Cole: An SRM is used to transfer values to other materials. Limited amounts and priced high. Chart of qPCR vs dPCR very similar #'s #GIAB
3:38pm August 27th 2015 via Hootsuite
Ken Cole (NIST) SRM Genomic DNA standards for HER2 measurements; 5 br ca lines; used qPCR and dPCR for copy umber. Validating with NCI #GIAB
3:36pm August 27th 2015 via Hootsuite
Salit: But ISO may not be helpful. EMQN - for augmenting CAP, called 'schemes'. Plea for del, dup, CNV info to NA12878 for proficiency #GIAB
3:06pm August 27th 2015 via Hootsuite
Salit: Nat'l metrology institutes don't have large genomics presence. ISO TC276 developing a set of standards around NGS. #GIAB
3:04pm August 27th 2015 via Hootsuite
Lincoln: EMQN run by Eurogentest, but funding Q's. @claritas4kids - how many of the 100 sample req's came from ex-US? Zook:will do #GIAB
3:02pm August 27th 2015 via Hootsuite
Salit: Representatives from Japan and Korea (Macrogen) have their efforts. Word getting out. People use it, but need to participate #GIAB
3:01pm August 27th 2015 via Hootsuite
Salit: Actionable mutations in clinically impt portions - may be a GeT-RM project. #GIAB
3:00pm August 27th 2015 via Hootsuite
de la Vega: What about EU, and other parts of the world to make it an int'l standard? Salit: A topic for Jan 2016 meeting #GIAB
2:59pm August 27th 2015 via Hootsuite
.@bioinfosm @mendelspod I'll have to dig into the assay, but one poss. explanation is the mutation occurs close to the end of the fragment
2:55pm August 27th 2015 via Hootsuite in reply to bioinfosm
Clinical samples has been handled by that group for many years. Zook: may need to look at other similar projects #GIAB
2:54pm August 27th 2015 via Hootsuite
Comment from UPenn: @hail_cser project for clinical dx downstream. 'CSER hadn't heard about #GIAB - exploratory research, NHGRI-sponsored.
2:53pm August 27th 2015 via Hootsuite
Schnieder: GRC wants to know regions that don't map. http://t.co/GiSU1rYHZq has mechanism to contact #GIAB
2:52pm August 27th 2015 via Hootsuite
Material from NA12878 lines; agrees that primary cell vs transformed cell comparison is needed #GIAB
2:51pm August 27th 2015 via Hootsuite
Comment from BioNanoGenomics: They need 350KB - 1MB long. Seeing long complex repetitive regions, sees EBV insertion 100's of times #GIAB
2:50pm August 27th 2015 via Hootsuite
Lincoln: Observed mis-handling of #GIAB data. 'Whatever can be done with education is certainly valuable'
2:47pm August 27th 2015 via Hootsuite
Salit: Why pre-analytic sample process is not part of #GIAB - excluded for a reason. Lincoln: even from whole blood, still a problem.
2:42pm August 27th 2015 via Hootsuite
Church: Hard to mimic handling; thus the need for larger 'real-world sample' collections. #GIAB
2:40pm August 27th 2015 via Hootsuite
Comment: Great that Horizon is doing FFPE. NIPT routinely extracts cfDNA. Heterogeneity is 'enormous'. Caution: real-world smpls cmplx #GIAB
Mason: FFPE on trios, with spike-ins, ABRF is onboard for doing this. #GIAB
2:30pm August 27th 2015 via Hootsuite
Mason: A 'Franken-genome' - with many genome types including arabidopsis, human, viral, fungal etc. #GIAB
Mason: Metagenomics standards - multiple sites, multiple kits, across vendors to happen this Fall. #GIAB
2:29pm August 27th 2015 via Hootsuite
Mason: cell-free DNA should keep epigenetic marks; having a good standard may be of interest. 'Family assembly' - a Christmas present #GIAB
2:28pm August 27th 2015 via Hootsuite
WashU: Creation of genomes that can be used as 'a reference if you want'. Plans to do that across multiple genomes, included with HGRC #GIAB
2:26pm August 27th 2015 via Hootsuite
Church: The Genome Ref Consortium has been hard at work, some regions not complete are very clinically important #GIAB
2:24pm August 27th 2015 via Hootsuite
Comment: Will we ever get to a stable genome? Salit: 25y of experience with reference materials at NIST, provides DNA in a tube #GIAB
2:23pm August 27th 2015 via Hootsuite
Turan (Coriell): There is (always) drift, but never had the level of #GIAB before. Large expansions it is inevitable. New level of detail.
