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PowerPoint Presentationgenomics.broadinstitute.org/data-sheets/POS_Liquid... · Title: PowerPoint...
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Development of Production Scale cfDNA Sequencing @ Broad Genomics Carrie Cibulskis, Viktor A. Adalsteinsson, Mark Fleharty, Katie Larkin, Justin Abreu, Michelle Cipicchio, Jonna Grimsby, Brendan Blumenstiel, Matthew DeFelice, Tom Mullen, Gavin Ha, Samuel S. Freeman, Kristisan Cibulskis, Atish D Choudhury, Daniel G. Stover, Heather A. Parsons, Nick Wagle, Gregory Gydush, Sarah C. Reed, Denisse Rotem, Justin Rhoades, Lee Lichtenstien, Stacey Gabriel, Todd R. Golub, Jesse S. Boehm, Gad Getz, J. Christopher Love, Matthew Meyerson, Niall Lennon Genomic profiling of cell free tumor DNA (Blood Biopsy) offers the potential to revolutionize cancer precision medicine. As a proxy for tumor tissue profiling, successful blood biopsy analysis can help select appropriate patients for clinical trials, provide useful data for treatment monitoring, and discover genomic mechanisms of disease resistance. cfDNA exomes provide an accurate proxy for tumor tissue biopsy Recognizing these potential benefits, we aim to enable large-scale genomic data generation and analysis of cfDNA samples in Broad Genomics. To support translational research at scale, Blood Biopsy products must be • Cost-effective, sensitive and accurate • Comprehensive in approach • Relatively quick to return data for clinical applications • Capable of scaling to > 100 samples per week Background & Motivation Blood Biopsy offerings at Broad Genomics will have three product options. Ultra Low Coverage Whole Genome (0.1x Coverage: Data will be used to estimate % tumor fraction of cfDNA library and for copy number analysis. Samples with > 10% purity are recommended for whole exome analysis and < 10% purity for deeper coverage targeted panel sequencing. Blood Biopsy Workflow @ Broad Genomics: Whole Genomes, Whole Exomes & Targeted Panels Targeted sequencing variant detection at high depth (>1000x) is sensitive to duplication of reads and sequencing errors. To increase sensitivity and specificity of predicted variants we are utilizing sequencing adaptors with unique molecular indexes (UMIs) to de-duplicate data and generate molecular consensus reads prior to variant calling with MuTect II. Targeted Panel Product Development Target Product Specifications Targeted Panel Content patients patients Whole Exome: Samples with adequate % ctDNA can be processed in whole exome sequencing using standard Illumina targeting reagents for the most comprehensive discovery potential. Targeted 400 Gene Panel: Samples with < 10% ctDNA can be processed in deeper coverage (>1000x) targeted panel sequencing for increased sensitivity. CLIA grade sequencing will be available if required. Preliminary targeted panel sequencing data of 2 individuals mixed at target % allele fraction (.2%, 1%, 5%). # of variants in plot = 470. Additional development experiments are underway aimed at increasing efficiency of adaptor ligation to generate more complex sequencing libraries from low input cfDNA material. • 402 Genes Targeted – Exon Territory (V2 = 581) • 1.9 Mb of Territory (V2 ~3 Mb) • Selected genes tiled in entirety, or with evenly spaced SNP probes for CNV analysis • 85% of current DFCI Oncopanel genes included • Will be refined before final product, continually accepting feedback Gene list is here: http://tinyurl.com/BROAD-CFDNA Timeline Product launch is targeted for July 2017. Stay Tuned! Cancer Program Data Sciences Platform Product Sample Input Territory Coverage Target Sensitivity Target* Specificity Target* Target Turn Around Time Target Launch Date Ultra Low Pass Whole Genome 5-10ml Blood, 4-6ml Plasma, or 5-20 ng cfDNA Whole Genome 0.1x – 0.3x - 1 Month May 2017 Blood Biopsy Whole Exome Whole Genome Library Whole Exome, 21K Genes 150x cfDNA Tumor, 60x gDNA Normal >90% of events at 5% AF (samples at 10% purity) < 0.5/Mb 1 Month May 2017 Blood Biopsy Targeted Panel Whole Genome Library 1.9Mb, Exon Territory 402 Genes 1000x cfDNA Tumor, 500x gDNA Normal >90% of events at 0.5% AF < 1/Mb 21 Day July 2017 Analysis Powered by FireCloud
Transcript of PowerPoint Presentationgenomics.broadinstitute.org/data-sheets/POS_Liquid... · Title: PowerPoint...
