Unger: A cell line data - showing subpopulation present as homozygotes across cells at specific het loci #AGBT14
4:55pm February 14th 2014 via Hootsuite
Unger: Clustering het alleles across 369 cells are variably distributed. Interesting - subpopulations of cells that are not het! #AGBT14
Unger: Targeted using AccessArray Oncogene panel, also map >95%. Reviewed different types of dropout, SNV and allelic dropout rates #AGBT
4:54pm February 14th 2014 via Hootsuite
Unger: #AWGS - coverage was ~75% at 10x; mapping >95%; l plot of fx of reads / fx of genome is 'as good as one can get' #AGBT14
4:52pm February 14th 2014 via Hootsuite
Unger: Using phi29 MDA WGA, implemented on the chip, export to WGS, WES, or targeted. Analyze via 'SINGuLAR' #AGBT14
4:50pm February 14th 2014 via Hootsuite
Unger: Highlight of Nature Methods 'method of the year' in 2013 #AGBT14
4:49pm February 14th 2014 via Hootsuite
Unger: 358 single cells, 16 cell groups, PCA: found groups by type. 200K reads/cell enough to get exact clustering as high-depth #AGBT14
4:48pm February 14th 2014 via Hootsuite
Unger: C1 information here http://t.co/2C8kLWCzHX Additive fluidics - capture, lyse, RT, pre-Amp #AGBT14
4:46pm February 14th 2014 via Hootsuite
Unger: Illustrates the average of a bimodal distribution. Bulk vs. individual variation: mutations may group / segregate differently #AGBT14
4:44pm February 14th 2014 via Hootsuite
.@notSoJunkDNA You are welcome. I grew up in Santa Monica, the beach is always there. Presentations have been uniformly GREAT.
4:43pm February 14th 2014 via Hootsuite in reply to
Next up: Fluidigm Corp., Marc Unger: New Insight in System Biology Through Single-Cell Sequencing #AGBT14
4:42pm February 14th 2014 via Hootsuite
Beecham: Able to monitor proteins from FNAs; can do 60 SNPs, 100 genes, several proteins on the same platform. #AGBT14
4:41pm February 14th 2014 via Hootsuite
Beecham: Publication shows protein detection with Ab. Down to single-cell. Science Trans Med reference http://t.co/mIUSjFWn4B #AGBT14
4:40pm February 14th 2014 via Hootsuite
Beecham: Detection of DNA fusions. "From research publication to LDT in <1y" #AGBT14
4:38pm February 14th 2014 via Hootsuite
Beecham: FFPE samples had low RIN numbers; didn't matter. Noise of 1-3%, upcoming publication #AGBT14
4:35pm February 14th 2014 via Hootsuite
Beecham: Named Prosignia, FFPE samples, 50 gene-based CodeSet, software output a pt report. 2634 samples in 2 clinical tests #AGBT14
4:34pm February 14th 2014 via Hootsuite
Beecham: WashU and Nanostring went to FDA for a PAM50 IVD for cancer, cleared 2012-13. Jan '14: now available to large testing org's #AGBT14
4:33pm February 14th 2014 via Hootsuite
Beecham: Can easily do 100 samples/day, looking at TCGA cancer driver pathway genes; Vogelstein's work.here http://t.co/5zsflHmzOj #AGBT14
4:31pm February 14th 2014 via Hootsuite
Beecham: Add reagents, incubate, purify via robot that also loads, then count. (Amplification free.) #AGBT14
4:25pm February 14th 2014 via Hootsuite
Beecham: Targeted RNA via Nanostring cp to RNA-seq: primers will locate, capture, and label all at once; optically barcoded #AGBT14
4:24pm February 14th 2014 via Hootsuite
Beecham: Single molecule, digital counting technology; sol'n phase 800-plex, 1M - 2M mapped 'aligned reads/lane' #AGBT14
4:22pm February 14th 2014 via Hootsuite
Beecham: Personal note from Joe - wanted to see discoveries to move downstream, thus the move from @LIFECorporation to Nanostring #AGBT14
4:21pm February 14th 2014 via Hootsuite
Up next: NanoString, Joe Beechem: A Proven Technology for the Rapid Translation of Genomic Discovery to a Clinically Validated Assay #AGBT14
4:20pm February 14th 2014 via Hootsuite
Descombes: Q:Metrics for platform choice? A: Largest choice of protocols, agnostic to reagents, price #AGBT14
4:19pm February 14th 2014 via Hootsuite
Descombes: Plan to automate: exome capture, PacBio large insert lib (50kb). Advice: "Move more, eat better, choose ancestors well" #AGBT14
