Nordland: Concern about overtreatment, given 95% OS rate. Interested in DNA methylation; looked at 756pts in '13 on 450K array #AGBT17
8:35pm February 15th 2017 via Hootsuite
Nordland: 200 cases/year. Transloc's are the core of subtype Dx. Non-random rearr; corr betw. cytogenetics, outcome #AGBT17
8:33pm February 15th 2017 via Hootsuite
Nordland: Ped ALL most common pediatric malignancy; immature B- or T-cells, 2-5y of age onset. Nordic society: OS >90% #AGBT17
8:32pm February 15th 2017 via Hootsuite
Jessica Nordland (Uppsala Univ): Dissection of the heterogeneous fusion gene landscape in pediatric acute lymphoblastic leukemia #AGBT17
8:31pm February 15th 2017 via Hootsuite
Perera: Also combined with metabolyte analysis of urine; set of lncRNA, mRNAs and metabolites enriched in PCa urine. GOT1 impt cmpd #AGBT17
8:29pm February 15th 2017 via Hootsuite
Perera: Collaborating with @Genomics_Guy from Illumina, helped with pan-cancer enrichment for urine RNA #AGBT17
8:25pm February 15th 2017 via Hootsuite
Perera: Gives overview of prostate ca and insufficiency of both PSA tests, prevalence of prostate cancer, and need for biomarkers #AGBT17
8:23pm February 15th 2017 via Hootsuite
Ranjan Perera (Sanford Burnham FL) Systems level invest. of urine enriched RNA and metabolites for early prostate cancer detection #AGBT17
8:22pm February 15th 2017 via Hootsuite
Boland: Sample input was only 1.5ng which they needed; not that cost-effective for Amazon instance; 2.8d of compute/2 samples #AGBT17
8:03pm February 15th 2017 via Hootsuite
Boland: '15 ref about integration sites https://t.co/DcVFtQLBZq Approach to use 10X with hg19 plus HPV as reference. #AGBT17
8:00pm February 15th 2017 via Hootsuite
Boland: Integrated shows clearly interruption of E2 gene. Cancer w/HPV integration, 1 or 2 sites observed. Each site is unique #AGBT17
7:58pm February 15th 2017 via Hootsuite
Boland: Episomal vs integrated HPV: Replication in episomal, integrated loses E2 fn. Shows 10X Genomics data of IGV alignment to HPV #AGBT17
7:57pm February 15th 2017 via Hootsuite
Boland: HPV 150 related viruses; 8kb in size, E6/E7 known oncogenes. 14 types are >98% of HPV-rel cancers worldwide #AGBT17
7:56pm February 15th 2017 via Hootsuite
Joe Boland (NCI, MD) A novel WGS method to comprehensively map all HPV16 integration events across multiple human genomes #AGBT17
7:55pm February 15th 2017 via Hootsuite
#AGBT17 (For a blog post, I wrote up some notes about NanoString's Hyb & Seq at https://t.co/buNCoKLIVB )
7:53pm February 15th 2017 via Hootsuite
Beechem: Able to pull-down DNA and RNA simultaneously, and sequence in parallel, long reads (up to 33K) and phased reads #AGBT17
7:52pm February 15th 2017 via Hootsuite
Beechem:File format output will be FASTA; 2 independent assemblers under development. Hexamer spectrum, and 'short stack' #AGBT17
7:48pm February 15th 2017 via Hootsuite
Beechem: Thus high coverage / high accuracy regions can be determined by the composition of the 'deck' of probes #AGBT17
7:46pm February 15th 2017 via Hootsuite
Beechem: Coverage map - can 'control the deck'. Since it is targeted, you know where the actionable variants are. #AGBT17
7:45pm February 15th 2017 via Hootsuite
Beechem: Their 4096 probes - separate perfect hexamer complements; separate high Tm vs low Tm. #AGBT17
7:44pm February 15th 2017 via Hootsuite
Beechem: Hexamer sequence, designed to interact with target. Reporter domain (74bp) designed to interact with reporters R1/R2/R3 #AGBT17
7:43pm February 15th 2017 via Hootsuite
Beechem: Targeted, clinical-grade sequencing, depends upon 2 color reporter probe, total of 8 colors (pairs of colors) #AGBT17
7:42pm February 15th 2017 via Hootsuite
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
