Tweets from Hootsuite

DeRisi: They work on malaria, viruses, pythons; but today is '2 day's worth of work': acute encephalitis. Fever, seizures, etc. #AGBT14

9:37am February 14th 2014 via Hootsuite

Up next: Joe DeRisi (University of California, San Francisco): NGS in the Context of Critical Care: A Case Example #AGBT14

9:35am February 14th 2014 via Hootsuite

Botstein: Q: Stable mixture persistancy? A: Each mut. can't 'do it themself'. Seen physical separation, where one sticks other not #AGBT14

9:34am February 14th 2014 via Hootsuite

Botstein: Q: (S. Plos) Haploid model vs diploid? Differences? A: Rel. few rearr. in haploids; rearr = lethal. SNV's have same effect.#AGBT14

9:33am February 14th 2014 via Hootsuite

Botstein: Q: (Mardis) Chemostat cp. to body? Microenv.? A: Microenv. is 'consistently reproducible' during metastasis. #AGBT14

9:31am February 14th 2014 via Hootsuite

Botstein: Genes found repeatedly - IRA 'neg regulator of Ras'. But cell wall assembly too. #AGBT14

9:29am February 14th 2014 via Hootsuite

Botstein: Notable trajectories of passengers and drivers: many passengers, but it takes time to determine the few drivers #AGBT14

9:28am February 14th 2014 via Hootsuite

Botstein: But which one, elo1 or gas1 gene is the important one? A yeast backcross provides the answer. elo1 passenger, gas1 driver #AGBT14

9:27am February 14th 2014 via Hootsuite

Botstein: With NGS deep sequencing on ILMN, earlier sweeps detected; fatty acid elongation, chrom. silencing, then mating. #AGBT14

9:26am February 14th 2014 via Hootsuite

Botstein: Steriles initially spread faster than expected. Showed Desai in 2000 was right. Lang 2011 ref http://t.co/neG5Sfkw8L #AGBT14

9:25am February 14th 2014 via Hootsuite

Botstein: Start with w/t, at the end can calculate % mutated at the end, and can measure it experimentally. Can view 'sweeps' #AGBT14

9:24am February 14th 2014 via Hootsuite

Botstein: Fitness cost of constitutive signalling through the mating pathway.. Ref Lang 2009 http://t.co/pkWWD6o3UE #AGBT14

9:23am February 14th 2014 via Hootsuite

Botstein: Theoretical framework for mutations over many generations in a distribution. Ref: Desai Fisher 2007 http://t.co/oOnn5eTYiM #AGBT14

9:21am February 14th 2014 via Hootsuite

RT @GenomeNathan: Botstein: Sugar-starved yeast burn more, ferment less. Clearly, they've read Biochemistry (Stryer). #agbt14

9:18am February 14th 2014 via Hootsuite

@deannachurch D. Botstein gave a similar talk in Jan. 2012 that you can watch: http://t.co/b1PLA3iWwH #agbt14

9:18am February 14th 2014 via Hootsuite

Botstein: 3 N2 sources for yeast; different chrom. rearr.'s. Successful strains were deletions, around repeated sequences #AGBT14

9:17am February 14th 2014 via Hootsuite

Botstein: If there are four breast cancer subtypes, the path may be different; then genetic predisposition (BRCA) will be 1 subtype #AGBT14

9:15am February 14th 2014 via Hootsuite

Botstein: Data from sulfate-reduced yeast environments. Gresham 2008 paper http://t.co/Je4YzNpegi #AGBT14

9:12am February 14th 2014 via Hootsuite

Botstein: CIT1 (citrate synthase) now run by a different promoter, just like the Philadelphia Chromosome (CML) (bcr-abl / Gleevec) #AGBT14

9:10am February 14th 2014 via Hootsuite

Botstein: Using aCGH, rearranged chromosomes in this clonal evolution; transloc. in a transposon element (CIT1) #AGBT14

9:09am February 14th 2014 via Hootsuite

Botstein: Using rate-limiting glucose, reported glucose limitation 1999 Ferea paper http://t.co/irB06ajMuE Some genes up / down #AGBT14

9:08am February 14th 2014 via Hootsuite

Botstein: Photo of Leo Szilard at CSHL - invented with Monod the Chemostat, enabling single-cell organism growth in a steady-state #AGBT14

9:04am February 14th 2014 via Hootsuite

Botstein: "Yeast... has provided a remarkably high fx of our knowledge abt the functions of individual euk. genes and proteins" #AGBT14

9:03am February 14th 2014 via Hootsuite

Up first: David Botstein (Princeton University): Yeast, Evolution and Cancer #AGBT14

9:01am February 14th 2014 via Hootsuite

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types | Science ($) http://t.co/057ekmDgju

7:20am February 14th 2014 via Hootsuite

Thanks to all who introduced yourselves to me at #AGBT14. From Sharon Plon (@splon) "Do you do anything else other than Twitter?"

