Reis-Filho: Other type of driver is tumor suppressor mutations - TCGA lollipop plot is even distribution (p53 in Br Ca) #AACR14
12:07pm April 5th 2014 via Hootsuite
Reis-Filho: One types of drivers: oncogenes (detected via hotspot or fusion genes via RNA-Seq); showed TCGA 'lollipop' freq plots #AACR14
Reis-Filho: Driver alteration defined: a net growth advantage, positively selected for in tumorigenesis #AACR14
12:05pm April 5th 2014 via Hootsuite
Reis-Filho: Showed Circos images - mutations he's never heard about, never described before, but may be of interest #AACR14
12:04pm April 5th 2014 via Hootsuite
Next up: Jorge Reis-Filho MSKCC: "Identification of driver versus passenger mutations " #AACR14
12:03pm April 5th 2014 via Hootsuite
Hatzis: "Treat", "SIMPLEX", "WEP" were three of the five samples of these integrated solutions #AACR14
12:01pm April 5th 2014 via Hootsuite
Hatzis: Other challenges: high bioinformatics barrier. But there are several integrated pipelines #AACR14
Hatzis: Challenges: NGS reads short: difficult to assemble / map; Bias; Ampl. bias (polymerase slippage in poly(A)); Errors #AACR14
12:00pm April 5th 2014 via Hootsuite
Hatzis: Also a figure to look at structural variant calling from Alkan 2011 PubMed: http://t.co/kpsuKFEG4U #AACR14
11:58am April 5th 2014 via Hootsuite
Hatzis: Showed briefly a chart of 8 different algorithms for var calling, from Nielsen et al (2011) PubMed http://t.co/btRciPyy8e #AACR14
11:56am April 5th 2014 via Hootsuite
Hatzis: A particular location may need a local assembly to solve alignment problems; outlined .BAM file format, getting to .VCF #AACR14
11:54am April 5th 2014 via Hootsuite
Hatzis: Illustrates the workflow overview for SNP calling pipeline from Altmann et al 2012 PubMed: http://t.co/VIEo7xUXyQ #AACR14
11:50am April 5th 2014 via Hootsuite
Hatzis: Best practice - GATK paper from the @BroadInstitute mentioned http://t.co/qdLMiVoq2Z
11:48am April 5th 2014 via Hootsuite
Hatzis: (DARPA's challenge was called 'all your shreds are belong to us') http://t.co/rnujGd8agT #AACR14
11:47am April 5th 2014 via Hootsuite
Hatzis: DARPA had a shredder puzzle challenge (10K pieces solved in 30d) in 2011 (fun with informatics) #AACR14
11:46am April 5th 2014 via Hootsuite
Hatzis: Analogy of the bioinformatics challenge - taking a journal, shredding it, and giving you the 'paper chads' #AACR14
11:45am April 5th 2014 via Hootsuite
Hatzis: 'Analyzing an exome... (is) like reading the Cliff Notes(TM) version of a classic book" #AACR14
Hatzis: A range of genomic tools for putative biomarker strategies: WGS, WES, PCR amplicon, RNA-Seq #AACR14
11:39am April 5th 2014 via Hootsuite
Hatzis: Moving from 'compound to trial' to 'biology to trial' paradigm shift #AACR14
11:38am April 5th 2014 via Hootsuite
Next up: C. Hatzis, Yale Cancer Center: "Bioinformatics analysis pipeline for exome sequencing data " #AACR14
11:37am April 5th 2014 via Hootsuite
Mardis: A (con't): Higher coverage for somatic (300x-500x) needed, higher bar for clinical research setting. #AACR14
Mardis:Q:Selection of QC metrics? A:Some common tools (@servingscience Qubit), also Agilent for up-front. Downstream: ave 100x #AACR14
11:36am April 5th 2014 via Hootsuite
Mardis:Q: Accuracy of fresh vs. FFPE? A: FFPE can be as good, but barrier to entry is higher for up-front QC. <200bp problematic #AACR14
11:35am April 5th 2014 via Hootsuite
Mardis: RNA / Protein data can provide orthogonal data, enh. precision; long read platforms may permit assembly, not alignment #AACR14
11:33am April 5th 2014 via Hootsuite
Mardis: "Will this ever get easier?" Mfrs providing highly tuned pipelines; cloud- or local pipelines; strengths/weaknesses char'd #AACR14
11:32am April 5th 2014 via Hootsuite
