Tabor: Wanted results: "Long term planning for children". Pt "We could use the help of a crystal ball I guess" #ASHG2013
2:22pm October 25th 2013 via TweetDeck
Tabor: Desire for awareness / preparation. Pt "better than being blindsided by it" #ASHG2013
2:21pm October 25th 2013 via TweetDeck
Tabor: A prevention example, BRCA and prophylactic mastectomy. Pt "She was able to make an informed decision (regarding A Jolie)" #ASHG2013
2:20pm October 25th 2013 via TweetDeck
Tabor: Results wanted are also for prevention: "there is always something you can do" #ASHG2013
2:19pm October 25th 2013 via TweetDeck
Tabor: Another: "Even if there's something that seems scary, I think it is valuable to know" #ASHG2013
2:18pm October 25th 2013 via TweetDeck
Tabor: Participant quote: "I can't necessarily tell that something not valuable today might be valuable later on" #ASHG2013
Tabor: Phone interview coded; five conditions. >85% 'wanted all' 'anything and everything that comes out of this study' #ASHG2013
2:17pm October 25th 2013 via TweetDeck
Tabor: Recruiting and reconsent 150 from indivs whose exomes already sequenced. Use of My46 for self-guided web-based tool. #ASHG2013
2:16pm October 25th 2013 via TweetDeck
H. Tabor (Seattle Children's): Individual expectations for return of secondary results from exome sequencing #ASHG2013
2:15pm October 25th 2013 via TweetDeck
Dulik: Conclude: ACMG IF list leads to efficient analysis. #ASHG2013
2:14pm October 25th 2013 via TweetDeck
Dulik: Comparing IF frameworks, ACMG has 56 genes, while PediSeq 2074. Unique vars/exome ave 1.6 / 13.8 respectively #ASHG2013
2:11pm October 25th 2013 via TweetDeck
Dulik: Uses a PediSeq freamework for Incidental Finding (IF) variant filtering (ACMG db) #ASHG2013
2:08pm October 25th 2013 via TweetDeck
Ethical, legal, social:: M.C. Dulik (CHOP) Practical assessment of incidental finding recommendations for use in clinical exome #ASHG2013
2:07pm October 25th 2013 via TweetDeck
RT @Diane_McKenna_: Why the U.K. Wants a Genomic National Health Service http://t.co/kncZUwyCy3
1:21pm October 25th 2013 via TweetDeck
RT @BBCWorld: Can it be done? The mobile phone that is built like Lego http://t.co/1bgPjItwdn http://t.co/wfKnxFw4Zi
12:21pm October 25th 2013 via TweetDeck
RT @canislatrans: "My friend's kid explains The Hulk: he's a big green monster; when he needs to get things done he turns into a scientist."
11:21am October 25th 2013 via TweetDeck
For US, tempting! RT @TUAW: [Deals] 100% free high speed 4G LTE internet with purchase of FreedomPop hotspot http://t.co/a3DEL6lWB7
10:21am October 25th 2013 via TweetDeck
@splon Great work reported here! Parsons: #ASHG2013
10:18am October 25th 2013 via TweetDeck in reply to
Parsons: Q&A: Germline discovery - not reported here, but yes, also significant incidental findings in some cases. #ASHG2013
10:16am October 25th 2013 via TweetDeck
Parsons: Q&A: PDF report is defined by the limitations of their EHR. Better interactive reporting in development. #ASHG2013
Parsons: Criteria for seq depth is '5% or more'. Seq is rel deep - about 300x. Fraction of reads is on report. #ASHG2013
10:15am October 25th 2013 via TweetDeck
Parsons: Q&A: CNV analysis using WES is something performed now. #ASHG2013
10:14am October 25th 2013 via TweetDeck
Parsons: May use RNA-Seq to ID fusion genes may be implemented (complementary method) #ASHG2013
Parsons:25-30% of samples ID tumor muts of potential clinical utility #ASHG2013
10:13am October 25th 2013 via TweetDeck
Parsons: NHGRI link about Clinical Sequencing Exploratory Research (Plon and Parsons at BCM http://t.co/1A5ddLtI3e ) #ASHG2013
