Nazneen Aziz, PhD. Director, Molecular Medicine Transformation Program Office

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1 2013 Laboratory Accreditation Program Audioconferences and Webinars Implementing Next Generation Sequencing (NGS) as a Clinical Tool in the Laboratory Nazneen Aziz, PhD Director, Molecular Medicine Transformation Program Office February 20, 2013

2 Topics Next Generation Sequencing o Technology overview o Rapidly evolving field o Factors driving adoption of NGS in diagnostic medicine o CAP/CLIA standards developed for NGS o NGS methods based PT in development 2013 College of American Pathologists. All rights reserved. 2

3 Introduction to Next Generation Sequencing Overview: History Human genome Project led the path to genomic medicine ( ) Now Human Genome Project 13 years $3 billion Research Applications Genomic medicine Sequence Compare Report Predict and diagnose diseases 2013 College of American Pathologists. All rights reserved. 3

4 Sanger Sequencing: Autoradiography Chromatograms The Human Genome Project (first reference sequence) was done using Sanger sequencing College of American Pathologists. All rights reserved. 4

5 Sanger vs Next Generation Sequencing Sanger Next Generation Sequencing 2013 College of American Pathologists. All rights reserved. 5

6 Sanger vs Next Generation Sequencing 2013 College of American Pathologists. All rights reserved. 6

7 Illumina Genome Analyzer Compiled Image A T C G Flow Cell Clusters

8 Qualitative and Quantitative Information G> A Illumina Ref Seq Coverage or number of reads 8

9 Next Generation Sequencing Bioinformatics Image Capture Variant Identification Annotation Giga-Terabyte Image Processing Conversion to Bases Base Quality Scores Sequence Read Files Signal to Noise 2013 College of American Pathologists. All rights reserved. 9

10 Rapid Evolution of Next Generation Sequencers First Wave Second Wave 454/Roche 2005 Illumina Life Tech Helicos Pacific Biosciences GS FLX Genome Analyzer SOLiD HeliScope SMRT Third Wave GS Junior GAIIx GAIIe HiScanSQ HiSeq SOLiD 5500 SOLiD 5500xl Ion Torrent PGS Ion Proton miseq Proton

11 Sequencing Chemistries and Signals are Varied Pyrosequencing 454 Reversible Dye Terminators Illumina Sequencing by Ligation SOLiD Ion Torrent Generation of Luminescent or Fluorescent Images or chemical signals Conversion to Sequence 2013 College of American Pathologists. All rights reserved. 11

12 Illumina HiSeq Independent Flow Cells 8 Lanes per Flow Cell Multiple Samples per Lane 2-3 Exome(s) per Lane 2 Genomes per Flow Cell 7 days/genome 2013 College of American Pathologists. All rights reserved. 12

13 New Platforms Lower throughput h t - faster turn around time Illumina miseq Ion Torrent PGM Reversible Dye Monitors H+ Terminators Release 2013 College of American Pathologists. All rights reserved. 13

14 Ion Proton DNA Sequencer Semiconductor chips form the heart of the machine. CMOS chips detect chemical changes instead of light. The Ion Proton I chip has 165 million sensors Mid The Ion Proton II Chip has 660 million sensors. Late Significant increase in speed and reduction of fthe cost of genome-level l sequencing College of American Pathologists. All rights reserved. 14

15 Oxford Nanopore: Single Molecule Sequencing 2013 College of American Pathologists. All rights reserved. 15

16 Alignment Software Academic Software In-house built Free Genome community support maq assemble [-sp] [-m maxmis] [-Q maxerr] [-r hetrate] [-t coef] [-q minq] [-N nhap] out.cns in.ref.bfa in.aln.map 2> out.cns.log Commercial Software Feature rich user interface $$$ Company support 2013 College of American Pathologists. All rights reserved. 16

17 Agenda Next Generation Sequencing o o Technology overview Rapidly evolving field o Factors driving i adoption of NGS in diagnostic medicine i o Standards developed for laboratory accreditation at CAP o NGS methods based PT in development 2013 College of American Pathologists. All rights reserved. 17

18 Growth in Sequencing Revenues: Genetic Testing Estimated to reach $5 billion : College of American Pathologists. All rights reserved. 18

19 The Cost of Genome Sequencing is Decreasing Rapidly and Driving Clinical Adoption of Genomic Analysis Cost per Genome Data Generation, Sep 2001 Oct 2011 $100,000, $10,000,000 $1,000,000 $100,000 $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 Cost for genome sequence data generation today is <$3, College of American Pathologists. All rights reserved. Source: National Human Genome Research Institute 19

