Tweets from Hootsuite

Santani: Many questions, each with a report. GATK calling, but filtering. Quality var, rare, mutation type, disease genes #NGDx15

9:47am August 19th 2015 via Hootsuite

Santani: Showed complex pipeline for their CAP compliant bifx pipeline. Reports,overall quality mgmt, low coverage. #NGDx15

9:46am August 19th 2015 via Hootsuite

Santani: Informatics - a challenge. 'It was like a foreign language exchange program' SAM? CAP? #NGDx15

9:44am August 19th 2015 via Hootsuite

Santani: On a V5 now, at 98% coverage at >20x. They had about 100 panels for their customers to accommodate. #NGDx15

9:43am August 19th 2015 via Hootsuite

Santani: Collaborated with Emory (M Hegde) and Partners (B Funke), 3y effort: targeted the low-coverage regions to supplement WES #NGDx15

9:42am August 19th 2015 via Hootsuite

Santani: Medical exome def'n: 5,000 genes of medical significance. Then sliced further into panels (e.g. cardiomyopathy) #NGDx15

9:41am August 19th 2015 via Hootsuite

Santani:Benchmarking - whole exome, medical exome, cardiomyopathy panel. Bases <20x, fully covered exon (>20x) metrics.75%/82%/85% #NG

9:40am August 19th 2015 via Hootsuite

Santani:Director, technical supervisor, data analysts, genetic counselors etc. An ongoing challenge - attracting top talent NGDx15

9:39am August 19th 2015 via Hootsuite

Santani: Request for PhD-level technologists: new job descriptions needed. Bioinformatics specialist is not a software developer. #NGDx15

9:38am August 19th 2015 via Hootsuite

Santani: There were no compliance checklist 7 years ago. Informed consent, spent time determining return of results #NGDx15

9:37am August 19th 2015 via Hootsuite

Santani: Surveyed needs across clinics and prioritized tests to demonstrate need. Also acquired an R&D budget. Composed compliance #NGDx

9:36am August 19th 2015 via Hootsuite

Santani:Has many platforms, both NGS and microarray. Composed a business plan with ROI - why important and who was it for. #NGDx15

9:35am August 19th 2015 via Hootsuite

Santani: Has been working on this for the 5-7 years. Working on inherited diseases, with pediatric setting in mind #NGDx15

9:33am August 19th 2015 via Hootsuite

Avni Santani (UPenn and Children's Hosp of Philadelphia) "Implementation of clinical exome sequencing" #NGDx15

9:32am August 19th 2015 via Hootsuite

Daber: Larger panels 310 genes, 4K bi-allelic SNPs, address fusions, inversions, CNV, merge DNA and RNA variants #NGDx15

9:28am August 19th 2015 via Hootsuite

Daber:Their metrics: 76% of samples have 1 or more actionable mutation; 1.3 per 0.16 VUS. <0.1% assay failure rate #NGDx15

9:27am August 19th 2015 via Hootsuite

Daber: ctDNA is fragmented, small input, may use same process for that in their development work #NGDx15

9:26am August 19th 2015 via Hootsuite

Daber: Shows sensitivity down to 4% at 20ng input. 500pg input down to about 20% #NGDx15

9:25am August 19th 2015 via Hootsuite

Daber: They can go down to 100pg (15-18 cells) but at cost of primer-dimer. Asks if they could construct from collection of few CTCs #NGDx15

9:24am August 19th 2015 via Hootsuite

Daber: FFPE tumor DNA varies in quality widely - need to optimize library prep for small fragments and low input (120bp, 1ng) #NGDx15

9:23am August 19th 2015 via Hootsuite

Daber: Showed pie chart of NSCLC genes. (Quoted the '85%' number from Foundation paper, a bit of a red herring there.) #NGDx15

9:22am August 19th 2015 via Hootsuite

Daber: Criteria - clinical utilty, cost effectiveness, fast turnaround, reduce 'QNS' rates #NGDx15

9:21am August 19th 2015 via Hootsuite

Daber: Selecting content? Listed @iontorrent @illumina RainDance, MS, Foundation One, MATCH - only 109 common from 486 genes#NGDx15

9:20am August 19th 2015 via Hootsuite

Daber: Gene fusions - PCR using RNA. DNA: "Brute force tiling'. They use Archer, semi-amplicon based (one-side known, other unk) #NGDx15

9:19am August 19th 2015 via Hootsuite

Daber: Even so with intermediate dels: bioinformatics has to accomodate - primer cross-talk, looking at read-pairs. #NGDx15