2:21pm August 27th 2015 via Hootsuite
Zook: How would this be used? A:Mason: Likely both. Drift of lines happens; PDx cells drift as well. No current sense of how quickly #GIAB
2:19pm August 27th 2015 via Hootsuite
de la Vega: NA12878 looked at typed pedigrees, artifacts thus removed. For AJ trios: would be nice to have #GIAB
2:18pm August 27th 2015 via Hootsuite
Rosenfeld (Rutgers): Pt samples are different than cell lines. Blood - 50 de novo mut's vs 1K in a cell line from that pt. #GIAB
2:16pm August 27th 2015 via Hootsuite
Robin (AMP): Expresses appreciation for #GIAB, and how to help the translation to clinic. Kalman, Salit: GeT-RM forum to make requests
2:15pm August 27th 2015 via Hootsuite
McCormack: Some 28 companies developing cfDNA, many academic centers. Thinking of partnership with FNIH, NIST, 'bigger device co's' #GIAB
2:12pm August 27th 2015 via Hootsuite
McCormack (Jenssen Oncology) Looking to partner to develop standards for cfDNA. FNIH association - 'get it all under control' #GIAB
2:11pm August 27th 2015 via Hootsuite
Representation of repetitive regions - Zook comment a lot of work done with @GA4GH without phase not helpful. #GIAB
2:09pm August 27th 2015 via Hootsuite
Comment2: FFPE block with severe formalin treatment - adding variables, in particular from limited samples from pts w/adv cancer #GIAB
2:07pm August 27th 2015 via Hootsuite
Comment: known mutations with somatic mutations; the fear of missing indels 'is always there'; EGFR known but a consistent question #GIAB
2:06pm August 27th 2015 via Hootsuite
Roadmap discussion: Church:Range of variation, and quality of samples and their effect on ability to detect low-freq alleles #GIAB
2:04pm August 27th 2015 via Hootsuite
Frampton: Chart of structural multiplex standard - fusion, CNV, SNV, short dels #GIAB
11:31am August 27th 2015 via Hootsuite
Frampton: Has data on formalin on DNA quantitation; slides will be available later. 40 people devoted to effort #GIAB
11:30am August 27th 2015 via Hootsuite
Williams: "A great need for cfDNA, not only reference material but also calibration materials' an important point #GIAB
11:29am August 27th 2015 via Hootsuite
Frampton: If any useful gene editing to be done, 'now is the time to ask for 2016' e.g. structural engineering into PGP's #GIAB
11:28am August 27th 2015 via Hootsuite
Turan: iPSCs for PGP in-process at Coriell. Salit: Keep in mind what is most important. Put PGP smples in cell-free format... #GIAB
11:27am August 27th 2015 via Hootsuite
Salit: But the challenge: drift for genome, transcriptome. Lincoln: Need methods-based validation. Reprod or homogeneous the need #GIAB
11:25am August 27th 2015 via Hootsuite
Lincoln: "One thing to remember is you will need 2 with RNA" Salit: PGP, go to iPSCs and build tissues from there. #GIAB
11:23am August 27th 2015 via Hootsuite
Turan: Interest in a large batch of RNA from these samples? A:Batch to batch variation may be 'a nightmare' (M Williams) #GIAB
11:22am August 27th 2015 via Hootsuite
Frampton: Q:Are fusions (clin relevant) helpful in AJ trio? A: Salit: does it matter that its edited? Or spiked into the background? #GIAB
11:21am August 27th 2015 via Hootsuite
Church: Gene fusions is challenging. Work, 'because there aren't good materials' Other input: hard b/c gene expression 'chaotic' #GIAB
11:18am August 27th 2015 via Hootsuite
Frampton: Q to group: is reference RNA needed? A:Salit - expression is arbitrary from cell line. Church: var calling from RNA #GIAB
Framptonin Q-Seq includes: Q1/15 Formalin compromised Q2/15: cell free DNA, structural standards, Q3/15 RNA #GIAB
11:17am August 27th 2015 via Hootsuite
Frampton: May do cell line base with 1,000's of SNVs. Their roadmap: Ash trio as FFPE sections, Asian son (same), Q-Seq ref stds. #GIAB
11:16am August 27th 2015 via Hootsuite
Frampton: Sample, extraction, quant, library, sequencing, alignment, var calling, analysis. Need reference materials all along. #GIAB
11:15am August 27th 2015 via Hootsuite
