Frampton: Asks the question of the impact of assay failure, its clinical impact. Variability sources - mentions FRUO status #GIAB
11:14am August 27th 2015 via Hootsuite
Frampton: Samples can be fixed from 1 minutes to the weekend; they have stds with differing amounts. Also cfDNA #GIAB
11:12am August 27th 2015 via Hootsuite
Frampton: Starts with the chaulkboard (old-skool) - gene editing technology, go into FFPE from cells. DNA, RNA, can do formalin harsh #GIAB
11:11am August 27th 2015 via Hootsuite
Salit: A set of genomes to get standard characterizations of variants with clinical utility; both natural and engineered #GIAB
11:07am August 27th 2015 via Hootsuite
Salit: Either a pure GeT-RM or #GIAB or both; opportunity for high-confidence char of a panel of regions in a wider set of sample variety
11:05am August 27th 2015 via Hootsuite
Lisa Kalman discuses several hundred samples and several hundred genes - generalized to clin relevant genes, both cancer & inherited #GI
11:04am August 27th 2015 via Hootsuite
Jonathan Frampton (Dir Products HorizonDx): 'Impact of formalin treatment on molecular assays - and how to use #GIAB samples to answer'
11:02am August 27th 2015 via Hootsuite
Turan: In the process of CAP certification, will get to that point. Salit: "First reference material that will get better as its used" #GIAB
10:57am August 27th 2015 via Hootsuite
Turan: Q (Lincoln from In Vitae) about low-level drift in NA12878. Disc. around tying lot number to batch, not currently provided #GIAB
10:55am August 27th 2015 via Hootsuite
Turan: Q:Do you detect drift? A:Occasionally, on the 'F or G expansion' and will go back to earlier ones. #GIAB
10:49am August 27th 2015 via Hootsuite
Salit: 10X had to grow up their own cells to get larger MW DNA. Turan: Has the capability as a custom project. #GIAB
10:48am August 27th 2015 via Hootsuite
Turan: Q (Salit):Fragment lengths about 60KB - normal for others? A:Kept procedures the same. #GIAB
10:47am August 27th 2015 via Hootsuite
Turan: Q:Test for drift? A: From cytogenetic and microarray on every expansion, sterility, along with culture QC #GIAB
10:46am August 27th 2015 via Hootsuite
Turan: Mentions the GET conference http://t.co/5xoeLKHTrU #GIAB
10:44am August 27th 2015 via Hootsuite
Turan: Some are HapMap consented, but PGP's are the most consented. Over 1K diseases, many collections, constantly thinking of needs #GIAB
10:43am August 27th 2015 via Hootsuite
Turan: PGP mainly B-lymphocytes. 2 trios; in process of working up larger numbers. Housing many samples for human variation #GIAB
10:42am August 27th 2015 via Hootsuite
Turan: From blood to PBMCs to cell lines. For NIST, much larger and complex operation due to batch size. #GIAB
10:41am August 27th 2015 via Hootsuite
Turan: Actively involed with NA12878, RM 8398. Also PGP collection - 120 lines, from LCL #GIAB
10:40am August 27th 2015 via Hootsuite
Turan: Collection, consent, inventory, data capture, inventory management. 50% of her time works with submitters on what they need #GIAB
10:39am August 27th 2015 via Hootsuite
Turan: TGP and HapMap samples; iPSCs, gDNA, total RNA. Continuously funded for >40y. NIGMS, NINDS, NHGRI, NIA. Since 1972. #GIAB
10:38am August 27th 2015 via Hootsuite
Turan: Grown stem cells (several 100, aim for several thousand), storage of biomaterials, cell cultures, cytogenetics #GIAB
10:37am August 27th 2015 via Hootsuite
Nihid Turan (NIGMS Human Genetic Cell Repository, Coriell) Introduces Coriells as the 'world's most diverse biobank' #GIAB
10:35am August 27th 2015 via Hootsuite
Salit: Mentions AMP's presence here, and importance. Expresses excitement around representation from clinical labs here. #GIAB
10:31am August 27th 2015 via Hootsuite
#GIAB session on RM's: Nahid (Coriell); Jonathan (HorizonDx) about PGP trios; Jason Lih NCI-Frederick; myself from @seracare; Ken Cole NIST
10:29am August 27th 2015 via Hootsuite
Zook: Long-range phasing - CGI LFR and 10X. 'Integration methods needed for phasing' #GIAB
