Witte: Manhattan plot of GWAS 'surprising': many pass significance (220 zeros before P-value); dozens of SNPs in blue unreported #TCGC15
12:26pm June 23rd 2015 via Hootsuite
Witte: Kaiser Permanente (Calif.) has GERA resource (Risch just published: http://t.co/LxqzKIZFtY ) 43K men, 7.6K w/PSA #TCGC15
12:22pm June 23rd 2015 via Hootsuite
Witte: Why not genetics for PSA screening? Genetics influences PrCa (prostate cancer). Genetics affecting PSA indep of PrCa is noise #TCGC15
12:20pm June 23rd 2015 via Hootsuite
Witte: AUA - counters PSA <40 no, 40-54 no if ave risk, maybe if +family history, or African American, 55-69 maybe, >70 no #TCGC15
12:19pm June 23rd 2015 via Hootsuite
Witte: Germline: can improve screening. PSA controversial, reflecting USPSTF graded as 'D' - harms of screening outweigh benefit #TCGC15
12:18pm June 23rd 2015 via Hootsuite
John Witte (UCSF) "Leveraging germline genomics to improve an individuals health" Asks audience how many men have had PSA test #TCGC15
12:16pm June 23rd 2015 via Hootsuite
Vasmatzis: (Title incorrect -"ID of indep primary tumors and intrapulmonary metastases using rearrangements in NSCLC") #TCGC15
12:15pm June 23rd 2015 via Hootsuite
Vasmatzis:Q:WGA using repli-g; what abt chimeras? A:2012 Murphy ref may have answer to that PubMed http://t.co/qudV2WBt1f #TCGC15
12:13pm June 23rd 2015 via Hootsuite
Vasmatzis: In summary - inexpensive, robust test using mate-pairs. Can be more specific than pathology. Can be done on FNA #TCGC15
12:09pm June 23rd 2015 via Hootsuite
Vasmatzis: Extrapulmonary mets: shows breakpoint analysis clearly shows lineage or independent primary cancers. #TCGC15
12:07pm June 23rd 2015 via Hootsuite
Vasmatzis: Breakpoints show (expected) heterogeneity of cancer within and between pts. Adjacent lesions: AD invasive vs AD lepic #TCGC15
12:04pm June 23rd 2015 via Hootsuite
Vasmatzis: Validating (via breakpoint PCR) 95% of what they find now. Shows busy signature table of genes, breakpts, commonality #TCGC15
12:00pm June 23rd 2015 via Hootsuite
Vasmatzis:Have done 1.3K, germ line events 10-40 per genome. Example: #TCGC15 TP63 paper: http://t.co/FZjKhxDJXf
11:57am June 23rd 2015 via Hootsuite
Vasmatzis:They do in situ WGA (!), and go to mate-pair protocol to look at breakpoints. 5Kb inserts. #TCGC15 Aligner: http://t.co/gLbu8Q21id
11:55am June 23rd 2015 via Hootsuite
Vasmatzis: Collected panel of domain experts; LCM separating AD component from Lepidic component. 200-300 cells apiece #TCGC15
11:53am June 23rd 2015 via Hootsuite
Vasmatzis: Shares complex example of chromoplexis, v. messy. Another w/fusion. Chr 21 dels - can vary betw. individs #TCGC15
11:51am June 23rd 2015 via Hootsuite
Vasmatzis: Linear graph uses colors for indels, SNVs, rearr's. Breakpoints via bold line. 2nd example of large del #TCGC15
11:49am June 23rd 2015 via Hootsuite
Vasmatzis: AmpliSeq RNA looking for ALK rearr - not the same as EGFR. Showed a linear genome plot: T/N pair, 30kb windows #TCGC15
11:48am June 23rd 2015 via Hootsuite
Vasmatzis: WGS $5K, 'lots of data, noise'; 'not very practical at the moment'. SNV/Indels $1K, rearr/CNV $500, fusions/exp $500 #TCGC15
11:47am June 23rd 2015 via Hootsuite
Vasmatzis: Pt presents w/multiple lung tumors - could be related, or not related molecularly. NGS - what scheme to use? #TCGC15
11:45am June 23rd 2015 via Hootsuite
George Vasmatzis (Mayo Clinic) "Leveraging germline genomics to improve an individual's health" #TCGC15
11:44am June 23rd 2015 via Hootsuite
Griffith:A2: Resources to maintain? Mycancergenome went with Genomeoncology; ultimately driven by community that engages with it #TCGC15
11:40am June 23rd 2015 via Hootsuite
Griffith: @gabeinformatics commends the effort. Q:How to release under CC? A:All info in CIViC are from public sources. #TCGC15
11:38am June 23rd 2015 via Hootsuite
Griffith:Q:What about clin trials like NCI-MATCH? A: 'Clin trial data models have not evolved for genomics'; data structure probs #TCGC15
11:37am June 23rd 2015 via Hootsuite
Griffith: CIViC freely available, open source, open access, client-server model. Now called the McDonnell Genome Inst at WashU #TCGC15
11:34am June 23rd 2015 via Hootsuite
