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
Rudy: Found HuRef-1 alignment - GRCh38 still doesn't match. @jcventer and he shares this sequence. #TCGC15
3:59pm June 22nd 2015 via Hootsuite
Rudy: Went back to raw data, BWA vs. other aligners - BLAT data showed uniqueness, but lines up to Chimp (!) Tried any other assy #TCGC15
3:57pm June 22nd 2015 via Hootsuite
Rudy: Another mutation - one base deletion on a splice donor site for PSPH gene. Very rare, damaging - many nearby novel muts #TCGC15
3:56pm June 22nd 2015 via Hootsuite
Rudy: "I'm a happy steak eater - so far"; OTC deficiency can be triggered by some kind of shock. #TCGC15
3:54pm June 22nd 2015 via Hootsuite
Rudy: ClinVar update path, late onset Dx. 'Now personal and interesting'. OTC gene - on chrX, one copy - affects protein metabolism #TCGC15
3:53pm June 22nd 2015 via Hootsuite
Rudy: His own exome; now with ExAC, has a hemizygote G/A that 2/60K individuals also have; ornithine transcarbamylase deficiency #TCGC15
3:51pm June 22nd 2015 via Hootsuite
Rudy: Shows utility of VarSeq. Shows interface to hide unneeded metadata; ability to setup filter chains to break down WES data. #TCGC15
3:50pm June 22nd 2015 via Hootsuite
Gabe Rudy @gabeinformatics has a personal family trio story too. Reviews structure of .vcf, and need for GUI (VarSeq) #TCGC15
3:43pm June 22nd 2015 via Hootsuite
Pickard: 'Data sharing is critical for insights' - blog here: http://t.co/yiJOKBTXTG #TCGC15
3:41pm June 22nd 2015 via Hootsuite
Pickard: "Homebrew computers in the '70's". Personal genomics is real; some dark alleys but not all "some promising leads" #TCGC15
3:40pm June 22nd 2015 via Hootsuite
Pickard: Pointed to this Lancet publication series on Autism by Geschwind and State http://t.co/Y6UXSy6YRu #TCGC15
Pickard Sifted de novo, compound hets; searched autism db's http://t.co/UrG9UD1cGU http://t.co/lRx654uNhg http://t.co/xKiV9M8llR #TCGC15
Pickard: VarSeq by Golden Helix (Gabe Rudy gave earlier talk) http://t.co/Ybe8tSBotM Divides out mutations by type (de novo, etc) #TCGC15
Pickard: Used VarSeq and DNANexus; cost for Amazon hosting via @dnanexus about same as DIY on Amazon cloud. #TCGC15
3:39pm June 22nd 2015 via Hootsuite
Pickard: Ran into problem with differing informatics pipelines; thus the need for FASTQ's. Found false-positive de novo var's #TCGC15
Pickard: Used @AllSeq for WGS as broker, cost via HiSeq X10 was $1.8K; did trio + add'l child; 325GB data/sample (81h to xfer) #TCGC15
Pickard: Adult child w/autism, he got an Rx and bought purple-cap tubes from Amazon; got a blood draw from a local clinic (!) #TCGC15
I just realized I was tweeting using a mis-spelled hashtag! Oh well - #TCGA15 #TCGC15 will need to re-send. (Sorry followers!)
3:38pm June 22nd 2015 via Hootsuite
Pickard: 'Data sharing is critical for insights' - blog here: http://t.co/yiJOKBTXTG #TCGA15
3:36pm June 22nd 2015 via Hootsuite
Pickard: "Homebrew computers in the '70's". Personal genomics is real; some dark alleys but not all "some promising leads" #TCGA15
3:30pm June 22nd 2015 via Hootsuite
Pickard: Mentioned @GA4GH and their work on genomic data sharing, and the Beacon Project "like the 'go fish' card game" #TCGA15
3:27pm June 22nd 2015 via Hootsuite
Pickard: Pointed to this Lancet publication series on Autism by Geschwind and State http://t.co/Y6UXSy6YRu #TCGA15
3:26pm June 22nd 2015 via Hootsuite
Pickard Sifted de novo, compound hets; searched autism db's http://t.co/UrG9UD1cGU http://t.co/lRx654uNhg http://t.co/xKiV9M8llR #TCGA15
3:24pm June 22nd 2015 via Hootsuite
Pickard: VarSeq by Golden Helix (Gabe Rudy gave earlier talk) http://t.co/Ybe8tSBotM Divides out mutations by type (de novo, etc) #TCGA15
3:22pm June 22nd 2015 via Hootsuite
Pickard: Used VarSeq and DNANexus; cost for Amazon hosting via @dnanexus about same as DIY on Amazon cloud. #TCGA15
3:19pm June 22nd 2015 via Hootsuite
