Lawrence: 'This won't work b/c...' but rec'd a high-risk NIH grant. First used ZFN to edit and paste 21kb transgene. #ASHG2013
6:38pm October 22nd 2013 via Hootsuite
Lawrence: Idea - take dosage imbalance from X-chrom inactivation. XIST is the 19kb non-coding RNA only from inactive X #ASHG2013
6:35pm October 22nd 2013 via Hootsuite
Lawrence: 'Chromosomal disorders remain largely outside hopeful advances of genetics and biomedicine' #ASHG2013
6:34pm October 22nd 2013 via Hootsuite
Lawrence: 1:140 births have a chrom. disorder. 1/700 T21; 400K in the US; 6M worldwide. 50% congen. heart disease #ASHG2013
6:33pm October 22nd 2013 via Hootsuite
Jeanne Lawrence 'Transl. dosage compensation to Trisomy 21' Translational epigenetics #ASHG2013
6:32pm October 22nd 2013 via Hootsuite
Useful! MT @girlscientist: If you don't want tweets from #ASHG2013 this week, here's one way to block a hashtag: http://t.co/IaoPO8jRQy
6:25pm October 22nd 2013 via Hootsuite
Loviglio: Correlated 49 differentially expressed genes in the deleted / dupl. regions. Of these 3 were correlated with ASD #ASHG2013
6:09pm October 22nd 2013 via Hootsuite
Loviglio: 5 genes in 600kb region selected for 4C analysis. 2 controls, 2 600kb del, 2 600kb dupl. #ASHG2013
6:02pm October 22nd 2013 via Hootsuite
Loviglio: Looked at region using 3C (chromosome conformation capture); higher-order chromosome organization affecting del. / dupl. #ASHG2013
6:00pm October 22nd 2013 via Hootsuite
Loviglio: 16p11.2 region proximal 600kb, microdeletion locus ass'd w/ autism, duplication w/ schiz. in addition to obesity. #ASHG2013
5:55pm October 22nd 2013 via Hootsuite
RT @Genomethics: DDD project aiming for 36,000 samples. Doing sequencing on trios #ASHG2013
5:46pm October 22nd 2013 via Hootsuite
RT @girlscientist: Don't forget #ASHG2013 tweetup tonight, 7:30pm, MJ O'Connor's Pub right next to the Westin.
4:25pm October 22nd 2013 via Hootsuite
RT @GeneticsSociety: Pack a coat for #ASHG2013! Highs only in the 50s this week; lows in the 30s. Forecast still calls for great science!
3:26pm October 22nd 2013 via Hootsuite
Mike McKenna, VP of Molecular Biology, wrapping up at #ionworld2013 http://t.co/HDpGUN6vqZ
2:31pm October 22nd 2013 via Hootsuite
McKenna: Showed 30Gb runs from a PII chip in October #ionworld2013
2:27pm October 22nd 2013 via Hootsuite
McKenna: System: not much to talk about. Built to handle PII capacity. 5 Gbps links robust, able to get to 14 Gbps #ionworld2013
2:26pm October 22nd 2013 via Hootsuite
McKenna: All core data rates have been tested, timeline listed for CMOS design, mfg. 30 layers of masks. Today: in mfg #ionworld2013
2:24pm October 22nd 2013 via Hootsuite
McKenna: Data transfer: Cisco routers 100 Gbps; PII will go 120 Gbps. 120 1Gb ethernet cables. 36K Netflix movies at once! #ionworld2013
2:23pm October 22nd 2013 via Hootsuite
McKenna: Sensor illustrated, then sensor plate, to the transistor. P1 electronics with P2 wells on top: 1/4 wells usable #ionworld2013
2:19pm October 22nd 2013 via Hootsuite
McKenna: Used a to-scale HiSeq cluster and compared it to the size of a PII well. Well geometry, sensor structure, materials #ionworld2013
2:18pm October 22nd 2013 via Hootsuite
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
