MT @LifeTech: Top 5 at #ASHG2013 1 @drbachansky 2 @DaleYuzuki 3 @girlscientist 4 @cureffi 5 @B_ologist Who will be on top at #ASHG14 ?
2:05pm October 16th 2014 via Hootsuite
RT @PolygenicPaths: Scientists find 18 new #viruses on NYC #rats - Futurity http://t.co/REDUkb341x
1:05pm October 16th 2014 via Hootsuite
.@NikiBarrPhD You're welcome - and I recommend you try the Authy app too. http://t.co/aUrmmOJg7M
12:52pm October 16th 2014 via Hootsuite in reply to
It's Time to Enable Two-Step Authentication on Everything. Here’s How. - Gizmodo http://t.co/pNixWvuQsb
12:02pm October 16th 2014 via Hootsuite
Affy signs deal with Ariosa to supply array-based NIP | Arrays | GenomeWeb http://t.co/htbJRdKdFQ
11:26am October 16th 2014 via Hootsuite
CM:A2:The challenge is bioinformatics space, 'it needs to be cleaned up'. #gensoltour Finished!
10:54am October 16th 2014 via Twitter Web Client
CM:Q:Use of NGS for forensics? A:It will be used for many, many applications, incl. infectious disease as it's fast #gensoltour
CM: Also identical twin astronaut study, DNA muts, RNA exp, methylation, microbiome, cytokines, etc. etc. ISS one year vs. twin #gensoltour
CM: Mapping the microbes in the subway system by location. eXtreme Microbiome data as well. Space Station microbes #gensoltour
CM: @nycpathomap Can we do real-time tracking of pathogens? Swabs of many places - from NY Mag Nov 2013 article #gensoltour
CM: 'Are you concerned that we might run out of things to sequence?' http://t.co/nPgfzjhp9O #gensoltour
CM: Getting involved? Genome in a Bottle (http://t.co/t9s5wLIKUC), Global Alliance for Genomics and Health #gensoltour
10:53am October 16th 2014 via Twitter Web Client
CM: Next step is for DNA sequencing - library protocols, aligners, enrichment methods for Phase II #gensoltour
CM: Summary: website is http://t.co/TVl4YNTPsT #gensoltour
CM: But see 100's or 1000's. Tools (PEER, SVA) suppress false pos. DEGs. Four areas of variation: biggest source is technician #gensoltour
CM: Large-scale studies (GTex, ENCODE...) DEGs between same sample across sites 'shoudl be zero, a perfect neg control' #gensoltour
CM: 3' shift on degraded RNAs. Purposefully degrading RNA, w/heat, RNAse, sonication. Got high correlation w/intact RNA #gensoltour
CM: DEGs consistent; PolyA and ribo- are comparable #gensoltour
CM: PolyA vs ribo-depleted: ribo-depleted shows more lincRNAs and snoRNAs. PolyA favors high expressors #gensoltour
10:52am October 16th 2014 via Twitter Web Client
CM: Inter-platform diff gene exp. shows 88-97% agreement. Showed a proportional Venn too. (interesting representation) #gensoltour
CM: Rare isoforms: a function of sequence depth. "not surprising" #gensoltour
CM: Coverage across bins, showing evenness; mRNA 5'-3'; fairly comparable. Proton efficient for junctions #gensoltour
CM: Made a table comparing platforms. 'Error models highly variable among platforms and aligners' Informatics a source of noise #gensoltour
CM: Reviewed quickly their QC metrics, read alignments, their publication (PubMed) http://t.co/4vK0qXOtUk #gensoltour
CM: ABRF did RNA-Seq in '12-'14; DNA-Seq '14-'16. Same samples (UHRR and HBRR) SeQC - laid out sites, platforms, replicates #gensoltour
CM: Nature Biotech piece in '08: MAQC but this time for NGS. SeQC started in '08, no longer 454 or Helicos #gensoltour
10:51am October 16th 2014 via Twitter Web Client
CM: Lays out >12 sources of technical noise... which types of known types of RNA... which platform... #gensoltour
CM: What you can look at via sequencing... fusions, ncRNAs, differential genes, splicing. But noise, wiggles? #gensoltour
CM: Studying splicing: refers to recent review here: http://t.co/tjLG9dHFSC #gensoltour
CM: (on Twitter at @mason_lab ) ENCODE review, Dan Gaur's critique, coding genes is 19,881, non-coding is 25,411. 60,155 'total' #gensoltour
Christopher Mason (Weill Cornell) "Multi-platform assessment of transcriptome profiling using RNA-Seq in the ABRF NGS study" #gensoltour
JB:Q:Hybrid genome? A:HPV is an add'l chromosome; split-read alignments come later to determine integration sites #gensoltour
JB:Presented at an IPV 2014 (In't Papilloma Virus) meeting. Using a 165-SNP ancestry panel, developing integration panels #gensoltour
10:50am October 16th 2014 via Twitter Web Client
JB: Genome completion rate of Ion NGS compared to Sanger noticeably higher. #gensoltour
JB: 35 cases of HPV16 co-infections discovered. Compared 10% of pilot group (89 samples), >99% concordance #gensoltour
JB: Of 660, 23 had high quality sequence with large deletions (evidence of integration) Discovered 81 novel variants #gensoltour
10:49am October 16th 2014 via Twitter Web Client
JB: Able to get 98% of the genome (44/47 amplicons cover well). From 824 samples: 660 high, 63 medium, 78 poor quality #gensoltour
JB: 384 samples/4d throughput. Alignment uses hg19-HPV hybrid reference (HPV integrates) #gensoltour
JB: Project started on Fluidigm AccessArray + 454; about 70% coverage, expensive. Moved to Ion AmpliSeq, 47 amplicons #gensoltour
JB: PaP: 100K samples, HPV Persistence and Progression cohort. #gensoltour
JB: HPV causes 99% of cervical cancer; 53% of initial samples HPV16. Goal: look at viral genetics tied to cervical ca risk #gensoltour
10:48am October 16th 2014 via Twitter Web Client
JB: Main res. area is cervical cancer: 400k new cases/y, 275k deaths WW. PAP smears not available in much of the world #gensoltour
Circulating, Cell-free Tumor DNA Detection with Ion PGM Sequencing - Read at Behind the Bench: http://t.co/smtQAdKu8x
JB: Describes the CGRL at NCI: staff of 50, est. '01, 6 PGMs + 4 Protons; 100 custom panels (familial cancer research) #gensoltour
Next: Joe Boland (NCI) "High-depth HPV16 WGS of 830 PaP cohort specimens using crude exfoliated cervical extracts" #gensoltour
The New York Genetic Solutions Tour Selfie! #gensoltour http://t.co/E7ptZ4P9uD
10:47am October 16th 2014 via Twitter Web Client
NT:Q:Unbalanced translocations? A:Can be done with larger targeted panels. Can use genotypes & phasing, with add'l technologies #gensolt
NT: Techniques for measuring mosaicism are limited; what is biological variation vs. technical variation (can't tell apart) #gensoltour
ML: Got 99.7% chromosome concordance, across >1800 samples. Mentioned limitation of mosaicism from the sample. #gensoltour
10:46am October 16th 2014 via Twitter Web Client
ML:Q:HiQ part of AmpliSeq panel now? Old enzyme? A:Retained for another 12 mos., available now #gensoltour