4:18pm February 14th 2014 via Hootsuite
Descombes: Conclude: improved walk-away (they like Nestle coffee-breaks!) robust, pooling is accurate, post-PCR is ongoing #AGBT14
4:17pm February 14th 2014 via Hootsuite
Descombes: After increase of throughput, next problem was QC and pooling; working on full QC automation (quant + pooling) #AGBT14
4:14pm February 14th 2014 via Hootsuite
Descombes: r2 values on the order fo 0.99. Fold-change r2 was 0.98 between methods. Recapitulated the ~700 TaqMan correlations #AGBT14
4:12pm February 14th 2014 via Hootsuite
Descombes: Size shifted +40bp; Data quality very similar at 150bp; overlap was 98.3% between methods. #AGBT14
4:10pm February 14th 2014 via Hootsuite
Descombes: New protocol had on-bead A-tailing + ligation steps. Used MAQC samples, HBR and UHR RNA's to validate / test #AGBT14
4:09pm February 14th 2014 via Hootsuite
Descombes: Uses Sciclone for pre-amp steps; post-PCR on the Zephry and GX. Std protocol 2011 and mid-12 'GOLD standard' (improved) #AGBT14
4:08pm February 14th 2014 via Hootsuite
Descombes: Main liquid handling autom. is PE / Caliper and Hamilton. Focus on RNA-Seq lib prep, and QC / pooling #AGBT14
4:06pm February 14th 2014 via Hootsuite
Descombes: Tech used is Hi/MiSeq, PacBio, Affy and ILMN arrays, with automation. 30M reads/sample RNA-Seq #AGBT14
Descombes: Nestle - contribution of environment to genetics, translate to improve health. Brain, metabolic, aging, etc. #AGBT14
4:04pm February 14th 2014 via Hootsuite
Up next: PerkinElmer, Patrick Descombes, Nestle Institute: Tuning Library Generation With Sequencing Throughtput #AGBT14
4:03pm February 14th 2014 via Hootsuite
Korlach:Q: Capture to pull out rare transcripts? A: Yes it has been done. #AGBT14
3:01pm February 14th 2014 via Hootsuite
Korlach: Q: Human assy with GRCh38? A: Not yet, data out to enc. comparisons. Regions in 38 have used PacBio data (e.g. Mucin) #AGBT14
Korlach: Q: 1/1M detection? A: 30K - 60K reads/cell; okay for mid-abundant transcripts #AGBT14
2:59pm February 14th 2014 via Hootsuite
Korlach: Now able to link phage to bacteria by the methyltransferase activity on both virus and host (!) #AGBT14
2:58pm February 14th 2014 via Hootsuite
Korlach: Human gut Virome doing meta-epigenomics: different base modifications, a unique tool to look at bacteriophage infection #AGBT14
2:57pm February 14th 2014 via Hootsuite
Korlach: Able to resolve ~25 plasmids, also char. the methylome in that same mock sample #AGBT14
2:56pm February 14th 2014 via Hootsuite
Korlach: Looking at metagenomics using NIAID's HMP Mock Community B, able to assemble 20 fully finished genomes #AGBT14
2:55pm February 14th 2014 via Hootsuite
Korlach: Looks like the PAG 2014 presentation by Gordon is on the PacBio website http://t.co/NIqHnvzzPw #AGBT14
2:54pm February 14th 2014 via Hootsuite
Korlach: PAG presentation by Sean Gordon shows fungal transcriptome, there were 118 isoforms, not 6 with short-reads #AGBT14
2:53pm February 14th 2014 via Hootsuite
Korlach: Also mentions the ABRF NGS RNA-Seq study (still yet to be published), cross-platform limitations (bias) shown clearly #AGBT14
2:49pm February 14th 2014 via Hootsuite
Korlach: Now have Iso-Seq protocol for getting full-length cDNA, they have a pipeline for isoform generation #AGBT14
2:48pm February 14th 2014 via Hootsuite
Korlach: Illus. transcript diversity, limitation of methods; Nature Methods reference highlighted http://t.co/GoiaVF8jKc #AGBT14
2:47pm February 14th 2014 via Hootsuite
Korlach: Transcript isoform sequencing - M Snyder quoted as 'kind of crazy' to 'blow things up' and then put them together again #AGBT14
2:46pm February 14th 2014 via Hootsuite
Korlach: Illustration of haploid assemblies across 2013 - 1MB, 12MB, 120MB, 170MB, 1GB and 3.2GB (human) #AGBT14
2:45pm February 14th 2014 via Hootsuite
Korlach: Whole fosmid sequencing of Killer Cell Ig-Like Receptors (KIR), reads include the entire fosmid. #AGBT14
2:44pm February 14th 2014 via Hootsuite
