JV:90 languages already machine-translated (same $GOOG engineer now at HLI). slide illus. 'Integrative approach to medicine' #AGBT15
12:36pm February 27th 2015 via Hootsuite
JV: Brain MRI is 2GB data; can reduce features to <10kB. Finding parameters in advance changes the scale of what can be done #AGBT15
JV: Using brain fMRI scanning - neuron locations and mapping structures. Huge list of phenotypes to measure #AGBT15
12:35pm February 27th 2015 via Hootsuite
JV:Working with metabolomics, from a few uL of blood. #AGBT15
12:34pm February 27th 2015 via Hootsuite
JV: HLI integrates EMR's organized with whole genomes. Now onto microbiome #AGBT15
12:33pm February 27th 2015 via Hootsuite
JV:'We can't tell more about my genome today than from 15 years ago' #AGBT15
JV: A slow process but 'already producing really interesting results' #AGBT15
12:32pm February 27th 2015 via Hootsuite
JV: Also pig xenotransplantation - a very complex problem, but they are working w/United Therapeutics w/ a humanized pig liver #AGBT15
JV:Working on reducing the size of a genome by a factor of 8; reordering genes #AGBT15
12:31pm February 27th 2015 via Hootsuite
JV: (Note: more info about their synthetic gene service/product is here http://t.co/kfzsOXVIli ) #AGBT15
JV: Panel of 6 synthetic bio papers - PNAS and Science - mentioned Synthetic Genomic's gene assembly instrument #AGBT15
12:30pm February 27th 2015 via Hootsuite
JV: "If a photo is embedded in the genome, the data then needs to be in a scure database." #AGBT15
12:29pm February 27th 2015 via Hootsuite
JV: "We're working with UCSD students - they don't know it yet" - predicting faces from genes. 'Confident that faces will work' #AGBT15
12:28pm February 27th 2015 via Hootsuite
JV: We need to generate global reference standard genomes #AGBT15
12:27pm February 27th 2015 via Hootsuite
JV: "I love these bubble graphs" - nicely illustrating where allelic variation occur #AGBT15
12:26pm February 27th 2015 via Hootsuite
JV: Compound heterozygotes 'is how our genome works'. Phasing largely ignored as it was not possible to study #AGBT15
12:25pm February 27th 2015 via Hootsuite
JV: Sperm cells - one crossover per chromosome. No two are alike; but can get large blocks from a few sperm cells. #AGBT15
JV: Hiring 200 bioinformatics people this year. Genome Res '13 paper http://t.co/Yi8v5aTTrf using sperm for phasing #AGBT15
12:24pm February 27th 2015 via Hootsuite
JV: One 10-X is ~350 3730xl's. New 110k sf on Executive Dr La Jolla. Also Mt View office for machine learning; Singapore offc too #AGBT15
12:23pm February 27th 2015 via Hootsuite
JV:First genome sequenced in 1995; his 2007 PLOS Biol paper http://t.co/ZaGDH60gK9 contrasted 3700's to X-10's at HLI #AGBT15
12:22pm February 27th 2015 via Hootsuite
JV:Need lots of phenotypes, lots of genomes; 'we're now in the 4th or 5th generation of scientists working in genomics...' #AGBT15
12:20pm February 27th 2015 via Hootsuite
JC: Starts with HLI - about 1y old now. 'Does DNA contain all necessary information for cellular life?' #AGBT15
12:19pm February 27th 2015 via Hootsuite
Craig Venter: "It's the first time on this island" (indeed! Some storied history between AGBT and the now-defunct Hilton Head GSAC) #AGBT15
12:18pm February 27th 2015 via Hootsuite
MH:Not commercialized yet (in terms of tools) but conceptually 'it's there' #AGBT15
12:17pm February 27th 2015 via Hootsuite
MH: N5010.4Mb; N90 1.3Mb. Showed large-scale heterozygous variation in HLA-DQA1/DQB1 (151kb region) phased automatically #AGBT15
12:16pm February 27th 2015 via Hootsuite
MH:Took HuRef-1 sample, did PacBio reads. Constructed diploid-aware contig represention ("FALCON"). DALIGNER (Myers), FALCON (chin) #AGBT15
12:14pm February 27th 2015 via Hootsuite
MH: Quotes @deannachurch in this '13 Bio-IT World http://t.co/yy11TgYzBR 'we have to have de novo assy' #AGBT15
12:11pm February 27th 2015 via Hootsuite
MH:Non-SNP variation is 22%; 35% of genes are encompassed by CNV's; less than 1% of var's present in CHM1 in newer assemblies #AGBT15
12:10pm February 27th 2015 via Hootsuite
Mike Hunkapiller @PacBio workshop: compares human de novo assemblies - N50 contig of 7.7kb for CHM1 far longer than rest #AGBT15
12:08pm February 27th 2015 via Hootsuite
MG:Q:How much sample for library prep? A:AML has almost unlimited amts of DNA/RNA ddPCR 'uses a ton' - a few ug #AGBT15
11:52am February 27th 2015 via Hootsuite
MG:Q:RNA-Seq data? A:Done to look for regulatory mut's (FOXP1 splicing defect, exon-skipping); validates some var's in this way #AGBT15
MG: Large dataset - to serve as a resource to help others choose optimal strategy. Hope to make it avail 'soon' #AGBT15
11:50am February 27th 2015 via Hootsuite
MG:As WGS depth downsampled - check this out (animation of downsampling) Cool!
