Q: Can you observe SNP profile over time? Grskovic: Not expected over time. A few 100 SNPs chosen #AGBT18
3:50pm February 15th 2018 via Hootsuite
Grskovic: Landmark prospective study, 400 pts and 2108 pt visits. Submitted all data to CMS, MolDx Palmetto https://t.co/hn98tJpJHR #AGBT18
3:47pm February 15th 2018 via Hootsuite
Grskovic: Range down to 0.2%; can go as high at 16%. '16 validation study https://t.co/jxmB4ga9uQ #AGBT18
3:44pm February 15th 2018 via Hootsuite
Grskovic: Payers: all the way through clinical utility. Their early devl use NGS guidelines (from CAP, ACMG, ASP, others), standards #AGBT18
3:43pm February 15th 2018 via Hootsuite
Grskovic: Walks through concept, test opt, CLIA, analytical process validation, clinical validation, clinical utility, clin use #AGBT18
3:41pm February 15th 2018 via Hootsuite
Grskovic: donor-derived cfNDA - have a specific signature. In stable recipients, concept around since '98 https://t.co/98HbWCSvps #AGBT18
3:38pm February 15th 2018 via Hootsuite
Grskovic: Serum creatinine suffers from poor sens/spec. Life-long immunosuppression leads to cancer, infection, side-effects #AGBT18
3:35pm February 15th 2018 via Hootsuite
Grskovic: First kidney xplant was to an identical twin. Still ave survival <10y. Limited organ avail, surveillance invasive #AGBT18
3:34pm February 15th 2018 via Hootsuite
Marica Grskovic (CareDx CA) dd-cfDNA, a transplant biomarker in clinical diagnostics – from discovery to clinical practice #AGBT18
3:33pm February 15th 2018 via Hootsuite
Cuppen: MLH1 deficiency as a driver for a group of mutation signatures in an organoid model '17 Science https://t.co/H56GOfrw9p #AGBT18
3:27pm February 15th 2018 via Hootsuite
Edwin Cuppen (Utrecht Netherlands) Use of CRISPR-modified stem cell organoids to study the origin of mutational signatures in cancer #AGBT18
3:25pm February 15th 2018 via Hootsuite
Keller comparing MiSeq to ONT RT @ncloonan: MK table of results #AGBT18 https://t.co/4aLWwByWcr
2:44pm February 15th 2018 via Hootsuite
Keller: MIA: Mobile Influenza Analysis - the future. https://t.co/8RbAkS7bK5
2:43pm February 15th 2018 via Hootsuite
Keller: Need improved read-level accuracy; improved since launch. Want mixed bases, sub-populations, modified bases #AGBT18
2:41pm February 15th 2018 via Hootsuite
Keller: Was able to get 100% coverage, 99.7% identity . First full-genome RNA-seq; a 'unique and tranformative technology'. #AGBT18
2:40pm February 15th 2018 via Hootsuite
RT @mason_lab: Update from this morning #AGBT18 about @Covaris -the transition and transversion artifacts can be corrected by simply fragme…
2:32pm February 15th 2018 via Hootsuite
Keller: Helicos - still indirect, as it was still cDNA being measured. ONT: RNA ligated to adapter, sequencing the molecule itself #AGBT18
2:31pm February 15th 2018 via Hootsuite
Keller: Direct RNA - the hard way was from '79: https://t.co/ls93wn6aDa Today cDNA's method is RNA via cDNA - but what is lost? #AGBT18
2:30pm February 15th 2018 via Hootsuite
Matthew Keller (CDC US) MinION nanopore sequencing of influenza #AGBT18
2:29pm February 15th 2018 via Hootsuite
Q: FAST5 files, any base mods on PromethION? McGrath: Didn't look at that, am interested in collaboration #AGBT18
1:58pm February 15th 2018 via Hootsuite
Q:Time for alignment/classification vs runtime? McGrath: One Codex was post-run. (didn't answer time it takes) #AGBT18
1:57pm February 15th 2018 via Hootsuite
McGrath: On MinION vs NextXeq: within 1h able to get a similar profile. (Also One Codex analyzed.) #AGBT18
1:54pm February 15th 2018 via Hootsuite
McGrath: Briefly reviews range of publications, including Cardiovasc disease. Shows a neat clip from Scrubs. 'Looking at your poo.' #AGBT18
1:53pm February 15th 2018 via Hootsuite
McGrath: Shorter reads can't assign at the spp level. Microbial ID by time- first 60 mins of run vs 48hr, identical. 1 min consensus #AGBT18
1:51pm February 15th 2018 via Hootsuite
