Beechem: 3D experiment looks at 5ng DNA, 50ng RNA, 500ng protein (min). 700 targets impt to cancer (RNA). And protein, SNV data too #AGBT16
11:19am February 13th 2016 via Hootsuite
Joe Beechem (NanoString) New optical barcode chemistries power 3D biology & sequencing #AGBT16
11:17am February 13th 2016 via Hootsuite
Hendrickson: Launch of NEB's Cancer Hotspot Panel set for April, can be contacted at nebnextdirect@neb.com #AGBT16
11:14am February 13th 2016 via Hootsuite
Hendrickson: Covers uniformity, uniformity by GC. Shows sensitivity down to well below 5%. Input down to 10ng as well. #AGBT16
11:11am February 13th 2016 via Hootsuite
Hendrickson: Individual bait synthesis allows addition to pre-existing panels. Can specify target size from 100 to 500bp's #AGBT16
11:07am February 13th 2016 via Hootsuite
Hendrickson: 2 IDs: i7 index, 120 UIDs available. i5, up to 12 bases of UMI (unique molecule IDs) #AGBT16
11:05am February 13th 2016 via Hootsuite
Hendrickson: Ligate to end of bait plus hyb'd DNA, Automation-friendly, no ampure-bead cleanups, moderate temps #AGBT16
Hendrickson: Input as low as 10ng; hyb is not tile-based, only 3' end for 90m. Bind to SA, Use enzymes to remove off-target DNA #AGBT16
11:04am February 13th 2016 via Hootsuite
Cynthia Hendrickson (Directed Genomics) Fully customizable hybridization-based enrichment technology w/ capture and library prep #AGBT16.
11:02am February 13th 2016 via Hootsuite
RT @sandiegoscience: Vision, tragedy lead Google exec to head Illumina cancer venture https://t.co/ZoU2hhwXgi https://t.co/OOZPmNHyEI
4:20am February 13th 2016 via Hootsuite
Mungall: NTC rearr 49/41 (78%), matching FISH break-apart pattern. BCL2 rearr 20/26 (77%) #AGBT16
9:05pm February 12th 2016 via Hootsuite
Mungall: On target bases ranged from 22-44% - usable from 7% - 24%. Adequate coverage to determine fusions #AGBT16
9:03pm February 12th 2016 via Hootsuite
Mungall: 220bp ave inserts; custom capture uses SureSelect. Pilot capture: 0.5MB, total is 7.8MB. #AGBT16
9:01pm February 12th 2016 via Hootsuite
Mungall: 100ng DNA, covaris, double bead-based size selection, end-repair with NEB, dA, adapter on Biomek FX. 4-6 PCR cycles #AGBT16
9:00pm February 12th 2016 via Hootsuite
Mungall: Automated FFPE DNA and RNA extraction, yields ranged from 200ng to 7ug (!), 120mm2 surface area1-5 10um scrolls #AGBT16
8:59pm February 12th 2016 via Hootsuite
Mungall: Saw a whole collection from 72 BAC clones and biotinylated baits. '15 J Path https://t.co/mVvNEN1VMp #AGBT16
8:57pm February 12th 2016 via Hootsuite
Mungall: Several new gene fusions ID'd, '12 Blood https://t.co/2ANMmji0QZ FFPE resource now available. Dev workflow, discovery #AGBT16
8:55pm February 12th 2016 via Hootsuite
Mungall: Survival of MYC or BCL2 and OS, K-M plot shows double-hit disease with very poor survival #AGBT16
8:53pm February 12th 2016 via Hootsuite
Mungall:B-cell lymphomas have recurrent translocations, all involve chr 14 where heavy-chain Ig located #AGBT16
8:52pm February 12th 2016 via Hootsuite
Mungall: B-cell lymphoma, dates back 50y Fig from this '15 Nat Rev Imm https://t.co/Q5IFYKxy2u #AGBT16
8:51pm February 12th 2016 via Hootsuite
Andrew Mungall (BCCA) Detection of genomic rearrangements in archival lymphoma tissues using targeted capture sequencing #AGBT16
8:49pm February 12th 2016 via Hootsuite
Aburatani: oxoG artifact flag (to suppress FFPE-induced artifacts) 15-22% samples affected #AGBT16
8:41pm February 12th 2016 via Hootsuite
Aburatani: DNA damage types can have unique signatures; '14 Nature Rev Gen ref https://t.co/VtIe8GMCdX #AGBT16
8:36pm February 12th 2016 via Hootsuite
.@h2so4hurts Not so surprising - very $$$ to stream video (or even just record it). Believe me, one event was $50K (won't say which one!)
