Goode: Have BaseSpace both as cloud and on-site flavors. mid-output has 8M reads, 1-8 panels, PE150 17h. High output 8-24 panels #ESHG2016
1:44pm May 22nd 2016 via Hootsuite
Goode: Local run-manager; analysis modules has 8 applications (amplicon, amplicon DS, TruSight tumor 15, resequencing, DNA enrich #ESHG2016
1:41pm May 22nd 2016 via Hootsuite
Goode: Integrated cartridge, shipped/stored frozen. Waste handling made simple; Formamide self-contained #ESHG2016
1:40pm May 22nd 2016 via Hootsuite
Goode: MiniSeq $49.5K price, $550-1500/run; PE150 80% >Q30, 1.9-7.5GB, 8-25M clusters. Flow cell looks like a MiSeq; 2-channel #ESHG2016
1:38pm May 22nd 2016 via Hootsuite
@illumina workshop here at #ESHG2016 Jason Goode, product manager presents new MiniSeq in context of MiSeq, NextSeq500, HiSeq series.
1:36pm May 22nd 2016 via Hootsuite
Lo: Typically, 1000 genomes / mL plasma, so 4,000 genomes #ESHG2016
1:22pm May 22nd 2016 via Hootsuite
Q: How much plasma needed for this hypothesis? Lo: Currently use 8mL blood, 4mL plasma, 1 library. Methylation 100M reads #ESHG2016
Q: What will be the first for the clinic? Lo: Known - like EGFR for NSCLC, usable now. Others viral-assoc'd. #ESHG2016
1:21pm May 22nd 2016 via Hootsuite
Q: Does 'delta M' handle heterogeneity? Lo: Selects for cancerous liver, not normal liver. #ESHG2016
1:20pm May 22nd 2016 via Hootsuite
Lo: Novel method of nucleosome footprint '16 Cell https://t.co/mk3Bkui3oZ "has many applications in the years to come" #ESHG2016
1:18pm May 22nd 2016 via Hootsuite
Lo: In one abnormal maternal plasma 11w, traced CNA in b-cells, woman had follicular lymphoma. Looked at lymph node #ESHG2016
1:15pm May 22nd 2016 via Hootsuite
Lo: Looking at difference of tissue contributions, can derive CNA. Other tissues won't find this difference. Shows liver CN data #ESHG2016
1:14pm May 22nd 2016 via Hootsuite
Lo: A specific approach, rather than genome-wide. But can't look at CNA when looking at specific regions. #ESHG2016
1:13pm May 22nd 2016 via Hootsuite
Lo: Their method late '15 PNAS: https://t.co/sQ2CoXj2yQ Recent PNAS: https://t.co/sa88GC7PTW alt method #ESHG2016
1:12pm May 22nd 2016 via Hootsuite
Lo: Now to cancer: how much liver DNA in plasma. Also look at allelic loss analysis #ESHG2016
1:10pm May 22nd 2016 via Hootsuite
Lo: Shows these four sources across 1/2/3 trimesters, data on fetal fraction and paternal SNPs correlation #ESHG2016
1:09pm May 22nd 2016 via Hootsuite
Lo: Showed data from mixture experiments. WG bisulfite seq, attributes origin to placenta, liver, lymphocytes, neutrophils #ESHG2016
1:08pm May 22nd 2016 via Hootsuite
Lo: Will a male liver form cfDNA in a female recipient of the ogan? Yes - '98 ref https://t.co/jbTlYd3j1c #ESHG2016
1:07pm May 22nd 2016 via Hootsuite
Lo: Fetal fraction comes from placenta - methylation ref '05 PNAS https://t.co/nVjxLy3eBt #ESHG2016
1:05pm May 22nd 2016 via Hootsuite
Lo: Need the total 5,800 methylation markers. Need DNA mixture experiments, clinical scenarios. #ESHG2016
1:04pm May 22nd 2016 via Hootsuite
Lo: Work made easier by organ-specific WG methylome data from others. 1013 markers Type I (less dense); 4807 Type II (less spec) #ESHG2016
1:03pm May 22nd 2016 via Hootsuite
Lo: Determine tissue-specificity via methylation of cfDNA '15 PNAS https://t.co/nsFX6BQeUC applied to whole range of settings #ESHG2016
1:01pm May 22nd 2016 via Hootsuite
Lo: Increased use of NIPT; unexpected results Dx cancer. '15 JAMA Onco. https://t.co/D7aNnMnfFV About 1/1000 pregnancies #ESHG2016
1:00pm May 22nd 2016 via Hootsuite
Lo: in HBV carriers - data suggests being able to detect HCC early '14 PNAS https://t.co/BsapcRNvol #ESHG2016
12:58pm May 22nd 2016 via Hootsuite
Lo: Focus on liver cancer: due to high prevalence of hepatitis. Shows circos plot, pre- and post-resection plots #ESHG2016
12:57pm May 22nd 2016 via Hootsuite
Lo: Decided to work on both ctDNA and non-invasive prenatal testing. Background '11 ref https://t.co/6OsUYrmIyE #ESHG2016
12:55pm May 22nd 2016 via Hootsuite
Dennis Lo (Chinese Univ HK) Genomewide plasma DNA sequencing for cancer detection and noninvasive prenatal testing #ESHG2016
12:53pm May 22nd 2016 via Hootsuite
Q: How do you see clinical implementation of CTCs? Dive: Turnaround time of about 2 weeks currently #ESHG2016
12:52pm May 22nd 2016 via Hootsuite
.@gtyrelle Thank you for the kind #ESHG2016 mention, Greg!
