van 't Veer: Big data: NIH's BD2K http://t.co/Jzi4Tx8eMW Global Alliance 4 Genomics and Health http://t.co/7ueY6hAmBU #TCGC15
8:31pm June 22nd 2015 via Hootsuite
van 't Veer: Second graduate - Neratinib for HER2+/HR- signature. 79% prob of PIII trial success #TCGC15
8:22pm June 22nd 2015 via Hootsuite
van 't Veer: Veliparib, 72 pts enrolled, and graduated for TNBC subtype. Est pCR rate was 2x the concurrent control (26% to 52%) #TCGC15
8:17pm June 22nd 2015 via Hootsuite
van 't Veer: 85% predicted likelihood of success; pCR is end-point. Bayes probability scores, est. pCR rates by signatures #TCGC15
8:16pm June 22nd 2015 via Hootsuite
van 't Veer: An adaptive design for new experimental drugs to enter (and exit) the trial. 4y to approval, already 2 graduated in 2y #TCGC15
8:15pm June 22nd 2015 via Hootsuite
van 't Veer:1435 registered. Accel. FDA endpoint saving a lot of time for this trial. Add'l randomization based on tumor biology #TCGC15
8:13pm June 22nd 2015 via Hootsuite
van 't Veer: I SPY 2: serial biopsy, imaging: 5 expt'l arms in parallel. Pts tumor size >2.5cm; Mammaprint high-risk ID'd #TCGC15
8:05pm June 22nd 2015 via Hootsuite
van 't Veer: Strategies for high risk cancers: tumor immune env, PARPi, Myc inh, Notch inh, TORQ 1/2 for PI3K, TKI's for HER2 #TCGC15
8:00pm June 22nd 2015 via Hootsuite
van 't Veer: "Companion therapeutics in the I-SPY 2 Breast Cancer Trial" - 30% of high-risk women - tumor gone; 70% room to improve #TCGC15
7:59pm June 22nd 2015 via Hootsuite
Laura J van 't Veer (UCSF) "Big data in translational cancer genomics" #TCGC15
7:56pm June 22nd 2015 via Hootsuite
Price:Q:How will the $ work? Pay to participate? A:Opt-in is below-cost. Year 1 "a few thousand $" #TCGC15
7:55pm June 22nd 2015 via Hootsuite
Price: Looked at GWAS results for elevated risk: hypertension med, bilirubin levels, IBD. Fitbit activity - 3 markers assoc'd #TCGC15
7:51pm June 22nd 2015 via Hootsuite
Price:Seeing clear patterns even with simplistic layering of information. Genetic risk across many variables. #TCGC15
7:46pm June 22nd 2015 via Hootsuite
Price: Microbiome results: highly diverse. Looked at composition to genetic risk for Crohn's: risk: linked to verrucomicrobia #TCGC15
7:45pm June 22nd 2015 via Hootsuite
Price: Overproducing iron: could see high Fe level, made Dx, treatment via monthly blood donation, breakdown of cartilage ceased #TCGC15
7:39pm June 22nd 2015 via Hootsuite
Price: Genetics plus environment: diet, lifestyle, pollution, medications, toxins. One person: hemochromatosis, cartilage breakdown #TCGC15
7:38pm June 22nd 2015 via Hootsuite
Price: Diabetes markers improved 33% in 6 mo. HbA1c improved 38%; HOMA improved 55% - importance of coaching. 7 prediabetic->normal #TCGC
7:37pm June 22nd 2015 via Hootsuite
Price: Lab tests: Everyone had actionable recommendations. 68% inflamm, 54% diabetes risk, 59% cardiovascular. Showed 6mo imprvmt #TCGC15
7:35pm June 22nd 2015 via Hootsuite
Price: WGS, labwork, proteome, microbiome, metabolome. Circos-style plot with lines running across. Thousands of datapoints plotted #TCGC15
7:33pm June 22nd 2015 via Hootsuite
Price: Take Larry Smarr 'times 100'; then 'times 100K'. Ages: 20's to >88. Showed statistical correlations between many points #TCGC15
7:32pm June 22nd 2015 via Hootsuite
Price: Data integration, monthly coaching sessions on actionable data. History, traits, lab results, genome, tracking datasets #TCGC15
7:30pm June 22nd 2015 via Hootsuite
Price: Pioneer 100: 9mo study started Mar 2014, IRB. WGS, blood, urine, saliva 3x, gut microbiome 3x, continual self-tracking... #TCGC15
7:29pm June 22nd 2015 via Hootsuite
Price: Many parameters, all diseases simultaneously. Cost at scale? Had to show value to justify cost. Origin, transitions to state #TCGC15
7:28pm June 22nd 2015 via Hootsuite
Price: Quantifying wellness - following individuals for 20-30y. Need large #'s of people for a long time. What to learn from 100K? #TCGC15
7:26pm June 22nd 2015 via Hootsuite
Price: Reviews aging population in dev world, P4 medicine's promise "personalized, predictive, preventive, participatory" #TCGC15
7:22pm June 22nd 2015 via Hootsuite