9:39am August 27th 2015 via Hootsuite
Zook: Progress on AJ Trio: 2 de novo assemblies (MHAP and Falcon/Bionano), structural variants - MetaSV, Parliament, svclassify #GIAB
(NB - you can follow webcast link on Google Groups: http://t.co/dveQcrTosG ) #GIAB
9:37am August 27th 2015 via Hootsuite
Zook: Busy slide of workflow to form high-confidence SNP/indel calls. Timeline of high-confidence calls on AJ Trio #GIAB
9:36am August 27th 2015 via Hootsuite
Zook: Refining integration of SNP/Indels on DNAnexus to others can easily reproduce results. Validating w/released NA12878 data #GIAB
9:34am August 27th 2015 via Hootsuite
Zook: Data release in real-time, open, public release, no embargo. Can publish whenever analyses are finished. #GIAB
9:33am August 27th 2015 via Hootsuite
Zook: Brought in 4 leaders for GIAB analysis (F de la Vega of Annai, @mason_lab, Tina Graves (WashU), V Schneider (NCBI) #GIAB
9:32am August 27th 2015 via Hootsuite
Zook: Short read, PE, Long MPs, Moleculo, 10X, CGI, CGI LFR, Proton Exome, BioNano Genomics, @PacBio and @nanopore from @mason_lab #GIAB
9:31am August 27th 2015 via Hootsuite
Zook: Stratifies data to GC content, indels and FP rates. Datasets across platforms for GIAB PGP trios (AJ and Asian) #GIAB
9:30am August 27th 2015 via Hootsuite
Zook: Onto @GA4GH benchmarking task team, defining TP/FP, also no-calls and half-calls across tools. Credits Rebecca Truty and CGI #GIAB
9:29am August 27th 2015 via Hootsuite
Zook: One paper that uses RM 8398 from @qiagen comparing somatic mutation calls across 5 callers http://t.co/LiYvboDbLr #GIAB
9:28am August 27th 2015 via Hootsuite
Zook: GeT-RM browser: a nice resource for feedback for corrections to make. Mentions 3 publications #GIAB
9:26am August 27th 2015 via Hootsuite
Zook: In July '15, 90K downloads from GIAB site. GeT-RM browser from NCBI and CDC here http://t.co/pyXoKNj1B5 #GIAB
9:25am August 27th 2015 via Hootsuite
Zook: NA12878 - high-confidence calls are updated onto FTP site. Working with NCBI to organize data; SNPs and indels covering ~77% #GIAB
9:24am August 27th 2015 via Hootsuite
Zook: Now at work on AJ (Ashkenazi Jewish) and Asian - goal is to make RM available in 2016. #GIAB
9:23am August 27th 2015 via Hootsuite
Justin Zook: Progress update since last workshop: release of RM 8398. Char for homogeneity, same as NA12878. 'Best for regulated uses' #GIAB
Salit: Others working on well-char genomes: @illumina Platinum, CDC GeT-RM, Korean Genome, @humanlongevity , Hyditaform mole haploids #GIAB
9:21am August 27th 2015 via Hootsuite
Salit: Other breakouts to carry out roadmap, split into analysis and RMs. Slides typically placed onto Slideshare. #GIAB
9:20am August 27th 2015 via Hootsuite
Salit: Highlights previewing this meeting: progress updates, breakouts for analysis and other RMs (spike ins, other genomes) #GIAB
9:18am August 27th 2015 via Hootsuite
Salit: Mentions http://t.co/CaOODNggON for access to Pilot NIST RM data #GIAB
9:14am August 27th 2015 via Hootsuite
Salit: Mentions @seracare working with Mickey Williams of NCI for spike-in calling for somatic calling. http://t.co/GvcsbAwAwm #GIAB
Salit: And not for clinical interpretation either. Working with Coriell, working with Acrometrix @servingscience @seracare #GIAB
9:12am August 27th 2015 via Hootsuite
Salit: Scope is analytical process (library through sequencing, alignment, var calls and confidence estimates). Not for pre-analytical #GIAB
9:11am August 27th 2015 via Hootsuite
Salit: Learn to resolve difficult structural var's; enable regulated apps. Was excited to see @10xgenomics using RMs as benchmark #GIAB
9:10am August 27th 2015 via Hootsuite
Salit: Well-characterized, stable RM's: metrics for validation, QC, QA, PT; sources of bias/error. Yellow lights are 'standard' #GIAB
9:08am August 27th 2015 via Hootsuite
Salit: 'Enabling performance assessment of sequencing and science-based regulatory oversight' Initiated in 2009, first meetings in '11 #GIAB
9:06am August 27th 2015 via Hootsuite