8:34pm February 12th 2016 via Hootsuite in reply to h2so4hurts
Aburatani:HGSOC TP53 is most frequent per TCGA; but PARP inhibitors play a role. 81 cases, WES, CN analysis, also methylation #AGBT16
8:30pm February 12th 2016 via Hootsuite
Hiroyuki Aburatani (Univ Tokyo) Genomic assessment of chemotherapy sensitivity in High Grade Serous Ovarian Cancer #AGBT16
8:28pm February 12th 2016 via Hootsuite
Otto:Q:95% indels, how large? A:From 1 to 40 bases, what's available in cell-lines. Hard to find cell lines with larger #AGBT16
8:25pm February 12th 2016 via Hootsuite
Otto:Q:How do you know unique? A:Barcoding, and unique ends (via shotgun) #AGBT16
8:23pm February 12th 2016 via Hootsuite
Otto: Acknowl. Travis Clark on the lab side, and Mark Kennedy on the computational biology side #AGBT16
Otto: Standard of care biopsies, you need to start with that for the best patient option, but ctDNA 'is a powerful option' #AGBT16
8:22pm February 12th 2016 via Hootsuite
OttoStreck shows ctDNA peak, and KRAS signal (as expected). Tissue vs ctDNA concordance lines up nicely (by disease stage) AGBT16
8:21pm February 12th 2016 via Hootsuite
Otto: Prolonged storage in EDTA, incomplete removal of buffy coat. Bioanalyzer shows no 170bp peak #AGBT16
Otto: Ave plasma 4.5mL, of 168, 69% yielded >2,500x even though low quality plasma samples #AGBT16
8:20pm February 12th 2016 via Hootsuite
Otto: Prelim clinical results: sample procurement of 172, majority had very poor quality plasma. Collection was poor. #AGBT16
8:19pm February 12th 2016 via Hootsuite
Otto: 99.9% PPV for subst, 98% or above for indel, fusions, CNA. Fully autom workflow. Inter- and intra-run concordance >95% #AGBT16
8:18pm February 12th 2016 via Hootsuite
Otto: 100% concordance in orthogonal validation via ddPCR. 87/87 somatic alterations, 47 of these at <5% MAF #AGBT16
8:17pm February 12th 2016 via Hootsuite
Otto: CNA: 39 TP, 3 FP, 1 NN, 93% sens, 98% PPV #AGBT16
8:16pm February 12th 2016 via Hootsuite
Otto: SNV: showed 168 TP, 2 FP, 0 FN, 100% sens, 98.8% PPV #AGBT16
Otto: Demonstrated contamination control and detection. Intra- and inter-run concordance. #AGBT16
8:15pm February 12th 2016 via Hootsuite
Otto: Best practices of FoundationOne - accuracy, PPV for subst, indels, fusions, CNA. Workflow, compatibility and contamination ctl #AGBT16
Otto: Maintain uniformity - normalized coverage plot look very good, down-sampling to 5,000x still 99% covered >2500x #AGBT16
8:14pm February 12th 2016 via Hootsuite
Otto: 90% of samples with >25ng of ctDNA yield >5000x unique exon coverage. #AGBT16
8:13pm February 12th 2016 via Hootsuite
Otto: Library construction and bioinformatics were the major effort. Initial data - overall 50-70% conversion from ctDNA to sequence #AGBT16
Otto: Need 5,000x unique (non-duplicate) coverage. Automating workflow - 18 mos of work. Will share detail 'in near future' #AGBT16
8:12pm February 12th 2016 via Hootsuite
Otto: Pef spec - as many pts as possilbe. PPVs >99% for subst. or >95% for rest (indels, rearr, CNA, CN>8, 10mL plasma 25-200 ng DN
Otto: Other - pts who have relapsed on targeted therapies. #AGBT16
8:11pm February 12th 2016 via Hootsuite
Otto: No way to assay tumor content. 2 key indications: some is better than none. (Biopsy unacceptable risk or unaccessable) #AGBT16
8:10pm February 12th 2016 via Hootsuite
Otto: Formalin fixation - can assay for tumor content. Liquid biopsies - exciting, but indirect interrogation. Apoptosis or necrosis #AGBT16
Otto: 5. Operational - it has to actually work, in a reasonable timeframe. For them - 14d #AGBT16
8:09pm February 12th 2016 via Hootsuite
Otto: 4. Analytic validation - validation results have to be made transparent tot he field. #AGBT16
