RT @kunal_bhutani: Rong Chen @RongChenBioinfo : Reference Variant Store database of 318 million of variants & VAF based on several publi
6:08pm October 22nd 2014 via Twitter Web Client
RT @girlscientist: .@RongChenBioinfo Resilience project: 600k indivs, 14 "final unexpected hero candidates" w/fully penetrant mutns but sti…
RT @ElissaRLevin: @RongChenBioinfo Impressive overview of the system he's developed at @IcahnInstitute for combining/querying massive data …
RT @trutane: .@RongChenBioinfo at #ASHG14 on the http://t.co/cNpNyLwjrg "A search for unexpected heroes." Send in your spit! http://t.co/s3…
RT @E_Carlen: Its been the Taq this whole time. After 1.5y I switched to @LifeTech HiFi Taq & got bright bands! http://t.co/BnAXx0k82z
5:37pm October 22nd 2014 via Hootsuite
How Building a Black Hole for Interstellar Led to an Amazing Scientific Discovery | WIRED http://t.co/Z2vnYV5K1U
4:06pm October 22nd 2014 via Hootsuite
I liked the one on Crying RT @23andMe: Our #ASHG2014 posters are collected here: http://t.co/uiCED0Y340 #genetics #research
3:16pm October 22nd 2014 via Hootsuite in reply to
RT @LifeTech: What a great last few days. 140 characters doesn't do it justice. #ASHG14 http://t.co/AWjviGRG5b
2:56pm October 22nd 2014 via Hootsuite
.@cathcoste You are welcome! TY for stopping by @LifeTech at #ASHG14, received a note from the rep; if you are ever in WashDC let me know!
2:50pm October 22nd 2014 via Hootsuite in reply to
.@drbachinsky Thank you for the kind words and all the RT’s David. Learned a tremendous amt this #ASHG14 mtg. And 4am - 11pm days!
2:19pm October 22nd 2014 via Hootsuite in reply to
#ASHG14 Thank you for a great mtg @GeneticsSociety! Over next few days I'll be posting at http://t.co/wPLC4TdyuC See you at #ASHG15!
1:57pm October 22nd 2014 via Hootsuite
DL:Q:Targeted me-Seq? A:Optimized bisulfite for WGS, working on other ideas (e.g MBP-based approach) #ASHG14
1:54pm October 22nd 2014 via Hootsuite
DL:Could it repl. colonoscopy? A:Curr. looking for follow-up e.g. liver MRI complement. Ultra-sens test not so useful here #ASHG14
1:53pm October 22nd 2014 via Hootsuite
DL:Q:How much has this approach has cost reduced? A:10M reads is similar to Downs screen is $1K #ASHG14
1:51pm October 22nd 2014 via Hootsuite
DL:A2:The question is how many CTC genomes can you afford to do? #ASHG14
1:49pm October 22nd 2014 via Hootsuite
DL:Q:Landscape bet. CTCs and cfDNA? A:Indep phenomena; CellSearch tech is 'only a few cells', 'limited info'. 4mL = 10K genomes #ASHG14
1:48pm October 22nd 2014 via Hootsuite
DL:Q:cfDNA before vs. after treatment? A:They do targeted seq approach, 1/2 life on order of hours #ASHG14
1:47pm October 22nd 2014 via Hootsuite
DL:Shows data across cancer types, combining ROC curves, 100M reads is really needed (correction to prior tweet - 1lane not 1M) #ASHG14
1:45pm October 22nd 2014 via Hootsuite
DL: ROC - area goes from 0.93 to 0.96 going from 1M to 10M reads for methylation, essentially same. But for ME-CNA: need 10M reads #ASHG14
1:44pm October 22nd 2014 via Hootsuite
DL:Getting sens 92%, spec 88% w/one set of algor. parameters. Est of tDNA fraction by Methylation & tumor size, some correl. #ASHG14
1:43pm October 22nd 2014 via Hootsuite
DL: Another indiv., persistent hypo-meth and CN, had recurrence. ME-CNA has no add'l cost as it is only add'l computation #ASHG14
1:41pm October 22nd 2014 via Hootsuite
DL: Pre-post surgery: showing hypo ring dissappearing. And for CN: same effect. #ASHG14
1:40pm October 22nd 2014 via Hootsuite
DL: Getting 30% tumor DNA from plasma. Next: copy-number from bisulfite NGS? Cp to normal NGS, can get CN from methylome #ASHG14
1:39pm October 22nd 2014 via Hootsuite
DL: Took 2y to dev. hypometh gene body NGS from cell-free DNA. Det. inter-indiv var <1.8% Circos plot of hypo (inner) hyper (outer) #ASHG
1:38pm October 22nd 2014 via Hootsuite
Dennis Lo (Chinese Univ HK) Genome-wide plasma DNA sequencing as a universal approach for cancer detection #ASHG14
1:35pm October 22nd 2014 via Hootsuite