Development of Production Scale cfDNA Sequencing @ Broad Genomics
Carrie Cibulskis, Viktor A. Adalsteinsson, Mark Fleharty, Katie Larkin, Justin Abreu, Michelle Cipicchio, Jonna Grimsby, Brendan Blumenstiel, Matthew DeFelice, Tom Mullen, Gavin Ha, Samuel S. Freeman, Kristisan Cibulskis, Atish D Choudhury, Daniel G. Stover, Heather A. Parsons, Nick Wagle,
Gregory Gydush, Sarah C. Reed, Denisse Rotem, Justin Rhoades, Lee Lichtenstien, Stacey Gabriel, Todd R. Golub, Jesse S. Boehm, Gad Getz, J. Christopher Love, Matthew Meyerson, Niall Lennon
Genomic profiling of cell free tumor DNA (Blood
Biopsy) offers the potential to revolutionize cancer
precision medicine. As a proxy for tumor tissue
profiling, successful blood biopsy analysis can help
select appropriate patients for clinical trials, provide
useful data for treatment monitoring, and discover
genomic mechanisms of disease resistance.
cfDNA exomes provide an accurate
proxy for tumor tissue biopsy
Recognizing these potential benefits, we aim to
enable large-scale genomic data generation and
analysis of cfDNA samples in Broad Genomics.
To support translational research at
scale, Blood Biopsy products must be
• Cost-effective, sensitive and accurate
• Comprehensive in approach
• Relatively quick to return data for clinical
applications
• Capable of scaling to > 100 samples per week
Background & Motivation
Blood Biopsy offerings at Broad Genomics will
have three product options.
Ultra Low Coverage Whole Genome (0.1x
Coverage: Data will be used to estimate % tumor
fraction of cfDNA library and for copy number
analysis. Samples with > 10% purity are
recommended for whole exome analysis and < 10%
purity for deeper coverage targeted panel
sequencing.
Blood Biopsy Workflow @ Broad Genomics: Whole Genomes, Whole Exomes &
Targeted PanelsTargeted sequencing variant detection at high depth
(>1000x) is sensitive to duplication of reads and
sequencing errors. To increase sensitivity and
specificity of predicted variants we are utilizing
sequencing adaptors with unique molecular indexes
(UMIs) to de-duplicate data and generate molecular
consensus reads prior to variant calling with MuTect II.
Targeted Panel Product Development
Target Product Specifications
Targeted Panel Content
patients patients
Whole Exome: Samples with adequate % ctDNA
can be processed in whole exome sequencing
using standard Illumina targeting reagents for the
most comprehensive discovery potential.
Targeted 400 Gene Panel: Samples with < 10%
ctDNA can be processed in deeper coverage
(>1000x) targeted panel sequencing for increased
sensitivity. CLIA grade sequencing will be
available if required.
Preliminary targeted panel sequencing data of 2 individuals mixed at
target % allele fraction (.2%, 1%, 5%). # of variants in plot = 470.
Additional development experiments are underway
aimed at increasing efficiency of adaptor ligation to
generate more complex sequencing libraries from low
input cfDNA material.
• 402 Genes Targeted – Exon Territory (V2 = 581)
• 1.9 Mb of Territory (V2 ~3 Mb)
• Selected genes tiled in entirety, or with evenly
spaced SNP probes for CNV analysis
• 85% of current DFCI Oncopanel genes included
• Will be refined before final product, continually
accepting feedback
Gene list is here: http://tinyurl.com/BROAD-CFDNA
Timeline
Product launch is targeted for July 2017.
Stay Tuned!
Cancer Program
Data Sciences Platform
Product Sample Input TerritoryCoverage
TargetSensitivity
Target*Specificity
Target*Target Turn
Around TimeTarget
Launch Date
Ultra Low Pass Whole
Genome
5-10ml Blood,4-6ml Plasma,
or 5-20 ngcfDNA
Whole Genome
0.1x – 0.3x - 1 Month May 2017
Blood Biopsy Whole Exome
WholeGenome Library
Whole Exome, 21K
Genes
150x cfDNATumor, 60x
gDNA Normal
>90% of events at 5% AF
(samples at 10% purity)
< 0.5/Mb1 Month May 2017
Blood Biopsy Targeted
Panel
WholeGenome Library
1.9Mb, ExonTerritory
402 Genes
1000x cfDNATumor, 500x
gDNA Normal
>90% of events at 0.5% AF < 1/Mb 21 Day July 2017
Analysis Powered by FireCloud
