2017 HTS-CSRS COMMUNITY PUBLIC WORKSHOP

Transcription

1 2017 HTS-CSRS COMMUNITY PUBLIC WORKSHOP

2 GenomeNext Overview Olympus Platform The Olympus Platform provides a continuous workflow and data management solution from the sequencing instrument through analysis, annotation, reporting, and interpretation, including a solution for multivariate discovery analytics and genetic association studies. Powerful Platform & Intelligent Infrastructure Fully Automated, Turn-Key NGS Genomic Data Analytics End-to-End Lab Integration Clinical or Research Discovery Analytics & Genomic Association Studies On Demand Compute & Storage; Unparalleled Security & Compliance DNA Germline, RNA-seq Tumor / Normal (Somatic) Custom Pipelines LIMS EHR/EMR Third Party Tools Multivariate Discovery Analytics and Genome Association Studies 2

3 GenomeNext Olympus Solution Analysis Pipeline AMI LIMS System NGS Sequencing Queue Service Analysis Requests Analysis Request Message Olympus Platform Analysis Status Updates Status Updates Analysis Message Listener Analysis Results Analysis Result Message Results Files Discovery Analytics & Genome Association Studies Storage 3

4 DNA-seq Germline & Tumor /Normal Analysis Pipelines Tumor / Normal (Somatic) Sequencer Automated Data Transfer FASTQ BCL Conversion FASTQ FASTQC Alignment/ Realignment BAM Deduplication Recalibration Genotyping Germline QC GenomeNext Genomic Data Knowledgebase Annotation Patient Demographics Biospecimen Data Clinical Assessment Treatment Decision / Response Integrated Patient Data Warehouse DNA Germline BAM (From previous NGS run) BAMèFASTQ Conversion* Genome Visualization Tumor/Normal Differential Discovery Analytics & Genomic Associations Interpretation, Discovery, Clinical Decision Support Automated Data Transfer Sequencer è Olympus Platform Primary Analysis: BCL è FASTQ Secondary Analysis: FASTQ è Annotation & Visualization Interpretation, Reporting & Discovery Analytics 4

5 Quality & Integrity LOWEST FALSE DISCOVERY RATE Validated with NA % 100% 5

6 6 OLYMPUS PLATFORM PERFORMANCE Sample Case Study: 34 Clinical Exomes FASTQ NGS Sequencing Automated Streaming 331 GB BCL Total Time Sequencer to Results <5 hours 0.25 Hours Clinical Decision Support Annotation Discovery Analytics

7 HEAR LOSS PROJECT

8 New Born Hearing Loss Use Case DNA Germline LIMS Pedigree Physician Sample Preparation Sample Sequencing Automated Data Streaming BCL FASTQ FASTQC Olympus Platform Fully Automated Pathology Sign-Off EMR (i.e. EPIC) Interpretation QC Visualization & Annotation

9 BLADDER CANCER PROJECT

10 Discovery Analytics Simplified Discovery analytics and genome association studies can now be performed with ease. Using and annotation data (and supporting clinical, demographic and biospecimen data if available) perform genomic pairwise and multivariate association studies for interpretation, discovery and clinical decision support. GenomeNext Genetic Knowledgebase This solution provides an optimized list of true candidates within minutes, delivering a seamless, automated workflow that enables researchers, physicians, and bioinformaticians to perform a wide variety of analyses including inheritance model analysis, mutation detection, genome-wide multi-family and cohort studies, and simultaneous analysis of DNA and RNA sequencing data. Patient Demographics Biospecimen Data GenomeNext Omic Pipelines Profiling and Characterization (RNA, DNA Germline, Tumor/Normal, etc.) Clinical Assessment Treatment Decision / Response Proprietary Databases Integrated Patient Data Warehouse Discovery Analytics & Genomic Association Studies Interpretation Discovery Clinical Decision Support

11 TCGA Bladder Cancer Data GenomeNext reanalyzed the TCGA BLCA dataset incorporating proprietary patient follow-up and clinical outcomes to discover novel causative mutations impacting pathways and disease. 412 Normal BAM Files 412 Biospecimen Files Olympus Platform Tumor / Normal 412 BLCA Cases Tumor / Normal 8.82 Tb Data Analyzed < 45 Hours 412 Tumor BAM Files 412 Clinical Files 1700 Files 412 Cases 8.82 Tb Data Upload / Parsed 30 HOURS BAM GenomeNext FASTQ Data Upload Olympus Platform 412 Annotation Files Automated Genomic Analysis & Annotation Gene / Variant Discovery: Pairwise Comparisons Bulked Segregant Fisher Exact Test 12 HOURS 3 HOURS GenomeNext GenomeNext Annotation Data Upload MuTect MuSe VarScan Somatic Sniper Analysis included combination of 5 genotyping workflows Discovery Analytics 11

12 Bladder Cancer Study 71 BLADDER CANCER CASES Clinical Assessment Genomic Analysis DNA Germline Tumor/Normal (Somatic) Genome Visualization < 3 Hours ANALYTICS 46 Deceased 25 Alive Sequenced File (BAM) Import Olympus Platform <10 Minutes 1.5 TB Data < 6 Hours Gene & Variant Level Candidate Dx/Px/PgX Markers & Signatures < 1 Minute DATA IMPORT Patient Demographics Biospecimen Data Clinical History Treatment Decision / Response Multivariate Analytics & 280 GB Data Genetic Association Studies 7 MB Data GenomeNext Clinical Outcomes Knowledgebase Tumor Stage / Grade Age / Gender / Environmental Therapy Response Potentially Causative Candidate Genes Discovered Germline 12,693 (31 Causative) Tumor/Normal 618 (30 Causative) 15 Common Causative Genes 12