Jay Flatley (Illumina) Beyond the $1000 Genome-What’s next for NGS? #AGBT16
9:03am February 12th 2016 via Hootsuite
Great to meet @mattloose here at #AGBT16 breakfast! Great stuff he’s working on.
9:02am February 12th 2016 via Hootsuite
New post: Circulating Tumor DNA Poster presented at Keystone Symposium | SeraCare Blog https://t.co/6AMm8j2aQc #AGBT16
6:45am February 12th 2016 via Hootsuite
A cancer’s surprise origins, caught in action | Harvard Gazette https://t.co/Ph4qfpHm91
6:05am February 12th 2016 via Hootsuite
The Tragedy of the Woolly Mammoth: Does An Economic Problem Explain Their Extinction? - Pacific Standard https://t.co/iTDxL28xwn
5:40am February 12th 2016 via Hootsuite
Invitae's Q4 Revenues Increase More Than Three Fold | GenomeWeb https://t.co/VXimmKCa8r
4:15am February 12th 2016 via Hootsuite
Huang:Q:Why only 2x needed? A:Enriched the target region has reprod higher coverage regions adjacent regions #AGBT16
9:29pm February 11th 2016 via Hootsuite
Huang: Acknowledges Sunney Xie now at Peking Univ #AGBT16
9:28pm February 11th 2016 via Hootsuite
Huang: Only need 2x WGS coverage for MALBAC makes this cost-effective, free from parent's monogenic disease #AGBT16
9:27pm February 11th 2016 via Hootsuite
Huang: Five embryos, one diploid polar body had homozygous deleterious mutation. 3/5 were unaffected. 2nd healthy delivery '14 #AGBT16
9:26pm February 11th 2016 via Hootsuite
Huang: Case 2, XLHED, X-linked hypohidrotic ectodermal dysplasia, no hair or teeth #AGBT16
9:25pm February 11th 2016 via Hootsuite
Huang: Summary of 18 embryos - 7 unaffected, showed first healthy delivery in late '14. #AGBT16
9:23pm February 11th 2016 via Hootsuite
RT @mason_lab: #AGBT16 The 20kb Oxford nanopore prep needs ~15ug of DNA due to serial loss during library prep. Good news for @10xgenomics
9:22pm February 11th 2016 via Hootsuite
Huang: '15 PNAS https://t.co/3gn8DmVTFR by combining MALBAC with linkage method called MARSALA #AGBT16
9:20pm February 11th 2016 via Hootsuite
Huang: They reviewed 5 methods of WGA here https://t.co/NVoVD7t6Rz Developed linkage analysis #AGBT16
9:19pm February 11th 2016 via Hootsuite
Huang: Use MALBAC '12 Science https://t.co/uH74HxEpMN For SNVs easy to get allele dropout or amplifcation error #AGBT16
9:18pm February 11th 2016 via Hootsuite
Huang: PGD/PGS - via polar body biopsy day 0, also blastocyst biopsy at day 5 #AGBT16
9:16pm February 11th 2016 via Hootsuite
Huang: Rises w/age of female to 70% aneuploidy rate, 50% miscarriage rate by 44yo. #AGBT16
9:15pm February 11th 2016 via Hootsuite
Huang: New method prevents both monogenic diseases and aneuploidy. Seq of polar bodies '13 Cell ref https://t.co/NnJRrXS3vY #AGBT16
9:14pm February 11th 2016 via Hootsuite
Lei Huang (Peking Univ) Live Births with monogenic diseases and chromosome abnormality simultaneously avoided by NGS-based PGD/PGS #AGBT16
9:12pm February 11th 2016 via Hootsuite
Bainbridge:Q:Adding algorithms? A:They can determine if one or the other is useful. #AGBT16
Bainbridge:Q:How to deal with updates? A:No official policy, but can update and move report forward or back in time #AGBT16
9:09pm February 11th 2016 via Hootsuite
Bainbridge: And these apps will have an automated pipeline behind it. Worked closely with DNANexus #AGBT16
9:08pm February 11th 2016 via Hootsuite
Bainbridge: expects a 'burst of recreational DTC WES companies' with inexpensive sequencing, and sell apps on top of that #AGBT16
9:07pm February 11th 2016 via Hootsuite
Bainbridge: Discusses their efforts beyond precuration: ensemble approach for variant effect. Showed tunable spec/sens for panel #AGBT16
Bainbridge: Var db based on Hadoop, uses Hive uses SQL and transl to noSQL. Two portals - controlled for external vs internal #AGBT16
