Fernandes: Going back to FDA and LTDs: Oct '14 framework for regulatory oversight; Reporting. Jan '15 Public meeting, comments #Tricon
5:19pm February 21st 2017 via Hootsuite
Helen Fernandes (Columbia Univ NY): Choosing an effective validation plan for NGS assays in oncology #Tricon
5:17pm February 21st 2017 via Hootsuite
Armstrong: Describes Paragon test for immuno-oncology. Escape - expresion arrays; activation via flow cytometry. #Tricon
3:09pm February 21st 2017 via Hootsuite
Armstrong: Reporting: all sample metadata provided; key genes highlighted; visual representation of flagged genes #Tricon
3:03pm February 21st 2017 via Hootsuite
Armstrong: Cofactor Pinnacle cp aberrant gene expression to other cancers of the same type. Report is 379 oncology-relevant genes #Tricon
3:02pm February 21st 2017 via Hootsuite
Armstrong: Goes through biology of ALK fusion. Shows 12 FFPE FISH as gold std; 8/12 by DNA; 8/12 by RNA; IHC was 10/12. #Tricon
2:57pm February 21st 2017 via Hootsuite
Armstrong: Illustrates challenge of finding breakpoints, and how much more sequence needs to be done; whereas RNA straitforward #Tricon
2:53pm February 21st 2017 via Hootsuite
Armstrong: DNA doesn't look at expression, large rearr detection limitations; but RNA has its own weakness: FFPE, variation in fix #Tricon
2:51pm February 21st 2017 via Hootsuite
Armstrong: Via sequencing-based Dx - majority DNA-based; most are tumor-only; #Tricon
2:49pm February 21st 2017 via Hootsuite
Armstrong: Molecular Dx - goal is to char difficult-to-understand biology on a molecula level. #Tricon
2:47pm February 21st 2017 via Hootsuite
Jon Armstrong (Cofactor MO) Reaching the Pinnacle: a unique cancer diagnostic tool that harnessess the power of RNA #Tricon
2:46pm February 21st 2017 via Hootsuite
Kuo: Have a two-tier classification: pathogenic or VUS. 30% are from BMT's, sometimes 2x or 3x. Thus germline SNPs w/varying AF #Tricon
2:34pm February 21st 2017 via Hootsuite
Kuo: Reviews complex calling pipeline. ClinVar, dbSNP, ESP100, ExAc, COSMIC, TCGA all involved. Links Mut Assessor, KEGG, GeneCard #Tricon
2:30pm February 21st 2017 via Hootsuite
Kuo: Run 30 samples/run; use 250ng; 1.8m reads at 1500x. No matched pairs, 2-3 runs/week. #Tricon
2:24pm February 21st 2017 via Hootsuite
Kuo: Decided to build custom TruSeq, 95 genes, 1330 amplicons, 175K. SNVs, indels to 55bp, CNV, FLT3-ITD. No translocations #Tricon
2:22pm February 21st 2017 via Hootsuite
Kuo: 1y costs of single-genes '14 on the order of $343K. Rapid heme panel goals: TAT of a few days, detecte low AF, cost-effective #Tricon
2:21pm February 21st 2017 via Hootsuite
Kuo: Shows very large menu of Non-NGS tests for solid and heme tumers;for NGS; Snapshot and Oncopanel #Tricon
2:19pm February 21st 2017 via Hootsuite
Kuo: Starts with JAMA editorial https://t.co/CfBP1lUY2f that TCGA was $675M, 10K samples. #Tricon
Frank Kuo (Brigham and Women's Hosp MA) NGS-based panel testing for hematologic malignancies #Tricon
2:16pm February 21st 2017 via Hootsuite
.@kennamshaw Wonderful talk Kenna! I really enjoyed it (unlike the, um, plenary <cough cough> session)
2:16pm February 21st 2017 via Hootsuite in reply to kennamshaw
MT @SeraCare: #TRICON We're launching new fusion #RNA reference materials developed in collaboration with @QIAGEN https://t.co/u1Sp4ByzHk
2:14pm February 21st 2017 via Hootsuite
Shaw: These were pts who had exhausted all treatment options. #Tricon
2:04pm February 21st 2017 via Hootsuite
Shaw: 7% of their pts with VUS enrolled. Showed unpublished K-M curve for OS afte doubling participation: clearly better #Tricon
2:03pm February 21st 2017 via Hootsuite
Shaw: They've now been able to get 25% of pts with mutations in actionable genes enrolled in clin trials #Tricon
2:02pm February 21st 2017 via Hootsuite
Shaw: VUS is 95% of the variants they see. Their website for their knowledge base for decision support: https://t.co/K3f3S6ZNZz #Tricon
2:00pm February 21st 2017 via Hootsuite
