Mason: Planetary protection: what if we find life? Or resequence a spore we sent out in the first place? Mars 202 rover #AGBT18
10:05am February 15th 2018 via Hootsuite
Mason: Swabs are low input samples. Shows a spacecraft being assembled. Showing what's in the cleanroom. #AGBT18
Mason: Chris asks no photos. Why low input? Clinical, irreplaceable, hard to obtain. Starts w/cool https://t.co/HL2K8Of6bD graphic #AGBT18
10:04am February 15th 2018 via Hootsuite
Chris Mason (New England BioLabs sponsored) Comprehensive metagenomic and transcriptomic characterization of astronauts #AGBT18
10:03am February 15th 2018 via Hootsuite
Q: Not cheap, targeted? Hoischen: Promised to kick down prices, but haven't done it. LR for HLA, but needs WGS for this work #AGBT18
10:02am February 15th 2018 via Hootsuite
Q: Missing data a caller or alignment? Hoischen: Go back and genotype; some events can go back, but not all. Need long reads #AGBT18
10:01am February 15th 2018 via Hootsuite
Hoischen: Got 15M Euro for 20K rare disease cases(!) aim for >500 long-read genomes. https://t.co/euHYBUaf1B #AGBT18
10:00am February 15th 2018 via Hootsuite
Hoischen: Concl: high quality coverage of 21Mb uncovered; 23K SVs/individual. SMRTbell express: 1.5h hands-on, 2-5ug, >7GB/cell #AGBT18
9:59am February 15th 2018 via Hootsuite
Hoischen: Other 'goodies' - zooming out with de novo SNVs, find heterozygous, maternally inh SNP (linkage). #AGBT18
9:57am February 15th 2018 via Hootsuite
Hoischen: How many indels novel? 21.1K, 58% of all called. Next - find genotype/phenotype recurrence in other cases #AGBT18
9:56am February 15th 2018 via Hootsuite
Hoischen: Chr16: 65bp deletion. Shows gel validation. Shows presence in parents. May not be single-copy locus: 1100 tandem repeat! #AGBT18
9:54am February 15th 2018 via Hootsuite
Hoischen: 23K SVs to 1000 SVs not in popln then to 5. But at #AGBT18 too early. Not validated yet. Of >30 validations, only one FP so far
9:53am February 15th 2018 via Hootsuite
Hoischen: SV dist over samples, looking for rare, private. Power of using trios: 5 cand de novo SVs per affected. #AGBT18
9:52am February 15th 2018 via Hootsuite
Hoischen: Shows IGV of 116 heterozygous deletion. Paternal, but short read track of affected were ambiguous #AGBT18
9:51am February 15th 2018 via Hootsuite
Hoischen: 15.4K (68^) novel. 80% insertions, 55% deletions are novel. Overlap: 5.8K. 1092 unique to short read: simple repeats (FPs) #AGBT18
9:50am February 15th 2018 via Hootsuite
Cawley: Acknowledgements - huge mosaic of individuals, forming a photo of their new platform (way cool). #AGBT18
Hoischen: Shows size dist; shows 300bp peak for Alu insertion/deletions. larger SVs (1kb->10kb), 6kb LINE insertions. #AGBT18
9:49am February 15th 2018 via Hootsuite
Hoischen: SV calling (joint calling across 15 samples); low-coverage comes up. 23K SVs/genome (50bp-50kb). #AGBT18
9:48am February 15th 2018 via Hootsuite
Hoischen: 21MB of high quality data not seen. 0.7% of WGS. 7MB overlaps w/geneic regions, 700kb coding region ! #AGBT18
9:47am February 15th 2018 via Hootsuite
Hoischen: Ave readlength 12kb; 4.5GB/SMRTcell. Longest reads >70kb. Now almost 20x coverage across trios still ongoing #AGBT18
Hoischen: Pat cohort (analysed by CNV-microarray, WES, WGS, NovaSeq). Now by PacBio: 880GB / 195 SMRTcells. 5 trios #AGBT18
9:46am February 15th 2018 via Hootsuite
Hoischen: Problem: de novos similar to FPs. '14 https://t.co/sFnB0Oyq9A 38% no diagnosis; about 1/3 de novo SNVs, about 1/4 SVs #AGBT18
9:44am February 15th 2018 via Hootsuite
Hoischen: Focus on de novo: reduces 'search space', b/c so few per genome. And severe, sporadic cases can ID novel paradigms #AGBT18
9:41am February 15th 2018 via Hootsuite
Hoischen: 30-100 de novo SNVs per genome per generation; 1-2 per exome. Mutatoin rates for CNVs is 0.2 per generation. Indels = unk! #AGBT18
Hoischen: Intellectual disability (IQ<70) severe, sporadic disorders. >60% of moderate-severe, sporadic ID is de-novo mutations #AGBT1
