Kulkani: Challenges - sample procurement; complexity of cancer genome; heterogeneity; structural var's; informatics #NGDx16
2:46pm August 23rd 2016 via Hootsuite
Kulkani: Why genomic aberrations via NGS for cancer? Still cost-effective precision medicine. 'Sitting on a fantastic technology' #NGDx16
2:45pm August 23rd 2016 via Hootsuite
Kulkani: After WGS - PML inserted into RARA, a 77,06bp insertion (!), and developed Fosmid to dev test #NGDx16
Kulkani: Pt with APL or AML w/unfavorable-risk cytogenetics Cp. cyto to two-color FISH for RARA-PML and converse (diff trtmt) #NGDx16
2:43pm August 23rd 2016 via Hootsuite
Kulkani: Pt died before results worked-up; w/3 minor children, results given to family. (anectdotally), all children then tested #NGDx16
2:42pm August 23rd 2016 via Hootsuite
Kulkani: Pt developed AML; spectral karyotyping showed multiple rearrangements. Skin/Bone Marrow showed TP53 germline deletion #NGDx16
2:41pm August 23rd 2016 via Hootsuite
Kulkani: At Baylor they are able to go from WGS discovery to Dx; starts with a case-study. 37yo female, T2N1 Breast Ca, ER/PR/Her2+ #NGDx16
2:39pm August 23rd 2016 via Hootsuite
Shashi Kulkani (Baylor Miraca) Clinical cancer genomics - driving precision medicine #NGDx16
2:37pm August 23rd 2016 via Hootsuite
Q: Variation in HGVS nomenclature? Voelkerding: Not had graded before on it, it is something that needs study by itself #NGDx16
Voelkerding: 'We need more inter-lab, inter-institution studies to guide development of NGS stds' (Well-said!) #NGDx16
2:33pm August 23rd 2016 via Hootsuite
Voelkerding: Summary - considerable multi-stakeholder discussion of NGS stds; prof testing provides one view into lab performance #NGDx16
RT @h2so4hurts: Oh good, Dale's here again, I can take a break. #NGDx16 https://t.co/kxQX1Yx6Ka
2:32pm August 23rd 2016 via Twitter Web Client
Voelkerding: (by 'missed', show it as heterozygous mutation rather than homozygous.) Of 46 labs, 60% preferred. Spread in responses #NGDx16
2:31pm August 23rd 2016 via Hootsuite
Voelkerding: EYS deletion, upstream of met initiation codon. Homozygous deletion - but problem w/reads not spanning repeat missed #NGDx16
2:30pm August 23rd 2016 via Hootsuite
Voelkerding: This deletion, 84% preferred and acceptable. 1 reported an SNV. #NGDx16
2:29pm August 23rd 2016 via Hootsuite
Voelkerding: 2016 PT - APB31 deletion (31bp). 52 labs tested, 44 detected, 4 didn't, 4 could not evaluate. 64% of the 44 preferred #NGDx16
2:28pm August 23rd 2016 via Hootsuite
Voelkerding: For 10 indels in study: preferred response 56%. SNV detection was solid; indels was variable. #NGDx16
2:26pm August 23rd 2016 via Hootsuite
Voelkerding: Germline insertions - majority confirm via Sanger. Didn't ask for Sanger confirmation for the survey, due to $ consid #NGDx16
2:24pm August 23rd 2016 via Hootsuite
Voelkerding: For insertions - 22/29 labs detected AKAP9 insertion. 4 missed; 3 couldn't evaluate #NGDx16
2:23pm August 23rd 2016 via Hootsuite
Voelkerding: In 200 positions, preferred response ave = 89% of 161 SNVs #NGDx16
2:21pm August 23rd 2016 via Hootsuite
Voelkerding: Grading scale for HGVS description completeness; ATB6V1B1 was tested by 23 labs. 20/23 gave 'preferred description'. #NGDx16
2:20pm August 23rd 2016 via Hootsuite
Voelkerding: Panels predominated (71 vs 20 WES vs 8 WGS). Diversity of platforms, 66% ILMN 43% Ion Torrent. #NGDx16
2:19pm August 23rd 2016 via Hootsuite
Voelkerding: Results form was 50pp long; 200 positions; filled-in var type, zygosity, how to desscribe in HGVS. #NGDx16
2:18pm August 23rd 2016 via Hootsuite
Voelkerding: Recognizes #GIAB and NIST for building the reference. Dev a 'CAP Genome', offered blinded samples, 139 labs in '15 #NGDx16
2:17pm August 23rd 2016 via Hootsuite
Voelkerding: '14 ref https://t.co/jvmVYnAvlD on methods-based PT within the context of CAP in historical context #NGDx16
2:15pm August 23rd 2016 via Hootsuite
Voelkerding: Proficiency testing (PT) offers a view into multiple laboratory performance. Can see state of the art, and gen practice #NGDx16
