Brenner: Some specific, others sensitive, others balance. What's the state of the art? ID progress, innovations, reveal bottlenecks #TCGC15
8:09pm June 23rd 2015 via Hootsuite
Brenner:Phenotypic consequences - CAGI 2013, 10 challenges, then assessment season. Not a competition, methods good 'in what way' #TCGC15
8:08pm June 23rd 2015 via Hootsuite
Brenner: Critical Assessment of Genome Interpretation (CAGI) - CASP-like contest in predicting protein structure. #TCGC15
8:07pm June 23rd 2015 via Hootsuite
Brenner: Newborn seq - Mendelian disorders still much unknown. Large wordcloud of mut prediction methods - like sift and PolyPhen #TCGC15
8:06pm June 23rd 2015 via Hootsuite
Brenner: First two genomes - Watson and Venter, back then what useful information derived from them? #TCGC15
8:05pm June 23rd 2015 via Hootsuite
Brenner:(title con't): "...a community experiment to evaluate phenotype prediction" Assessing how clin interpretation of genomes #TCGC15
8:04pm June 23rd 2015 via Hootsuite
Steven Brenner (Univ Calif Berkeley) "Findings from the critical assessment of genome interpretation" #TCGC15
8:03pm June 23rd 2015 via Hootsuite
Sieh: Recent 2014 ref: http://t.co/RgmtMVY7bO Genetics has comparable information as lifestyle factors #TCGC15
8:02pm June 23rd 2015 via Hootsuite
Sieh:Using currently known br ca risk alleles, model shows more useful, guiding cost-effective screening, lifestyle choices #TCGC15
7:58pm June 23rd 2015 via Hootsuite
RT @ecancer: New project designing tools for cancer patients to manage illness from mobile phones http://t.co/w7BZIgCjzL #iManageCancer
7:45pm June 23rd 2015 via Hootsuite
Sieh: Cp partial risk of known br ca risk alleles (93 alleles) to theoretical 'all known' and predict probabilities #TCGC15
Sieh:Can WGS at birth guide br ca prevention? '12 Science Trans Med ref http://t.co/64xQ4FjP2x NYT "DNA predictive power is limited" #TCGC15
7:43pm June 23rd 2015 via Hootsuite
Weiva Sieh (Stanford Univ) "Role of genome sequencing in personalized breast cancer prevention" #TCGC15
7:41pm June 23rd 2015 via Hootsuite
Mittelman:Needed for annotation as well - to test annotation across platforms and companies. Benchmarks and stds slows us down #TCGC15
7:40pm June 23rd 2015 via Hootsuite
Mittelman:Q:How much attn needed for library prep? A:Partners need to repeat NA12878 maybe every six months. #TCGC15
7:39pm June 23rd 2015 via Hootsuite
Mittelman:Q:Validated means? A: Can get metrics around FP, FN that would be needed for regulatory agencies #TCGC15
7:37pm June 23rd 2015 via Hootsuite
Mittelman: Tool at Tute has a filter cascade; developing a dashboard to support deep dives into variant analysis 'by ASHG' #TCGC15
7:35pm June 23rd 2015 via Hootsuite
Mittelman: Did you miss a gene or exon in your panel? There are dropouts - unacceptable in clinical setting. QC steps passed along #TCGC15
7:33pm June 23rd 2015 via Hootsuite
Mittelman: Var callers depends on the application. BioIT launched; 200K on it. Acknowledges @gabeinformatics and @gholsonlyon #TCGC15
7:28pm June 23rd 2015 via Hootsuite
Mittelman: Same var caller (GapK) but Venn diagram showed - different variants. Worked with J Zook NIST Genome in a Bottle (GIAB) #TCGC15
7:26pm June 23rd 2015 via Hootsuite
Mittelman: Bowtie is good - but insensitive to quality. GCAT gives insight to other metrics. 'You may get different variants' #TCGC15
7:25pm June 23rd 2015 via Hootsuite
Mittelman: Can do read alignment comparisons, next several examples. Novoalign and BWmem both are best, but have variation. #TCGC15
7:24pm June 23rd 2015 via Hootsuite
Mittelman:Highnam '15 ref http://t.co/NTRCBWs7Mi pipeline free to use called GCAT here: http://t.co/p1UwqF8u1F catching best methds #TCGC15
7:23pm June 23rd 2015 via Hootsuite
Mittelman: Partnered with DNANexus (alignment and var calling) Tute does annotation and reporting. '12 ref http://t.co/FpWJMj0ufI #TCGC15
7:21pm June 23rd 2015 via Hootsuite
Mittelman: Curated datasources, private and other public ones, fast and scalable annotation. Prenatal to inherited disorders #TCGC15
7:18pm June 23rd 2015 via Hootsuite