Pearson: Story of Smarr - thought he'd come down with IBD, and he did. From disease state, doesn't come back to baseline. #TCGC15
7:14pm June 22nd 2015 via Hootsuite
Price: 100K genomes, microbiomes. 'Hundred Person Wellness Project' company kicked off today. Larry Smarr: TR http://t.co/iuAR5ghdn5 #TCGC15
7:13pm June 22nd 2015 via Hootsuite
Nathan Price (Inst System Biology) "Integrating the principles of preventative and personalized medicine to advance wellness" #TCGC15
7:10pm June 22nd 2015 via Hootsuite
Pearson: Q: A challenge computationally; we need a good model. A: Not easy but the ones we know about we shld report and prepare #TCGC15
7:06pm June 22nd 2015 via Hootsuite
Pearson: Privacy worry: presumes widespread genomic data. Asks to structure data wider than 2 or 3 sites at a time. #TCGC15
6:54pm June 22nd 2015 via Hootsuite
RT @theNCI: The rate of new cases for all U.S. cancers combined continued to fall from '02-'11 http://t.co/RkMynubxFe http://t.co/A4eYT7Ggo2
6:50pm June 22nd 2015 via Hootsuite
Pearson: Genotypes abound, overlap, and are very rare ('each mark a few people') in vitro work 'can greatly help'. #TCGC15
6:49pm June 22nd 2015 via Hootsuite
Pearson: Shift to a genotype-centric view: Gawande's '13 New Yorker http://t.co/P44AJzR3X1 Anesthesiology vs hand-washing uptake #TCGC15
6:38pm June 22nd 2015 via Hootsuite
Pearson: Also other rare genotype-driven health prion resistance in PRP1. MSH2 var's and cancer risk http://t.co/SYVnkmIqKP #TCGC15
6:36pm June 22nd 2015 via Hootsuite
Pearson: Other stably diverse local haplotypes mtDNA, HLA, CYP haplotypes. Still others: rare compound heterozygosity #TCGC15
6:32pm June 22nd 2015 via Hootsuite
Pearson: Illustrates non-additivity, known from the start 'we often overlook it': dominance. XX/XY-dependencies #TCGC15
6:31pm June 22nd 2015 via Hootsuite
Pearson: variant<>element; genotype<>molecule; zygosity<>stoichiometry; coinheritance<>bond; imprinting<>stere
6:29pm June 22nd 2015 via Hootsuite
Pearson: And these combinations cross locations, can cross chromosomes, can effect non-additively. 1+ vars, 1+ sites, 1+ chrs #TCGC15
6:26pm June 22nd 2015 via Hootsuite
Pearson: But impenetrance 'swept under huge rug'; we should clinically classify and report genotypes (combinations of var's) #TCGC15
6:25pm June 22nd 2015 via Hootsuite
Pearson: Conventional: classification and reporting of variants. "Presumes simple, strong effects, rooted in classical genetics" #TCGC15
6:24pm June 22nd 2015 via Hootsuite
Pearson: Photo of Telluric Helix, a recurring periodic table http://t.co/pG8JRNZX5P 56 elements known; reminiscent of ACMG list #TCGC15
6:17pm June 22nd 2015 via Hootsuite
Pearson: Alice, meet bottle: C, N, H, O and 'may be harmful'. 1865 Darwin on speaking circuit, Mendel plants peas, de Chancourtois #TCGC15
6:15pm June 22nd 2015 via Hootsuite
Pearson: His own genome - CLEC7A assoc'd w/fungal disease susceptibility. 'Uncommon nonsense... I should like to have it explained' #TCGC15
6:12pm June 22nd 2015 via Hootsuite
Pearson: Starts w/a photo of a person w/a limp, collecting water from a spa. A metaphor of a bottle: inside, a large message... #TCGC15
6:11pm June 22nd 2015 via Hootsuite
.@genomeNathan First up at #TCGC15 from @nygenome "Common sense, beyond uncommon nonsense" "deliberately cryptic and somewhat coy title"
6:06pm June 22nd 2015 via Hootsuite
.@eperlste @gabeinformatics And @kthomaspickard is scoping out the bar at the Kabuki hotel lobby for Tues PM #TCGC15 tweetup. :)
6:04pm June 22nd 2015 via Hootsuite
.@gabeinformatics @kthomaspickard Great to meet both of you at #TCGC15 at lunch! Fun conversations - lots of learning & sushi cc:@eperls
6:03pm June 22nd 2015 via Hootsuite
Rudy: PFKL gene: shows comparison to ExAC, NHLBI frequencies. Not in ClinVar, completely novel to ExAC, TGP (G>C), no OMIM entry #TCGC15
4:04pm June 22nd 2015 via Hootsuite
Rudy: His son's exome sequence - Cp to father & mother, right at splice site a de-novo mut. 1-2 de novo mut's per generation #TCGC15
4:03pm June 22nd 2015 via Hootsuite
Rudy: Q about aligners and paralogous genes; great answer about limitations of alignment and reference genome sequence completeness #TCGC15
4:02pm June 22nd 2015 via Hootsuite
