EA: Mentions this Nature Methods paper http://t.co/27rKd5sKTu for improved indel calling #AGBT15
9:53am February 27th 2015 via Hootsuite
EA: Showing data from @personalisinc ACE exome paper '14 http://t.co/pRlIDUjRdr #AGBT15
9:52am February 27th 2015 via Hootsuite
EA: Instead of 1400 var/singleton, <20 var/trio. Showed JAMA paper from Baylor saying the same #AGBT15
9:49am February 27th 2015 via Hootsuite
EA: Sharing of unsolved phenotypes important; SNX1 gene described by another group in '14 #AGBT15
9:48am February 27th 2015 via Hootsuite
EA:Can sequence family style. PLOS Genet 2011 http://t.co/ciyYLuNiKP #AGBT15
EA: An indiv var takes about an hour of time; what's the answer to this? Brought up http://t.co/t9s5wLIKUC http://t.co/7vHIseiUiP #AGBT15
9:46am February 27th 2015 via Hootsuite
EA: Certain classes hard to call - indels. Data from JAMA 2014 http://t.co/5GbYeyilLM #AGBT15
9:44am February 27th 2015 via Hootsuite
EA: Shows data from @dgmacarthur's Exac server http://t.co/bIUhg7rxHJ Still challenges #AGBT15
9:42am February 27th 2015 via Hootsuite
EA: The genome is complex; repeats, paralogous seq; duplications, families, pseudogenes. 'It gives me a cold sweat at night' #AGBT15
9:41am February 27th 2015 via Hootsuite
EA: In the NICU: before and after; from 5 genes to WES. JAMA ref: http://t.co/zqauNyHBo2 What about the other 75%? #AGBT15
9:40am February 27th 2015 via Hootsuite
.@TorontoGenomics I'm guessing maybe 25232850 but check the list here: http://t.co/8GrWWHMTsc #AGBT15
9:37am February 27th 2015 via Hootsuite in reply to
Euan Ashley, Stanford Univ "Towards Clinical Grade Whole Genome Sequencing” #AGBT15
9:35am February 27th 2015 via Hootsuite
GJ:Q:Evidence / interpretation of phenotypes? A:Some ClinVar annotations are outdated. #AGBT15
9:31am February 27th 2015 via Hootsuite
GJ:Q:CSER and commercial lab interaction? A:Very interested in integrating interests. 'See me'. #AGBT15
9:30am February 27th 2015 via Hootsuite
.@h2so4hurts Hilarious. Haven't seen Comic Sans since, oh, my 7th-grader's homework. #AGBT15
9:29am February 27th 2015 via Hootsuite in reply to
GJ:Q:How to overcome ClinVar submission challenge? A:Get the current data in. 20y of data exists; a resource issue. #AGBT15
9:28am February 27th 2015 via Hootsuite
GJ:Over 100 papers published under the consortium; points out several listed here http://t.co/JX23mFu7Om #AGBT15
9:27am February 27th 2015 via Hootsuite
GJ: Points to this '14 Genetics in Med piece http://t.co/NjU32P9OfJ She discusses FDA regulatory changes of LDT's #AGBT15
9:21am February 27th 2015 via Hootsuite
GJ: Clinvar has 76.6k var's so far; 'far from the millions we need'. We need to get annotations into it. 'Insuff resources' #AGBT15
9:19am February 27th 2015 via Hootsuite
GJ: GERP++ (ref http://t.co/tYt4hBshMw ) cp to CADD (ref http://t.co/UlqObz5cye ) plotted against each other shown #AGBT15
9:18am February 27th 2015 via Hootsuite
GJ: Incidental findings 'is what all labs will need to be good at'. #AGBT15
9:16am February 27th 2015 via Hootsuite
GJ: Biased toward overcalling var's. In the end final calls had very good match with SCRP, LMM projects #AGBT15
9:15am February 27th 2015 via Hootsuite
RT @bioinformer: GJ: criteria for pathogenic variants at CSER #AGBT15 @HAIL_CSER http://t.co/oaBjeKzJTm
9:13am February 27th 2015 via Hootsuite
GJ: Caveats - no CNV included. 'Very interesting about this: QC'. 53 reviewers, online training; 'errors at all expertise levels' #AGBT15
GJ: Cites Amendola Genome Res '15 http://t.co/hc0fow9Az9 Expected rate of actionable var's by ancestry N=4300 / 2203 (EU/AF) #AGBT15
9:12am February 27th 2015 via Hootsuite
GJ: Came up with 112 actionable genes; showed overlap with ACMG list (they selected only the more prevalent ones) #AGBT15
9:10am February 27th 2015 via Hootsuite
