 2.4. Countries of participants in SEQ 2016

Country %

USA 21.2

Italy 7.4

UK 6.9

Spain 6.5

France 6

China 4.6

Brazil 3.7

Germany 3.7

Australia 3.7

Denmark 3.2

Canada 3.2

Finland 1.8

Belgium 1.8

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2015 Study

Figure 2.2. Top ten countries of participants in SEQ 2015

Table 2.2. Countries of participants in SEQ2015

Country %

USA 13.4

Italy 8

China 7.6

UK 7

France 5.1

Spain 5.1

Canada 3.8

Germany 3.8

Australia 3.5

Netherlands 2.5

Rep Korea 2.2

India 1.9

Sweden 1.9

Findings in the 2016 study relating to the countries of participants show that the top ten are USA at 21%, followed by Italy, UK, Spain, France, China, Brazil, Germany, Australia and Denmark. Together, these countries represent around 69% of the participants. Overall, 46 countries participated in this study. Findings in the 2015 study relating to the countries of participants show that the top ten are USA at 13%, followed by Italy, China, UK, France, Spain, Canada, Germany, Australia and the Netherlands.

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Together, these countries represent around 60% of the participants. Overall, 47 countries participated in this study. 2.5. Experience 2016 Study

Figure 2.6. Top ten experience levels in DNA and RNA sequencing, of SEQ 2016 participants

Table 2.6. Experience levels in DNA and RNA

sequencing, of SEQ 2016 participants

Experience %

15 years 10.6

10 years 10.1

5 years 8.8

20 years 8.8

25 years 7.8

4 years 6.9

8 years 4.1

6 years 3.7

2 years 3.2

3 years 2.8

7 years 2.8

12 years 2.8

<1 year 2.8

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Table 2.6. Experience levels in DNA and RNA sequencing, of SEQ 2016 participants

Experience %

16 years 2.8

>30 years 2.8

14 years 2.8

9 years 1.8

18 years 1.8

30 years 1.8

11 years 1.8

1 year 1.4

13 years 1.4

26 years 1.4

28 years 0.9

24 years 0.9

22 years 0.9

19 years 0.9

17 years 0.5

27 years 0.5

23 years 0.5

2015 Study

Figure 2.4. Top ten experience levels of participants in SEQ2015

In the 2016 study, findings show that the average experience levels of participants in the use of DNA sequencing is 12.9 years. Findings in the 2015 study also showed average experience levels in the use of DNA sequencing is 12.9 years.

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Table 2.4. Experience levels of participants in SEQ2015

Experience %

10 years 11.8

20 years 9.2

5 years 7.6

15 years 6.7

6 years 5.4

3 years 4.8

12 years 3.8

16 years 3.8

25 years 3.5

14 years 3.5

7 years 3.5

4 years 3.2

8 years 2.9

>30 years 2.9

2 years 2.9

18 years 2.5

24 years 2.5

13 years 2.2

23 years 2.2

9 years 2.2

22 years 2.2

<1 year 2.2

11 years 1.9

30 years 1.3

1 year 1.3

27 years 1.3

17 years 1

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Table 2.4. Experience levels of participants in SEQ2015

Experience %

28 years 0.6

29 years 0.3

21 years 0.3

26 years 0.3

2.6. Organisation Types 2016 Study

Figure 2.7. Top ten organisation types of participants in SEQ 2016

Table 2.7. Organisation types of participants in SEQ 2016

Organisation Type %

University 31.8

Research Institute 26

Government Organisation 9.7

Hospital 9.1

Medical School 7.5

Teaching Hospital 4.9

Laboratory Services 4.2

Clinic 2.9

Veterinary Organisation 1

Company - Small 0.6

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Table 2.7. Organisation types of participants in SEQ 2016

Organisation Type %

Company - Large International 0.6

Company - Medium Sized 0.3

Other 1.3

2015 Study Figure 2.5. Organisations types of participants in SEQ 2015

Table 2.5. Organisations types of participants in SEQ2015

Organisation %

University 43

Research Institute 25.8

Government Organisation 13.4

Hospital 7

Teaching Hospital 4.5

Small Company 1.9

Veterinary Organisation 1

Large International Company 1

Clinic 1

Medium Sized Company 0

Other 1.6

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2.7. Roles 2016 Study

Figure 2.8. Roles of participants in SEQ 2016

Table 2.8. Roles of participants in SEQ 2016

Role %

Laboratory Scientist 72.8

Laboratory or Clinical Manager 9.7

Physician or Clinician 4.6

Veterinarian 0.5

Other 12.4

Figure 2.6. Roles of participants in SEQ2015

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Table 2.6. Roles of participants in SEQ 2015

Role %

Laboratory Scientist 73.9

Laboratory or Clinical Manager 8.3

Physician or Clinician 6.1

Veterinarian 0.3

Other 11.5

2.8. Main Purpose

Figure 2.7. Top ten main purposes of sequencing activities of participants in SEQ2015

Findings on the general purpose of participants’ sequencing activities show that the top ten are genomics, microbiology, fundamental biological research, diagnostics research, disease research, diagnostic screening, clinical research, disease biomarkers routine diagnostics and cell research. Together these represent 78% of those cited.

