McKenna: Bead formulation has been finished for PII. Microwells: more like nanowells. 3um to 1.3um to 0.6um for PII #ionworld2013
2:16pm October 22nd 2013 via Hootsuite
McKenna: Really not beads, more like microscopic jellyfish. #ionworld2013
2:15pm October 22nd 2013 via Hootsuite
McKenna: Dynal beads, partnered since Nov '10. Size control: 450nm +/- 20 nm reproducibility. #ionworld2013
2:14pm October 22nd 2013 via Hootsuite
McKenna: Bringing up PII sensor: Beads, Microwells, Sensors, Instrument (Proton) #ionworld2013
2:13pm October 22nd 2013 via Hootsuite
McKenna: XT kit for AmpliSeq Exome had different ISPs, better seq enzyme, improved breaking droplets (how duplicates lowered) #ionworld2013
2:09pm October 22nd 2013 via Hootsuite
McKenna: PI v3 on Proton now up to 14Gb. Benefits of Ion XT chemistry, 30% reduction of duplicate rates, 45m shorter OT2 time #ionworld2013
2:08pm October 22nd 2013 via Hootsuite
McKenna: Early access of isothermal starts Nov 2013. #ionworld2013
2:07pm October 22nd 2013 via Hootsuite
McKenna: Used over 600bp libraries. Also works with Proton at 300bp 'ports directly'. Early access supports both PGM, Proton #ionworld2013
2:06pm October 22nd 2013 via Hootsuite
McKenna: Seeing ~20% fewer reads due to lack of partitioning that emulsions bring. (!) #ionworld2013
2:05pm October 22nd 2013 via Hootsuite
McKenna: Add'd time needed for 10 min setup, 15 min wash and cleanup, another 30 min for enrichment. #ionworld2013
2:04pm October 22nd 2013 via Hootsuite
McKenna: Rapid isothermal template prep: formerly known as 'Avalanche'. Single tube amplification, lyophilized tube, 2h #ionworld2013
2:03pm October 22nd 2013 via Hootsuite
McKenna: 'I have never worked in an environment where such a depth of disciplines are needed." #ionworld2013
2:02pm October 22nd 2013 via Hootsuite
Williams: Technology access starting in Nov. for Hi-Q, 6-8w leadtime, available July 2014. #ionworld2013
2:00pm October 22nd 2013 via Hootsuite
Williams: 'Dramatic improvements seen' on a strand-specific basis #ionworld2013 http://t.co/LGFSeSumHP
Williams: "Systematic errors reduced 90%' from 0.224% down to 0.027%. #ionworld2013
1:57pm October 22nd 2013 via Hootsuite
Williams: 10K enzyme variants screened, Hi-Q chemistry is 'massive reduction in indel errors' #ionworld2013
1:55pm October 22nd 2013 via Hootsuite
Williams: Chef Proton (in development) performance at 10.1 - 11.7GB; PGM on Chef first, Proton to launch later. #ionworld2013
1:52pm October 22nd 2013 via Hootsuite
Williams: Iterated the x/y/z stage (more reliability, tolerances), electronics, loading rotor, 6-bucket breaking rotor #ionworld2013
1:48pm October 22nd 2013 via Hootsuite
Williams: Goal of Ion Chef is to 'remove the 'art' from the workflow'. Review of 15min setup time. Two runs/day, two chips/run #ionworld2013
1:47pm October 22nd 2013 via Hootsuite
Williams: Will be talking about the Ion Chef developments and Hi-Q, McKenna will talk about PII and Avalanche #ionworld2013
1:43pm October 22nd 2013 via Hootsuite
Next up: Alan Williams VP Eng and Software and Mike McKenna VP Molecular Biology, "Innovations from Ion Torrent" #ionworld2013
1:41pm October 22nd 2013 via Hootsuite
Photo of Dagan Wells presenting at #ionworld2013 http://t.co/vNfsXymihV
1:38pm October 22nd 2013 via Hootsuite
Wells: Conclude: PGM is a powerful method for aneuploidy screening; shortened time allows fresh embryo xfer #ionworld2013
1:37pm October 22nd 2013 via Hootsuite
Wells: Elevated mtDNA may be useful clinically for implantation. Reported last week, normal blastocysts with +mtDNA did not #ionworld2013
1:35pm October 22nd 2013 via Hootsuite
Wells: Looked at mtDNA in aneuploid embryos - found that mtDNA increases with both age and with aneuploidy #ionworld2013
1:33pm October 22nd 2013 via Hootsuite
Wells: Now looking at single genes: looking at CF (deltaF508) #ionworld2013
1:32pm October 22nd 2013 via Hootsuite