.@bioinfomagician Yes but for one year it'll be a nice change-up. Expect lots of mouse-ears, reminiscent of ABRF a few years ago #AGBT15
9:07am February 27th 2015 via Hootsuite in reply to
CJ: >200 clinicians; @hail_cser is their handle. (IMHO as a marketer that's an interesting choice.) #AGBT15
9:06am February 27th 2015 via Hootsuite
CJ: CSER explores in a clinical setting the application of genomic data http://t.co/4tnHx3dxgP #AGBT15
9:05am February 27th 2015 via Hootsuite
Gail Jarvik, Univ Washington: Clinical Genomics: Lessons From the Clinical Sequencing Exploratory Research (CSER) Consortium #AGBT15
9:04am February 27th 2015 via Hootsuite
Listen up, kids! RT @MySOdotCom: Why Productive People Take Better Notes http://t.co/sg4DNSgvmh via @FastCompany http://t.co/kWvvFIvXYW
7:25am February 27th 2015 via Hootsuite
Lessons from a High School Student: Motivation + Perseverance = Success | NIH Director's Blog http://t.co/AHXHlooJ1o
7:20am February 27th 2015 via Hootsuite
.@obahcall Awesome time with @nelsondl @h2so4hurts @illumina @splon and @GenomeLiberty! Alas, no photos of feet
5:58am February 27th 2015 via Hootsuite in reply to
RT @pathogenomenick: Just finished my second genome with the new @nanopore assembly strategy ... this time GC ~35%
5:15am February 27th 2015 via Hootsuite
RT @matthewherper: How to Develop New Antibiotics http://t.co/J9yUu9vx9T Zeke Emanuel says we need a $2 BILLION per company prize.
4:30am February 27th 2015 via Hootsuite
RT @msgbi: In Mysterious Pattern, Math and Nature Converge | Quanta Magazine #math394 http://t.co/D8Etq6Havj
11:40pm February 26th 2015 via Hootsuite
Order in which mutations in cancer crop up affect disease progression | GenomeWeb Scan http://t.co/OblexCuC4l
10:10pm February 26th 2015 via Hootsuite
MS: Future goals: det differences in asthmatics vs healthy; det biomarkers & pathways specific to resp virus #AGBT15 http://t.co/BI0XHl9
9:28pm February 26th 2015 via Hootsuite
MS: Low-depth polyA-WT seq can be used to 'detect nearly all common resp viruses'; simultaneous w/ host transcriptome #AGBT15
9:27pm February 26th 2015 via Hootsuite
MS: Building co-expression models, found seven modules w/ WGCNA #AGBT15
9:26pm February 26th 2015 via Hootsuite
MS: Showed nice heatmap between virus / no virus. Many GO hits for viral infection #AGBT15
9:25pm February 26th 2015 via Hootsuite
MS: Asymptomatic virus carriage is ass'd with dramatic shift in host transcriptome. Found 5k genes diff exp >2-fold #AGBT15
MS: 100 reads to 164K reads/smpl; none of the chemokine low samples had virus #AGBT15
9:24pm February 26th 2015 via Hootsuite
MS: Did low-depth RNA-seq on @iontorrent Proton; 10M reads/sample, poly-A Kapa protocol; found 11 chemokine high all had virus #AGBT15
9:23pm February 26th 2015 via Hootsuite
MS:Affect on host transcriptome: did qPCR on two most highly induced genes (both chemokines). Most very low exp; 11 were very high #AGBT15
9:22pm February 26th 2015 via Hootsuite
MS: Read depth seemed uniform across diff transcripts. Can determine virus strain, 'from all we're finding' #AGBT15
9:20pm February 26th 2015 via Hootsuite
MS:100M reads/sample; 10 asthmatic samples, 10 ctls. Found viral reads in 2 ctrl samples. 3.1K viral reads / 140M; 1.2K / 112M #AGBT15
9:19pm February 26th 2015 via Hootsuite
MS:Listed many common resp viruses: rhinovirus, coronavirus, RSV, influenza etc. All RNA viruses #AGBT15
9:17pm February 26th 2015 via Hootsuite
MS: Looking for viral RNA (asymptomatic). Community-based recruitment; ask whether host transcriptome affected. #AGBT15
9:16pm February 26th 2015 via Hootsuite
MS: GALA - large nasal airway study in Latino asthmatics (Puerto Rico). Nasal specimens from 700. RNA + DNA; doing polyA RNA-Seq #AGBT15
9:15pm February 26th 2015 via Hootsuite
