KY: Discovered 2.87 de novo indel (1-20bp)/gen; 0.14 de novo SNv (>20bp)/gen #ASHG14
1:43pm October 21st 2014 via Hootsuite
RT @claritas4kids: #ASHG14 Erin Riggs: dosage sens for CNVs, to get highest score of 3, need >= 3 indep events, not present in normal,+ m
1:42pm October 21st 2014 via Hootsuite
KY: Pointed to this 2011 NAR Yu ref: http://t.co/GeLlvln9BW microhomology end-joining for one mechanism #ASHG14
1:41pm October 21st 2014 via Hootsuite
KY:Cross-platform - including both MiSeq, Sanger and @iontorrent for validation of var's. With paternal origin: pat ~2x of maternal #ASHG14
1:38pm October 21st 2014 via Hootsuite
KY: Est sensitivity of their effort: 89.2% for 1-20bp; 69.4% for 21-99bp; 85.8% for >11bp (results submitted) 14x for MZ = 28x #ASHG14
1:36pm October 21st 2014 via Hootsuite
KY: 231 trios, 8 dizygotic twin quartets, 11 monozygotic twin quartets. Chart of 11 callers for 1bp to >10kb indels to struct var's #ASHG
1:34pm October 21st 2014 via Hootsuite
Session:Structural and Somatic Var. Kai Ye WashU Origin, frequency & functional impact of de novo struct changes in the human genome #AS
1:33pm October 21st 2014 via Hootsuite
AT: Uncertainty results in anxiety, and full certainty is an illusion. Acceptance of limits of certainty, accept a dual reality #ASHG14
12:33pm October 21st 2014 via Hootsuite
AT: Points to BRCA counseling in this '13 ref Vos http://t.co/IDjrBEKGZb Predictor of distress of interpretation, not understanding #ASHG14
12:32pm October 21st 2014 via Hootsuite
AT: 141 expecting parents, 2014 van der Steen http://t.co/DOKUapDZbF similar findings: elect to get maximum information #ASHG14
12:30pm October 21st 2014 via Hootsuite
AT: 2014 Sapp ref http://t.co/lb7xG4lLRa for children w/undiagnosed conditions. Parents describe their success in coping w/results #ASHG14
12:27pm October 21st 2014 via Hootsuite
AT:25yo, testing for Huntington's. Needed approval to get tested, 60-80% would apply for certainty. Health system 'not ready' #ASHG14
12:26pm October 21st 2014 via Hootsuite
Last: Aad Tibben, Leiden Univ. Med. Ctr. Managing the ambiguity and complexity of genome sequencing #ASHG14
12:25pm October 21st 2014 via Hootsuite
BB: Brought up this '12 Kaye reference: http://t.co/JiWwQHmHr2 #ASHG14
12:23pm October 21st 2014 via Hootsuite
BB: Majority had expected uncertainty, knowing ClinSeq was a work in progress, rather than becoming disillusioned. #ASHG14
12:20pm October 21st 2014 via Hootsuite
BB: Early pt adopters enthusiastic to participate, learn results. Tend to be optimistic, similar to other studies w/other new tech #ASHG14
12:19pm October 21st 2014 via Hootsuite
BB: Among ClinSeq participants - results reported in '14 Genet Med publ http://t.co/FIzbm1f4MI #ASHG14
12:15pm October 21st 2014 via Hootsuite
BB: Scope of uncertainties 'may be unprecedented in medicine'. #ASHG14
12:14pm October 21st 2014 via Hootsuite
Barbara Biesecker (NIH) Uncertainties in consenting to participate in sequencing studies and receive results #ASHG14
12:11pm October 21st 2014 via Hootsuite
LB: '14 Nature paper called 'heroic effort': "Guidelines for investigating causality of sequence var's" http://t.co/KwZbPFy81i #ASHG14
12:10pm October 21st 2014 via Hootsuite
LB:Analytic sufficiency: WES and WGS are not 'whole'; "we can all agree on that". #ASHG14
12:06pm October 21st 2014 via Hootsuite
LB:5 domains: technical, diagnostic, prognostic, therapeutic, personal/psychological #ASHG14
12:04pm October 21st 2014 via Hootsuite
LB:Task: to go from exome to pt mgmt; what are all attributes of this process and uncertainties? #ASHG14
LB:Genomics is 'new' in terms of scale and breadth; proteomics in newborn-screening have gone before. Moving huge amts of data thru #ASHG14
12:02pm October 21st 2014 via Hootsuite
LB:'Our entire knowledge of biology is based upon the concepts of taxonomy' going back to Linneaus. A dynamic, responsive system #ASHG14
12:00pm October 21st 2014 via Hootsuite
