LG: An alternate transcr. profile: can tell a substantial subset that will be indifferent to targeted therapy. #AGBT15
10:29am February 27th 2015 via Hootsuite
LG: Does FNAs, pleural effusions, other biopsies: can cluster T-cells and tumors cells. Aviv Regev's group - distinct transc. states #AGBT15
10:28am February 27th 2015 via Hootsuite
LG: Other factors than mutations and their frequency - want single-cell RNA-seq for subsets of tumor cells; see predictive markers #AGBT15
10:27am February 27th 2015 via Hootsuite
LG: Some respond, others don't: 'the mother of all biomarker projects' Shows Lawrence mut freq plot #AGBT15
10:26am February 27th 2015 via Hootsuite
LG: DNA/RNA: of particular interest due to immunotherapy. Shows melanoma tumor; interior region of clearing #AGBT15
10:25am February 27th 2015 via Hootsuite
LG: Shows nice WES-only signal - but does the fusion occur via chromoplexy? Redid analysis on both sides, found ERG cognates #AGBT15
10:24am February 27th 2015 via Hootsuite
LG: To assess - mentions Kristina Giorda and Mirna Jarosz from 10x - WGS vs WES TMPRSS2-ERG fusion from VCaP Prostate line #AGBT15
10:22am February 27th 2015 via Hootsuite
LG: Of interest - pull down exonic DNA w/phasing into surrounding introns; thus rearrangements easily pulled. #AGBT15
10:21am February 27th 2015 via Hootsuite
LG: Puts up a 10X Genomics slide - 100kb region from 1ng DNA; linked exonic reads. Random priming w/barcodes in pL volumes #AGBT15
LG: No obv. way to do this other than WES; already targeted is difficult enough to interpret. #AGBT15
10:20am February 27th 2015 via Hootsuite
LG: PTEN observed 10/60 freq; disrupted by chromoplexy, invisible to current panels. What implications for #precisionmedicine? #AGBT15
10:19am February 27th 2015 via Hootsuite
LG:Busy slide from Baca et al Cell 2013 http://t.co/kEg0N5IEnw Cancer genes often disrupted by chromoplexy #AGBT15
10:18am February 27th 2015 via Hootsuite
LG: DNA and RNA; pharmacodynamics, splice and fusion isoforms, and accout for tumor heterogeneity #AGBT15
10:17am February 27th 2015 via Hootsuite
LG: Next: 'ideal' profiling, ID all major categories of somatic var: incl. complex rearrangements. 'Beyond targeted but not WGS' #AGBT15
10:16am February 27th 2015 via Hootsuite
LG: Application of state-of-the art tech: targeted panels, CanSeq (CSER grant) for WES to oncologists #AGBT15
10:15am February 27th 2015 via Hootsuite
LG: Another example - response/resistance determinants may be hetergeneous. (same Wagel paper) #AGBT15
10:14am February 27th 2015 via Hootsuite
LG: A case of resistance to combined RAF/MEK inh - Wagel Cancer Disc '14 http://t.co/5NVjQ4FJVr #AGBT15
10:13am February 27th 2015 via Hootsuite
LG: RAF/MEK inh - the long tail of drivers detailed here in Nature Med '14 http://t.co/tXE2TtM6Gl #AGBT15
10:12am February 27th 2015 via Hootsuite
LG: Idea of liquid biopsy (Note: Cynvenio liquid biopsy blog http://t.co/MYOMToe0s5 ) #AGBT15
10:10am February 27th 2015 via Hootsuite
LG: Exceptional responders - goal is new therapeutics and combinations agains molecularly defined tumors #AGBT15
10:08am February 27th 2015 via Hootsuite
LG: Future trials can be designed; some still aspirational, others in place now. Genotype to Phenotype; reversed too #AGBT15
LG: Shares a figure "Engine of Cancer Precision Medicine" from his 2013 JCO review http://t.co/TYmfweUJqy #AGBT15
10:07am February 27th 2015 via Hootsuite
.@CIgenomics "And this is not a joke."
10:05am February 27th 2015 via Hootsuite in reply to
LG:Shares story of last year he shared a joke. Twitter sent it worldwide, of course he heard about it later. (No jokes today.) #AGBT15
10:05am February 27th 2015 via Hootsuite
Levi Garraway, Dana Farber. Genomic Frontiers in Cancer Precision Medicine #AGBT15
10:04am February 27th 2015 via Hootsuite
EA:Q:NLP for EHR's? A:Emerging technology, yet a degree of manual curation is req'd. #AGBT15
EA: From the HGP to 1M genomes: the end of the beginning. Precision oncology, PGx, inf disease. "Boundless possibilities" #AGBT15
9:59am February 27th 2015 via Hootsuite
EA:His own work - MyoKardia, Gilead for longQT syndrome. Feb 28 Rare Disease day, collab w/Bill Gahl NHGRI http://t.co/JUuv8ftTws #AGBT15
9:57am February 27th 2015 via Hootsuite
EA:'Practice precision medicine' - presidential reference to this CFTR paper NEJM 2011 http://t.co/4zwxV5rDNP #AGBT15
9:56am February 27th 2015 via Hootsuite
EA: 'we need to share and connect': Phenotips, GenomeConnect, Matchmaker Exchange, Rare Genomics Inst #AGBT15
9:54am February 27th 2015 via Hootsuite
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