Wells: Avalanche data looking at monosomy 6, clear results presented in Ion Reporter screenshot. #ionworld2013
1:28pm October 22nd 2013 via Hootsuite
Wells: Had access to Avalanche; 'extremely excited', down to ~8h, no need to freeze embryos. #ionworld2013
1:27pm October 22nd 2013 via Hootsuite
Wells: Time: 12.5h, cost: ~$70/sample. 30%-50% cheaper than microarrays. #ionworld2013
Wells: Array Comparative Genomic Hybridization (aCGH) tested embryos (52) tested 100% via NGS #ionworld2013
1:24pm October 22nd 2013 via Hootsuite
Wells: WGS is via Multiple Displacement Amplification (MDA). Some amplify better than others; chr 19 is GC-rich. Reproducible #ionworld2013
1:23pm October 22nd 2013 via Hootsuite
Wells: Do not want WGS on embryos. Only 2.5M reads/run, 52K - 110K reads/sample; 1K - 7K reads/chromosome 'enough' #ionworld2013
1:22pm October 22nd 2013 via Hootsuite
Wells: Strategy: WGA after lysing and NGS. Criteria: simple, robust, accurate, but not too expensive; scalable too. #ionworld2013
1:19pm October 22nd 2013 via Hootsuite
Wells: Before, FISH was used but would miss problems. Recent publications (5 listed in past 2y) ~30% increased implantation #ionworld2013
1:16pm October 22nd 2013 via Hootsuite
Wells: PGD = preimplantation genetic diagnosis: inherited disorders, familial disorders. PGS: screening for abnormal embryos #ionworld2013
1:14pm October 22nd 2013 via Hootsuite
Wells: Embryo at 5d - extraction of trophectoderm cells, embryos are 'incredibly robust', tolerating this kind of insult at 5d #ionworld2013
1:13pm October 22nd 2013 via Hootsuite
Wells: Video of single cell isolation with the zona pellucida being broken with a weak acid, and a single cell extracted. #ionworld2013
1:11pm October 22nd 2013 via Hootsuite
Wells: Aneuploidies increase from 15% to 75% with maternal ages 20y to 40+y, implantation rate decreases #ionworld2013
1:09pm October 22nd 2013 via Hootsuite
Wells: 85% of embryos transferred do not implant. But end up with multiple pregnancies, which increase risk for everyone #ionworld2013
1:06pm October 22nd 2013 via Hootsuite
@bioinformer This morning there were two tracks. Alas I can't be in two places at once! (I missed out, friend from Baylor got a lot from it)
1:05pm October 22nd 2013 via Hootsuite in reply to
Wells: Only 30% IVF cycles result in a pregnancy. Embryo viability is based primarily on morphology. #ionworld2013
1:04pm October 22nd 2013 via Hootsuite
Wells: IVF is highly successful, but inefficient. 5M babies worldwide born following IVF; 1-5% in indust. countries #ionworld2013
1:03pm October 22nd 2013 via Hootsuite
Up next: Dagan Wells, University of Oxford, 'Ultra-rapid aneuploidy detection in single-cells using low-pass whole genome NGS #ionworld2013
1:01pm October 22nd 2013 via Hootsuite
Breakthrough award being presented now to Anna Cebula reference: http://t.co/qxlPz70IDC #ionworld2013 Finalists http://t.co/m48Yt7bXHi
1:00pm October 22nd 2013 via Hootsuite
Sandra Maria Cardoso speaking about 16S rRNA profiling of HIV-positive samples using PGM #ionworld2013 http://t.co/fqBGWFqW83
11:48am October 22nd 2013 via Hootsuite
Cardoso: Challenge - a better alignment tool with highly variable HIV genome #ionworld2013
11:45am October 22nd 2013 via Hootsuite
Cardoso: Sanger-based typing only on short regions; now with NGS can do phylogenetic analysis across geography #ionworld2013
11:43am October 22nd 2013 via Hootsuite
Cardoso: Last section, anti-retroviral treatment, appearance of drug-resistant mutations. And can infect others. #ionworld2013
11:41am October 22nd 2013 via Hootsuite
Cardoso: Overall concordance between PGM and Sanger was only 85%. Sanger too $, labor intensive #ionworld2013
11:39am October 22nd 2013 via Hootsuite
Cardoso: Used Omixon for analysis, discrepancies to Sanger, cross-validated against MiSeq; PGM fully concordant to MiSeq #ionworld2013