Shaw: Shows a figure from '11 JAMA https://t.co/6idiXfwFMP showing every gene is not equally actionable #Tricon
1:59pm February 21st 2017 via Hootsuite
Shaw: One person's actionable alteration is another's germline varient. Gives illustration of a MET mutation. #Tricon
1:58pm February 21st 2017 via Hootsuite
Shaw: Of 429 pts w/mutations in highly actionable genes: 17% never came back. Of those who came back: 2/3'rds never went on another #Tricon
1:53pm February 21st 2017 via Hootsuite
Shaw: Lack of enrollment not due to lack of available matched trials. MDAnderson has a lot of clinical trials. #Tricon
1:51pm February 21st 2017 via Hootsuite
Shaw: % of pts with potentially actionable gene: 40% (o 2K); ultimately 4% went to a clinical trial. #Tricon
1:50pm February 21st 2017 via Hootsuite
Shaw: 'We are all equally bad at doing this" - who tested, how much to sequence, how to pay for it, how to demonstrate effectiveness #Tricon
1:48pm February 21st 2017 via Hootsuite
Shaw: "NGS 'big' data are necessary, but insufficient, to drive precision medicine" #Tricon
1:47pm February 21st 2017 via Hootsuite
Shaw: Doesn't matter how many genes you sequence - only 125 'actionable' genes. 1/2 of FMI's panel - you can't match to a drug #Tricon
Shaw: NGS cost decrease 'leads to increases in data generation'. 'Same exact crappy hit rate' 11% for 50 genes; 5% for WES #Tricon
1:46pm February 21st 2017 via Hootsuite
Shaw: Only unless you have particular cancers with particular markers. Most the time - sequential chemo #Tricon
1:43pm February 21st 2017 via Hootsuite
Shaw: Away from population work getting to individual pt shift. 'We are not providing PM to the majority of our pts' #Tricon
1:42pm February 21st 2017 via Hootsuite
Kenna Mills Shaw (Sheikh Khalifa @kennamshaw MD Anderson TX) Precision oncology decision support #Tricon
1:41pm February 21st 2017 via Hootsuite
Q: OncoSkins at Dana Farber? Gray: A version is being used now. Wants to build more applications on top @stacywgray is her handle :) #Tricon
1:40pm February 21st 2017 via Hootsuite
Gray: Moving beyond academic cts, need for reimbursement for genetic counseling, and testing info returned to pt #Tricon
1:38pm February 21st 2017 via Hootsuite
Gray: Shows summary slide of challenge of 'actionability', access. Trial participation from 11% down to 5% https://t.co/gcDfwLOFwP #Tricon
1:37pm February 21st 2017 via Hootsuite
Gray: 10% have OOP costs of >$18K. 84% of oncologiest consider OOP costs. Need to think about systemic solutions #Tricon
1:35pm February 21st 2017 via Hootsuite
Gray:Tractable challenges: pt's "financial toxicity". 25% spend most or all savings during cancer trtmt #Tricon
Gray: Instead of static PDFs, OncoSkins project to innovate genomic reporting, want to publish this soon. #Tricon
1:34pm February 21st 2017 via Hootsuite
Gray: Innovation is needed to support providers w/result comprehension, increase confidence in genomic knowledge #Tricon
1:33pm February 21st 2017 via Hootsuite
Gray: Also ID'd the need for physician education. Need to explain tests, decide, sequence, return results, understand findings #Tricon
1:32pm February 21st 2017 via Hootsuite
Gray: Oncologist want to provide seq data to pts 80% predictive for clin trial; 60% for off-label; 55% prognostic favorable #Tricon
Gray: Most pts want somatic and germline results - typically >90%. CanSeq study '16 https://t.co/Qf2WIe2V1P #Tricon
1:30pm February 21st 2017 via Hootsuite
Gray: https://t.co/S58yFEEEpZ EHR problems - mentions https://t.co/JNKlPL0OKx - where data was locked in PDFs, system from '91 #Tricon
1:29pm February 21st 2017 via Hootsuite
Gray: Some providers express low confidence in genomic knowledge. Dana Farber - survey of Dr. attitudes https://t.co/zkme1EilFN #Tricon
1:26pm February 21st 2017 via Hootsuite
Gray: Insufficience evidence: only 6% of NCCN guidelines based on high-level evidence. Abernathy '10 - only 5 datapts used #Tricon
1:24pm February 21st 2017 via Hootsuite
