August 2015

Lin: Very conservative regarding annotation and implications for clinical care, access to many resources. #NGDx15

9:05am August 18th 2015 via Hootsuite

Lin: Somatic SNV via BWA-mem, GATC, Mutect. Somatic index via Strelka. Medium/large indels are still hard for high sens. #NGDx15

9:04am August 18th 2015 via Hootsuite

Lin: Somatic clalers: Strelka, Mutect, Varsan, Lofreq - here is where the most development and ongoing work is being done #NGDx15

9:02am August 18th 2015 via Hootsuite

Lin: Bioinformatics: aligners: BWA, BWA-mem, Novoalign. Var callers: Unified genotyper, haplotype caller, Platypus, BAM2MPG #NGDx15

9:02am August 18th 2015 via Hootsuite

Lin: IT system - highly backed-up. FASTQ on Biowulf. BAM is intermediate; also VCFs. Looking into more efficient compression #NGDx15

8:59am August 18th 2015 via Hootsuite

Lin: WES Specificity: 99.99% across ('a funny metric to calculate') but sens is 95.6% - 98.5%; PPV 89% - 98% #NGDx15

8:58am August 18th 2015 via Hootsuite

Lin: For WES, goal is 90x, median 124x coverage. Compared to MyCancerGenome 191 hotspots, ave coverage 459x, 11 expts #NGDx15

8:57am August 18th 2015 via Hootsuite

Lin: Targeted tumor coverage median coverage 346x (goal 300x); germline goal is 150x #NGDx15

8:56am August 18th 2015 via Hootsuite

Lin: Whole-exon is 564 genes/9442 exons; whole-genes (6); PGx (1906 markers) #NGDx15

8:55am August 18th 2015 via Hootsuite

Lin: Two panels - one for mutations, another for CNV and fusions. Design - listed a large number of existing pane. NCI, @iontorrent #NGDx15

8:54am August 18th 2015 via Hootsuite

Lin: Wet lab: did WES comparison between SureSelect, SeqCap EZ - fold-coverage by % of exome covered. Comparable but SureSelect won #NGDx15

8:53am August 18th 2015 via Hootsuite

Lin: Can get good germline data from saliva, with their bacterial DNA informatics filtering. #NGDx15

8:51am August 18th 2015 via Hootsuite

Lin: Macro-dissection is important - removal of as much normal tissue as possible. ("Not micro-dissecting, yet") #NGDx15

8:49am August 18th 2015 via Hootsuite

Lin: Mark Raffeld, Liqiang Xi, Keith Killian acknowledged for their work here. (Good people I know at the NCI.) #NGDx15

8:48am August 18th 2015 via Hootsuite

Lin: Tissue: optimize extraction, path review, macro-dissect, track sample, integrate into IT and EMR systems, transport #NGDx15

8:48am August 18th 2015 via Hootsuite

Lin: They work closely with pathology for the right tissue. "Doesn't help if you sequence all you want and you had the wrong tissue' #NGDx15

8:46am August 18th 2015 via Hootsuite

Lin: PDXs are sequenced again (exome and panel, also RNA-seq). Workflow covers tissue proc, wet lab, IT, Bifx, clinical, protocol. #NGDx15

8:45am August 18th 2015 via Hootsuite

Lin: 2 db's - a research clinomics, another clinical EMR. Biopsies: Most is FFPE, used for both DNA, RNA; fresh tissue goes to PDX #NGDx15

8:44am August 18th 2015 via Hootsuite

Lin: Omics goes to research data, germline data, and somatic data. 2 separate tumor boards: one to sign out, another to decide care #NGDx15

8:42am August 18th 2015 via Hootsuite

Lin:Plasma for ctDNA, urine for add'l biomarkers. Workflow of patents are on two different protocols - 'Omics' and 'Precision Rx' #NGDx15

8:41am August 18th 2015 via Hootsuite

Lin: 'We use a lot of DNA, RNA' - and sure that in a few years much less will be needed; importance of biobanking of tissues, smpls #NGDx15

8:41am August 18th 2015 via Hootsuite

Lin: Also pt-derived tumor models (patient-derived xenografts, PDX), and biobanking, tissue repository of tumor, germline #NGDx15

