Hyland: Optimized with buccal swabs; validated with TaqMan assays via OpenArray#ASHG15
3:39pm October 7th 2015 via Hootsuite
Hyland: This panel launched a few weeks ago. Ampliseq product info here: http://t.co/K8HVUSByth #ASHG15
3:37pm October 7th 2015 via Hootsuite
Hyland: Goal: SNPs, indels, and CNV in gene to cover pharmacogenomic genes. Lots of paralogues, CYP2D6, etc. 119 amplicons. #ASHG15
3:35pm October 7th 2015 via Hootsuite
Fiona Hyland (Thermo Fisher) " Detection of relevant PGx variants and CYP2D6 copy number using a highly multiplexed NGS Assay" #ASHG15
3:32pm October 7th 2015 via Hootsuite
Tzika: 10 normal sample pools; data shown for chr1 cp to aCGH. Showed a few cases, one with a 4x copy of a gene, 'cat-eye syndrome' #ASHG15
3:29pm October 7th 2015 via Hootsuite
Tzika: After BWA and BAM file, extract read start locations to text file. Scripts for analysis '13 ref http://t.co/ADJHS7gvWd #ASHG15
3:24pm October 7th 2015 via Hootsuite
Tzika: If sub-optimal DNA - CNVseq; also referrals from precious, non-repeatable samples. Can confirm array findings #ASHG15
3:20pm October 7th 2015 via Hootsuite
Tzika CNVseq method; unexplained learning difficulties, dev delay in children. aCGH front-line test if good quality DNA #ASHG15
3:19pm October 7th 2015 via Hootsuite
Antigoni Tzika (St James Hosp Leeds UK) The application of the CNVSeq method for whole genome copy number variant detection. #ASHG15
3:18pm October 7th 2015 via Hootsuite
Saris: Used 4 samples for training, 24 cardiomyopathy. Z-score analysis; value minus mean over std dev; >5 or < -5:Gain/loss #ASHG15
3:08pm October 7th 2015 via Hootsuite
Saris: Goal was to replace MLPA; asked if their gene panel could call CNVs; they use JSI SeqPilot SW; based upon depth of coverage #ASHG15
3:03pm October 7th 2015 via Hootsuite
Jasper Saris (Erasmus Medical Center) "Supplemental CNV analysis in NGS genepanel data in a diagnostic setting" #ASHG15
3:02pm October 7th 2015 via Hootsuite
Muzzey:Q:Could use 'regular' NGS? A:Yes, hardest is statistically clean calling for CNV, and enough coverage of gene +pseudogene #ASHG15
3:01pm October 7th 2015 via Hootsuite
Muzzey:Q (Lincoln) Where else could this could be used? A: Where CNV has high homology, many other pseudogenes #ASHG15
2:59pm October 7th 2015 via Hootsuite
Muzzey: From 100K samples - showed distribution of mutations in CAH. #ASHG15
2:58pm October 7th 2015 via Hootsuite
Muzzey: Seeing 93% of samples w/interchanged sequence between gene and pseudogene. Q319X + duplication 2% of pts, non-carrier #ASHG15
2:56pm October 7th 2015 via Hootsuite
Muzzey: Shows a 30kb deletion - collection of CN data, SNPs aren't informative as it is to large a region to span #ASHG15
2:54pm October 7th 2015 via Hootsuite
Muzzey: P31L mutation - shows example of carrier: CN of gene, CN of pseudogene across gene lengths, w/SNP data overlaid #ASHG15
Muzzey: Key: Use SNP and CNV data and look for mis-match. Look where CN gene vs. CN of gene at site - part of pseudogene has moved #ASHG15
2:51pm October 7th 2015 via Hootsuite
Muzzey:CYP21A1P and CYP21A2 are highly homologous; 8 of 15 sites that distinguish gene/pseudogen are deleterious. Many FN results #ASHG15
2:50pm October 7th 2015 via Hootsuite
Muzzey CAH is the 7th most-common severe recessive disease; carrier rate is 1:60. Missing from 'nearly all commercial screens" #ASHG15
2:49pm October 7th 2015 via Hootsuite
Dale Muzzey (Counsyl) "An NGS-based carrier screen for congenital adrenal hyperplasia with 95% detection rate" #ASHG15
2:48pm October 7th 2015 via Hootsuite
.@markgenome Thanks for the shout-out, Mark! I just run around #ASHG15 all day long, powered by coffee and free vendor lunches :)
2:47pm October 7th 2015 via Hootsuite in reply to markgenome
Yang: Q:Details on error correction? A: After alignment, can look at freq and determine source of error (homopolymers), normalize #ASHG15
2:45pm October 7th 2015 via Hootsuite
Yang:Tool Amplicon Long Read Error Correction (ALEC); publication in-press. Proof of concept for PacBio for large struct var's #ASHG15