9:16am August 19th 2015 via Hootsuite

Daber: AmpliSeq two different primers in same pool; RainDance amplicons within same drop; TSCA same DNA strand. Archer - no problem #NGDx15

9:15am August 19th 2015 via Hootsuite

Daber:What about larger deletions? Hyb-based will work better than PCR-based; you can but takes effort - 'it's complicated' #NGDx15

9:14am August 19th 2015 via Hootsuite

Daber: Homologous regions are eliminated in order to improve sensitivity / specificity. #NGDx15

9:13am August 19th 2015 via Hootsuite

Robert Daber (BioReference) "Development and implementation of clinical NGS testing: assay development and informatic challenges" #NGDx15

9:12am August 19th 2015 via Hootsuite

Fernandez:Second case of intrahepatic cholangiocarcinoma, had IDH1, common according to #TCGA. In clinical trial, 'pt doing well' #NGDx15

8:59am August 19th 2015 via Hootsuite

Fernandez: Concludes with a papillary thyroid case report: sample had both BRAF and NRAS mutations. Debate regarding classification #NGDx15

8:57am August 19th 2015 via Hootsuite

Fernandez: Variants via cytology vs resection smpls: concordance of 13 samples, 92%. 1/13 cellularity low #NGDx15

8:54am August 19th 2015 via Hootsuite

Fernandez: Same looked at via NGS: 29% cytology, # of indeterminates go down to 3% from 8% prior. Surgical: 27% about same #NGDx15

8:53am August 19th 2015 via Hootsuite

Fernandez: Comparing real-time PCR results for both cytology and surgical samples: 22% vs 31% mutation (more material) #NGDx15

8:52am August 19th 2015 via Hootsuite

Fernandez: Cytollogy vs surgical resection for lung ca: ave neoplastic cellularity of FNA was 23%, sig lower than resections 67% #NGDx15

8:50am August 19th 2015 via Hootsuite

Fernandez: Showed pie chart of NSCLC EGFR 26%, KRAS 28%, BRAF 3%. Has made a difference in clinical care. #NGDx15

8:49am August 19th 2015 via Hootsuite

Fernandez: Their costs for 450 genes about $250. #NGDx15

8:47am August 19th 2015 via Hootsuite

Helen Fernandez (Weill Cornell NY) "Utility of implementing clinical NGS assays as standard of care in oncology" #NGDx15

8:44am August 19th 2015 via Hootsuite

RT @softwareguru1: Introducing the single-cell maze runner http://t.co/2VefGK2bKy via @physorg_com

8:01am August 19th 2015 via Hootsuite

RT @rahman_nazneen: First almost fully-formed human brain grown in lab, researchers claim http://t.co/F4Fd680rrq

7:01am August 19th 2015 via Hootsuite

RT @aphillippy: @m_croxen For best accuracy, we currently recommend MHAP w/ PacBio -> Quiver w/ PacBio -> Pilon w/ Illumina

5:48am August 19th 2015 via Hootsuite

RT @illumina: Illumina, Warburg Pincus, Sutter Hill Ventures Form Helix to Accelerate Consumer Adoption of Genomics http://t.co/uiTT0qgBCf

10:10pm August 18th 2015 via Hootsuite

Helix, a New Gene Sequencing Venture, Aims to Create Digital Hub for Genomics - NY Times http://t.co/HPp0fRIzxU

10:10pm August 18th 2015 via Hootsuite

Patterson:In lung ca - CD45- tumor cell and inflammatory population both PD1/PDL1, as well as aneuploidy and other markers #NGDx15

5:40pm August 18th 2015 via Hootsuite

Patterson: Lung ca:stroma, inflammatory cells, able to disaggregate and quantify PD1/PDL1 on the subsets. 4h assay, scalable to 96 #NGDx15

5:38pm August 18th 2015 via Hootsuite

Patterson: Antibodies stain both surface and intracellular. Were able to also derive a metastatic prediction for br ca #NGDx15

5:37pm August 18th 2015 via Hootsuite

Patterson: Using FNA - 6mm punches, also FFPE material on br cores; derived 'malignancy score' now in clinical trial (MDAnderson) #NGDx15

5:36pm August 18th 2015 via Hootsuite

Patterson:Showed data for tissue suspension from lung. Kit now RUO, will be IVD, tube-based assay, w/non-shearing homogenizer #NGDx15

5:35pm August 18th 2015 via Hootsuite