Jeremiah McDole, PhD Product Manager, Oncology Illumina · Challenge Iterative testing §Roth AD1,...
Transcript of Jeremiah McDole, PhD Product Manager, Oncology Illumina · Challenge Iterative testing §Roth AD1,...
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Jeremiah McDole, PhD
Product Manager, Oncology
Illumina
Enabling Advancements in Cancer Research
2
New cases Deaths Living with
http://www.cancer.org/cancer/cancerbasics/lifetime-probability-of-developing-or-dying-from-cancer (current 02/09/2016)Globocan 2012: http://globocan.iarc.fr/Pages/fact_sheets_cancer.aspx
14M 8M 32M
Global Cancer
1 in 3 1 in 2
The War on Cancer
3
Understanding The Puzzle of Cancer Biology Through Genomic Solutions Enabled by Illumina
Identification
of Driver
Mutations
Pathway
Analysis
Tumor Micro-
environment
Understanding
Drug
Resistance
The Role of
Germline
Variants
Gene
Regulation &
Epigenetics
Understanding
Response To
Therapy
The Role of the
Microbiome
Tumor Sub-
type
Classification
Building a Catalog of Driver MutationsIdentification
of Driver
Mutations
The Cancer Genome Atlas Pan-Cancer analysis project, Nature Genetics 45, 1113–1120 (2013)
Building a Catalog of Driver MutationsOver 3,000 tumor samples, 12 tumor types
TCGA Pan-Cancer Analysis Kandoth et al., Nature, Oct 2013See: http://www.nature.com/tcga/
Identification
of Driver
Mutations
Lawrence, et al. Nature 2014
Building a Catalog of Driver MutationsHow much more is there to discover?
“We now know what it would take to get a complete catalog. And we now know we’re not close to done. We have a lot left to learn.”
ERIC LANDERNYT Interview,
Feb 6, 2014
“Creating a comprehensive catalogue of genes in which somatic point mutations propel cancer at both high (>20%) and intermediate (2–20%) frequency will require analysing an average of approximately 2,000 tumours for each of at least 50 tumour types, corresponding to approximately 100,000 tumours.”
Lawrence et al., Nature 2014
Identification
of Driver
Mutations
Towards a Molecular Classification of Tumors
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Tumor Sub-
type
Classification
Mechanisms of Response
9
Understanding
Response To
Therapy
Understanding The Puzzle of Cancer Biology Through Genomic Solutions Enabled by Illumina
Identification
of Driver
Mutations
Pathway
Analysis
Tumor Micro-
environment
Understanding
Drug
Resistance
The Role of
Germline
Variants
Gene
Regulation &
Epigenetics
Understanding
Response To
Therapy
The Role of the
Microbiome
Tumor Sub-
type
Classification
11 For Research Use Only. Not for use in diagnostic procedures.
Portfolio of Sequencing PlatformsTo serve every application
High ThroughputWGS | WES | T-OME
Personal ScaleFew samples | Run
Low ThroughputTGRS | WGS (Microbes)
Production ScaleMany samples | Run
MiniSeq MiSeq
NextSeq 500HiSeq Series
NextSeq 500
Serious
Production Scale
HiSeq X Series
HiSeq Series
Translate
Apply
Discover
Transforming the Practice of Oncology with Genomics Scientists, Clinicians, Pharma, Regulatory Bodies and New Technologies
Mapping the biology of cancer
Defining clinical utility
Responsible implementation
The Sample Challenge
Small tissue samples:
Lung biopsies Fine Needle Aspirates
An increasing number of variants of known significance
More variants to query More tests to be performed
The ChallengeHow to find more with less?
Image from Chen et al., J Thorac Dis. 2013 Jun;5(3):E93-7. doi: 10.3978/j.issn.2072-1439.2013.04.17. Figure 2
ChallengeIterative testing
§Roth AD1, Tejpar S, Delorenzi M, et al. Prognostic role of KRAS and BRAF in stage II and III resected colon cancer: results of the translational study on thePETACC-3, EORTC 40993, SAKK 60-00 trial. J Clin Oncol. 2010 Jan;28(3): 466-474.*Irahara N, Baba Y, Nosho K, et al. NRAS mutations are rare in colorectal cancer. Diagn Mol Pathol. 2010 Sep;19(3): 157-163.**Duration of testing time begins after the sample material becomes available. Turn-around time and cost will vary from lab to lab.
Today:Iterative testing increases demands for tissue, time, and costs
Colon Cancer investigation
Cumulative testing time** 7 days 14 days 21 days…
Cumulative cost** $400 $800 $1200
Cumulative sample needed 10 ng 135 ng 145 ng
Positive30%-50% of results§Negative
KRAS test
Positive5%-10% of results§Negative
BRAF test
Positive1%-3% of results*
Negative
NRAS test …
Colon sample
Multi-Gene AssaysAccelerate investigation
*Duration of testing time begins after the sample material becomes available. Turn-around time and cost will vary from lab to lab.**Cost of library prep and sequencing consumables per sample on MiSeq®.
Colon Cancer investigation Savings
Testing Time *3 days 21 days
Reagent Cost **$167 $400-1000+
Sample needed 20 ng No additional biopsy
Comprehensive solutions designed with your cancer research in mind
Minimize tissue burden Potential to reduce time to action
NGS cancer assay(15 genes)
Positive
Investigationaldata analyzed
PositiveColon sample
For Research Use Only. Not for use in diagnostic procedures.
Multi-Gene NGS Test Maximizes Resources
Faster time to results Cost savings Maximized results withminimal tissue
Improved stratification
Multi-Gene NGS Cancer AssaysNow available
TruSightCancer
TruSightMyeloid
TruSight RNAPan-Cancer
TruSeqAmplicon
Cancer Panel
TruSightTumor 15
TruSeqCustom
Amplicon Low Input
PanelType
Germline Hematology Pan-cancer Solid Tumor Custom
Genomic content
94 genes 54 genes 1385 genes 48 genes 15 genesUp to 1536 amplicons
Variant detection
(frequency)Germline As low as 5%
Detects gene expression, fusions and
SNVs
As low as 5% As low as 5% As low as 5%
Blood, FFPEBlood Blood, FFPEBlood, Bone
Marrow, FFPE
For Research Use Only. Not for use in diagnostic procedures.
Multi-Gene Cancer PanelTruSight® Tumor 15
Single assay:Detect pathogenic variants for 7 types of cancer
BRAFEGFRERBB2KRASMETPIK3CARETTP53
Lung
BRAFGNA11GNAQKITPDGFRATP53
Melanoma
AKT1ERBB2PIK3CA
Breast
KITKRASMETPDGFRA
Gastric
BRAFKRASMETTP53
Colon
PIK3CA
Prostate
FOXL2TP53
Ovary
For Research Use Only. Not for use in diagnostic procedures.
Precision Oncology Treatment From companion diagnostics to companion therapeutics
Patient Multi-target test
Target 1
Target 2
Target 3
The Drug
CRx
Partners