Wang: PGM Avalanche 500bp seq: 'heavy chain antibody-ome'. Looking for HIV-1 neutralizing Ab #ionworld2013
5:39pm October 21st 2013 via Hootsuite
Wang: Immune repertoire sequencing: H chain locus 1250kb on chr 14, presented chart of V / D / J 10^10 poss. B-cells #ionworld2013
5:37pm October 21st 2013 via Hootsuite
Wang: Exome coverage of 100x can be obtained in 1 run, fine for monogenic disorders. #ionworld2013
5:36pm October 21st 2013 via Hootsuite
Wang: SNV concordance cross-platform very similar. Indels highly discordant though. Unk. which is truth. #ionworld2013
5:35pm October 21st 2013 via Hootsuite
Wang: Exomes comparing HiSeq to Proton: with the same amt of data, 72x vs. 84x coverage #ionworld2013
5:34pm October 21st 2013 via Hootsuite
Wang: Glioblastoma (GBM) looking at intratumor hetergeneity, RNA-Seq first, very consistent metrics, up/down reg. genes #ionworld2013
5:32pm October 21st 2013 via Hootsuite
Wang: Corrrelate RNA-Seq on Proton to qPCR, Proton to HiSeq 'very good'. Also technical replicates r2=0.997 #ionworld2013
5:30pm October 21st 2013 via Hootsuite
Wang: 41 runs in Sept, 92% of their runs >70M reads/run. #ionworld2013
Wang: First application: RNA-Seq; the workflow is 3d 'quite amazing actually'. '~14G per run!' 144bp RL #ionworld2013
5:29pm October 21st 2013 via Hootsuite
Wang: Protons to be installed:2 Shenzhen, 31 China, 5 US, 1 Europe. #ionworld2013
5:27pm October 21st 2013 via Hootsuite
Wang: "We pursue faster, cheaper and better sequencing technologies"; clinical priority: time and accuracy, then cost. #ionworld2013
5:26pm October 21st 2013 via Hootsuite
Wang: "Biology has become information" #ionworld2013
5:24pm October 21st 2013 via Hootsuite
Up next: Jun Wang from BGI on 'Solutions from benchside to bedside' #ionworld2013
5:23pm October 21st 2013 via Hootsuite
Milan Radovich presenting at Ion World, they have a Facebook page #ionworld2013 http://t.co/M2tJh9OyAK
5:22pm October 21st 2013 via Hootsuite
Radovich: MSK database - observed the same gene to validate their results #ionworld2013
5:20pm October 21st 2013 via Hootsuite
Radovich: Ion Reporter 4.0 - SNPs, indels, as well as CNV. Tested pipeline with exome-seq, SYBU gene had a 4x in tumor vs norm #ionworld2013
Radovich: Figure using FFPE RNA, 1000ng vs. 50ng, R=0.92 and the Ambion kit. #ionworld2013
5:19pm October 21st 2013 via Hootsuite
Radovich: Multi-sites, samples 'you get what you get'. You have to work with what you get. Ion Proton - low input FFPE #ionworld2013
5:18pm October 21st 2013 via Hootsuite
Radovich: Correlative science: looking at resistance after neo-adjuvant chemo; looking at cir tumor DNA, also PGx #ionworld2013
5:17pm October 21st 2013 via Hootsuite
Radovich: PARP inhibitor clinical trial: looking at pts with sig residual disease; looking at RNA-Seq, exome-seq, plasma-seq #ionworld2013
5:16pm October 21st 2013 via Hootsuite
Radovich: PI3K / Wnt inhibitor at low nanomolar combination effect. Then RNA-Seq pre- and post-treatment. 'Whack-a-mole' #ionworld2013
5:13pm October 21st 2013 via Hootsuite
Radovich: Using RNA-Seq to look for candidates to target; genes involved with epithelial dev. - Wnt pathway gene ID'd #ionworld2013
5:12pm October 21st 2013 via Hootsuite
Radovich: TN BrCa - review of EGFR, c-KIT and PARP overexp., microarray, RNA-Seq, clinical trial outcome of treatments. #ionworld2013
5:10pm October 21st 2013 via Hootsuite
Radovich: The comparison were breast tissue reductions, mainly adipose tissue. Tumor vs. tumor comparisons have difficulties #ionworld2013
5:08pm October 21st 2013 via Hootsuite
Radovich: Showing a PCA plot of normal from TN Ca samples (manuscript in press). Prior studies using microarrays however... #ionworld2013
5:07pm October 21st 2013 via Hootsuite
