OncoCartaOncoCarta™™ Panel v1.0Panel v1.0
OncogeneOncogene Rare Somatic Mutation Rare Somatic Mutation DetectionDetection
Jennifer DangJennifer DangGenome Analysis Core FacilityGenome Analysis Core Facility
March 3March 3rdrd, 2010, 2010
Validated panel of 187 assays, designed for
profiling 238 rare somatic mutations in 19 oncogenes within
24 multiplexes
OncoCartaOncoCarta™™
Ready: Ready: --PrePre--validated and prevalidated and pre--mixed for mixed for immediate useimmediate use
Rapid: Rapid: --8 hour workflow (18 hour workflow (1--4 Chips, up to 4 Chips, up to 62 samples)62 samples)--Characterization of large sample Characterization of large sample populations with short turn around populations with short turn around times times
Accurate:Accurate:--Detection asDetection as low as 10% mutation low as 10% mutation frequency in mixed tumor samples frequency in mixed tumor samples
Little DNA neededLittle DNA needed: : --Minimum Minimum 540540ng DNA per sample ng DNA per sample at 10ng/at 10ng/µµll
Why OncoCarta™?
OncoCartaOncoCarta™™ Assay DesignsAssay DesignsAssayAssay –– a pair of PCR a pair of PCR
primers and a single primers and a single base extension primer base extension primer
““SimpleSimple”” AssayAssayOne assay used to One assay used to determine mutationdetermine mutation
““CompositeComposite”” AssayAssayMultiple assays are used Multiple assays are used to resolve mutationto resolve mutation
24 Wells multiplexed with all 187 assays24 Wells multiplexed with all 187 assaysLow Low mulitplexingmulitplexing levelslevels
One 384-well plate fits 15 samples and a non-template control
Assays across 24 plexes
Sam
ples
OncoCartaOncoCarta™™ KitKit
OncoCartaOncoCarta™™ Kit ComponentsKit ComponentsTypePlexTypePlex®® ReagentsReagentsGen II Matrix ChipsGen II Matrix ChipsPrePre--validated and prevalidated and pre--mixed mixed oilgooilgo sets:sets:
--24 PCR primer tubes24 PCR primer tubes--24 Extend primer tubes24 Extend primer tubes
Gen II Chip data from Sequenom®
Mutation ReportMutation Report
--Mutation frequency cutMutation frequency cut--off changeable off changeable --CoreCore’’s standard cuts standard cut--off 5%off 5%
--Genome Core reviews mutation report and spectraGenome Core reviews mutation report and spectra
WTMutation
FrequencyWT
FrequencyDetected Mutation
Oncogeneof Interest
Genome Core Findings Genome Core Findings
--Missed 2 KRAS mutations Sequencing detectedMissed 2 KRAS mutations Sequencing detected--Found 5 KRAS mutation Sequencing missedFound 5 KRAS mutation Sequencing missed--Found up to 35 other mutations in EGFR, MET, PIK3CA, BRAFFound up to 35 other mutations in EGFR, MET, PIK3CA, BRAF--Composite assays may not resolve which mutation or mutations areComposite assays may not resolve which mutation or mutations are presentpresent
-- 3/49 KRAS mutations found were unresolved3/49 KRAS mutations found were unresolved-- 4/26 EGFR mutations found were unresolved4/26 EGFR mutations found were unresolved
140 Tumor samples sequenced for KRAS mutations were processed with OncoCarta™ on 9 chips in 8 days
OncoCarta™ Projects
ProsPros
Ready for immediate useReady for immediate use
Rapid Rapid
Accurate detection as low as Accurate detection as low as 10% 10%
Little DNA needed: under Little DNA needed: under 600ng600ng
Limitation
Some composite assays may Some composite assays may not resolve which mutation or not resolve which mutation or mutations are presentmutations are present
CostCost
Kit SizeKit Size
OncoCarta™
OncoCartaOncoCarta™™ PricingPricing
$16.59$16.59$10.17$10.17Labor Cost Per SampleLabor Cost Per Sample
$263.16$263.16$141.94$141.94Reagent Cost Per Reagent Cost Per SampleSample
$10,000$10,000$22,000$22,000Total Kit CostsTotal Kit Costs
331010ChipsChips
2255ControlsControls
3838155155SamplesSamples
40 Sample Kit**40 Sample Kit**160 Sample Kit*160 Sample Kit*
*Minimum Run: 31 samples & 1 control on 2 chips *Minimum Run: 31 samples & 1 control on 2 chips Total Charges (Kit + labor): $4,715.15Total Charges (Kit + labor): $4,715.15
**Full kit must be run**Full kit must be runTotal Charges (Kit + labor): $10,630.30Total Charges (Kit + labor): $10,630.30
Thanks to…
Allan Balmain
Il-Jin Kim
Kirsten Copren
Kate Thompson
Langdon Smythe
Sonia Mirza
Sequenom®
Genome Core ListservGenome Core Listserv®®
From your UCSF email addressFrom your UCSF email addressTo: To: [email protected]@listsrv.ucsf.eduSubject Heading: optionalSubject Heading: optionalBody of email: Body of email: ““subscribe CC_GENCOR_EDsubscribe CC_GENCOR_ED””
oror““subscribe CC_GENCOR_ANsubscribe CC_GENCOR_AN””
Non UCSF addressNon UCSF addressplease email: please email: [email protected]@cc.ucsf.edu
