Agilent NGS Solutions : Addressing Today s Challenges

Transcription

1 Agilent NGS Solutions : Addressing Today s Challenges Charmian Cher, Ph.D Director, Global Marketing Programs 1

2 10 years of Next-Gen Sequencing 2003 Completion of the Human Genome Project 2004 Pyrosequencing hits the market 2006 Launch of Genome Analyzer and SOLiD 2010 High-throughput sequencing enabled 2011 Benchtop and singlemolecule sequencing 2015 Promise of the $1000 genome What s Next? Innovative technologies to make NGS faster, cheaper, more accurate NGS tools to probe the genome and transcriptome in greater depth to enhance understanding of phenotype and disease Precision medicine 2

3 Entering an Exciting Era in Advancing Human Health Technologies and disease understanding are moving through the research-clinical continuum Precision medicine enable physicians to identify and treat maladies more effectively at a lower cost Building on a strong legacy and expertise within bio-reagents, automation solutions and informatics capabilities For Research Use Only. Not for use in diagnostic procedures. 3

4 Focus on Constitutional and Cancer Research Addressing today s challenges Prenatal Pre-implantation screening Sample Prep Challenging samples : FFPE, single cells, cfdna Sample heterogeneity Hard to capture/sequence regions Structurally complex regions Cost efficiencies Shorter time from sample to data Streamlined workflows Postnatal Data analysis Cumbersome and difficult bottleneck Cancer 4

5 8 years of Agilent NGS Innovation along the research-to-clinical continuum 2011 Launch of first model organism exome, the SureSelect Mouse All Exon 2014 Most comprehensive Clinical Research Exome and SureSelect QXT launched >2000 Agilent NGS publications 2015 Agilent acquires Cartagenia enabling clinical analysis of genomics data Introduced HaloPlex HS for low allele frequency variants & OneSeq for CNV detection SureSelect Human All Exon V6 and ClearSeq Comprehensive Cancer 2009 Launch of SureSelect Human All Exon kit, the first target enrichment system 2012 Launch of HaloPlex, an amplicon-based target enrichment system Agilent acquires Dako, a leading cancer diagnostics company 2016 OneSight for cfdna analysis $80M investment in Lasergen 5

6 Agilent s Core Capability : High-Fidelity Oligo Synthesis The foundation of Agilent s target enrichment solutions Production of custom microarrays and NGS target enrichment Leading platform for generating long, highfidelity oligos High volume & low cost production capability (1) 6

7 Advantage of Ultra-Long RNA baits 7

8 What s New? 1. Beyond the Exome : resolving structural complexities and variation OneSeq CNV Backbone + Custom Panel Collaboration with 10X Genomics on a Premium Exome 2. High sensitivity detection of rare variants (<1% VAF) HaloPlex HS Target Enrichment System incorporating molecular barcodes 3. Quality control of DNA from single cells for NGS Agilent D5000 ScreenTape Assay 4. Visualization of chromosomal aneuploidies in cell-free DNA sequencing data OneSight software platform 5. Investment in NGS technology for clinical sequencing Lasergen 8

9 1. Beyond the Exome : resolving structural complexities and variation OneSeq CNV Backbone + Custom Panel Computational methods that identify CNVs from WES are based on analysis of read depth These methods assume that read depth is proportional to the number of copies of that region Differences in bait efficiencies and sequencing biases result in highly variable read depth Distribution of read depth in exome Asymmetric read depth makes CNV calling from WES very difficult Same WES dataset analyzed with different CNV-callers produce significantly different results (Tan et al., 2014) WGS can identify all variants in one assay but remains cost-prohibitive How do we study all variants in one cost-effective NGS assay? 9

10 1. Beyond the Exome : resolving structural complexities and variation OneSeq CNV Backbone + Custom Panel Backbone Exon Exon Exon SureSelect XT Library Prep and OneSeq Target Enrichment Probes selected for calling copy number High minor allele frequency SNPs targeted Probes covering coding regions Select CNV backbone Select content for SNVs & indels High resolution backbone (300Kb genomewide + 25Kb in ClinGen regions) Low resolution backbone (1Mb) Catalog ClearSeq gene panels SureSelect Exomes, Clinical Research Exome, Focused Exome SureSelect Custom OneSeq Target Enrichment 10

11 1. Beyond the Exome : resolving structural complexities and variation OneSeq CNV Backbone + Custom Panel Detection of Trisomy 13 in NA02948 Detection of 364kb duplication upstream of SOX9 300kb OneSeq backbone Microarray 1Mb OneSeq backbone Detection of 5Mb LOH in NA20409 OneSeq Copy number [Log 2 Ratio] LOH data [B allele freq] 11