David Mittelman (Tute Genomics) "Democratizing regulated clinical sequencing" #TCGC15
7:16pm June 23rd 2015 via Hootsuite
Fortney:Q:HLI's approach is big data - does clinical data help? A:It can help (healthy vs. not), not clear-cut how best to use it #TCGC15
6:42pm June 23rd 2015 via Hootsuite
RT @GenomeNathan: My #TCGC15 deck: http://t.co/e3F6d06sYi Or, why drug labels don't list elements...and what that says, long-term, for geno…
6:39pm June 23rd 2015 via Twitter Web Client
.@gabeinformatics Yes it also would have been nice to have a list of graded callers (okay it was only 1 .vcf but still) #TCGC15
6:31pm June 23rd 2015 via Twitter Web Client in reply to gabeinformatics
RT @gabeinformatics: Kristen Fortney: Talk on whole genome sequencing of 17 supercentenarians - available for public study: http://t.co/IlO…
6:30pm June 23rd 2015 via Twitter Web Client
RT @gabeinformatics: Thanks Kristen Fortney for making the supercentenarians public! I enjoyed analyzing them! Blog on my analysis http://t…
Fortney: Used GWAS data from disease for overlap to longevity SNPs. Traits and disease GWAS listed, developed p-value weighting #TCGC15
6:28pm June 23rd 2015 via Hootsuite
Fortney:WGS via Complete Genomics; didn't find any replicated. Used PGP data, made data available '14 PLOS http://t.co/UjtGaaiuor #TCGC15
6:24pm June 23rd 2015 via Hootsuite
Fortney: Only 17 supercentarians alive in the US. Many highly functional, ave age of death 113. 2/17 had major age-rel disease #TCGC15
6:18pm June 23rd 2015 via Hootsuite
Fortney: Centenarian GWAS - only APOE - but low #'s (100's of samples). Two stories: rare var's w/17 >110yo (super-centenarians) #TCGC15
6:17pm June 23rd 2015 via Hootsuite
Fortney: One example of longevity - about 25%. Kahn family, four siblings all >100yo. They work for a long time. 83% less stroke etc #TCG
6:16pm June 23rd 2015 via Hootsuite
Kristen Fortney (Stanford Univ) "Whole-genome sequencing of the world's oldest people" #TCGC15
6:14pm June 23rd 2015 via Hootsuite
Kong: Concludes:(one of many): "analytical validity of current state-of-the-art algorithms is not satisfactory" #TCGC15
6:08pm June 23rd 2015 via Hootsuite
Kong: Comparison of VCFs from 1 FASTQ file (from GIAB) illustrated. Fig from '11 ref http://t.co/UOQSoCAj4j #TCGC15
6:04pm June 23rd 2015 via Hootsuite
Kong: Using @hail_cser and 100 WGS as part of a project called MedSeq '14 Genet Med ref: http://t.co/4xwcBXGWdJ Polygenic risk score #TCGC15
5:50pm June 23rd 2015 via Hootsuite
Kong: How can probabilistic predictions of disease be incorporated into personal and clinical decision-making? #TCGC15
5:48pm June 23rd 2015 via Hootsuite
Kong: What if we had WGS of millions of individuals? '13 ref http://t.co/gUswQ96U25 Actionable muts and for offspring #TCGC15
5:45pm June 23rd 2015 via Hootsuite
Kong: Mentions Mark Cuban's tweets about getting a quarterly blood baseline. Human exposome (Dean Jones) 400K chemicals #TCGC15
5:39pm June 23rd 2015 via Hootsuite
Kong: Eric Topol's 2014 Cell paper http://t.co/bHjl40SfN4 From prewomb to tomb: prevent disease, infectious disease #TCGC15
5:37pm June 23rd 2015 via Hootsuite
Kong: Near-term focus on cancers, longer term to improve healthcare. Snyder's personal 'omics '12 Cell ref http://t.co/Dt5Pxzafax #TCGC15
5:35pm June 23rd 2015 via Hootsuite
Sek Won Kong (Harvard Medical School and Boston Children's Hospital) "An approach to WGS as a lifelong health resource" #TCGC15
5:32pm June 23rd 2015 via Hootsuite
Garlick:Q:Curation of info, db's? A:Will be doing an integrated QC study, look at QC metrics to pinpoint where QC should take place #TCGC15
4:17pm June 23rd 2015 via Hootsuite
Garlick:Q:Stability? A:Patent method filed last month. Q:FFPE is simulated? A:Not planning cell lines, PDX instead. #TCGC15
4:16pm June 23rd 2015 via Hootsuite
Garlick:Q:Tools to FDA - how to correlate w/assay mfrs? A:SeraCare is agnostic to assays. Validation of product to intended use. #TCGC15
4:14pm June 23rd 2015 via Hootsuite
Garlick:Q:Shared data with Illumina? A:Yes the conversation will start #TCGC15
