Jackson: SafetyMAP showed risk of diff treatment arms, report convinced change of treatment. Safety + genomic info to primary pt #TCGC15
1:20pm June 23rd 2015 via Hootsuite
Jackson: Gave ex of woman w/br cancer and Foundation report. SafetyMAP recommended change of treatment, difficult to do in Germany #TCGC15
1:19pm June 23rd 2015 via Hootsuite
Jackson: Open trial info also provided; drug-drug interaction analysis also. Reviewed SafetyMAP info. #TCGC15
1:18pm June 23rd 2015 via Hootsuite
Jackson: Includes reimbursement, safety, approval status information about medication, germline predictors of toxicity #TCGC15
1:14pm June 23rd 2015 via Hootsuite
Jackson: Their system mimics what a physician would do. Report limited to 7pg; focus on top 3 treatment options #TCGC15
1:13pm June 23rd 2015 via Hootsuite
Jackson: Treatment, safety, outcome, insight, risk (all "-MAP") extract info and report out. TreatmentMAP illustrated #TCGC15
1:10pm June 23rd 2015 via Hootsuite
Jackson: Have text data-mining tech est in '08, >23M publications. Uses dictionaries and NLP, curated. Also n=1 studies captured #TCGC15
1:07pm June 23rd 2015 via Hootsuite
Jackson: Molecular Health produced an evidence-driven panel design of 613 genes. Has data warehouse, clin interpretation #TCGC15
1:05pm June 23rd 2015 via Hootsuite
Jackson: For CR ca: EGFR amplification but germline toxicity to Irinotecan. Lastly in lung, EGFR erlotinib but toxic to paclitaxel #TCGC15
1:03pm June 23rd 2015 via Hootsuite
Jackson: Dominant Dx strategy is tumor-spec info on cancer gene seq. Ex of germline mut predicting toxicity to Dabrafenib #TCGC15
1:02pm June 23rd 2015 via Hootsuite
Jackson: Showed drug-drug interaction at different levels - lots of drugs, targets, metabolizing enzymes, then adverse events #TCGC15
1:00pm June 23rd 2015 via Hootsuite
Jackson: Pt extrinsic mechanism: co-medications. Showed distribution of # of drugs/Pt - between 4 and 5 per patient #TCGC15
12:59pm June 23rd 2015 via Hootsuite
Jackson: Tumor intrinsic mechanisms; KRAS and cetuximab in '04 for CR cancer. ID resistance mechanism (many); heterogeneity. #TCGC15
12:56pm June 23rd 2015 via Hootsuite
Jackson: $85B spent on oncology drugs, low likelihood of responding (25% response rate) #TCGC15
12:54pm June 23rd 2015 via Hootsuite
Jackson: Physicians have two people in mind: the patient and Hippocrates. "abstain from whatever is deleterious and mischievous" #TCGC15
12:52pm June 23rd 2015 via Hootsuite
David Jackson (Molecular Health) "Beyond the cancer genome: computational enablement of holistic, evidence-driven pt care" #TCGC15
12:49pm June 23rd 2015 via Hootsuite
Witte:Q:Commercial plans? A:Haven't published this, suspect Kaiser will implement as genotyping inexpensive to do. #TCGC15
12:45pm June 23rd 2015 via Hootsuite
Witte: PSA or adj PSA' and Gleeson score: both highly sig., PSA' had better fit. #TCGC15
12:44pm June 23rd 2015 via Hootsuite
Witte: Showed results of reclass. between controls and cases (PSA >3). Raises question about FP, 4 is no longer cutoff (urologists) #TCGC
12:38pm June 23rd 2015 via Hootsuite
Witte: 7 prev PSA loci, new 24 at p <5x10-8. Summarizes genetic normalization method. Q:Normal? LT followup? A:Yes, but LT in system #TCG
12:36pm June 23rd 2015 via Hootsuite
Witte: Same plot shows previously assoc'd PrCa genes. comparison of PSA to PrCa 'hits': some both, some PrCa only, several PSA only #TCGC15
12:28pm June 23rd 2015 via Hootsuite
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
