Jennifer Ishii (NY Genome Center) #AGBT19 Advances in whole genome methylation profiling - prelim HS-X data with EM-Seq (sponsored by NEB)
2:39pm March 1st 2019 via Twitter Web Client
Mason #AGBT19 Rank on gene expression and epitope tag. Larger difference in expression of mRNA than protein. mRNA v… https://t.co/k1gl3wSsNa
2:37pm March 1st 2019 via Hootsuite Inc.
Mason #AGBT19 Looking at clinical CAR trials increase in China esp last 18 mos. Looking at markers on BD panels. Yo… https://t.co/l66fhDQ1Nx
2:35pm March 1st 2019 via Twitter Web Client
Mason #AGBT19 Trivial to look at major lineage markers used to ID clusters. Major shift between pre- and post-Rx. N… https://t.co/2eeI58AvW6
2:31pm March 1st 2019 via Twitter Web Client
Chris Mason (Weill Cornell) #AGBT19 T-cell lymphoma clinical samples - 1 pre and 1 post Rx samples, BD Rhapsody, 500 mRNAs, 100 epitopes
2:30pm March 1st 2019 via Twitter Web Client
Blumenstiel #AGBT19 the drive to switch is in the right - 85% at 20x ‘with a lot less sequencing’ (about 50% less f… https://t.co/oNUk1ssiNW
1:20pm March 1st 2019 via Hootsuite Inc.
Blumenstiel #AGBT19 A fold-80 coverage plot showing penalty of coverage - lower is better. https://t.co/MMV8JaVIkk
1:18pm March 1st 2019 via Hootsuite Inc.
Blumenstiel #AGBT19 Sample number, target territory, and third dimension now of depth.
1:11pm March 1st 2019 via Twitter Web Client
Blumenstiel #AGBT19 Automated blood extraction (Q QiaSymphony, 240/week). Also couple with Hamilton easyBlood camer… https://t.co/FNIsJ4wRQj
1:06pm March 1st 2019 via Twitter Web Client
Blumenstiel #AGBT19 Also less than 1 FP per MB of target.
1:03pm March 1st 2019 via Twitter Web Client
Blumenstiel #AGBT19 Wanted a single workflow. Wanted 10's to 100's of genes, sensitivity to 1% or less. Future: MRD… https://t.co/lI2OftZmTF
Blumenstiel #AGBT19 Have to use UMI's, as cfDNA is only about 166bp, reduce duplicates and PCR errors.
1:02pm March 1st 2019 via Twitter Web Client
Blumenstiel #AGBT19 Blood biopsy - WGS ultra low-pass of cfDNA 0.1x to determine healthy or cancer. '18 Nature Comm https://t.co/8NlmKrUwzY
1:01pm March 1st 2019 via Twitter Web Client
Blumenstiel #AGBT19 They generate a WGS equivalent of data every 12 minutes at the Broad. (whew.)
12:59pm March 1st 2019 via Twitter Web Client
Blumenstiel #AGBT19 The Broad genomics platform (research and clinical, tech dev too) and data sciences platform. T… https://t.co/FyoNd5lFez
12:58pm March 1st 2019 via Twitter Web Client
Brendan Blumenstiel (Broad) #AGBT19 Enabling disease specific research using dynamic targeted sequencing
12:57pm March 1st 2019 via Twitter Web Client
Renata Pellegrino da Silva (CHOP) #AGBT19 Twist technology - will not tweet as this is unpublished data.
12:37pm March 1st 2019 via Twitter Web Client
Lee #AGBT19 Evaluating performance of an exome - callability vs. total yield. https://t.co/3zsSAmHgLB
12:34pm March 1st 2019 via Hootsuite Inc.
Lee #AGBT19 Designed separate pools for high and low GC region probes, and it didn't work. Then took mismatch probe… https://t.co/Bl21iduR2F
12:32pm March 1st 2019 via Twitter Web Client
Lee #AGBT19 Showed downsampling experiment and function on # of variants called. At half coverage of V2, same number of variants as V1.
12:29pm March 1st 2019 via Twitter Web Client
Lee #AGBT19 Only 6 months and 3 iterations to production. Evaluation of 290K SNPs, measure performance on imputatio… https://t.co/UDXmYVuOGP
12:28pm March 1st 2019 via Twitter Web Client
Lee #AGBT19 v2 had around 400K custom probes, in addition to the core exome. Shows timeline - first design in April… https://t.co/phviw4RyL1
12:27pm March 1st 2019 via Twitter Web Client
RT @TwistBioscience: @EmilyLeproust touts our 15 min hybridization assay- allowing samples to be sequenced in a single day #AGBT19 #AGBT2019
12:24pm March 1st 2019 via Hootsuite Inc.
