EE:Q:Consensus reads? A:Not SMRTbells, after Quiver 99.99% Qv 40 to 50, Cp to Sanger as well as BAC sequencing #AGBT15
9:35am February 26th 2015 via Hootsuite
EE:Q:Implications for Dx? A:100's in coding seq; largely untapped space to explore #AGBT15
9:34am February 26th 2015 via Hootsuite
EE:Q:Upper limit of detection size? A:Insertions is 50bp-5kb is novel; Phase III data not included. Tandem dupl: to 40kb due to RL #AGBT15
9:33am February 26th 2015 via Hootsuite
EE: Shoutout to Jason Chin of @PacBio. Q:FP/FN rate of genotyping? A:No metrics yet #AGBT15
9:31am February 26th 2015 via Hootsuite
EE:Eddie Rubin once joked 'if we can generate 200kb reads you (EE) will finally shut up' #AGBT15
9:30am February 26th 2015 via Hootsuite
RT @jgreid: EE: many contigs shatter right over segmental duplications, justifies a de novo approach #AGBT15
9:29am February 26th 2015 via Hootsuite
EE: Summary - 'we are missing most of the variation from 50bp - 2kbp in size'. Estimate >50% can be genotyped if we can discover it #AGBT
EE: Shows a large table of ~18 ongoing projects, targeting 20x to 60x, across 4 institutions #AGBT15
9:28am February 26th 2015 via Hootsuite
EE:De novo human genome assy: recommend a hybrid approach with targeted BAC clone-based sequence #AGBT15
9:27am February 26th 2015 via Hootsuite
RT @mjcgenetics: Hm, we were doing a lot of this stuff with long mate-pairs on SOLiD back in 2008/09. Why’d the field ignore LMP again? #ag…
9:26am February 26th 2015 via Twitter Web Client
EE:W/a relatively few number of samples char in this way, can get a much better reference. Can use BACs to resolve complex regions #AGBT15
9:25am February 26th 2015 via Hootsuite
EE:3.9kb deletion from TGP data - now can go back and genotype, find 10% of TGP samples have this deletion #AGBT15
9:24am February 26th 2015 via Hootsuite
EE:Now at work on CHM13 w/P6C4 chemistry; increase in read length as distribution. Similar bar chart. Huddleston et al unpubl #AGBT15
9:22am February 26th 2015 via Hootsuite
EE:Retrotransposon biases - 20% inc in detection of SVA elements (repeat + GC composition) #AGBT15
9:19am February 26th 2015 via Hootsuite
EE:Relevance - implications of STRs in disease. Resolving complex repeats - very busy slide, illus. the complexity of the task #AGBT15
9:18am February 26th 2015 via Hootsuite
EE:Longer and new STRs - 3x more and 2.8x longer in CHM1 cp to reference genome #AGBT15
EE:Alu and L1HS sites. 22.1k novel var's correspond to 11Mbp of sequence. 6.7k events in 3.4k genes, 169 w/in coding regions #AGBT15
9:17am February 26th 2015 via Hootsuite
EE:Despite thousands of genomes sequenced, most of this var 50bp-5kbp 'never seen before' #AGBT15
9:16am February 26th 2015 via Hootsuite
EE:Fn relevalence - 20 exons, containing 12 genes. Payoff slide: event size against count. 92% ins, 60% dels are novel 50bp-5kbp #AGBT15
9:15am February 26th 2015 via Hootsuite
EE:'Signif. enrichment of tandem repeats'. Sometimes >10kb; flanked w/GC-rich on both sides. Sequence tech marched through it #AGBT15
9:14am February 26th 2015 via Hootsuite
EE:Summarizing: 90 gaps closed or extended; 26K 'structural var's' resolved at bp level resolution; 460 STR/VNTR >1kb #AGBT15
9:13am February 26th 2015 via Hootsuite
EE:An enucleated egg, 45.8x via RSII P5/C3 data released in late 2013 here: http://t.co/o6Qi3I5XeX Ref: http://t.co/x3HMrC3WdD #AGBT15
9:12am February 26th 2015 via Hootsuite
EE:Non-random 15% error is a feature, due to lack of bias. CHM1 hydatidiform mole is the 'Platinum Genome Assy' - not quite finished #AGBT15
9:10am February 26th 2015 via Hootsuite
EE: @PacBio histogram: 10.8kb mean, max 47.6kbp, very little G-C bias demonstrated "almost flat" cp to PCR-free illumina sequence #AGBT15
9:09am February 26th 2015 via Hootsuite
EE: 'We don't know how big that whole is'. Introduces @PacBio, they've been using it for 4y. ZMW's sequence directly (3rd gen) #AGBT15
