Alexander (Sasha) Zarenek (PGP):Comments of the need for open software. #GIAB
10:08am August 28th 2015 via Hootsuite
Han Cao (BioNanoGenomics) Q:About emphasis on SNVs A: Definitely not focused only on SNVs, but there is tech-dependence #GIAB
10:04am August 28th 2015 via Hootsuite
Mansfield: There can't be a 'read-depth standard' - and know why you set it that way. #GIAB
10:02am August 28th 2015 via Hootsuite
Mansfield: FDA doesn't want to be restrictive, not expecting indiv labs to use everything 'out of the box'. #GIAB
10:00am August 28th 2015 via Hootsuite
Lincoln: Q:Some labs have really tuned their analysis and metrics around specific platforms. Tezak: Asking for input #GIAB
9:59am August 28th 2015 via Hootsuite
Zook: Difficulty arises with platform-spec quality scores. Tezak: Even with bioinformatics definitions of quality too. #GIAB
9:57am August 28th 2015 via Hootsuite
Liz Mansfield (FDA): Invites input on how to make this tech-agnostic and not stifle innovation. Want it to be 'current all the time' #GIAB
9:55am August 28th 2015 via Hootsuite
Tezak:Q:(Salit) Is this technology-agnostic? A:Not what they are thinking, but 'really hard', is working to find the middle #GIAB
9:53am August 28th 2015 via Hootsuite
Tezak:Q:About specific documentation A:One general one and one specific one to gather feedback/input #GIAB
9:50am August 28th 2015 via Hootsuite
Tezak: Precision Medicine requires: safe and accurate Dx; learning health systems; dev of targeted Rx; updated research and reg policy #GIAB
9:44am August 28th 2015 via Hootsuite
Tezak: precisionFDA: a crowd-sourced, cloud-based platform for advancing accuracy and reprod of NGS. Tools and open access resources #GIAB
9:42am August 28th 2015 via Hootsuite
Tezak: Need built-in flexibility; stakeholders may be able to convene (e.g. FDA's SEQC) #GIAB
9:40am August 28th 2015 via Hootsuite
Tezak: Among collection of existing standards - NYSDOH, CAP, MolDx, GA4GH, Tex-StoCT, ACMG, HGVS, CPIC, CLSI: what are gaps? Timeline? #GIAB
9:39am August 28th 2015 via Hootsuite
Tezak: Common stds - methology (types of variants, allelic ratio, technology); test building blocks. #GIAB
9:36am August 28th 2015 via Hootsuite
Tezak: Areas for separate stds - targeted germline, somatic. Exome, WGS-based (both germline and somatic). #GIAB
9:35am August 28th 2015 via Hootsuite
Tezak: And definition of 'standards' - what performance standard doc? ACMG, CLSI, etc. Build a general framework: a roadmap. #GIAB
9:31am August 28th 2015 via Hootsuite
Tezak: Analytical evaluation, bioinformatics, and clin sig. Since Feb 20th: before 'go blind' - now: clear indications for use #GIAB
9:29am August 28th 2015 via Hootsuite
Tezak: Disclaims that these are preliminary ideas. #GIAB Shared this link to the Feb 20 public FDA workshop on NGS http://t.co/Cz5sm8lR4E
9:28am August 28th 2015 via Hootsuite
Zivana Tezak (FDA OIR CDRH) Analytical evaluation standards for NGS. Starts with mention of last year's discussion w/ Liz Mansfield #GIAB
9:24am August 28th 2015 via Hootsuite
Salit: How can a kb like ClinVar or PharmGKB be evaluated for completeness? #GIAB
9:23am August 28th 2015 via Hootsuite
Salit: And the regulatory agencies need fluency for accreditation. For Precision Med - identify knowledge gaps, build standards #GIAB
9:20am August 28th 2015 via Hootsuite
Salit: The 'yellow light': from DNA to .vcf - the analytical/technical performance assessment. 'We need ways to evaluate VCFs' #GIAB
9:17am August 28th 2015 via Hootsuite
Salit: Standards for WGS: Preanalytical, seq, bifx, functional var annotation, clinical var kb query, interpretation, reporting, EHR #GIAB
9:13am August 28th 2015 via Hootsuite
RT @ldtimmerman: Informed Consent Isn't Working. @Sagebio and Apple Just Might Be Onto Something Better. https://t.co/dFk1FCcStP
8:35am August 28th 2015 via Hootsuite
RT @NatureNews: Long-term collaborations yield 17% boost in citation rate for resulting papers http://t.co/5Rox0il7Z0 http://t.co/0V0PQtYiOh
7:21am August 28th 2015 via Hootsuite
A new book answers why it’s so hard for educated women to find dates - The Washington Post http://t.co/Yd9jEkYjVR
8:55pm August 27th 2015 via Hootsuite
RT @pickover: A clock for math teachers. http://t.co/6N5AwOjhiZ http://t.co/3YqHzkhKIt
6:40pm August 27th 2015 via Hootsuite
Church: "Variants from 15bp to 50kb really worries me." "A complete blind-spot" NA12878 has very few SVs >50kb #GIAB
4:48pm August 27th 2015 via Hootsuite
Church: Concerned about variants we haven't seen before. Lincoln: "We know today we miss a lot of indels" #GIAB
4:44pm August 27th 2015 via Hootsuite
Lincoln:Would love to have a shoot-out. Perhaps #GIAB contribution would be to come up with the consensus list of mutations to test for.