11:49am February 27th 2015 via Hootsuite
MG: Primary tumor VAF, plot against relapsed tumor VAF; each driver corresponds to variant cluster #AGBT15
11:47am February 27th 2015 via Hootsuite
MG: Plot of PPV against sensitivity - with 8 different callers. Many callers were similar PPV, sens had a range #AGBT15
11:46am February 27th 2015 via Hootsuite
MG: Complex list of ~8 datasets; ended up with 'platinum var's' list. Downsampled to test sensitivity of 'std' coverage levels #AGBT15
11:45am February 27th 2015 via Hootsuite
RT @bioinformer: Great example of CBEP efforts by @broadinstitute for genomics in Africa. @illumina @USAID #AGBT15 http://t.co/ywyxKLUAjB
11:43am February 27th 2015 via Hootsuite
MG: 350X WGS, 350x WES, 1200x of 260 AML genes, 10,000x 144 high priority SNV sites. 240K ddPCR (15 sites) 30 'lanes' RNA-Seq #AGBT15
11:42am February 27th 2015 via Hootsuite
MG:Indiv. w/AML31 char in Ding et al 2012 http://t.co/r7SdJ3kMbY After WGS 400x targeted validation. Showed fish-eye plot figure #AGBT15
11:40am February 27th 2015 via Hootsuite
MG:Heterogeneity and aneuploidy: non-optimal strategies WGS/30-60x and WES/100x- insufficient coverage. Same w/RNA-Seq read numbers #AGBT15
11:38am February 27th 2015 via Hootsuite
Malachi Griffith, Washington Univ. Optimizing Tumor Genome Sequencing and Analysis #AGBT15
11:36am February 27th 2015 via Hootsuite
CM:Q:(Plon) How were you contacted? A:'We were poised and ready'. Obv. other places affected #AGBT15
CM:Q:Samples from Africa or seq in-country? A:'A lot of hurdles', still gets samples shipped #AGBT15
11:35am February 27th 2015 via Hootsuite
.@clcbio I WANT. Will
11:34am February 27th 2015 via Hootsuite in reply to
CM:Was able to track spread through Sierra Leone, published in Science '14 http://t.co/oByvytKOg4 Mut's cluster into clades #AGBT15
11:29am February 27th 2015 via Hootsuite
CM: Also carryover of poly(A) carrier a problem; depletes w/method. Showed coverage plot pre- and post-depletion. #AGBT15
11:28am February 27th 2015 via Hootsuite
CM: Cold chain a challenge. Have est relationships with local hospitals. RNA quality/qty. RIN of 1.2 (!) Need qRTPCR for quant #AGBT15
11:25am February 27th 2015 via Hootsuite
CM: Goals - Dx, therapy, origins, transmission, host-interaction. Had lessons from working with Lassa virus - logistics is hard #AGBT15
11:24am February 27th 2015 via Hootsuite
CM: Starts with Genome Biol '14 ref: http://t.co/NJo4sq96ji Suspected: 22.8K; >9K deaths. Unprecedented outbreak #AGBT15
11:23am February 27th 2015 via Hootsuite
Christian Matranga, Broad Inst Rapid Full-Length Sequencing of Lassa and Ebola Viruses: A Model for Genomic Pathogen Surveillance #AGBT15
11:21am February 27th 2015 via Hootsuite