Mardis: FP: one strand, end of read, coverage insuff., pseuogene/paralog (mismapped), too high sensitivity of the caller #AACR14
11:31am April 5th 2014 via Hootsuite
Mardis: Illus. their somatic variant discovery pipeline. FP/FN: most FN's are due to lack of coverage. FP have many sources #AACR14
11:30am April 5th 2014 via Hootsuite
Mardis: Calling SNVs, illustrates the IGV (http://t.co/VfYNXpYo8h), they developed http://t.co/R0l6FJ0Nq3 #AACR14
11:29am April 5th 2014 via Hootsuite
Mardis: Illustrates repetitive elements where reads may map to multiple loc's: dupl. reads, local misalignments, recalc Qv scores #AACR14
11:27am April 5th 2014 via Hootsuite
Mardis: Data alignment is the important first step. Puzzle analogy using 'Bliss'-style graphic #AACR14
11:25am April 5th 2014 via Hootsuite
Mardis: Consensus on Ion: "Low subst. error rate, in/dels problematic, no PE reads" "Inexpensive and fast turnaround" "improv. SW" #AACR14
11:24am April 5th 2014 via Hootsuite
Mardis: Showing @iontorrent PGM & Proton, TP range, 400bp RL's on PGM, mentions Ion Chef, only single-reads #AACR14
11:23am April 5th 2014 via Hootsuite
Mardis: Also feeling that improving kits and SW pipeline #AACR14
Mardis: Illumina's offerings, consensus: "high accuracy, range of capacity & TP" "longer RL's on some platforms (MiSeq)" #AACR14
11:22am April 5th 2014 via Hootsuite
Mardis: Ion Torrent incorporation is label-free due to sequential addition of nucleotides #AACR14
11:21am April 5th 2014 via Hootsuite
Mardis: Lays out optical-based NGS: "the S/N will build up"; the limit to readlength. @iontorrent laid out via pH detection #AACR14
11:20am April 5th 2014 via Hootsuite
Mardis: Duplicate reads via PCR can over-represent a false positive, often when low-input, low-complexity sample #AACR14
11:18am April 5th 2014 via Hootsuite
Mardis: Multiplex PCR (@iontorrent AmpliSeq not mentioned), points out PCR-related problems ("jackpotting", FP artifacts, bias) #AACR14
11:16am April 5th 2014 via Hootsuite
Mardis: Reviewed hybrid capture and exome defined. 1.5% of the genome usually covered at 100x; also gene panels #AACR14
11:14am April 5th 2014 via Hootsuite
Mardis: "Digital" readout (as it began from single library molecule), dependent on mapping back to reference. #AACR14
11:12am April 5th 2014 via Hootsuite
Mardis: NGS linker ligation, amplification, coupled detection with incorporation, massively parallel throughput #AACR14
11:10am April 5th 2014 via Hootsuite
Educ Session: "Next Generation Sequencing: from Bench to Bedside". First at #AACR14: Elaine Mardis, WashU: "Next Generation Seq Platforms"
11:06am April 5th 2014 via Hootsuite
It’s great to be at #AACR14 this morning. Some 18K cancer research scientists expected. http://t.co/0SdYENykxf
10:23am April 5th 2014 via Hootsuite
RT @matthewherper: 7 other things successful people never say. hysterical. http://t.co/7p7G5Dd11D
9:20am April 5th 2014 via Hootsuite
RT @WSJpersonaltech: 3-D Printer Makers Get Reality Check http://t.co/9T8cNsLlDl
8:20am April 5th 2014 via Hootsuite
How Can I Help My Kids Develop Better Social Skills? - Lifehacker http://t.co/1xvThmifXM
7:20am April 5th 2014 via Hootsuite
Myth About Harvard Book Made of Human Skin Debunked - Boston Magazine http://t.co/0ZBg9hSUBJ
6:20am April 5th 2014 via Hootsuite
This Japanese animation music video is hard to describe but sure is a lot of fun - YouTube http://t.co/QqU72js3gN
5:20am April 5th 2014 via Hootsuite
▶ Unbelievable Rube Goldberg Machine version from OK Go - This Too Shall Pass - YouTube http://t.co/4hqkpiZxTR
3:20am April 5th 2014 via Hootsuite
See A Classic 'Painting' That's Actually A Spellbinding CGI Masterpiece | Co.Create http://t.co/pF91kjESJd
2:20am April 5th 2014 via Hootsuite