8:40am August 18th 2015 via Hootsuite

Lin: Leaders at CCR (NCI), Paul Meltzer and Javed Khan for Clinical Omics program: clin platform; research (RNA and methylation) #NGDx15

8:39am August 18th 2015 via Hootsuite

Lin: Working at Hopkins with Vogelstein and Velculescu, worked on the first human exome (2006) http://t.co/4gv3by7DEp #NGDx15

8:38am August 18th 2015 via Hootsuite

Lin: Starts with a story about designing >10K primers and seeing many failures at Hopkins. Now WES for patients 'is routine' #NGDx15

8:35am August 18th 2015 via Hootsuite

Here at #NGDx15 Jimmy Lin (NCI) "NCI Clinomics Program: Clincal Cancer Panel and Exome Sequencing and Beyond"

8:33am August 18th 2015 via Hootsuite

Transparency Weaponized Against Scientists http://t.co/8nfOjnDv6c

5:10am August 18th 2015 via Hootsuite

NIH to Award Up to $12M to Fund DNA, RNA Sequencing Research | GenomeWeb http://t.co/Mgm5az7vtm

4:40am August 18th 2015 via Hootsuite

Every county in America, ranked by natural beauty - The Washington Post http://t.co/XcCWPCLcl1

7:50pm August 17th 2015 via Hootsuite

RT @Helena_LB: These images of crystallized DNA by L. Gledhill are fantastic. #sciart http://t.co/o7caPKXqIr http://t.co/Wp7J5mxYus

6:20pm August 17th 2015 via Hootsuite

RT @kirkenglehardt: A science conference restricts live tweeting and confusion ensues. http://t.co/hGFFDv5rPV @ta_wheeler #scicomm #socialm…

5:10pm August 17th 2015 via Twitter Web Client

RT @aaronquinlan: Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene. (tx Evan Eichler) http://t.co/KcSUSoA20f

3:30pm August 17th 2015 via Hootsuite

Personal Genome: Rather Boring, Actually | GenomeWeb http://t.co/k3CeER7baA

2:20pm August 17th 2015 via Hootsuite

RT @GholsonLyon: Beacon Project Cracks the Door for Genomic Data Sharing - Bio-IT World http://t.co/5SPgeSuC4c

1:30pm August 17th 2015 via Hootsuite

RT @AppliedBio: Wouldn't this #ScienceHero Award looking smashing in your lab?http://t.co/KzMYIFcRc6 http://t.co/lPFd7AlgEr

12:30pm August 17th 2015 via Hootsuite

Also attending #NGDx15 http://t.co/Dp9Q2rGUkr RT @SeraCare: Meet the SeraCare #PrecisionMedicine team at #AACC2015! http://t.co/iPPJ6Nvmcv

11:25am August 17th 2015 via Hootsuite

If any of you are attending #NGDx15 in DC (starting tomorrow), be sure to pay me a visit @seracare ! Great lineup: http://t.co/Dp9Q2rGUkr

10:15am August 17th 2015 via Hootsuite

The Buffett Formula - reading is only part of the equation | Farnham Street http://t.co/hLWodd9afO

9:05am August 17th 2015 via Hootsuite

RT @rahman_nazneen: Great new word - Metagrobology: the study of puzzles. I'm a practitioner. A couple to amuse/confuse you here! http://t…

6:49am August 17th 2015 via Hootsuite

RT @deannachurch: ICYMI: Come join my group @PersonalisInc http://t.co/u5teMiHucy #bioinformatics #jobs

6:25am August 17th 2015 via Hootsuite

RT @nytimes: Archaeologists think they've found clues to the fate of the "lost colonists" of Roanoke http://t.co/O2zZxQWiUU

5:25am August 17th 2015 via Hootsuite

Star Wars-Themed Lands Coming to Disney Parks | http://t.co/HnWL91xbLK http://t.co/ibEkx0YoMZ

4:40am August 17th 2015 via Hootsuite

RT @wef: Is online #education reaching the masses? http://t.co/HSvI1xky56 #MOOCs http://t.co/9RIe8vJi9j

10:15pm August 16th 2015 via Hootsuite

RT @NatGeoScience: Scientists can guess where users are going in life by the photos they upload: http://t.co/CNE2dJ8niv

9:15pm August 16th 2015 via Hootsuite