Griffith: CIViC is not: storing VUS. Interesting != clinically relevant. Unpublished n=1 anecdotes. For anything non-cancer. #TCGC15
11:30am June 23rd 2015 via Hootsuite
Griffith: Also commercial solutions, other private (pharma) db's. Reviews requirements for their data model and goals for CIViC #TCGC15
11:27am June 23rd 2015 via Hootsuite
Griffith: Know of a dozen cancer hospitals all building their own db's. All doing this, repeating everyone else's effort, silo'd #TCGC15
11:20am June 23rd 2015 via Hootsuite
Griffith: Closest- http://t.co/BFEZ1qYxUg and MD Anderson PCT http://t.co/4rWLFOJnlb also ClinVar and Gene Drug Knowledge db #TCGC15
11:19am June 23rd 2015 via Hootsuite
Griffith: DoCM requires published relevance: both clinical and functional evidence. Gap in clinical interpretations #TCGC15
11:18am June 23rd 2015 via Hootsuite
Griffith: DoCM moves beyond gene level - has API for interoperability. Muts relevant to ca 751 vars from 74 genes and 69 ca types #TCGC15
11:17am June 23rd 2015 via Hootsuite
Griffith: DGIdb allows known drug-gene interactions to query V2 to be complete in Aug, 22 sources data, 37K interactions, 9.1K drugs #TCGC15
11:15am June 23rd 2015 via Hootsuite
Griffith: DGIdb, DoCM, CIViC: Drug-gene interaction http://t.co/pQMhrDf4jv, db of Curated Muts http://t.co/8F8sZeDXIL, CIViC #TCGC15
11:14am June 23rd 2015 via Hootsuite
Griffith: CIViCs is for comprehensive interpretation. Shows Found. Med. sample rpt. 'clin significance of var's a non-trivial task' #TCGC15
11:12am June 23rd 2015 via Hootsuite
Griffith: CNV, SV, SNVs, Indels, GEx, pipeline here http://t.co/kAPNMhpyPv upcoming publication in PLOS Bio #TCGC15 http://t.co/lL0J6ZUwHq
11:10am June 23rd 2015 via Hootsuite
Griffith:Tech dev - if $ (and time) were no object, what could clinical cancer genomics look like? #TCGC15
11:08am June 23rd 2015 via Hootsuite
Griffith: Is part of genomics tumor board, exome and panels; diverse clinical goals. Also: clinical tech dev - cases explored deeply #TCGC15
11:07am June 23rd 2015 via Hootsuite
Griffith: Omics map of sequencing capacity http://t.co/KWrR2Yar3Q Now have an X10, sequencing tumors at scale. #TCGC15
11:06am June 23rd 2015 via Hootsuite
Malachi Griffith (WashU) CIViC - Clinical intepretation of variants in cancer #TCGC15 http://t.co/TFRIgOIEid @malachigriffith
11:04am June 23rd 2015 via Hootsuite
RT @bjornkuiper: These hackers warned the Internet would become a security disaster. Nobody listened. | WaPo http://t.co/uuBu3fk5Js
10:40am June 23rd 2015 via Hootsuite
RT @genome_gov: Bone up on cloning facts before heading to see the new Jurassic World movie! http://t.co/QKNd9VO8BJ http://t.co/FJGrcPEuXG
9:40am June 23rd 2015 via Hootsuite
RT @bengoldacre: In almost every industry sponsored head-to-head trial, the sponsor co. gets the answer they want. http://t.co/jAJOWLddKP
8:25am June 23rd 2015 via Hootsuite in reply to bengoldacre
RT @theNCI: The rate of new cases for all U.S. cancers combined continued to fall from '02-'11 http://t.co/RkMynubxFe http://t.co/A4eYT7Ggo2
7:50am June 23rd 2015 via Hootsuite
.@AllSeq @BarbourAnalytix At #AGBT15 both speakers who used ONT did not make any public comments about accuracy, so any word was off-record
7:48am June 23rd 2015 via Hootsuite in reply to AllSeq
Sequencing Ebola in the field: a tale of nanopores, mosquitos and whatsapp http://t.co/wZMZ9vkSjO
6:45am June 23rd 2015 via Hootsuite
RT @AACR: Exploring the next generation of anti-#EGFR therapies: http://t.co/sqZSuRHdbQ #EAS2015 http://t.co/HlxN0ysR9j
5:15am June 23rd 2015 via Hootsuite
Technophrenia: What are we afraid of, really? — Bad Words — Medium http://t.co/KvUAapkBmy
4:30am June 23rd 2015 via Hootsuite
.@MolecPath Sure - it was arthritis caused by the overly high amounts of Fe in blood. Rx was regular blood donations.
10:18pm June 22nd 2015 via Hootsuite in reply to MolecPath
The Hunt for the Financial Industry's Most-Wanted Hacker - Bloomberg Business http://t.co/lJQOJoxj7u #longread
9:05pm June 22nd 2015 via Hootsuite
Hold on to Your Seats: NASA Breathes New Life Into Supersonic Flight - GE Reports http://t.co/yBO6ddkIwP
8:55pm June 22nd 2015 via Hootsuite