2:44pm October 7th 2015 via Hootsuite
Yang: Has developed a VCF translator, showed new genotpe in NA16688, a hybrid allele #ASHG15 Resource via lab site: http://t.co/TdExjUjz2A
2:42pm October 7th 2015 via Hootsuite
RT @MollyGasp: A great re-read during #ASHG15 in Baltimore this year: http://t.co/l72vU50hbg
2:38pm October 7th 2015 via Hootsuite
Yang: 3-round PCR, universal tag, about 5kb target. Upstream duplication similar size, seq via @PacBio unusable for haplotype caller #ASHG15
2:37pm October 7th 2015 via Hootsuite
Yang: CYP2D6 Reference: http://t.co/eGBJIrEpXV Figure from '04 review: http://t.co/DknOsC1JJg 97% homology to other CYP #ASHG15
2:36pm October 7th 2015 via Hootsuite
Yang: CYP2D6 metabolizes 20-25% of all medications; >100 star (*) alleles ID'd, including full gene deletion, duplications #ASHG15
2:34pm October 7th 2015 via Hootsuite
Yao Yang (Ichan School Mt Sinai) Long read single-molecule real-time (SMRT) full gene sequencing of cytochrome P450 2D6 (CYP2D6) #ASHG15
2:32pm October 7th 2015 via Hootsuite
Itan: 'A medium cohort of 30 pts with 1000 genes - more information than in the universe' (10^111 power, an NP-complete problem) #ASHG15
2:09pm October 7th 2015 via Hootsuite
Itan: Their '14 HGC publication: http://t.co/LUTEUmDEzQ #ASHG15
2:08pm October 7th 2015 via Hootsuite
Ivey: How many potential users we lose due to command-line interfaces? #ASHG15 Their revised tool: http://t.co/ANxyZxQXn7
2:04pm October 7th 2015 via Hootsuite
Ital: Illustrates with a Google map problem - known connected routes, and secondary connections to get from A to B #ASHG15
1:59pm October 7th 2015 via Hootsuite
Ital: Case of encephalitis - look for genes ';closest' to Herpes Simplex Enceph. known genes. Time-consuming, 'doomed to fail' #ASHG15
1:55pm October 7th 2015 via Hootsuite
Yuval Itan (St Gile Lab, Rockefeller) "Finding a needle in a haystack - new approaches to ID new variants" #ASHG15
1:53pm October 7th 2015 via Hootsuite
Solomon: Q: Turnaround time? A:They prioritize, can do better (currently on the order of months) #ASHG15
1:52pm October 7th 2015 via Hootsuite
Solomon:Q:WGS vs WES? A:Tend to concentrate on NICU, not neuro. 60% answers; for non-exonic, roughly 10-20% interesting struct var #ASHG15
1:51pm October 7th 2015 via Hootsuite
Solomon:Q:Incomplete penetrance? A:Hard problem; illus. with cardiac conditions. #ASHG15
1:48pm October 7th 2015 via Hootsuite
Solomon: Online chat with their experts. Lesson: "It's a ridiculously fun time to be a geneticist/genomicist" #ASHG15
1:47pm October 7th 2015 via Hootsuite
Solomon: Another lesson: we need to provide help and guidance to clinicians. Next PGx testing for free for every baby at INOVA #ASHG15
1:46pm October 7th 2015 via Hootsuite
Solomon: Another: we need to manage perceptions. We're early - the Wright Bros stage. For Pers Med: What inning? "Bldg the stadium" #ASHG15
1:45pm October 7th 2015 via Hootsuite
Solomon: Lessons: the Dx paradigm has shifted! 'No longer the "House" model' WGS in the NICU #ASHG15
1:44pm October 7th 2015 via Hootsuite
Solomon: Literature is 'constantly changing'; mother of affected kid sending him papers all the time. New pipelines, datasets #ASHG15
1:43pm October 7th 2015 via Hootsuite
Solomon: Adam-Oliver syndrome '14 ref http://t.co/mhuToPTZLY NOTCH1, dominant mutation #ASHG15
1:39pm October 7th 2015 via Hootsuite
Solomon: Another case: a unique imprinted gene. Only 11 others in the world affected '14 ref: http://t.co/Xee7zBik2W Gave steroids #ASHG15
1:37pm October 7th 2015 via Hootsuite
Solomon: Ingenuity: analysis was "Unbelievable" - in 30sec time, with the same dataset, indicating Niemann-Pick #ASHG15
1:36pm October 7th 2015 via Hootsuite
Solomon:Showed timeline for Dx odyssey; after about 1.5 y; another imaging where WGS indicated Niemann-Pick, now much better #ASHG15
1:34pm October 7th 2015 via Hootsuite
Solomon: 49.8%: A different intervention w/molecular cause; 95.6% during infancy/childhood #ASHG15 '13 PNAS http://t.co/jNQkvNrB5n
1:32pm October 7th 2015 via Hootsuite