9:40am February 15th 2018 via Hootsuite
Alexander Hoischen (Radboud Nijmegen Netherlands) Medical genetics: ID of hidden structural variants with long-read sequencing #AGBT18
9:39am February 15th 2018 via Hootsuite
Q: HD avail? Cawley: Expected launch mid-year 2018 #AGBT18
9:37am February 15th 2018 via Hootsuite
Cawley: Higher All Variant sensitivity - 92% vs 93% w/HD; PPV 98% vs 84%. (Nota bene: unclear what the sensitivty being measured is) #AGBT18
9:36am February 15th 2018 via Hootsuite
Cawley: New lib chemistry: 'method of choice', now made available to Illumina. Now HD: ability to go to 0.1%, cutom, 2-3h prep #AGBT18
9:35am February 15th 2018 via Hootsuite
Cawley: Shows data from partner @OmniSeq and their Immune Report card; show low/intermed/high, using their immune resp assay, TMB #AGBT18
9:34am February 15th 2018 via Hootsuite
Cawley: Co-infiltrates and effect on I-O; can explore of cell lines, T-cell expansion doesn't expand; myeloid supp gene signature #AGBT18
9:33am February 15th 2018 via Hootsuite
Cawley: show clonality and betachain sequence assessment 'without interference from primer bias' #AGBT18
9:32am February 15th 2018 via Hootsuite
Cawley: 1.7MB target for TMB. Launched Immune Repertoire Assay Plus, TCR-beta. All 3 CDRs, germline TRBV from blood #AGBT18
Cawley: 1200 clinical trials for I-O Rx. But key need for biomarkers. Have Tumor Mutation Load assay. #AGBT18
9:31am February 15th 2018 via Hootsuite
Simon Cawley of @thermosci at #AGBT talking about ImmunoOncology - important topic. https://t.co/IuGqnUMk13
9:30am February 15th 2018 via Hootsuite
Cawley: Saw 11 failures w/ddPCR and only 1 w/Oncomine cfDNA. 11 failures 4 were T790M EGFR #AGBT18
9:28am February 15th 2018 via Hootsuite
Cawley: Retrospective study at Princess Margaret (Dr. Stockley): shows ddPCR of EGFR at 0.5%; cfDNA 0.1% (validated) #AGBT18
Cawley: Acrometrix, shows titration down to 0.1% LOD at 20ng input. 30ng input 0.05%. 10ng at 0.15%; 5ng at 0.25%; 1 ng at 0.6% #AGBT18
9:27am February 15th 2018 via Hootsuite
Cawley: cfDNA: pan-cancer, 52 genes, both DNA/RNA, SNVs, indels, fusions, CNVs. Lung cfTNA - 12 genes. Breast: CNVs, broad TP53 #AGBT18
9:26am February 15th 2018 via Hootsuite
Cawley: Small pack sizes (low upfront cost), web UI. Oncology: liquid biopsy and I-O here; FFPE and heme-onc (Myeloid) #AGBT18
9:25am February 15th 2018 via Hootsuite
Cawley: Fits into atuomated AmpliSeq lib prep (<30m hands-on), sequencing (<15m hands-on). On-demand AmpliSeq: 5K genes (inh dis) #AGB
9:24am February 15th 2018 via Hootsuite
Cawley: Field-upgradable from S5, Plus to Prime. 15Gb/30Gb/50Gb. 80M/160M/260M reads across three platforms. #AGBT18
9:23am February 15th 2018 via Hootsuite
Cawley: 550 chip: 100-130M reads to 200bp. 510 low-end 2-3M reads to 400bp. Shows raw read acc of 99.02% to 99.5%. To 600bp on 510 #AGBT18
9:22am February 15th 2018 via Hootsuite
Cawley: Will talk about GeneStudio S5, targeted seq (inh dis), liquid biopsy, I-O, and new technology. Ion GeneStudio S5 Plus, Prime#AGBT18
9:21am February 15th 2018 via Hootsuite
Cawley: 68K employees at TMO (!), from Affy to CE, to MS, EM, pharma services. FDA approved NGS multi-drug, multi-var CDx #AGBT18
9:20am February 15th 2018 via Hootsuite
Simon Cawley (Thermo Fisher) Innovations on Ion Torrent Platform, now in HD #AGBT18
9:19am February 15th 2018 via Hootsuite
Geldart: ctDNA targeted (17 NCCN genes 81kb); ctDNa expanded (77genes 192kb); ctDNA surveillance (197 genes 198kb) TMB #AGBT18
9:15am February 15th 2018 via Hootsuite
Geldart: Have their own Roche Oncology Analysis Server, and secondary analysis. aa changes, allele freq, UMIs, background polishing #AGBT18
9:14am February 15th 2018 via Hootsuite
Geldart: Designed around NextSeq 500/550, and analysis. 5d turnaround time. Library plus is SeqCap probes plus Hypercap reagents #AGBT18
Geldart: AVENIO ctDNA: first 'end-to-end' - sample collection, extract, QC etc. 3 assays, RUO, 4mL plasma, 16 sample thruput #AGBT18
9:13am February 15th 2018 via Hootsuite
