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
Korlach: Human de novo assemblies - from HuRef and six others - 3.25Gb total assy size for PacBio (since the N50's are ~4.5k) #AGBT14
2:43pm February 14th 2014 via Hootsuite
Korlach: 2d ago released 54x long-read coverage de novo PacBio assembly Press Release: http://t.co/n27XN2Tt3e #AGBT14
2:42pm February 14th 2014 via Hootsuite
Next up: Pacific Biosciences, Jonas Korlach: No Assembly Required: Extremely Long Reads for Full-length Transcript Isoform Seq #AGBT14
2:40pm February 14th 2014 via Hootsuite
Ohgami: Looked at mut type against AML subtype (of 4); survival and U2AF1 mutation; retrospective samples several mis-classified #AGBT14
2:37pm February 14th 2014 via Hootsuite
Ohgami: 77 AML samples, went through HaloPlex Molecular Inversion Probe method, sequenced on MiSeq and used SureCall s/w #AGBT14
2:34pm February 14th 2014 via Hootsuite
Ohgami: A well-defined genomic world for myeloid neoplasms (genes and pathways). Chose ~20 genes + 2000x coverage + HaloPlex #AGBT14
2:33pm February 14th 2014 via Hootsuite
Ohgami: But for hematologic neoplasms: classification involves many factors; now molecular data is much more prominent #AGBT14
2:31pm February 14th 2014 via Hootsuite
Ohgami: 'Targeted NGS of AML in Clinical Research'. Speakers background is pathology. Majority of cancers are carcinomas. #AGBT14
2:29pm February 14th 2014 via Hootsuite
Yi: SureCall software, free of charge, both HaloPlex and SureSelect, both exomes and custom. http://t.co/ARMXmwEqSM #AGBT14
2:26pm February 14th 2014 via Hootsuite
Yi: Transposase-based, 90min hyb. "<7h, 30m hands-on time, no fragmentation equipment req'd Better performance than 'competitor I' #AGBT1
2:24pm February 14th 2014 via Hootsuite
Yi: Preview of a new product: SureSelect^QXT - sample-to-seq in 1 day; 3x faster and 50ng input. Exomes & custom #AGBT14
2:23pm February 14th 2014 via Hootsuite
Up next: Yong Yi (Agilent Technologies) and Bob Ohgami (Stanford) New Agilent NGS Products – Advances in NGS Clinical Research #AGBT14
2:21pm February 14th 2014 via Hootsuite
Bready: Q: (Grills) Throughput? A: Data is immediate, 8 indep. on-deck; typically about 1h/sample #AGBT14
2:19pm February 14th 2014 via Hootsuite
Bready: Q: Any work with PacBio users (for long molecule sample prep)? A: Yes, but can't comment. #AGBT14
Bready: Q: Presumably not working on FFPE? A: Primarily focused on long molecules. Liquid tumors, not focus now. #AGBT14
2:18pm February 14th 2014 via Hootsuite
Bready:Looking at a cytogenetic application (FISH, karyotyping, aCGH): dense chart shows (?) much better resolution #AGBT14
2:16pm February 14th 2014 via Hootsuite