Les Biesecker (NGHRI) A taxonomy of uncertainty for clinical genomics #ASHG14
11:58am October 21st 2014 via Hootsuite
PH:Going into Source: 20% probability of benefit. Figures from '11 ref here: http://t.co/80MWx0IijE #ASHG14
11:54am October 21st 2014 via Hootsuite
PH:Source is composed of probability, ambiguity, and complexity. Issue can be scientific (data), practical (system) or personal #ASHG14
11:52am October 21st 2014 via Hootsuite
PH:Developed a medical taxonomy to conceptualize uncertainty in health care. By source, by issue, by locus (expert vs pt) #ASHG14
11:50am October 21st 2014 via Hootsuite
PH:In healthcare - rise of evidence-based medicine, visibility of medical controversies (w/mass media). It is unavoidable. #ASHG14
11:48am October 21st 2014 via Hootsuite
PH: Defining uncertainty: a metacognition, the conscious awareness of ignorance (knowing one does not know) #ASHG14
11:46am October 21st 2014 via Hootsuite
Paul Han (Maine Med. Ctr. Res. Inst.) Conceptualizing and communicating uncertainty #ASHG14
11:45am October 21st 2014 via Hootsuite
RP: Eliminating uncertainty - knowing what all 6B bp means. J Shendure's paper looking at 4K variants of only 6 bp - a start #ASHG14
11:44am October 21st 2014 via Hootsuite
RP: Cheaper seq data - but at a cost of increasing uncertainty. '13 Reiff ref - What does it mean? http://t.co/cfo2hB86fM #ASHG14
11:43am October 21st 2014 via Hootsuite
RP: In the context of reproductive medicine, uncertainty from the patient's perspective 1979 ref: http://t.co/BuiskGqH1k #ASHG14
11:39am October 21st 2014 via Hootsuite
RP: Points to work of UPenn's Renee Fox recommended in '57 that medical students be trained in uncertainty #ASHG14
11:38am October 21st 2014 via Hootsuite
RP:Quotes Bernoulli's (300yo) Ars Conjectandi on uncertainty, also Thomas Bayes. #ASHG14
11:37am October 21st 2014 via Hootsuite
RP:1956:number of chr is fixed. Today: a SNV. measured 'ever more precisely has increased, so has uncertainty' #ASHG14
11:34am October 21st 2014 via Hootsuite
Reed Pyeritz (UPenn): History of uncertainty in genomic medicine #ASHG14
11:32am October 21st 2014 via Hootsuite
#ASHG14 Building Bridges session next: Finding Global Agreement on Topical Disc'ns in Genetics: Evolving Uncertainties in Genomic Medicine
11:31am October 21st 2014 via Hootsuite
GA:Q:Data format development from TGP? A:BAM now becomes cumbersome with 10's of K genomes. CRAM format FAQ: http://t.co/dDKFq9kgji #ASHG14
11:24am October 21st 2014 via Hootsuite
GA:Q:How will TGP inform the 100K UK project? A:Guiding their analytic approach #ASHG14
11:22am October 21st 2014 via Hootsuite
GA:Advances to human disease through imputation. TGP Ph 3 release now available http://t.co/M7Jr0cXtGU #ASHG14
11:20am October 21st 2014 via Hootsuite
GA: a summary point: great benefits to integrated analyses, but takes time 'comparable to data generation' #ASHG14
11:19am October 21st 2014 via Hootsuite
GA:One goal - to enable other studies via imputation; chart of imputation accuracy (r2 vs AF) per population. #ASHG14
11:17am October 21st 2014 via Hootsuite
GA:Chart after Ph 3: 80M in dbSNP, 61.9M novel from TGP, 62% of dbSNP contributed by Ph 3. Shows private vs. shared var by geography #ASHG14
11:11am October 21st 2014 via Hootsuite
GA:Validation of inversions via PacBio; shows simple and complex SV (mix of dup's and multiple inversions) #ASHG14
11:09am October 21st 2014 via Hootsuite
GA:Now est 5% FP rate; 26 indivs using PCR-free deep seq. Multi-allelic SNPs and multi-allelic indes 4.91%/4.95% #ASHG14
11:08am October 21st 2014 via Hootsuite
GA:Ph 3 goes from raw data, 24 initial callsets, 4 consensus callsets, integration incl phasing. (He calls it complex!) #ASHG14
11:07am October 21st 2014 via Hootsuite
GA:Today: 84TB of BAM files. Data complete 5/13; just now finished analysis. 10 SNP/indel callers listed, 12 struct var callers #ASHG14
11:05am October 21st 2014 via Hootsuite