12 1. Beyond the Exome : resolving structural complexities and variation Collaboration with 10X Genomics on a Premium Exome 1. Reach beyond the exome while maintaining high quality SNP/indel performance 2. Phase thousands of genes and assign cis or trans to heterozygous variants with megabase-scale phase blocks 3. Detect translocations, gene fusions and enable CNV detection with precise insertions, deletions events. Standard Exome Baits Linked-Reads from Standard Exome Baits SureSelect Optimized Exome Baits Linked-Reads from Optimized Baits Chromium Controller Agilent Target Enrichment Sequencer 10x Long Ranger 10x Loupe Launching in October 2016! 12

13 2. High Sensitivity Detection of Rare Variants HaloPlex HS Target Enrichment System Incorporating Molecular Barcodes How molecular barcoding works HaloPlex HS Workflow Step 1 Step 2 Step 3 Step 4 Align reads Group read pairs to designed probes based on read start-stop position Group reads with an identical molecular barcode sequence for each probe Consolidate read information to one read per molecule (remove PCR duplicates) Complete library prep-free target enrichment in <6hr Detects SNVs down to <1% allele frequency Analysis using Agilent SureCall software 13

14 2. High Sensitivity Detection of Rare Variants HaloPlex HS Target Enrichment System Incorporating Molecular Barcodes HaloPlex HS performance with FFPE samples Detection down to 0.5% allele frequency in HapMap dilutions 14

15 2. High Sensitivity Detection of Rare Variants HaloPlex HS Target Enrichment System Incorporating Molecular Barcodes HaloPlex HS makes the cover of the Journal of Medical Genetics! High Sensitivity Sequencing Reveals Multi-Organ Somatic Mosaicism Causing DICER-1 Syndrome Leanne de Kock et al (2015) Dept of Human Genetics, McGill University Journal of Medical Genetics Tumors associated with DICER1 Syndrome Deep sequencing of gdna from blood, tumor and normal tissue Detected RNaseIIIb mutations at % frequency in constitutional DNA Mosaic DICER1 RNaseIIIb missense mutations important genetic cause of DICER1 syndrome 15

16 3. Quality Control of DNA from Single Cells for NGS Agilent Sample QC Systems NEW Agilent 2100 Bioanalyzer System Widely accepted QC standard Integrated in many protocols & extensively cited Widest range of applications Includes protein Small footprint Agilent 4200 TapeStation System 96 sample walkaway operation Scalable throughput at a constant cost Easy to use Ready-to-use consumables 16

17 3. Quality Control of DNA from Single Cells for NGS Agilent D5000 ScreenTape Assay A B Agilent Application Note ( EN): Morris & Eberwine, Penn University 17

18 4. Visualization of chromosomal aneuploidies in cell-free DNA sequencing data OneSight software platform OneSight Compatible with most common NGS library prep kits Compatible with the most common NGS sequencing platforms Upload NGS data Select analysis pipeline and reference set Visually inspect chromosome plots OneSight offers genetics laboratories a cost-effective way to perform high-quality cell-free DNA analysis in-house 18

19 4. Visualization of chromosomal aneuploidies in cell-free DNA sequencing data OneSight software platform Normal Segmental aberration Trisomy Complex aberrations 19

20 5. $80M Investment in NGS Technology for Clinical Sequencing Lasergen Library Prep / Capture Automation QC Sequencing Analysis Interpretation / Reporting Lasergen Houston, TX Focused on advancement and commercialization of unique nucleotide chemistries Proprietary photocleavable nucleotide chemistry ( lightning terminators ) fast reaction times, robust cleavage Potential to be faster, cheaper and more accurate than current NGS technologies Ultimate goal: Provide a complete workflow for routine clinical testing Intended to support applications within Human & Reproductive Genetics and Cancer Exomes and panels Integrated solution, including automation and analysis / reporting 20

21 Building a Complete Agilent NGS Solution HaloPlex Target Enrichment SureSelect Target Enrichment Interpretation support and reporting Sample prep Research Mix & match Clinical Integrated workflow Automated Target Enrichment Automation Sample QC Alignment & Variant Calling Next Generation Sequencing Data Analysis (q)pcr OneSeq Target Enrichment 21

22 Learn Festival of Genomics Boston Stop by Agilent Booth #322! 22