9:08am February 26th 2015 via Hootsuite
EE: Missing heritability may be hiding in this missing variation due to short-read methods. 'We want to be comprehensive & precise' #AGB
9:07am February 26th 2015 via Hootsuite
EE: Structural var detection is indirect: read depth, read pair, split reads: all dep. on context Nature Rev http://t.co/Q4XdYaCs6w #AGBT15
9:06am February 26th 2015 via Hootsuite
EE: 1,000 genes in complex areas not well char. Alkan Nature Meth 2011 'we've been seduced' by NGS http://t.co/ZUC34dqd2v #AGBT15
9:05am February 26th 2015 via Hootsuite
EE: Most attn on SNV's & indels; today structural var >50bp, microsatellites, mobile elements 300bp-10kb #AGBT15
9:03am February 26th 2015 via Hootsuite
First: Evan Eichler, University of Washington: Resolving the Complexity of Human Genetic Variation by Single-Molecule Sequencing #AGBT15
9:02am February 26th 2015 via Hootsuite
The US Supreme Court has affirmed that fish are not an information-storage device - Quartz http://t.co/sbXZUX2NAv
7:15am February 26th 2015 via Hootsuite
Beautiful beach walking here at #AGBT15, although rain in the forecast. http://t.co/cZ98rXncVq
7:05am February 26th 2015 via Hootsuite
Star talker: Neil deGrasse Tyson on fame, education and tweets - The Washington Post http://t.co/N0xJceQd76
6:15am February 26th 2015 via Hootsuite
.@howitts_done Here's the NEJM ref ($) http://t.co/fVVdZVAoug 'myeloid cancers' (general).
5:26am February 26th 2015 via Hootsuite in reply to
Eating peanuts prevents peanut allergies http://t.co/3n4rH984gg
5:10am February 26th 2015 via Hootsuite
Here’s Why You Shouldn’t Put Your Baby Photos Online — Matter — Medium http://t.co/QDvcvMlTYo
4:10am February 26th 2015 via Hootsuite
Corrected YouTube link RT @DaleYuzuki: RT @CIgenomics: YE: see the video here http://t.co/mfZgcOfYfa #AGBT15
11:29pm February 25th 2015 via Hootsuite
Astronomers find a shockingly ancient black hole the size of 12 billion suns - The Washington Post http://t.co/JRRFCQTDve
11:10pm February 25th 2015 via Hootsuite
A Few Citizen Scientists Do Most of the Work - Inkfish (Discover) http://t.co/npU7qiMdMZ
10:40pm February 25th 2015 via Hootsuite
Nanocrafter: Playing a Game of Synthetic Biology - Citizen Science Salon (Discover) http://t.co/uvUCwPJ12p
9:40pm February 25th 2015 via Hootsuite
SM: Could this have been seen in WGS 3y before cancer dx? This work recently published in NEJM Genovese et al http://t.co/FzYq7LdBc0 #AGBT15
6:57pm February 25th 2015 via Hootsuite
SM:Is there a window for early detection for blood cancer from WES data? Data from 2mos before cancer dx suggests it's possible. #AGBT15
6:53pm February 25th 2015 via Hootsuite
SM:Looked at clonal hematopoiesis affecting subsequent cancer risk; Swedish EHR showed 12x increased risk #AGBT15
6:50pm February 25th 2015 via Hootsuite
.@milospm1206 Thank you for the kind word, Patrice!
6:49pm February 25th 2015 via Hootsuite in reply to
.@deannachurch @drgitlin @obahcall IIRC last year one was organized on an impromptu basis (Marriott bar). I missed it though!
6:48pm February 25th 2015 via Hootsuite in reply to
SM:DNMT3A, TET2, ASXL1, PPM1D; most disruptive; some missense; none synonymous. Suggests positive selection #AGBT15
6:46pm February 25th 2015 via Hootsuite
SM:Looked for somatic mutations in blood: 10-20% MAF putative from WES; 3.1K / 12.3K indiv.; 64/64 validated; found 4 genes #AGBT15
6:45pm February 25th 2015 via Hootsuite
SM: What happens in the years before disease becomes apparent? Looking for schizophrenia risk via blood DNA. No probands #AGBT15
6:42pm February 25th 2015 via Hootsuite
Steven McCarroll, Harvard Medical School “A Common Pre-Malignant State, Detectable by Sequencing Blood DNA” #AGBT15
6:40pm February 25th 2015 via Hootsuite
RT @GenaliceDNA: @erlichya: http://t.co/i4vIISEc5w User: Demo PW: Demo #AGBT15
6:38pm February 25th 2015 via Hootsuite