12:49pm May 22nd 2016 via Hootsuite in reply to gtyrelle
Dive: Can find CellSearch CTCs in pulmonary vein blood (not in venous) in Stg I-III NSCLC. W/ Swanton, TRACERx generate phylogeny #ESHG2016
12:48pm May 22nd 2016 via Hootsuite
Dive: Now clinical trial for SCLC will start at MSKCC this Fall by AZ. #ESHG2016
12:45pm May 22nd 2016 via Hootsuite
Dive: W/ AstraZeneca, a Wee1 inhibitor, combine with PARP inhibitor for SCLC. In CDX3, efficacy shown. Mice: 1y SCLC survivor! #ESHG2016
Dive: Shows chemosens/chemorefractive CDX, where models mirror patient response. #ESHG2016
12:42pm May 22nd 2016 via Hootsuite
Dive: Markers, looks at CNA analysis of 13 genes; biopsy vs CDX. Unpublished data have a CNA classifier w/predictive value #ESHG2016
Dive: Now can observe progression of the biology. Have 5 CDX matched pairs (presentation and progression) Shows histology cp #ESHG2016
12:40pm May 22nd 2016 via Hootsuite
Dive: Called CDX - CTC-derived patient eXplants. '14 Nature Med ref https://t.co/EQQfI6h3vJ Can use as few as 5 cells regenerate #ESHG2016
12:39pm May 22nd 2016 via Hootsuite
Dive: High number of CTCs in SCLC with large dynamic range - a pharmacodynamic marker #ESHG2016
12:37pm May 22nd 2016 via Hootsuite
Dive: Change in CTC number is a surrogate of response, prognostic for PFS and OS; also a ready source of predictive biomarkers #ESHG2016
12:36pm May 22nd 2016 via Hootsuite
Dive: Shows figure from '15 Nature ref https://t.co/YrVaTZwCed extraordinary heterogeneous mutation pattern #ESHG2016
12:35pm May 22nd 2016 via Hootsuite
Dive: Others - Spiral Chip ('dev in Singapore', likely ClearBridge); Parsortix, others. SCLC - 12-20% of lung ca cases. 5y surv 5% #ESHG2016
12:33pm May 22nd 2016 via Hootsuite
Dive: Switching to CTCs: has a multitude of technologies; marker-dep, CellSearch finds EpCAM+ cells; Gilupi as well #ESHG2016
12:32pm May 22nd 2016 via Hootsuite
Dive: 35/40 TARGET pts have at least 1 mutation ID'd in ctDNA, input 6-12mL plasma, 5-25ng input DNA #ESHG2016
12:31pm May 22nd 2016 via Hootsuite
Dive: And then 653 gene panel enrichment from WGS library; ddPCR on original cfDNA sample. Current status, TARGET Ph II is 40 pts #ESHG2016
12:30pm May 22nd 2016 via Hootsuite
Dive: Describes TARGET exp'tl plan, with matched patient-derived xenograft, ctDNA collection. Does a WGS library from cfDNA #ESHG2016
12:29pm May 22nd 2016 via Hootsuite
Carolyn Dive (Cancer Res UK Manchester) Circulating Tumour DNA & Circulating Tumour Cells: Complimentary Approaches #ESHG2016
12:28pm May 22nd 2016 via Hootsuite
Eichler: Class II: private inh SNV and CNV LGD; maternal transmission, >8%. Class III: smaller CNVs, disruptive in reg regions #ESHG2016
12:20pm May 22nd 2016 via Hootsuite
Eichler: ASD divided into different classes: class I, de novo, necessary and sufficient, correlate w/paternal age. ~30% #ESHG2016
12:19pm May 22nd 2016 via Hootsuite
Eichler: (Note: powerful case just made for WGS over WES for studies like this one.) 'I think this is where the action will be' #ESHG2016
12:18pm May 22nd 2016 via Hootsuite
Eichler: Comparing WES to WGS: picked up add'l 65 de novo mutations (from 190 via WES alone). Two novel large de novo by WGS #ESHG2016
12:17pm May 22nd 2016 via Hootsuite
Eichler: Study n=50 WGS '16 AJHG https://t.co/BfrrM0cQtw and shows an example of de novo and private disruption of non-coding seq #ESHG2016
12:15pm May 22nd 2016 via Hootsuite