20 Decline in Sequencing Costs Likely to Continue 2013 College of American Pathologists. All rights reserved. 20

21 Genomic Analysis by Next Gen Sequencing Currently Used Past and Continuing Molecular Pathology Tests Single/Few Mutations Genomic Analysis: Most commonly used Gene Panels Genomic Analysis: Growing and perhaps common in the near future Genome Single Gene/Pathogen Exome Transcriptome Few Genes Genomic Analysis by Next Gen Sequencing 2013 College of American Pathologists. All rights reserved. 21

22 NGS Survey of CAP PT Customers 19% current users 55% plan to begin NGS 20% within 6 months 14% within 12 months 21% within 1 3 years 176 responders 19% do not plan to begin using NGS technology Of those using NGS technology, 61% perform less than 10 tests per month 2013 College of American Pathologists. All rights reserved. 22

23 Disease Area NGS Tests 2012 College of American Pathologists. All rights reserved. 23

24 NGS Tests Offered: Panel, Exome, Genome 2013 College of American Pathologists. All rights reserved. 24

25 Expansion Plans of NGS Test Offered 2013 College of American Pathologists. All rights reserved. 25

26 Confirmation Using Alternate Technologies 41% always use Sanger or other technologies to confirm pathogenic variants prior to reporting 22% use it only for specific cases/assays 2013 College of American Pathologists. All rights reserved. 26

27 Bioinformatics Support 30% require outsourced bioinformatics support 2013 College of American Pathologists. All rights reserved. 27

28 Clinical Genomic Analysis Process Pre-Analytical Sequence Data Generation Sequence Data Interpretation Reporting & Billing Clinical Consultation 2013 College of American Pathologists. All rights reserved. 28

29 Pre-Analytical aytca Determine if testing ti is clinically i ll useful Determine appropriate p test, specimen, and laboratory Obtain sample and patient consent 2013 College of American Pathologists. All rights reserved. 29

30 Sequence Data Generation Sequencing Process Data QA & Sequence Alignment 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 sequence 6 Billion bases (maternal and paternal) 4 Million variants (10% complex variants: indels, SV, CNVs ) 2013 College of American Pathologists. All rights reserved. 30

31 Sequence Data Interpretation Variant tassessment Clinical i l Interpretation t ti Compare variants to databases (OMIM, COSMIC, dbsnp, 1000 Genomes, ENCODE, etc.) Variant impact analysis (evolutionary conservancy analysis, protein structural analysis, pathway analysis, etc.) Integration of potentially t significant variants with clinical phenotype of the patient, family, and literature Interpretive report generation Literature reviews 2013 College of American Pathologists. All rights reserved. 31

32 Reporting & Billing Report in LIS, EHR., and PHR Code and bill for testing & interpretation 20123College of American Pathologists. All rights reserved. 32

33 Clinical Consultation Physician i consults Clinical conferences Patient consultations with physician and genetic counselors 2013 College of American Pathologists. All rights reserved. 33

34 Clinical Genomic Analysis Process Sequence Data Generation Pre-Analytical Determine if testing is clinically useful Determine appropriate test, specimen, and laboratory Obtain/document patient consent Sequencing Process DNA extraction DNA fragmentation Fragment selection Adapter ligation Clonal amplification Sequencing Data QA & Sequence Alignment Quality assessment of sequence data (depth of coverage, variant frequency, etc.) Align sequence data to reference sequence Identify variants based on reference sequence 6 Billion bases (maternal and paternal) 4 Million variants (10% complex variants: indels, SV, CNVs ) Sequence Data Interpretation Variant Assessment Compare variants to databases (OMIM, COSMIC, dbsnp, 1000 Genomes, ENCODE, etc.) Variant impact analysis (evolutionary conservancy analysis, protein structural analysis, pathway analysis, etc.) Literature reviews Clinical Interpretation Reporting & Billing Clinical Consultation Integration of Report in LIS, Individual potentially EHR and PHR physician significant variants Code and bill consults with clinical, family, for testing & Clinical and literature interpretation Write interpretive report Conferences Patient consultations 2013 College of American Pathologists. All rights reserved. 34

35 CAP/CLIA Steps in Clinical Genomic Testing Process Work Flow Physician Genome CLIA lab Deliver data Patient orders IGS for patient Sequencing and QC delivers results to physician to patient Understands Implications CAP s standards in accreditation, PT services, reporting of NGS labs

36 Agenda Next Generation Sequencing o Technology overview o Rapidly evolving field o Factors driving adoption of NGS in diagnostic medicine o Standards developed for laboratory accreditation at CAP o NGS methods based PT in development 2013 College of American Pathologists. All rights reserved. 36