LG: Turnaround time - up to 3mos. Now CGEC is no longer linear to speed the time. #ASHG
1:31pm October 22nd 2014 via Hootsuite
LG:The kind of challenge - third mutation may be useful in the future, there is a clinical trial. CGEC review is 2-3 cases /1.5h #ASHG14
1:29pm October 22nd 2014 via Hootsuite
LG:Example CanSeq report: Lu ca w/3 somatic muts; one well-known; a 2nd gene ass'd with thyroid cancer, druggable; a 3rd pt mut #ASHG14
LG: Chart of germline muts and freq among 19 voted to return: all different except for TP53. PGx var's: 'reduced enthusiasm' #ASHG14
1:27pm October 22nd 2014 via Hootsuite
LG: CGEC=Cancer Genome Eval. Committee (Note: found some of LG's '13 IOM slides here http://t.co/8Y1hDYQEx5 while looking for CGEC) #ASHG14
1:25pm October 22nd 2014 via Hootsuite
LG: CGEC results for 1st 46 indiv's: of 205 somatic det., 154 (75%) voted to be returned. 166 germline det., 11% voted returned #ASHG14
1:22pm October 22nd 2014 via Hootsuite
LG: Long tail of actionable cancer genes:for the typical indiv., a VUS. Report? Laid out choices to audience, asks for feedback #ASHG14
1:15pm October 22nd 2014 via Hootsuite
LG:CanSeq project, WES starts w/consent down to review to report. All linear: do WES from FFPE 'routinely' http://t.co/2f1cwg3BrI #ASHG14
1:13pm October 22nd 2014 via Hootsuite
LG: Illust. balance of cost to coverage between WGS, WES, targeted. Atul NYMag "Path to outcome' highway to... dirt road... #ASHG14
1:10pm October 22nd 2014 via Hootsuite
LG: From bench to beside, example of OncoMap starting publication 2007 Nature Gen ref: http://t.co/TbN1ovySzr #ASHG14
1:08pm October 22nd 2014 via Hootsuite
L. A. Garraway (Harvard) Return of “actionable”, uncertain, and incidental findings in cancer #ASHG14
1:06pm October 22nd 2014 via Hootsuite
TM:Screen for causal alleles in erythroid GWAS loci in a model. Described work that found 23 SNPs overlap. #ASHG14
12:58pm October 22nd 2014 via Hootsuite
TM: % of eQTL peaks with fn hit, cp EU to YRI. 20-40% of LCL eQTLs contain one or more var's that would show allelic skew. #ASHG14
12:55pm October 22nd 2014 via Hootsuite
TM:Of 29.1K segments tested: 13% functional seg's; 3% shows activity + skew. Went onto est. assay sens. -log(P) graph by SNP #ASHG14
12:54pm October 22nd 2014 via Hootsuite
TM:More/less gene activity, higher RNA than expected plasmid DNA input amount would suggest. Another SNP: alllelic skewing #ASHG14
12:52pm October 22nd 2014 via Hootsuite
TM: Now: large-scale screen for causal alleles in eQTLs. Huge numbers: 29K SNPs, showed reprod plot, detected positive reg regions #ASHG14
12:51pm October 22nd 2014 via Hootsuite
TM: Determined putative HLA-G enh, used CRISPR/Cas9 to validate in cell line #ASHG14
12:49pm October 22nd 2014 via Hootsuite
TM: Another example: looking for regulator of HLA-G, protection of non-self in placenta. 20kb reg region, found 3 strong hits #ASHG14
12:48pm October 22nd 2014 via Hootsuite
TM:Dissecting TGV-beta-inducible promoter: 1 sequence (of 2K) is sensitive to TGFB. Zoom in, found 4 distinct binding sites #ASHG14
12:47pm October 22nd 2014 via Hootsuite
TM:Zoom in on one region: 2nd round 50k random vars for a single nt footprint to map exact nt for enhancer activity #ASHG14
12:45pm October 22nd 2014 via Hootsuite
TM: Tiled region 200nt window across 200kb: 2k frags in cells (HMEC/p15): strong evidence of enh activity 4/6 regions overlap #ASHG14
TM: MPRA finds novel regulatory elements in 9p2; in primary epithelium, does it correspond to known chromatin marks? (H3K4me3 etc) #ASHG14
12:43pm October 22nd 2014 via Hootsuite
TM: Crystal structure shows 'no direct interaction between this nucleotide and the bound TFs'. #ASHG14
12:42pm October 22nd 2014 via Hootsuite
TM: Saturation mutagenesis of hIFNB enhancer: classical promoter-bashing expt, single nt in the WT enh 'explains' its activity #ASHG14
12:40pm October 22nd 2014 via Hootsuite
TM:Assay can bue used to assay promoter, enh, silencers, rna-stability enz, genome integration. Can study 100's of K sequences #ASHG14
12:37pm October 22nd 2014 via Hootsuite