7:10am February 14th 2014 via Hootsuite

Interactive genetic history map | Biosci Technology http://t.co/HK9Vv3U0iE

5:25am February 14th 2014 via Hootsuite

RT @insidehighered: Record share of wives are "marrying down" educationally http://t.co/ksZBQhyvUc

4:35am February 14th 2014 via Hootsuite

Seshagiri:Used in vitro assay systems to probe ERBB3 mutants; look at cell survival as a proxy for oncogenic signalling #AGBT14

9:04pm February 13th 2014 via Hootsuite

Seshagiri:Hotspot mutations' effect on conformation? Also muts on kinase domain, but none regain kinase activity #AGBT14

9:03pm February 13th 2014 via Hootsuite

Seshagiri:Now looking at ERBB3 somatic mutations - only one of the ERBB family with a impaired kinase domain. Works w/ ERBB2 #AGBT14

9:02pm February 13th 2014 via Hootsuite

Seshagiri:Another was EIF3E-RSPO2 has a deletion, under control of a different promoter. R-spondin fusions activates Wnt #AGBT14

8:57pm February 13th 2014 via Hootsuite

Seshagiri: PTPRK-RSPO3 fusion, rearrangement results in functional protein. #AGBT14

8:57pm February 13th 2014 via Hootsuite

Seshagiri:WES, WGS; RNA; SNP arrays from 72 tumor/normal pairs. Looking at RNA fusions, seeing a number of fusions in solid tumors #AGBT14

8:55pm February 13th 2014 via Hootsuite

Seshagiri: Colon cancer, 3rd most freq., 1.2M WW, 140K in US annually. 608K WW, 51k deaths in US annually. Drugs to treat few. #AGBT14

8:53pm February 13th 2014 via Hootsuite

Up next: Somasekar Seshagiri (Genentech) Exome Sequencing Identified Oncogenic ERBB3 Mutations #AGBT14

8:52pm February 13th 2014 via Hootsuite

Lipson: Q: (Plon) Any reporting of germline? A:If they suspect it they report it. #AGBT14

8:51pm February 13th 2014 via Hootsuite

Lipson: Q:Are fusions picked up in the routine pipeline? A:Defined capture of introns. Intron 19 of ALK will pull down other exon #AGBT14

8:51pm February 13th 2014 via Hootsuite

Lipson: 2nd individual, KIF5B-RET fusion identified, completely novel. Looked for recurrence: of 600, 1% Cauc, 6.3% Asians #AGBT14

8:47pm February 13th 2014 via Hootsuite

Lipson: A complex ALK rearr. - 2012 Peled et al paper here http://t.co/A8yz0wnX7k #AGBT14

8:45pm February 13th 2014 via Hootsuite

Lipson: Gene fusions seen in 10% of NSCLC; a whole collection of them #AGBT14

8:44pm February 13th 2014 via Hootsuite

Lipson: 851/893 samples (95%) successfully seq.; 1,313 unique alterations, 181 genes; actionable targeted in >60 cases #AGBT14

8:44pm February 13th 2014 via Hootsuite

Lipson: Base subst, indels, CNA, fusions with known cell line pools; hundreds of FFPE samples to compare to classical assays #AGBT14

8:42pm February 13th 2014 via Hootsuite

Lipson: Reporting their performance metrics from Nature Biotech paper Nov 2013 http://t.co/FxLKXl96qx #AGBT14

8:41pm February 13th 2014 via Hootsuite

Lipson: Turnaround time is 14 d. >99.5% of exons at >100x; 236 known relevant cancer genes, all coding regions & select introns #A

8:39pm February 13th 2014 via Hootsuite

Lipson: Data from their Nature Biotech paper - 46% had mut freq <20%. Their test has specialized sample prep, hybrid capture, HiSeq #AGBT

8:37pm February 13th 2014 via Hootsuite

Lipson: Many NSCLC are fine needle aspirates, fixed small needle biopsies, and low tumor purity. Little control over amt of tumor #AGBT14

8:36pm February 13th 2014 via Hootsuite

Lipson: Listed many relevant genes for NSCLC - yet just a handful of gene-specific tests. And all the different types - not only SNV #AGBT14

8:35pm February 13th 2014 via Hootsuite