FYI #AGBT17 folks https://t.co/8enIYvnNeb
7:40pm February 15th 2017 via Hootsuite
Beechem: Reviews how it works; the workflow does include a step after the FFPE dissolving and filtration; there is a bead-pur step #AGBT17
7:39pm February 15th 2017 via Hootsuite
Joseph Beechem (NanoString WA) Library-free, targeted sequencing of native gDNA from FFPE samples using Hyb & Seq technology #AGBT17
7:38pm February 15th 2017 via Hootsuite
RT @bmaher: A verdict in the bitter battle over CRISPR patents: Broad wins https://t.co/Xj5dTSZ4mN
4:04pm February 15th 2017 via Hootsuite
Cereb: Transitioning to Sequel: enables increased throughput #AGBT17
Cereb: Here phasing (cis-trans) ambiguities can be clarified, with several patterns DQB1 shown due to long reads #AGBT17
4:02pm February 15th 2017 via Hootsuite
Cereb: 17 out of 60K had null and alt expressed II variation #AGBT17
3:56pm February 15th 2017 via Hootsuite
Cereb: Have gone through 150K samples. In their 60K samples had 179 null and alt-express alleles #AGBT17
Cereb: Both 5' and 3' untransl regions. Now have 7x RS II's (!!) #AGBT17 #NGSoffthehook
3:54pm February 15th 2017 via Hootsuite
Cereb: Exon 2 for class I/II, Exon 3 for I. Used nested PCR for MiSeq. Typing reports using long-reads of RS II much simpler #AGBT17
Cereb: Jan '16 HLA alleles was 14.4K; submitted by Histogenetics: 7K. Started with 3730xl; 6M on Sanger, 1M on MiSeq. July RS II #AGBT17
3:51pm February 15th 2017 via Hootsuite
Cereb: First report of HLA matching demonstrated at MSKCC in 1990 NEJM https://t.co/8eJMLQUTIK for transplants. Took off from there #AGBT17
3:49pm February 15th 2017 via Hootsuite
Cereb: MHC molecules modulate immune response by TCR interaction (I II) and NK-KIR (I), modulates graft rejection #AGBT17
3:47pm February 15th 2017 via Hootsuite
PacBio Workshop: Nezih Cereb (Histogenetics NY) Hight-throughput HLA Class I whole gene and HLA Class II long-range typing #AGBT17
3:46pm February 15th 2017 via Hootsuite
.@RaviSachidanand I was very close to saying something on the order of 'Only At the Broad' given their (basically) unlimited budgets...
3:39pm February 15th 2017 via Hootsuite in reply to RaviSachidanand
RT @nanostringtech: Back live in the sequencing suite! #AGBT17 https://t.co/13f8lezxat
3:38pm February 15th 2017 via Hootsuite
Macarthur: Also pilot studies of recontacting individuals with 'extreme genotypes' (i.e. non-functional but critical genes) #AGBT17
2:54pm February 15th 2017 via Hootsuite
Macarthur: No restriction on publication, usage. Next up is improving methods for rare-disease diagnosis. #AGBT17
2:53pm February 15th 2017 via Hootsuite
Macarthur: Will be soon releasing the VCFs; shows one example APOE where WGS offers much better coverage on genes cp to WES #AGBT17
2:52pm February 15th 2017 via Hootsuite
Macarthur: Showed cool 3D 8-population PCA using random forest approach, 40K known ancestry samples, 40K SNPs #AGBT17
2:50pm February 15th 2017 via Hootsuite
Macarthur: gnomad website: https://t.co/rbipgjHQ38 16TB for 123K exomes (from 1.3PB raw); 24TB for 14.3K genomes (from 1.6PB raw). #AGBT17
2:46pm February 15th 2017 via Hootsuite
Macarthur: Now gnomAD - 123K exomes, 15.4K WGS, called separately analyzed together. New populations, >5K AJ smpls #AGBT17
2:44pm February 15th 2017 via Hootsuite
Macarthur: "60K exomes is still not enough", for well-powered studies, constraint in many genes; older exome data; missing WGS #AGBT17
2:43pm February 15th 2017 via Hootsuite
Macarthur: can lok for genes depleted for LoF, where obs vs expected,; less LoF variants than by chance. Est how strong LoF effect #AGBT17
2:40pm February 15th 2017 via Hootsuite
McArthur: ExAC relasted 60.7K 'reference' samples; high-quality exomes, unrelated individuals; website: https://t.co/4nSUzXz1AZ #AGBT17
2:37pm February 15th 2017 via Hootsuite
