ML:Q:AmpliSeq Any Genome - how complete does the reference need to be? A:All about specificity #gensoltour
10:46am October 16th 2014 via Twitter Web Client
ML: What's new today: HiQ for PGM OT2; AmpliSeq for Transcriptome, Exome, hearing loss, RNA lung fusion; 16S; TruMate mate-pair #gensoltour
ML: AmpliSeq RNA Fusion Lung Cancer Res Panel - 98.4% concordance with FISH, IHC and qPCR in 61 sampls #gensoltour
ML: AmpliSeq inputs can go down to 100pg via 'tips and tricks' #gensoltour
Mike Lelivelt (Thermo Fisher) "New tools for the research and clinical research laboratories" #gensoltour
10:45am October 16th 2014 via Twitter Web Client
Catching a quick word w/ @jdudley of @IcahnMountSinai, Interview to be on Behind the Bench soon. http://t.co/7cJKEDmqNa
JD:Q:How to benchmark success? A:To identify a novel drug target would be one; another db generation for disease mutations #gensoltour
JD:Q:How to get e-consent of healthy individuals? Incidental results? A:Acknowledges the challenges & concerns for both. #gensoltour
JD:A2:Also helped analyze Steven Quake's genome at Stanford several years ago. #gensoltour
JD:Q:How to train MD's in the future? A:Near-term: training in genomics. Wrote book 'Exploring Personal Genomics' to help #gensoltour
JD:Q:How to pull environmental data? A:New project soon for env. exposure data, $GOOG's Project Baseline similar lines #gensoltour
10:44am October 16th 2014 via Twitter Web Client
JD:A2: Their proof-of-concept paper 'is coming out'. Allele freq of deleterious mutations higher than orig. expected #gensoltour
JD:Q:Elaboration on Resilience? A:Finding a hero genome, can do deep profiling to find compensating mutations #gensoltour @jdudley
JD: Ended w/ 3D map, with video w/3D animation of hills and valleys and environmental insults, and effect on indiv. network #gensoltour
JD: Enabling high-throughput 'end-to-end' - electronic consent, at-home sample collection, e-results. #gensoltour
JD: (Resilience project on Behind the Bench: http://t.co/spyGrtqnH5 ) #gensoltour
JD: Resilienceproject.me. Super-design panel, >700 genes,>4k disease-ass'd genes, 26K amplicons. #gensoltour
10:43am October 16th 2014 via Twitter Web Client
JD: 'Where will most of the health data be in 5-10 years?' Apple, Google are not dabbling; consumer health tools will be driver #gensoltour
JD: Printable tatoo'ed biosensors, mentions Pixie Scientific with a 'smart diaper', theranos in a local Walgreens #gensoltour
JD: 'We are on the crest of a tsunami in consumer sensor technologies' Headbands, Tricorder X-prize (Qualcomm) w/10 finalists #gensoltour
JD: Shows F1 car with 200 data feeds, 5Gb/lap. Oracle boat: 300 feeds, >200Gb/d, 30k var/sec. But a newborn human? #gensoltour
JD: Drills down in hotspot of the map, finds CACNA1E gene (described in T2D here: http://t.co/lnRogGrEMY ) #gensoltour
JD: "Who does Joel look like and does he look like anyone else?" Unsupervised clustering: by health status (T2D example) #gensoltour
10:42am October 16th 2014 via Twitter Web Client
JD: Have 30K samples; showed network of these samples from different measurement types; clustered together in a visual map #gensoltour
JD: Looking at whole-system perturbations between disease state and drug-treatment state. Now to many individuals #gensoltour
JD: Showed data from this recent paper on SCLC in a triple knockout mouse model http://t.co/O0QWah8vHn #gensoltour
JD: Connection bet. diseases - can drug be repurposed? Drug perturbation w/matching profile IBD '11 paper http://t.co/atU5jpVE98 #gensoltour
JD: Figure from 2010 paper http://t.co/saJLsZ1Jo6 'redefining disease with data' Different diseases similar at gene exp level #gensoltour
JD: Points out GEO http://t.co/oajIyBRFYd and points out >1M whole-genome microarray datasets available. #gensoltour
Dr. Joel Dudley of @IcahnMountSinai on stage at #gensoltour http://t.co/BlSR0xj30U
10:41am October 16th 2014 via Twitter Web Client
JD: Icahn Inst. embraces the complexity for better models of disease. Cloudera, $50M of infrastructure; Hadoop & Minerva #gensoltour
JD: A want to embrace stories; our ability to embrace complexity is limited... Our (outdated) orthodoxy: simple pathways #gensoltour
JD: We must embrace complexity to fully understand physiology and disease: environment, interacting networks, across organs #gensoltour
J Dudley: Reslience Project website: http://t.co/MvbWPD5sBb 'There are rarely smoking guns in human health' #gensoltour
Joel Dudley (Icahn Sch Med at Mount Sinai) "Resilience project: a targeted sequencing search for unexpected heroes" #gensoltour
10:40am October 16th 2014 via Twitter Web Client
HF: Comparing std. Var Caller (v.4.0) to Softgenetic's NextGene, at 4% - 16% AF, showed very comparable results #gensoltour
HF: They have been able to get down to 3.4% mutation AF, even when coverage was down to 220x (typically >1000x) #gensoltour
HF: Points out that for 25% neoplastic cells, for a heterozygote 12.5% detection; if 40% have a mutation, need 5% detection #gensoltour
HF: Methods across solid tumor types: real-time PCR, sequencing, FISH, aCGH, fragment analysis, RT-PCR. Chart of types of var's #gensoltour
Helen Ferandes (Weill Cornell Medical Coll., NYC) "Practical applications of NGS-based assays in molecular oncology" #gensoltour
AP:Q:Allelic expression and gene dosage effects? A:Even depends on compartment (nucl. vs. polysomes vs. cytosol) Haplotypes too #gensoltour
10:39am October 16th 2014 via Twitter Web Client
AP:Q:SNPs in coding vs nc regions? A:90-95% in non-coding regions, splicing regions #gensoltour
AP:Q:Ovation bias? A:rRNA reduction, a 3' bias as it amplifies, shearing method is another nuance w/secondary structure #gensoltour
AP:Q:Exonic rate in AmpliSeq whole transcriptome? A: It's all exons, no introns detected in the platform #gensoltour
AP:Q:Allelic ratio partioning shift? A:Nucleus to polysomes many times consistent. But to cytosol higher variability #gensoltour
AP:Q:'Value of ncRNA?' A:Annotations are hard; biomathematicians looking at modeling of networked hubs. Have to look for it. #gensoltour
AP: "It's not what you look at that matters, it's what you see" - Thoreau. #gensoltour
AP: But between methods, in the 0.64-0.68 range. RNA var calls between RNA-Seq and Ovation 94%, but caveats #gensoltour
AP: Comparing methods: 0.95 to 0.99 expression correlation between AmpliSeq RNA, RNA-Seq and NuGEN. #gensoltour
AP: % of reads mapped by # of reads: by 2-3M reads you hit saturation of detection. Showed graph at 9M-15M reads, flat ~70% #gensoltour