37 Why do we need to have standards for NGS clinical tests? Million variants/genome Dramatically increased complexity Test results need to capture not only the unique genetic differences but also the patterns of differences 2013 College of American Pathologists. All rights reserved. 37

38 NGS Work Group Charter 1 Identify, Refine, and drecommend dlaboratory Accreditation ti Standards for the Analytical and Bioinformatics Workflow for Clinical Tests Using NGS 2 Recommend Proficiency Testing Protocols, Reference Materials, and Product Development 3 Other Goals: Adapt to Meet Growing Questions/Needs Raised by Next Generation Sequencing 2013 College of American Pathologists. All rights reserved. 38

39 Process We Follow Employ Existing Applicable Requirements Introduce New Requirements Where Needed Find the Right Balance 2013 College of American Pathologists. All rights reserved. 39

40 Next Generation Sequencing: Steps in Workflow Analytical Wet Bench Process: sample handling, library preparation, sequence generation Bioinformatics process: Alignment, variant calling, and variant annotation Clinical Interpretation 2013 College of American Pathologists. All rights reserved. 40

41 NGS Accreditation Checklist Themes: Documentation Test Validation Quality control and quality assurance 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 Data storage and data transfer cloud computing and HIPAA Clinical interpretation of variants - using professional guidelines Reporting of unexpected and significant findings (incidental findings) 2013 College of American Pathologists. All rights reserved. 41

42 MOL.XXX02 The laboratory validates the analytical wet bench process and revalidates after changes or 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 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 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 2013 College of American Pathologists. All rights reserved. 42

43 MOL.34936: Validation - Wet Bench Analytical The laboratory validates the analytical wet bench process and revalidates 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 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 determined and documented using an alternative method which may include an alternate NGS chemistry. Indexing I d i (barcoding) and sample pooling methods must be validated d to ensure that individual sample identity is maintained throughout the analytical wet bench process. 43

44 MOL.34940: Confirmatory Testing The laboratory has a policy for when confirmatory testing of identified d or reported variants will be determined d 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 data obtained during the validation process. Evidence of Compliance: Policy or procedure that describes the indications for confirmatory testing College of American Pathologists. All rights reserved. 44

45 MOL.34944: Patient t Reports The specific methods, instrument(s) and reagents are traceable for each patient t report College of American Pathologists. All rights reserved. 45

46 MOL.34948: Monitoring i of Upgrades The laboratory has a policy for monitoring and implementing upgrades to instruments, sequencing chemistries, and reagents or kits used to generate next generation sequence data College of American Pathologists. All rights reserved. 46

47 MOL Sequence Variants: Interpretation/Reporting Interpretation 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 College of American Pathologists. All rights reserved. 47

48 MOL.34954: Clinically i ll Significant ifi Genetic Findings The 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 significant genetic findings unrelated to the disorder for which the patient is undergoing testing College of American Pathologists. All rights reserved. 48

49 MOL.34958: Process/Pipeline Documentation ti The 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, vendordeveloped 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 2013 College of American Pathologists. All rights reserved. 49

50 MOL.34968: Version Traceability The specific version(s) of the bioinformatics process or pipeline(s) used 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 College of American Pathologists. All rights reserved. 50

51 MOL.34972: Data Transfer Confidentiality Policy There are procedures in place to ensure that internal and external storage 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 access restrictions College of American Pathologists. All rights reserved. 51

52 Agenda Next Generation Sequencing o Technology overview o Rapidly evolving field o Factors driving adoption of NGS in diagnostic medicine o Standards developed for laboratory accreditation at CAP o NGS methods based PT in development 2013 College of American Pathologists. All rights reserved. 52

53 Plans for Proficiency Testing in NGS Offer a pilot product in 2013 Learn from this offering: Technology platforms used WGS, Exome, gene panels used Troubleshoot Full fledged PT offering by College of American Pathologists. All rights reserved. 53

54 Types of Next Generation Sequencing PT Analytical Wet Bench Process: sample handling, library preparation, sequence generation Bioinformatics process: Alignment, variant calling, and variant annotation Wet challenge Dry challenge Total challenge Clinical Interpretation 2013 College of American Pathologists. All rights reserved. 54

55 Relevant 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 Assuring the quality of next-generation sequencing in clinical laboratory practice. Nature Biotechnology. Vol. 30, No. 11, November College of American Pathologists. All rights reserved. 55

56 Acknowledgements Karl Voelkerding for some slides on NGS methods NGS Work Group at CAP for development of the NGS checklist The Case-for-Change M4 Team at CAP for some slides 2013College of American Pathologists. All rights reserved. 56

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