Table 2.7. Main purposes of sequencing activities of participants in SEQ2015

Purpose %

Genomics 17.8

Microbiology 10.4

Fundamental biological research 9.1

Diagnostics research 8.9

Disease research 8

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Table 2.7. Main purposes of sequencing activities of participants in SEQ2015

Purpose %

Diagnostic screening 5.5

Clinical research 5.4

Disease biomarkers 4.5

Routine diagnostics 4.4

Cell research 4.3

Virology 4.3

Environmental tests 3.5

Preclinical research 2.5

Clinical trials 1.9

Proteomics 1.5

Treatment monitoring 1.3

Histology 1.1

Drug targets 1

Drug R&D 0.7

Toxicology 0.6

Food monitoring 0.5

Screening blood products 0.2

Other 2.7

2.9. Discussion Findings presented in this chapter show that participants have substantial professional experience in the use of DNA sequencing, which averaged at 12.9 years. Disclosures on participants’ professional titles also show professional seniority in this group, and this indicates the breadth and depth of participants’ experience in this field. Overall, these data confirm the commercial relevance of the findings coming out of this study to company suppliers operating in the DNA sequencing field.

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6.1. This Chapter More than twenty different methods are used in DNA and RNA sequencing and this chapter presents findings relating to the techniques used by participants in this study, both currently and anticipated by end-users in three years from now (to 2019). 6.2 2016 Study In the case of the 2016 study, the top ten most cited sequencing techniques were [edited]. Together, these represented 93% of those cited.

Figure 6.3. Top ten current sequencing methods of SEQ 2016 participants

Table 6.3. Current sequencing

methods of SEQ 2016 participants

Sequencing Methods %

Edited 25.8

Edited 16.6

Edited 14

Edited 8.8

Edited 8.3

454 Pyrosequencing (Roche) 7.1

Edited 5.7

Edited 3.1

Edited 2.4

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Table 6.3. Current sequencing methods of SEQ 2016 participants

Sequencing Methods %

Edited 1.7

Edited 1.4

Edited 0.9

Edited 0.2

Edited 0.2

Edited 0.2

Edited 0.2

Edited 0.2

Edited 0.2

Other 2.8

Regarding the techniques that participants in the 2016 study anticipate using in three years, the top ten most cited techniques were [edited]. 89% of those cited.

Figure 6.4. Top ten future anticipated

sequencing methods of SEQ 2016 participants

Table 6.4. Future anticipated sequencing

methods of SEQ 2016 participants

Sequencing Methods %

Edited 19.8

Edited 12.2

Edited 11.3

30

Edited 9.9

Edited 9

Edited 8.7

454 Pyrosequencing (Roche) 6

Edited 4.8

Edited 2.8

Edited 2.5

Edited 2.1

Edited 1.6

Edited 1.6

Edited 1.4

Edited 1.1

Edited 0.7

Edited 0.7

Edited 0.5

Edited 0.5

Edited 0.2

Edited 0.2

Edited 0.2

Edited 0

Other 2.3

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The Author

Our global market studies profile the laboratory activities of research scientists and clinicians. Our findings assist suppliers to keep pace with and support end-users' activities and needs. We are committed to helping suppliers profile these needs, to source market information cost-effectively, and to provide accurate data that give valued insights into today's evolving life science and clinical laboratory fields. Our market reports are based on conducting well-designed market studies that profile the laboratory activities of specialist groups of scientists and clinicians. Findings from these studies, based on 'real world' data, are available as off-the-shelf reports that assist decision making in marketing and sales, planning, innovation and customer support.

Dr. John Bates is a laboratory market consultant and works in life science and clinical fields. After a degree in biochemistry and chemistry (1978) and a Ph.D in cancer research in 1981, John joined Upjohn Ltd (now Pfizer), where he managed a team of research scientists in the department of biopharmaceutical sciences and drug metabolism. In 1985 he took a similar role with Glaxo Group Research (now GSK), in the department of Biochemical Pharmacology. John has over 20 years laboratory experience and has worked as a market consultant since 2003, covering technologies in the fields of analysis, molecular biology and diagnostics.

Copyright© Laboratory Markets Limited Molecular Diagnostics 2016 and the associated study data in excel format has been produced and published by Laboratory Markets Limited. All Rights Reserved. The reproduction or redistribution of this report is prohibited, without the prior permission of Laboratory Markets Limited. The information in this report and the opinions, views and conclusions contained herein, are those of the author and publisher. While the information contained in this report is believed to be accurate at the time of publication, Laboratory Markets Limited accepts no liability for the information contained herein, nor for its completeness in any respect. Laboratory Markets Limited accepts no liability for any decisions or actions that are taken based on the content, views or conclusions contained in this report. END

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