Hakonarson: NOTCH3 inhib. for myofibramatosis, can put together a PGx model in rare disease. Can go from rare disease to fast-track #AGBT14
1:56pm February 15th 2014 via Hootsuite
Hakonarson: 50% of 49 genes found are novel; many of therapeutic interest with repositioning oppy's. NOTCH and many others #AGBT14
1:54pm February 15th 2014 via Hootsuite
Hakonarson: Diagnostic odyssey paper here in Genome Med. http://t.co/Kwvbj2gSBr #AGBT14
1:53pm February 15th 2014 via Hootsuite
Hakonarson: Everything through IVA, 280 rare dis families, 49 genes so far. List of several new genes. A 20-y diag. odyssey solved #AGBT14
1:52pm February 15th 2014 via Hootsuite
Hakonarson: They use AMZN for everything; <14h / exome, laid out their pipeline. 10GB seq, 12GB align, 100MB vars (not bases, bytes) #AGB
1:51pm February 15th 2014 via Hootsuite
Hakonarson: Also rare disease prog; 525 families, 1598 indiv's. 49 disease genes to-date 'just scratching surface' of samples onhand #AGBT14
1:50pm February 15th 2014 via Hootsuite
Hakonarson: Medication repositioning of a therapy - based on molecular phenotyping. Neuroblastoma ALK #AGBT14
1:49pm February 15th 2014 via Hootsuite
Hakonarson: ADHD - est $76B/y cost in US; most common disease among children; discovered var's Nature Gen '11 http://t.co/4UHoqVRDoG #AGBT14
1:48pm February 15th 2014 via Hootsuite
Hakonarson: And neuroimaging to boot; interview-based dis. class.; top and bottom 15% of the population (extreme phenotypes) #AGBT14
1:46pm February 15th 2014 via Hootsuite
Hakonarson: Power of the biobank - 10K recruited back for add'l phenotyping, assessment, 'computerized neurocognitive battery' #AGBT14
1:45pm February 15th 2014 via Hootsuite
Hakonarson: Biobank a key asset: EHR has unlimited potential - longitudinal followup, history of medications, track complex pheno's #AGBT14
1:44pm February 15th 2014 via Hootsuite
Hakonarson: Focus on neurodevelopmental studies, other developmental ones. History: Linkage, then GWAS, then WES. #AGBT14
1:43pm February 15th 2014 via Hootsuite
Hakonarson: CHOP Center for Applied Genomics - 2006 founded; 75 staff; 60K children recruited. Target: 100K. EHR goes 12y back #AGBT14
1:42pm February 15th 2014 via Hootsuite
Hakonarson: Where medicine is headed: stem-cell therapy has major promise, will take time for acceptance. 'Opportunities are huge' #AGBT14
1:41pm February 15th 2014 via Hootsuite
Hakonarson: Disclosing as a founder of neuroFix Therapeutics. Chronic diseases are growing. 15% of children (10M) US have spec needs #AGBT14
1:40pm February 15th 2014 via Hootsuite
Up next: Hakon Hakonarson (CHOP): Impact of optimized seq analysis pipeline on decision making in genomic medicine #AGBT14
1:38pm February 15th 2014 via Hootsuite
Freeman: Seeing democratization, as they've gone from a few genes and up-scaled; great training of 'next gen of scientists' #AGBT14
1:37pm February 15th 2014 via Hootsuite
RT @westr: #AGBT14 current analytics: 7.5M impressions - http://t.co/D0BohlPFWy #pm101 #genomics
1:33pm February 15th 2014 via Hootsuite
Freeman: Correlated to RNA-Seq data; rate-limiting is bisulfite primer design. #AGBT14
1:30pm February 15th 2014 via Hootsuite
Freeman: Bisulf. Amplicon Sequencing (BSAS) analyzed via GUI, in-silico reference conversion. Nice data across several CpC sites #AGBT14
1:28pm February 15th 2014 via Hootsuite
Freeman: Co-isolated DNA and RNA (Q); TruSeq/HiSeq; CLCbio; IPA. Needed targeted methylation; 2-20kb, invented Bisulf. amplicon #AGBT14
1:27pm February 15th 2014 via Hootsuite
Freeman: Using rat model (less genome annotation, no capture reagents, limited tissue); small effects, hetergeneous tissue #AGBT14
1:24pm February 15th 2014 via Hootsuite
RT @will_fitzhugh: Alan Williams from @iontorrent: v4.2 of Ion Reporter will support gene fusion detection and reporting #AGBT14
1:23pm February 15th 2014 via Hootsuite
QIAGEN: Poor glycemic control - cause complications years afterward. Large studies over a 10y timeframe. May be epigenetic. #AGBT14
1:22pm February 15th 2014 via Hootsuite
Freeman: Diabetic retinopathy is leading cause of vision loss (12k - 24k in US lose some vision/ year) #AGBT14
