MT @IcahnMountSinai: “We don’t know the language yet of #biology." Eric Schadt @IcahnInstitute discusses http://t.co/njWHh586Tl #biotech
10:05pm September 30th 2014 via Hootsuite
BRAIN: Launching America’s Next Moonshot | NIH Director's Blog http://t.co/gaL6EXVEy3 $46M awarded
9:00pm September 30th 2014 via Hootsuite
Why I'm returning my iPhone 6 (well, maybe) | Macworld http://t.co/WQKdC0abLl Agree with this, seeing it in-use today (co-workers').
8:00pm September 30th 2014 via Hootsuite
How to double your free OneDrive storage to 30GB | PCWorld http://t.co/DAMwT2YSnK Before Oct 1st!
7:05pm September 30th 2014 via Hootsuite
Personal genomics: The test for everything (with video) | Vancouver Sun http://t.co/xsLznP6u4V
6:00pm September 30th 2014 via Hootsuite
CDC Confirms First Case of Ebola in U.S. - WSJ http://t.co/6w5M0qAOhQ
5:36pm September 30th 2014 via Hootsuite
RT @NewsfromScience: Just how big is Google Scholar? http://t.co/B0XnDu5SGU
5:01pm September 30th 2014 via Hootsuite
To repeat "Don't try this at home" RT @michaelpollan: Jeff Leach gets fecal transplant from a hunter gatherer. http://t.co/Q2q2fGbcmT
4:00pm September 30th 2014 via Hootsuite
RT @moorejh: Our United Genomes Project http://t.co/9DuJ7Xf5WQ #genomics #africa
3:03pm September 30th 2014 via Hootsuite
Strauss: Points out that CTC data and cfDNA data aren't completely concordant, pointing out the need to analyze both #gensoltour
2:04pm September 30th 2014 via Twitter Web Client
Strauss: For their CTC sequencing effort, >2000x depth down to 1% with high sensitivity. Showed cell line titration #gensoltour
Strauss: Have a method of enumeration & scanning as well; after counting cells can be recovered for downstream analysis #gensoltour
Strauss: Cynvenio is a small company, have a rare-cell isolation service, 'think about future applications' #gensoltour
Last: William Strauss (Cynvenio) "Circulating tumor cells and cell-free DNA" #gensoltour
Zhu:Q:Transient Ab response in a 'normal' donor? A:Nothing 'normal' in a 'normal donor' #gensoltour
2:03pm September 30th 2014 via Twitter Web Client
Zhu:Q:600-700bp readlengths? A:Isothermal amplification. #gensoltour
Zhu: Another is HPV-induced Ab response, also disease progression in HIV virus in a population #gensoltour
Zhu: Can apply to a wide range of problems in rational vaccine development. Two examples of HIV longitudinal infection #gensoltour
Zhu: They did an improved emulsion-based template prep ('new OT2') + Hi-Q, getting 560bp read length #gensoltour
Zhu: Also developed a single-molecule barcoding technology. #gensoltour
Zhu: Showed biased vs. unbiased germline analysis; then functionally validated (from seq data, synthesize Ab, show activity) #gensoltour
2:02pm September 30th 2014 via Twitter Web Client
Zhu: bnAbs not the most dominant (IgHV4-59 from IAVI 17) only 8.5% of the repertoire #gensoltour
Zhu: Recent review http://t.co/1OdJZKD5co Points out 5'RACE approach, need for 600bp reads #gensoltour
Zhu: 'Seq depth matters' - many single nodes expand with PGM-derived data #gensoltour
Zhu: PGM identify six H / two L chains; ID all H and L chain, 1,022H and 2,282 L chains. Cp to 454, visual rep that PGM better #gensoltour
Zhu: Mentions HiQ and Iso. ampl as other improvements. Case-study: IAVI donor 17 (list of 4 papers, impt anti-HIV Abs) #gensoltour
Zhu: Other considerations - types of error. Chose PGM due to affordability. Technical improvement: 400 - >600 - >800 - >1K bp #gen
2:01pm September 30th 2014 via Twitter Web Client
Zhu: Historically 454 has only been used for Ab repertoire seq; long-reads needed (~450bp). Using 5' RACE, need 600bp #gensoltour
1:59pm September 30th 2014 via Twitter Web Client
Zhu: Affinity maturation by somatic hypermutation and clonal selection - V genes of mature bnAbs #gensoltour
Zhu: 100K possible V(D)J recombination (heavy-chain); then affinity maturation (up to 100nt mutations (>30%) in V genes) #gensoltour
Zhu: Points to this recent review http://t.co/xv5c66c4zi for accelerating global vaccine development #gensoltour
Zhu: First paper in '09 http://t.co/KWk5pcj6OX of Ab repertoire in zebrafish #gensoltour
1:58pm September 30th 2014 via Twitter Web Client
Zhu: Antibody-omics: computational pipeline, and then in-depth analysis (divergence-grid and other analyses) #gensoltour
Zhu: From PBMC's, find broadly neutralizing Abs, also ID maturation pathways & intermediates; also optimize Ab function #gensoltour
Zhu: Brief immunology review: humoral and cellular immunity, and protective Ab are the 'hallmark of any successful vaccine' #gensoltour
Next: Jiang Zhu (Scripps Center for HIV/AIDS Vaccine Immunol.) "Antibody discovery and vaccine design - a PGM solution" #gensoltour
Cardoso: Was able to get to species level of Prevotella sp.; before ART and 6mos post-ART; showed Krona charts changed #gensoltour
Cardoso: Now longitudinally: for this used Ion 16S Metagenomics kit (V2-4, V6-9) for early access (to launch soon) #gensoltour
1:57pm September 30th 2014 via Twitter Web Client
Cardoso: Found NNRT-based cART increased fusobacteria phyla, decreased baceroides; Prevotella/bacteriodes ratio low also #gensoltour
Cardoso: Used a V3- fusion primer approached on Ion PGM and 200bp chemistry. Analysis used QIIME 1.8.0 and Greengenes #gensoltour
Cardoso: Illust. from 2012 review http://t.co/dz1S90HVQ5 ; there are some 20 approved retroviral medications #gensoltour
Cardoso: Chronic untreated HIV: lower diversity, +Prevotella, -Bacteriodes; anti-retrovirals don't restore gut microbiota #gensoltour
Cardoso: Investigational at this point: we know HIV infection is ass'd with microbiota alteration. 5 publications this year #gensoltour
Next: Sandra Cardoso Nat'l Inst of Resp Dis MX Exploring gut microbiota alterations ass'd with HIV infection in archived samples #gensoltour
1:56pm September 30th 2014 via Twitter Web Client
Starcevic: Acknowledgements include Jeff Smith "he answered the phone" from @LifeTech; Eric Schadt, Robert Sebra, Andrew Uzilov #gensoltour
Starcevic: Their results on the AmpliSeq Cancer Hotspot panel, 5% MAF, >1200x coverage, 12-plex on a 318 #gensoltour
Starcevic: IRB allows return of results electronically for this project. #gensoltour
Starcevic: Need to look at a large # of individuals; many elements, incl. recruitment, e-consent, sample collection... #gensoltour
1:55pm September 30th 2014 via Twitter Web Client
Starcevic: http://t.co/ROKRY9MrI9 description: high-penetrence mutations but not affected. I.e. CFTR, looking for protective #gensoltour
Starcevic: Analysis to-date hasn't been optimized yet; sensitivity 97.9%; FDR 7.1%; originally 92.3% and 2.4% respectively #gensoltour