2:13pm August 23rd 2016 via Hootsuite
Voelkerding: Referring to 'standards' - what to expect: sens for detection of germline SNVs, and LoD for somatic SNVs #NGDx16
2:12pm August 23rd 2016 via Hootsuite
Karl Voelkerding (ARUP) Assessing the feasibility of performance stds for NGS-based genetic testing #NGDx16
2:11pm August 23rd 2016 via Hootsuite
Wang: Recruiting >300pts for metastatic prostate ca; endpt is PFS; plan to go 501K, CE-IVD. #NGDx16
1:23pm August 23rd 2016 via Hootsuite
Wang: Larger 8-sample/day automated system for staining and separate scanner. Onto favorable comparison to CellSearch (PLoS One '16) #NGDx16
1:22pm August 23rd 2016 via Hootsuite
Wang: Cell enrichment - 4mL with RosettaSep, density gradient, enrich. Shows 230 cell spike-in; recovery of 278; 417 ave WBCs; 4mL #NGDx16
1:17pm August 23rd 2016 via Hootsuite
Wang: Can do Ab staining on-chip, DNA/mRNA FISH, and CTC count. Can do retrieval, for NGS or PCR assays #NGDx16
1:14pm August 23rd 2016 via Hootsuite
Wang: 4-8mL whole blood; shows video of cells being collected. Small device, compact, inexpensive. Shows capture efficiency of 85% #NGDx16
1:13pm August 23rd 2016 via Hootsuite
Wang: Founded in '10 in Michigan; issued 4 patents, launched system '15. 11 pending patents . 56K wells, 8um pore #NGDx16
1:08pm August 23rd 2016 via Hootsuite
Yixin Wang (Celsee Dx) An automated, sensitive microfluidic device for capturing and characterizing CTCs from whole blood samples #NGDx16
1:07pm August 23rd 2016 via Hootsuite
Q: Of the 7 lines, how many cells from these samples? Zeillinger: From 15 to 100's per mL #NGDx16
1:01pm August 23rd 2016 via Hootsuite
Q: Of 7 lines, how many attempts? Zeillinger: 12 mos of work, 120 pt samples, a rough number. Cell aggregates may have some value #NGDx16
12:57pm August 23rd 2016 via Hootsuite
Q: Staining in-cassette or post? Which better? Zeillinger: Both work; in-cassette is larger vols. RNA = in-cassette lysis #NGDx16
12:54pm August 23rd 2016 via Hootsuite
Pantel Q: Micromanip. needed to count cells accurately. 4.5um is leukocyte size Zeillinger: Decided to use 6.5um b/c of contam #NGDx16
12:53pm August 23rd 2016 via Hootsuite
Zeillinger: Need to address first unmet clinical needs, reliable tech, tailored Dx. #NGDx16
12:51pm August 23rd 2016 via Hootsuite
Zeillinger: Diff physical, biological properties, may interact w/blood components. Likely 'no gold std' for enrichment, det, char #NGDx16
Zeillinger: 'Beware - healthy donor blood samples spiked w/cell lines are artificial samples'. Cell lines from tissue <> CTC-derived #
12:50pm August 23rd 2016 via Hootsuite
Zeillinger: Angle now has multiple gap sizes (8um, 6.5um, 4.5um). Shows data on different degree of cell loss across diff cell lines #NGDx16
12:48pm August 23rd 2016 via Hootsuite
Robert Zeillinger (Univ Vienna, Angle PLC-sponsored) CTCs for SCLC, with Parsortix enrichment. Observed EpCAM+; est 7 cell lines #NGDx16
12:44pm August 23rd 2016 via Hootsuite
Raponi: One gene RAD51C are tBRCA-ligh (high LOH) and responded to rucaparib. 3/4 were germline. #NGDx16
12:23pm August 23rd 2016 via Hootsuite
Raponi: Shows waterfall plot of response rates with germline and somatic BRCA mutations - both important, response rates similar #NGDx16
12:21pm August 23rd 2016 via Hootsuite
Raponi: Shows genomic LOH a robust predictor of responsiveness to rucaparib. Moving onto ARIEL2 another clinical trial #NGDx16
12:20pm August 23rd 2016 via Hootsuite
Raponi: n=206, fresh biopsies were more likely to fail NGS compared to archival, due to lower tumor content. #NGDx16
12:17pm August 23rd 2016 via Hootsuite
Raponi: ARIEL2 clin study, 3 prosp-defined molecular subgroups. Capped known germline BRCA. tBRCAmut, tBRCA-like, biomarker neg #NGDx16
12:13pm August 23rd 2016 via Hootsuite
Raponi: Used TCGA and AOCS OS data following Platinum Rx for LOH cutoff. Prospective data pre-specified for trial #NGDx16
12:11pm August 23rd 2016 via Hootsuite