Radovich: Does laser-capture microdissection (LCM) of the normal ductal tissue. They detail via RNA-seq what normal is #ionworld2013
5:06pm October 21st 2013 via Hootsuite
Radovich: Doing a normal control, using a Komen tissue bank (women who donate a normal 16 gauge needle biopsy for this effort) #ionworld2013
5:05pm October 21st 2013 via Hootsuite
Radovich: 15% of BrCa are Her2+; 15% triple negative; neg ER/PR/HER2. No targeted therapy; figure from Dent 2007 #ionworld2013
5:04pm October 21st 2013 via Hootsuite
Radovich: From the midwest, he named his Protons after the 1985 Chicago Bears. Ditka etc. (etc. etc.) #ionworld2013
5:02pm October 21st 2013 via Hootsuite
Radovich: Majority of their studies are in triple-negative breast cancer; clinical question, to seq, to bioinf. then clinic #ionworld2013
5:01pm October 21st 2013 via Hootsuite
Radovich: Brings up TCGA and leverages that dataset. DNA mutations, RNA dysregulation. 30y cancer treatmt 'largely unchanged' #ionworld2013
4:59pm October 21st 2013 via Hootsuite
Radovich: Figure from MR Stratton in Nature 2009 #ionworld2013 PubMed http://t.co/QWmk2UkE7Z
4:57pm October 21st 2013 via Hootsuite
Next speaker is Milan Radovich, 'next-gen RNA-Seq and Exome-Seq ... for translational oncology research'. #ionworld2013
4:55pm October 21st 2013 via Hootsuite
Photo of Richard Allcock speaking #ionworld2013 http://t.co/YWtAmz0dpF
4:54pm October 21st 2013 via Hootsuite
Allcock: "The sequencing is helping define diagnosis. And this is really powerful." #ionworld2013
4:52pm October 21st 2013 via Hootsuite
Allcock: 'Amplification SHOULD be much more 'controllable'' and look forward to subsequent iterations of AmpliSeq #ionworld2013
Allcock: AmpliSeq more sensitive to GC-rich compared to TargetSeq (hyb-based). (Room for improvement.) #ionworld2013
4:51pm October 21st 2013 via Hootsuite
Allcock: Mean depth is very different hyb vs AmpliSeq - due to the on-target numbers. 75% vs 95% at 20x, similar seq capacity #ionworld2013
4:50pm October 21st 2013 via Hootsuite
Allcock: AmpliSeq exome - 8am to analyzed data by midnight of day 2. Consistent loading of 80M reads. #ionworld2013
4:48pm October 21st 2013 via Hootsuite
Allcock: Capture-based enrichment (hybridization) - large input req (1.5ug); probes that run outside exons; hyb takes too long #ionworld2013
4:47pm October 21st 2013 via Hootsuite
Allcock: Titan a challenging gene due to its repetitive nature, will become a focus for them. #ionworld2013
4:44pm October 21st 2013 via Hootsuite
Allcock: A Titan mutation called as missense, turned out it was a splicing variant, reported previously. #ionworld2013
Allcock: Multi Minicor disease, recessive mutation in RYR1 gene, 1350 variants then reviewing his filtering. Found Titan muts #ionworld2013
4:43pm October 21st 2013 via Hootsuite
Allcock: Have taken 336 genes covering multiple diseases, targeting 1.9Mb Neuromuscular disease, also neg's from other group #ionworld2013
4:36pm October 21st 2013 via Hootsuite
Allcock: At least 10Gb per Proton PI chip, 56 runs. #ionworld2013
4:32pm October 21st 2013 via Hootsuite
Allcock: Doing metagenomics work, 2 PGMs with 400bp, viral metagenomes 200bp, Protons doing Alpaca RADseq, exomes on SOLiDs #ionworld2013
4:31pm October 21st 2013 via Hootsuite
Next up: Richard Allcock, Royal Perth Hospital Univ. Western Australia Perth #ionworld2013
4:29pm October 21st 2013 via Hootsuite
Photo of Patrice Milos presenting on behalf of Claritas. #ionworld2013 http://t.co/2d8je3GUuo
4:28pm October 21st 2013 via Hootsuite
Milos: 230K samples already collected; biobank in Boston up and running; >18K exomes scheduled this year. #ionworld2013
4:27pm October 21st 2013 via Hootsuite
Milos: Million Veteran Program announcement this AM: goal is 1M veterans in 5y, the largest genomic project in the US #ionworld2013