Parsons: n=67: recurrent genes include CTNNB1 (6) TP53 (3), BRAF (3) #ASHG2013
10:10am October 25th 2013 via TweetDeck
Parsons: 86 / 105 tumors/normal pairs acceptable for WES. Median 8 mutations per patient. Range 78 to 0. Many <5. #ASHG2013
10:09am October 25th 2013 via TweetDeck
Parsons:105 of 129 enrolled. Median age 5 y.o. TAT <15 weeks. First exomes Dec '12. Reports as part of EHR #ASHG2013
10:07am October 25th 2013 via TweetDeck
Parsons:The oncologist is also enrolled - and surveyed for their opinions of 'what if' given the WES data #ASHG2013
10:06am October 25th 2013 via TweetDeck
Parsons: Examples: Class I ALK, II MET, III PHF6, IV XIAP. #ASHG2013
Parsons:All muts are listed; categorized I to IV: est. clinical utility, potential, in consensus Ca gene, 'all other' #ASHG2013
10:04am October 25th 2013 via TweetDeck
Parsons:Process of interpretation and ranking, confirmation by Sanger, reviewed again. #ASHG2013
Parsons: Workflow for WES is by the Baylor GC. Variant review, clinical reporting applying filters. #ASHG2013
10:03am October 25th 2013 via TweetDeck
Parsons:ID types of muts, measuring impact of oncologist's decisions - clinical trials, oncologist opinions too. #ASHG2013
10:02am October 25th 2013 via TweetDeck
Parsons: Focus for today is the ped tumor exome results. Germline results for inherited factors. #ASHG2013
Parsons: Study Q's include ethics and psychosocial effects - recordings during counseling and return of results by oncologists. #ASHG2013
10:01am October 25th 2013 via TweetDeck
Parsons: BASIC3= Baylor Advanced Sequencing Into Childhood Cancer Care. #ASHG2013
10:00am October 25th 2013 via TweetDeck
Cancer: D.W. Parsons (Tx Children's): Diagnostic yield of clinical tumor exome seq for newly dx'd pediatric solid tumor patients #ASHG2013
9:59am October 25th 2013 via TweetDeck
Villani: High correlation betw. cis CNV and expression level #ASHG2103
9:50am October 25th 2013 via TweetDeck
Villani: Exp arrays & SNP arrays, ID CNV / dels. 14K / 11K gene #ASHG2103
9:49am October 25th 2013 via TweetDeck
Villani: 773 solid tumor lines from 22 tissues analyzed, part of the Cancer Cell Line Encycl. (CCLE) #ASHG2103
9:48am October 25th 2013 via TweetDeck
Cancer: A. C. Villani (Broad): integrative genomic and transcriptomic analysis of 775 human cancer cell line #ASHG2103
9:46am October 25th 2013 via TweetDeck
H. Choudhry: lncRNAs are regulated by HIF, ass'd with clinical outcome #ASHG2013
9:40am October 25th 2013 via TweetDeck
H. Choudhry: Looked at paused RNApol2 sites and increase of gene expression as a result of hypoxia #ASHG2013
9:37am October 25th 2013 via TweetDeck
H. Choudhry: Looking at new mechanism - piwiRNA, snoRNA etc.and hypoxia in MCF-7 #ASHG2013
9:33am October 25th 2013 via TweetDeck
Cancer: H. Choudhry (Oxford) Transcriptome and epigenome sequencing of hypoxic breast cancer reveals non-coding RNAs . #ASHG2013
9:32am October 25th 2013 via TweetDeck
Wong: ID of several novel candidate sarcoma driver genes, in both human and mouse #ASHG2013
9:28am October 25th 2013 via TweetDeck
Wong: 3.1M to 4.1M tumor variants across tiers. Example Circos plot observed many translocations, inversions. #ASHG2013
9:23am October 25th 2013 via TweetDeck
Wong: Did WGS via both ILM and CGI. Looking for shared genes, pathways. Coding var, then non-coding, then 'everything else' #ASHG2013
9:21am October 25th 2013 via TweetDeck
Wong: In human samples, het in normal, homozy in tumor. #ASHG2013
9:20am October 25th 2013 via TweetDeck