McGrath: Cp between metagenomic control HiSeq vs PromethION; 29M vs 198K reads; representation different. One Codex analysis #AGBT18
1:49pm February 15th 2018 via Hootsuite
McGrath: Shows PromethION video of chip and loading. Developed ABRF-MGRG 10 strain even mix genomic material. Even but not by size #AGBT18
1:48pm February 15th 2018 via Hootsuite
McGrath: Shows 2014 first run on R6. PromethION: 120GB/flowcell, up to 48 in parallel, in pre-beta mode. #AGBT18
1:41pm February 15th 2018 via Hootsuite
McGrath: Cost / (Quality of base * length of read of that base) $/QBL "cost per quibble"? #AGBT18
1:39pm February 15th 2018 via Hootsuite
McGrath: Slide called 'dollar per base fallacy': all bases are equal, some moreso than others. Read quality impt #AGBT18
1:38pm February 15th 2018 via Hootsuite
McGrath: Cp short vs long reads for metagenomics; short 'perfect reads' vs a long 'noisy' one; 2kb = 1-2 unique organisms. 5kb = 1sp #AGBT18
1:37pm February 15th 2018 via Hootsuite
McGrath:Flongle (flow cell dongle) MinIT (GPU accelerators) on-deck. #AGBT18
1:36pm February 15th 2018 via Hootsuite
McGrath: ONT’s next platform. #AGBT18 #sequencinghumor https://t.co/fm7uSbnoIY
1:35pm February 15th 2018 via Hootsuite
McGrath: The Game of Thrones analogies at #AGBT18 https://t.co/csLYmTwtXX
1:34pm February 15th 2018 via Hootsuite
Ken McGrath (Australian Genome Res AUS) For richer; for pore-er: Resolving metagenomic richness, diversity with nanopore sequencing #AGBT18
1:32pm February 15th 2018 via Hootsuite
RT @bioinformer: @illumina The @Illumina iSeq up close and personal #AGBT18 https://t.co/9pQckXdfYi
12:25pm February 15th 2018 via Hootsuite
Horejsh: Onto ProNex NGS Library Quant for Illumina. Bright Green ('it's brighter') and better reproducibility cp to KAPA #AGBT18
11:19am February 15th 2018 via Hootsuite
Horejsh: Shows double-cutoffs; shows 0.9% CV against 6% C of AMPure XP, and recovery 60% vs 80%+ #AGBT18
11:17am February 15th 2018 via Hootsuite
Horejsh: Also wanted lower viscosity, and kits with wash and elution buffers. Shows data for buffer exchange w/ladder DNAs w/cutoffs #AGBT18
11:16am February 15th 2018 via Hootsuite
Horejsh: Offers software, internal control. Also ProNex size-selection: want greater % recovery, better sizing, lower HMW carryover #AGBT18
11:15am February 15th 2018 via Hootsuite
Horejsh: cfDNA from plasma - yields of 10ng by Maxwell in HT. Next: QC, called ProNex, human-spec, size via 75, 150, 300bp amplicons #AGBT18
11:13am February 15th 2018 via Hootsuite
Douglas Horejsh (Promega Corporation WI) Optimized NGS Workflow Solutions #AGBT18
11:11am February 15th 2018 via Hootsuite
Mason: Shows NEBNext Ultra II data - consistent gene body coverage from these space samples #AGBT18
10:19am February 15th 2018 via Hootsuite
Mason: Shows fascinating video of an astronaut self-drawing blood. 95% viability 36h post-extraction in Houston #AGBT18
10:18am February 15th 2018 via Hootsuite
Mason: How many genes are there? 23,347 in v27 GENCODE. Pesudogenes: 14,694 #AGBT18
10:17am February 15th 2018 via Hootsuite
Mason: DNA can be used irectly - water, tris, TE. Now twin astronaut metagenomes. Using metaSUB pipeline https://t.co/ZoWEWrDoTm #AGBT18
10:12am February 15th 2018 via Hootsuite
Mason: This is the 'scariest paper I've read in some time' '17 https://t.co/Saj4DbGKEx #AGBT18
10:10am February 15th 2018 via Hootsuite
Mason: Ultra II FS: fragmentation. 100pg to 500 ng. 8m-14min hands-on. 1.5h total time. Shows nice titration from200ng to 100 pg #AGBT18
10:09am February 15th 2018 via Hootsuite
Mason: Built environment microbes. Showed cleanroom data, commented on the inability to determine people genomes from JPL #AGBT18
10:08am February 15th 2018 via Hootsuite
Mason: Mars 2020 rover: not a sequencer yet. Shows JPL sign 'alien crossing'. Sampling sites; Found elizabethkingia miricola #AGBT18
10:07am February 15th 2018 via Hootsuite
Mason: Snows NEB reagensts plus a ceiling fan as a centrifuge. Magnet from a fridge 'limited resource settings'. #AGBT18
10:06am February 15th 2018 via Hootsuite