1:20pm February 15th 2014 via Hootsuite
Up next at the Q workshop: William Freeman, Univ OK HSC: Metabolic memory and transcriptomic signatures in diabetic retinopathy #AGBT14
1:18pm February 15th 2014 via Hootsuite
QIAGEN: 1-20 independent runs on the GeneReader (GR); hotspot panel throughput x 250 samples/day #AGBT14
1:16pm February 15th 2014 via Hootsuite
QIAGEN: New GeneRead FFPE kit for small-scale purification; REPLI-g single-cell portfolio. #AGBT14
1:15pm February 15th 2014 via Hootsuite
QIAGEN GmbH Workshop:Used the words 'dominant player'; '14 plans include 12 new tech kits; 14 new gene panels; GeneReader #AGBT14
1:14pm February 15th 2014 via Hootsuite
QIAGEN GmbH Workshop: >80% of NGS runs use Q sample-prep; 2.3k inst. using CLCbio; 15K use Ingenuity tools, including IPA (10y old) #AGBT
1:12pm February 15th 2014 via Hootsuite
QIAGEN GmbH workshop: illustrating the largest bottlenecks, and the large number of paraffin-embedded sample collections #AGBT14
1:11pm February 15th 2014 via Hootsuite
Williams: Hi-Q data now avail; universal 200 / 400 bp kit; 70% red. in deletion error, 30% reduction in insertion error #AGBT2014
1:00pm February 15th 2014 via Hootsuite
Williams: Chef: For PGM in late Mar, for Proton soon after. 79% loading, 80-90M PI reads/run. 1.5% run failure rate #AGBT2014
12:58pm February 15th 2014 via Hootsuite
Williams: Room to improve, target early acces in 'May or June', full launch of PII in 2nd half of 2014 #AGBT2014
12:55pm February 15th 2014 via Hootsuite
Williams: L. Moroz data, 342M extrapolated reads. Cp. the PI to PII, r^2 of 0.99 across different samples #AGBT2014
12:54pm February 15th 2014 via Hootsuite
Williams: 91bp human frag lib data shown, extrapolated 291M reads. Are where we are in 3w w/PII what took 4mo with PI #AGBT2014
12:52pm February 15th 2014 via Hootsuite
Williams: Now 3w with new PII design; biggest risk was 5Gb/s data output. #AGBT14
12:50pm February 15th 2014 via Hootsuite
RT @lexnederbragt: Radovich: early access data by new Ion AmpliSeq Exome RDY - dried down primer pools in plates for easier workflow #AGBT14
12:47pm February 15th 2014 via Hootsuite
RT @iontorrent: Radovich: Using combo of Ion PGM System and Open Array qPCR in CLIA lab for PGx #AGBT14
12:46pm February 15th 2014 via Hootsuite in reply to
RT @OmicsOmicsBlog: Boland: Had Chef since mid-Nov; 37 runs. 200 bp chemistry. Challenge: titrating library. Uses 1 Chef for 2 PGMs #AGBT14
12:45pm February 15th 2014 via Hootsuite
Nice #AGBT14 crowd in the Palms Ballroom to hear about @iontorrent Chef and Proton updates. http://t.co/gHX4NrfPhe
12:12pm February 15th 2014 via Hootsuite
Tang: Q: SNP analysis from indiv cells? A: de novo point muts - need 3 cells. Several oocytes each with 2 PB's (same donor) #AGBT14
11:57am February 15th 2014 via Hootsuite
Tang: scRRBS of indiv. cells shows considerable var; also looking at haploid cell methylation status (sperm): 92% of sites 100%/0% #AGBT14
11:55am February 15th 2014 via Hootsuite
Tang: Single-cell RRBS publication in Genome Res here. http://t.co/ceJQOshNFG #AGBT14
11:54am February 15th 2014 via Hootsuite
Tang: RRBS development to the single-cell level: remove pur steps, combine to single-tube reaction, only heat #AGBT14
11:53am February 15th 2014 via Hootsuite
Tang: Discussion of a method called Super-Seq (alas missed any ref, can't locate) for lncRNA analysis for single-cell #AGBT14
11:52am February 15th 2014 via Hootsuite
Tang: PCA of 120 cells for single-cell transcr.: can separate 3 distinct celltypes. Nature Struct Biol ref: http://t.co/F9UyFQPnpE #AGBT14
11:49am February 15th 2014 via Hootsuite
Tang: Illus. a method of NIPT for post-fertilized embryos. First MALBAC-based implantation is underway (presum. in China) #AGBT14
11:47am February 15th 2014 via Hootsuite
Tang: Able to deduce maternal SNVs of indiv. zygotes; validated via Sanger 32/33 alleles. 1: amplification via MALBAC allele dropout #AGBT14
11:45am February 15th 2014 via Hootsuite
Tang: After micromanipulation, use MALBEC with 8 donors. Cell publication of 8 human embryo's in Cell 2013 http://t.co/IPVqqGwE3w #AGBT14
11:44am February 15th 2014 via Hootsuite
