DC: 100kb deletion in this CCL3 region. Now onto GChr37, burst of activity in alternative loci and genes. Many seq's under-annotated #AGBT15
1:12pm February 27th 2015 via Hootsuite
DC: CCL3 region - CNV could affect HIV susceptibility; but genotype is incorrect. CHM1 data ref: http://t.co/hiYW4BMzzA #AGBT15
1:09pm February 27th 2015 via Hootsuite
DC:The prior model was compressing 2 haplotypes into one that wasn't reflective of reality. New model: represent both w/alt locus #AGBT15
1:06pm February 27th 2015 via Hootsuite
DC: (And errors in reference confuse or dilute that variant signal - only gene 1 is 'present' in reference) #AGBT15
1:05pm February 27th 2015 via Hootsuite
DC:Need high-quality ref to call variants - and annotate them. Illus w/paralogous gene, where sample has deleterious var in gene 2 #AGBT15
DC: @personalisinc w/ACE WES can solve 50% of cases (good) but what about the other 50%? Var ID but not matched to phenotype #AGBT15
1:03pm February 27th 2015 via Hootsuite
Deanna Church (Personalis) "Finishing genomes: why does it matter?" #AGBT15
1:01pm February 27th 2015 via Hootsuite
GM: Briefly goes through idea of scrubbing (cleaning up artifacts in reads); module DAscrub. Illus beautifully w/ 30x Ecoli data #AGBT15
12:59pm February 27th 2015 via Hootsuite
GM: "I pulled every trick I ever learned" with Daligner to get 25x - 40x speed improvement over BLASR #AGBT15
12:57pm February 27th 2015 via Hootsuite
GM: http://t.co/DRwyr36HqT is where his code lives. Lossless compression at 14x, can analyze compressed; Daligner module fast #AGBT15
12:56pm February 27th 2015 via Hootsuite
GM: An assembler is a pipeline of modules; HGAP, Falcon; plug-and-play. It takes time to build good modules for all components #AGBT15
12:55pm February 27th 2015 via Hootsuite
GM: Current assemblers 'already competitive'. Melanogaster using PB 100x or Ref 6 (hand curated) comparable #AGBT15
12:54pm February 27th 2015 via Hootsuite
GM: Surprised w/lack of assembler. Not restricted by error rate; need was efficient in seq coverage & computer time w/15% error #AGBT15
12:53pm February 27th 2015 via Hootsuite
GM: Sufficiently var repeats are resolvable. As long as you can span. 1 het per every 2kbp for P6/C4 #AGBT15
12:52pm February 27th 2015 via Hootsuite
GM:Thus - just a function of coverage 3) Spanned repeats are resolvable. Unique flank on both sides solves it http://t.co/kX2c8cxvh7 #AGBT15
12:50pm February 27th 2015 via Hootsuite
GM: 2) Read error is Random - Q score (consensus of k sequences) increases linearly in k #AGBT15
12:47pm February 27th 2015 via Hootsuite
GM: 1)Poisson: At any desired level of coverage, amt of coverage approaches 100% (Lander-Waterman 1988) #AGBT15
GM:As a mathematician - near-perfect assy back on the table. After 10y hiatus - "I'm back" @thegenemyers #AGBT15
12:46pm February 27th 2015 via Hootsuite
GM: 10kbp+ length (P6/C4), 10-15% error (mostly insertions), but: random 'at any given point'. Read sampling also random. #AGBT15
12:45pm February 27th 2015 via Hootsuite
Gene Myers: #AGBT15 My favorite talk from 2014 here: http://t.co/YY0rHw7cGO
12:44pm February 27th 2015 via Hootsuite
RT @DNAmlin: Terrific fun @DNAnexus with @JCVenter @PacBio assembly! Here cmp'd to HuRef+@GenomeRef #AGBT15 http://t.co/vT2Pmg7jOU http://t…
12:43pm February 27th 2015 via Twitter Web Client
JV:Q:What abt epigenetics? A:We need the equiv for the methylome - HTP and accurately. But: epigenetics still encoded by genome #AGBT15
12:42pm February 27th 2015 via Hootsuite
JV:Insurance co's are not interested in prevention, long-term health; large companies though that self-insure, do. #AGBT15
12:41pm February 27th 2015 via Hootsuite
JV: 'I know 5 technologies down at the single molecule level' 'We're counting on $30 genomes in 3-4y' (seriously) #AGBT15
12:40pm February 27th 2015 via Hootsuite
RT @chrisamiller: Finishing up the paper and dbGaP submissions now! MT @DaleYuzuki Hope to make it avail 'soon' #AGBT15
12:38pm February 27th 2015 via Hootsuite
JV:Goal is 1M genomes + phenomes by 2020. Genomics moving forward at a 'much more rapid pace in a much more predictive fashion' #AGBT15
12:37pm February 27th 2015 via Hootsuite
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