Daniel McArthur (Harvard Med Sch MA) A unified resource of genetic variation spanning >138K genomes #AGBT17
2:36pm February 15th 2017 via Hootsuite
Beechem: Wants to engage on key applications; open for partnerships; plan beta-instruments 'in 2019' #AGBT17
1:40pm February 15th 2017 via Hootsuite
Beechem: With a photo-cleavable linker, able to detect protein quantitation (and RNA in the future) in FFPE in x-y coordinates #AGBT17
1:39pm February 15th 2017 via Hootsuite
Beechem: Concludes with a description of their newest system, the Digital Spatial Profiler (in Tech-Access) #AGBT17
Showing live sequencing at #agbt17 of Hyb & Seq. New blog post: https://t.co/buNCoKLIVB #AGBT17 https://t.co/Bj9iCbf5wK
1:36pm February 15th 2017 via Hootsuite
Parker: #AGBT17 (For details on PREVAIL this from Medivation https://t.co/0TT1bt675A ) PAM 50 captures heterogeneity of BC gene exp
1:29pm February 15th 2017 via Hootsuite
Parker: Looking at basal vs luminal activity in TNBC - PFS doubling that are PREDICT AR+, 5x to recurrance (9w to 40w) #AGBT17
1:26pm February 15th 2017 via Hootsuite
Parker: Working with NanoString's PAM50 classifier, looking at Enzalutamide w/TNBC patients. Did some Monte Carlo and other modeling #AGBT17
1:24pm February 15th 2017 via Hootsuite
New Post: NanoString’s Hyb & Seq single-molecule sequencing platform at #AGBT17 - Next Generation Technologist https://t.co/buNCoKLIVB
1:22pm February 15th 2017 via Hootsuite
Parker: Working with Medivation, Enzalutamide is an inhibitor of AR signaling. #AGBT17
1:16pm February 15th 2017 via Hootsuite
Joel Parker (Univ NC CH) NGS for biomarker discovery and companion Dx development #AGBT17
1:15pm February 15th 2017 via Hootsuite
@coregenomics loading the @nanostringtech instrument at #agbt17 https://t.co/wPV3NnZyOl
1:14pm February 15th 2017 via Hootsuite
Nusbaum: Detection of modified bases - 5-meC, 5-OHmeC, 5-formylcyltosine, 8-oxoguanine. RNA - shows 5 variants at 1% #AGBT17
1:10pm February 15th 2017 via Hootsuite
Nusbaum: 2-3d test by blood culture; need very fast readout, within an hour. #AGBT17
1:09pm February 15th 2017 via Hootsuite
Nusbaum: Speed - often days to get answers, fine. Shows fig from '06 https://t.co/gxQW18lddE surv fx by hour #AGBT17
1:06pm February 15th 2017 via Hootsuite
Nusbaum: Asking for 1 in a million error rate, at a cost of $1,000/sample. Bonus is great reduction in data storage #AGBT17
1:04pm February 15th 2017 via Hootsuite
Nusbaum: Tumor fraction in cfDNA WGS in met cancer: Of 391 pts, 167 from 0.8% to 0.1%; 118 0.1%. Long tail of undetectable #AGBT17
1:03pm February 15th 2017 via Hootsuite
Nusbaum: Why impt? Often you only get one shot - NIPT, cancer ctDNA, monitoring. T21 could be detected in 1955 by cytology. #AGBT17
1:01pm February 15th 2017 via Hootsuite
Nusbaum: Next Accuracy. 'Now this drives me nuts.' 0.5% to 1% since '10. Hasn't progressed at all, oversampling sets a floor on sens #AGBT17
1:00pm February 15th 2017 via Hootsuite
Nusbaum: "I want SVs at the same cost as SNVs, or a small premium." #AGBT17
Nusbaum: Missing data problem - lots of cheap short reads, losing lots of larger variation. Wants structural variation the same way #AGBT17
12:59pm February 15th 2017 via Hootsuite
Nusbaum: Max read length of 150bp, cheap but short. SV's from this '15 TGP paper https://t.co/W3T8jTToyh Need 50kb-500kb cheap #AGBT17
12:58pm February 15th 2017 via Hootsuite
Nusbaum: From $0.10 (to $0.001), for single-cell sequencing. Cheap reads are short - about 150bp. SV graph https://t.co/SaNJBZ3kH1 #AGBT17
12:56pm February 15th 2017 via Hootsuite
Nusbaum: 10K cells? Impractical limits of cost. Asking for a '3-log reduction in the next 10 years'. Sample prep $0.10 for scells #AGBT17
12:54pm February 15th 2017 via Hootsuite
Nusbaum: The cost equation - perhaps hitting a bit of a floor, but it is log-scale. Cost - brain has 10^12 cells; immune is 10^10 #AGBT17
12:53pm February 15th 2017 via Hootsuite
