Bennette: For generally healthy individuals: across 10K patients age 45y, $58K/QALY the pop-based cost #TCGC15
11:22am June 24th 2015 via Hootsuite
Bennette: Results published '14 ref http://t.co/ZestkzSIPh Wide range of health benefits - 0.1 to 2y QALY #TCGC15
11:21am June 24th 2015 via Hootsuite
Bennette: Even with 7, still economic QALY model would take too much time. 5/7 used existing published work. Used 3 populations #TCGC15
11:18am June 24th 2015 via Hootsuite
Bennette: Of 24 conditions, 7 comprised 95% of expected IF's. Top: familial hypercholderolemia, then hereditary br and ov cancer #TCGC15
11:16am June 24th 2015 via Hootsuite
Bennette: IF (incidental finding) found or not found, known effect or not; all based on the 56 genes. #TCGC15
11:15am June 24th 2015 via Hootsuite
Bennette: Quality Adjusted Life Year (QALY) - the life-years gained, adjusted for quality. Starting with WGS: evaluate return of VUS #TCGC15
11:14am June 24th 2015 via Hootsuite
Bennette: Goal to evaluate health outcomes and guide policy. Guidelines released in '13. Derive probabilities, expected benefits #TCGC15
11:13am June 24th 2015 via Hootsuite
Bennette: ACMG list of 56 genes, 24 inh conditions. Considerable uncertainty about returning 'secondary findings' #TCGC15
11:11am June 24th 2015 via Hootsuite
Caroline Bennette (Fred Hutchinson Cancer Ctr) " Estimating the Cost Effectiveness of Returning Incidental Findings from NGS" #TCGC15
11:10am June 24th 2015 via Hootsuite
Tynan: AMP has assumed a leadership role to describe the cost and value of GSP (Genomic Seq Procedure) here http://t.co/hdskjIGIiI #TCGC15
11:09am June 24th 2015 via Hootsuite
Katherine Tynan (Tynan Consulting) "Clinical genomics: a good investment?" #TCGC15
11:06am June 24th 2015 via Hootsuite
RT @westr: “@kirkwillmarth: Bianchi (tufts): 40% of women w t21 continue pregnancy #GenomicsFest” #Down's #NIPT #PM101
9:32am June 24th 2015 via Hootsuite
RT @Becky_Kusko: Rehm: just showed us this trailer made by 12 year old http://t.co/EIpVP71JK0 #GenomicsFest
9:31am June 24th 2015 via Hootsuite
"One of the earliest examples of precision medicine in the US" GERA Aging http://t.co/KpJjvwIlB9 PDF http://t.co/nNIfasI3Xu HT @divabiotech
8:01am June 24th 2015 via Hootsuite
MT @nxtstop1: The superb journal chat #nephjc on 'Social Media in Medicine' Storify http://t.co/OKF0Gm2uHy Thx 4 all you do! @kidney_boy
7:10am June 24th 2015 via Hootsuite
MT @TCGAupdates: Pan-cancer analysis suggests novel indications for existing cancer drugs #TCGA Biomarker Res (OA) http://t.co/Vt0cR7sgSk
6:10am June 24th 2015 via Hootsuite
Latest @mason_lab RT @kellyquek: The impact of read length on quantification of DEGs and splice junction detection http://t.co/UNMeDNGJkO
5:55am June 24th 2015 via Hootsuite
RT @vanessashen: I was asked to document my software development process http://t.co/9CSu3EdUvq
4:50am June 24th 2015 via Hootsuite
RT @JenniferRedig: Know PCR/next gen. sequencing? Want to become a part-time science writer w/Bitesizebio? email me jredig@gmail.com #altac
10:50pm June 23rd 2015 via Hootsuite
RT @BioMickWatson: From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows http://t.co/6EE3NXPyuK
9:50pm June 23rd 2015 via Hootsuite
RT @TCGAupdates: Landscape of driver mutations in #melanoma in @CellCellPress http://t.co/SS9CgjmYDY http://t.co/8gvb3Yhibz
8:50pm June 23rd 2015 via Hootsuite
Brenner:Q:What's next? A:Gearing up for next challenge. Some enhancer mutations, some CRISPR muts, exome data, splicing #TCGC15
8:37pm June 23rd 2015 via Hootsuite
Brenner:A huge wall of acknowledgements. Board, Council, Data Providers, Assessors, Web Dev & Data Analysis #TCGC15
8:35pm June 23rd 2015 via Hootsuite
Brenner: False confidence - correlating noise rather than signal. #TCGC15
8:34pm June 23rd 2015 via Hootsuite
Brenner: Predictors 'are not ready for the clinic'. Using multiple methods don't get you better results. Use just one rather than 2 #TCGC15
Brenner: Need methods that work on an individual disease, on an individual gene. #TCGC15
8:33pm June 23rd 2015 via Hootsuite
Brenner: Caveat - CAGI is anecdotal. Predictions are highly significant - but 'predictive accuracy for any spec var is low' #TCGC15
8:32pm June 23rd 2015 via Hootsuite
Brenner: PGP with trait prediction: 239 total binary traits, 77 genomes. 1 group got 6 right, another 5. #TCGC15
8:29pm June 23rd 2015 via Hootsuite
Brenner: Chrohn's disease affected people had high levels of homozygosity; explaining why groups did well. German affected individ's #TCGC15
8:24pm June 23rd 2015 via Hootsuite
Brenner:Another example: Hypoalphalipoproteinemia (HA). Predict most severe phenotype. @genomenathan did best #TCGC15
8:18pm June 23rd 2015 via Hootsuite
Brenner: Top methods had Spearman's correlation of 0.6. For that gene - advise against any prediction method. #TCGC15
8:17pm June 23rd 2015 via Hootsuite
Brenner: Cystathionine beta-synthase aa subst: which truly causative? Yeast had human enzyme put in, actual activity vs predicted #TCGC15
8:15pm June 23rd 2015 via Hootsuite
Brenner: 10 challenges CAGI website: http://t.co/LdulOarebz Discordant MZ twins: asthma prediction - no better than random #TCGC15
8:12pm June 23rd 2015 via Hootsuite
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