9:01pm February 11th 2016 via Hootsuite
Bainbridge:QA/QC critical; sample prep, var validation, sequencing. Heart of system is variant warehouse; limited annotation #AGBT16
9:00pm February 11th 2016 via Hootsuite
Bainbridge: LIMS is basically a Oracle Java/JS web-services oriented. Sample tracking, batch reagent failures #AGBT16
8:59pm February 11th 2016 via Hootsuite
Bainbridge:Fast, reliable, accurate. SNV, CNVs, SNP-arrays, automated QC/QA, automated reporting, new variants #AGBT16
8:57pm February 11th 2016 via Hootsuite
Bainbridge: Correction: 25K was eMERGE, Carrier testing at 1K-4K samples/month #AGBT16
8:56pm February 11th 2016 via Hootsuite
Bainbridge:Automated methods balance sensitivity, specificity. Baylor/Miraca wants to handle 4K samples/mo. SFARI 25K in 4y #AGBT16
Bainbridge: Thought in 2011 that WES would spell the death of panels. But they have proliferated - shorter TAT, lower cost, analysis #AGBT16
8:55pm February 11th 2016 via Hootsuite
Matthew Bainbridge (Baylor) Neptune: an automated pipeline for clinical reporting of carrier-tests #AGBT16
8:54pm February 11th 2016 via Hootsuite
Moore: Another example - current biopsy can be 'substantially different than the primary'. Need to treat metastatic disease #AGBT16
8:48pm February 11th 2016 via Hootsuite
Moore Certainly an N=1, but 1y cancer-free. #AGBT16
8:47pm February 11th 2016 via Hootsuite
Moore: Examples - high JUN expression. Hypertension medication (approved) and 'the tumor completely disappeared' "like a miracle' #AGBT16
Moore: Lists driver genes(expected list). Getting diagnosis, inform potential therapy, enable clinical trial enrollement #AGBT16
8:44pm February 11th 2016 via Hootsuite
.@East_OnWest Your welcome - like @becky_kusko, I'm just sharing my own notes with everyone.
8:42pm February 11th 2016 via Hootsuite in reply to East_OnWest
RT @East_OnWest: @DaleYuzuki Thanks for all the great #AGBT16 coverage today, you're a #tweetmaster
8:42pm February 11th 2016 via Hootsuite
Moore: Using integrated pathway analysis with RNA-Seq data. Several reports generated #AGBT16
8:41pm February 11th 2016 via Hootsuite
Moore: Many tools - SV, CNV, Somatic SNV. KB has many annotations, 8042 refs etc 'the most valuable part of all of this' #AGBT16
8:39pm February 11th 2016 via Hootsuite
Moore: Generate 'as many types of data as we can' CNV, LOH, gene exp, infectious agents, mutation sig, SNV, indels, fusions and SV #AGBT16
8:38pm February 11th 2016 via Hootsuite
Moore: About a 8w turnaround time; molecular tumor board; both DNA and RNA. Now they want WGS, before just a panel #AGBT16
8:37pm February 11th 2016 via Hootsuite
Moore: Personalized oncogenomics: 437 cases enrolled, incl 24 pediatric. Long array (50) different cancers represented #AGBT16
8:35pm February 11th 2016 via Hootsuite
Moore:First patient in 2010, 'took a month of sequencing' '10 ref https://t.co/PqaRSP2taS but felt this N=1 study did help #AGBT16
8:34pm February 11th 2016 via Hootsuite
Moore: Mentions this work in current issue of CSHL Molecular Case Studies as part of the #AGBT16 event bag https://t.co/3WHLrvh9wl
8:32pm February 11th 2016 via Hootsuite
Richard Moore (BC Cancer Agency) Whole genome and transcriptome sequencing for personalized cancer therapy: first 300 cases #AGBT16
8:30pm February 11th 2016 via Hootsuite
Keating: In transplantation, microbiome important, as well as proteomics, working on those fronts as well. #AGBT16
8:27pm February 11th 2016 via Hootsuite
Keating: Also using Roche 5MB capture for MHC. They have outcome data for 15y. #AGBT16
Keating: 35K samples now part of iGeneTRAiN int'l consortium for GWAS; are working with @10xgenomics to phase MHC around HLA-A. #AGBT16
8:26pm February 11th 2016 via Hootsuite