Lee #AGBT19 v1 had 5k genes, other genes, ncSNPs 180K. v2 had 600 hi-priority genes, 3600 med priority genes, GWAS/… https://t.co/1eUBLvQ3Ps
12:22pm March 1st 2019 via Twitter Web Client
Lee #AGBT19 99% of targeted bases >10x. Cheaper - less cost/sample. Better - covering more of ROI's more often. Fas… https://t.co/lMk0OTa
12:21pm March 1st 2019 via Twitter Web Client
Lee #AGBT19 Processes documented, traceable, and can be improved. Think of Exome+ as medical-grade, >98.5% targeted… https://t.co/zU8w4Rv
12:19pm March 1st 2019 via Twitter Web Client
Lee #AGBT19 Application partners - Nat'l Geo, Mayo, some 20+ partners. Exome+ 'unlocks over 100 times more data tha… https://t.co/JyONHcy34K
12:17pm March 1st 2019 via Twitter Web Client
Lee #AGBT19 Backed by $320M, genome-as-a-service, consumer ecosystem, on-demand DNA 'pay as you go' with low up-front costs.
12:16pm March 1st 2019 via Twitter Web Client
Lee #AGBT19 Helix has an Exome Plus, Helix wants to 'Empower every person to improve their life through DNA'; one o… https://t.co/5euQ2nSWRJ
12:15pm March 1st 2019 via Twitter Web Client
William Lee (Helix) #AGBT19 Design and optimization of an enhanced medical genome
12:14pm March 1st 2019 via Twitter Web Client
LeProust #AGBT19 Adding covaris mechanical frag. Maximizing efficiency and now least effort. Last: lots of gene synthesis.
LeProust #AGBT19 New universal blockers - one blocking solution for multiple adapter applications. Fast hyb: 16h fo… https://t.co/uGxop8Eo2T
12:11pm March 1st 2019 via Twitter Web Client
LeProust #AGBT19 Adding UDI adapters - last step added thru PCR: maximizing yield cp to Y-adapters. No dimers, high… https://t.co/mvHNgslbtC
12:10pm March 1st 2019 via Twitter Web Client
LeProust #AGBT19 Last year launched them, gene list to pilot in 2-3w. Flexibility - enz frag, combinatorial adapters, enrichment, and beads.
12:09pm March 1st 2019 via Twitter Web Client
LeProust #AGBT19 Goal is to get as even as possible - an average 30x, lowering peaks (wasted sequencing) and raising valleys (dropouts).
12:07pm March 1st 2019 via Twitter Web Client
Emily LeProust (Twist) #AGBT19 Founded on the principle of 'rewriting DNA with the power of silicon'. Benefits: fas… https://t.co/0gmn81XldX
12:06pm March 1st 2019 via Twitter Web Client
RT @nanostringtech: “With data demonstrating up to 60-plex protein assays and over 1,400 gene targets, the ability… https://t.co/huNEBWzvcr
12:05pm March 1st 2019 via Hootsuite Inc.
Levy #AGBT19 8- and 10-base UDI, color-balanced, performance-tested, tested on MiSeq, and automated on Beckman i-series robots.
11:45am March 1st 2019 via Twitter Web Client
Shawn Levy (Hudson Alpha) #AGBT19 Removal of technical bias in large-scale sequencing Poster 606. From library crea… https://t.co/dWiME6EgC7
11:44am March 1st 2019 via Twitter Web Client
Guo #AGBT19 Developed a duplex sequencing method, a enzymatic treatment to eliminate damage, and applied to 16 indi… https://t.co/Kkaf0xuheV
11:43am March 1st 2019 via Twitter Web Client
Yirui Guo #AGBT19 Mitochondrial heteroplasmy - linked to several diseases. Accurate detection impt. Challenges - it… https://t.co/82yCEagGad
11:42am March 1st 2019 via Twitter Web Client
Dobin #AGBT19 STARsolo can do a cell / gene exp matrix much faster (poster 212).
11:40am March 1st 2019 via Twitter Web Client
Alex Dobin (CSHL) #AGBT19 STARsolo - mapping and quant of scRNA-seq
11:38am March 1st 2019 via Twitter Web Client
Nattestad #AGBT19 Shows a photo of the height GWAS dataset.
11:37am March 1st 2019 via Twitter Web Client
Nattestad #AGBT19 Thinking of visualizations of data. Manhattan plots, Circos plots. Used a Manhattan plot to start… https://t.co/4ZdbL1o01T
11:36am March 1st 2019 via Twitter Web Client
Maria Nattestad (DNAnexus) #AGBT19 Is VR useful in genomics? Poster 218: 3D objects in biology are useful. But in genomics?
11:35am March 1st 2019 via Twitter Web Client
Hajirasouliha #AGBT19 WGS reveals somatic muts and tumor heterogeneity. Contrasts sc vs bulk: sc has FN and noisy.… https://t.co/cHzgZ4Ta2A
11:34am March 1st 2019 via Twitter Web Client
Iman Hajirasouliha (Weill Cornell) #AGB19 Tumor phylogeny reconstruction via integrative single cell and bulk sequencing
11:32am March 1st 2019 via Twitter Web Client
Q: Use of methylation for binning? Liachko #AGBT19 No limit to other techniques to overlay.
11:30am March 1st 2019 via Twitter Web Client
Liachko #AGBT19 Shows 'lil Bub' (a cat with polydactyly). https://t.co/sl5VHQVw9C Cow rumen '18 Nature Comm https://t.co/LFK3dHH58Q
11:25am March 1st 2019 via Twitter Web Client
