New post: NanoString’s Hyb & Seq Single Molecule Sequencer at #AGBT18 https://t.co/1c9RUMc6wu

8:20am February 16th 2018 via WP to TWTR on Yuzuki.org

New post: Highlights from the #AGBT18 Advances in Genome Biology and Technology Orlando Florida https://t.co/UxsAqjqZel

6:56pm February 15th 2018 via WP to TWTR on Yuzuki.org

McCombie: 'Long reads are crucial for accurate SV calling'. Resovles FPs, detection of potential cancer risk factors #AGBT18

4:07pm February 15th 2018 via Hootsuite

McCombie:Sample and DNA req's 'one of the largest barriers for clinical application'. Organoids can get larger amts. #AGBT18

4:06pm February 15th 2018 via Hootsuite

McCombie: Summary - long read platforms have 'matured significantly'; PACB and ONT producing similar length distributions #AGBT18

4:05pm February 15th 2018 via Hootsuite

McCombie: #AGBT18 Shows nice slide of differential methylation in organoid using this method '17 https://t.co/dUcL34IJx7

4:04pm February 15th 2018 via Hootsuite

McCombie: ONT saw 62bp repeat expansion in BRCA1, 'surprised us' #AGBT18

4:03pm February 15th 2018 via Hootsuite

McCombie: CNA: normal, tumor organoid, cell line comparison looks clean. SV analysis shown. SVs only tumor: 3662 lost via short read #AGBT18

4:01pm February 15th 2018 via Hootsuite

McCombie: a ton of methods for organoid interrogation. #agbt18 https://t.co/ZYotpnTdwz

4:00pm February 15th 2018 via Hootsuite

McCombie: Organoids: an improved method for cancer. Figure https://t.co/oYIjDCGeQK Grow in 3D, stable genotype #AGBT18

3:59pm February 15th 2018 via Hootsuite

McCombie: 10,099 PACB and ONT overlap. 5.4K unique to PACB; 4.4K unique to ILM PCR shows most are FP, esp translocs #AGBT18

3:57pm February 15th 2018 via Hootsuite

McCombie: For SVs, comparison of SKBR3 agree very well between PACB and ONT #AGBT18

3:56pm February 15th 2018 via Hootsuite

McCombie: Importance of SVs in cancer '06 ref https://t.co/e4HuaO7Hzt Now via Pacbio - https://t.co/aRWm5RmJF1 analysis cell line #AGBT18

3:54pm February 15th 2018 via Hootsuite

Dick McCombie (Cold Spring NY) Analyzing -omic Instability in breast cancer with nanopore sequencing of patient-derived organoids #AGBT18

3:51pm February 15th 2018 via Hootsuite

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: 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