4:40pm August 27th 2015 via Hootsuite
Salit: Challenge is not having #GIAB background with somatic mutations. Horizon: has 40-45 cancer-spec mutations.
4:32pm August 27th 2015 via Hootsuite
Discussion about merits/demerits of spike-ins. Nothing else is available however. Lincoln: assay dependency. #GIAB
4:29pm August 27th 2015 via Hootsuite
Sims (NCI) Choice of mutations for inter-lab study would need to stress informatics pipelines as well. #GIAB
4:27pm August 27th 2015 via Hootsuite
Comment: "I wish someone would do it" Mason for ABRF: Engineered cell lines at lower %. Timing of inter-lab study, FFPE too. #GIAB
4:18pm August 27th 2015 via Hootsuite
Salit: Had talked in prior meeting of inter-lab study with spike-in study? Utility of synthetic constructs for somatic calling? #GIAB
4:15pm August 27th 2015 via Hootsuite
Salit: Could be a relative calibrator - ensuring the same amount is there over time. Analytic and clinical pieces - a dynamic #GIAB
4:11pm August 27th 2015 via Hootsuite
Williams: As long as the assay is consistent with a set # of molecules/mL - what alarms him is claims being made now #GIAB
4:08pm August 27th 2015 via Hootsuite
Comment (UPitt): If V600E at 0.1%, what does that mean? Top 5 or 10 genes, actionable, prospective will it help? #GIAB
4:05pm August 27th 2015 via Hootsuite
Lincoln: Do we need all cell-free assays? But we don't know what these assays are... with 27 providers. CML bcr-abl RNA - an example #GIAB
4:04pm August 27th 2015 via Hootsuite
Salit: cfDNA is not that far from what #GIAB has done before. Robin (AMP) availability of ref materials important.
4:00pm August 27th 2015 via Hootsuite
Williams: MRD 'all over again' but without standards... Comment: Not only ref material but kits. Ends' chemistry? #GIAB
3:58pm August 27th 2015 via Hootsuite
Q: Salit:Are these ref materials? A:Used as a generic phrase. Q:How currently benchmarked? A:Williams:Pubs have no controls at all #GIAB
3:56pm August 27th 2015 via Hootsuite
Cole: Can get BRAF V600E down to 3% using ddPCR, 20ng ~6700 copiies/rcn. Mentioned used for RainDance 0.01% means almost 1 ug load #GIAB
3:51pm August 27th 2015 via Hootsuite
Cole: Tested with dPCR on QX200:can detect down to 50 copies/uL. HER2, 2PR4 (intron 4), and 4Q5 (exon 3). Assay amplicon is 97-122bp #GIAB
3:49pm August 27th 2015 via Hootsuite
Cole: Nuclei, either micrococal nuclase (MN-treat) or Atlantis dsDNse treatment. #GIAB
3:47pm August 27th 2015 via Hootsuite
Cole: Either sheared or nuclease digestion (~200bp); effect of spike-in at low AF. Covaris to 200bp. #GIAB
3:46pm August 27th 2015 via Hootsuite
Cole: cfDNA for cancer a promising technique; mentioned yesterday's news item #GIAB BBC on work in Sci Trans Med: http://t.co/QtvxHF9RzQ
3:45pm August 27th 2015 via Hootsuite
Cole: 'Ref material for measuring pre-analytical variables - a much harder task' (collection, storage, extraction, matrix etc.) #GIAB
3:43pm August 27th 2015 via Hootsuite
Cole: Onto circulating cfDNA, part of NCI early detection research network (EDRN). Is synthetic different than endogenous? #GIAB
3:42pm August 27th 2015 via Hootsuite
Cole: Using SRM 2370 for qPCR as a reference. CN for EGFR and MET data shown as well (in development) six ATCC lines #GIAB
3:41pm August 27th 2015 via Hootsuite
