P. Mickey Williams, NCI "NCI-MATCH: A national precision medicine study" #AGBT15
6:35pm March 3rd 2015 via Twitter Web Client
BS: "@iontorrent team, you have been great" #AGBT15
6:34pm March 3rd 2015 via Twitter Web Client
BS:DNA extraction - 192 to 384 libraries/day. 192 across 8 Ion Chef/8 Ion Protons. 16 12-plex runs/d w/only 2 FTE's #AGBT15
BS:8 gDNA in, normalized/pooled libraries out w/Ion Chef automating AmpliSeq #AGBT15
BS:100K/year, thruput needs to increase; compared manual and auto. AmpliSeq on Ion Chef. 93% uniformity and 97% on-target for both #AGBT15
BS:NIST rev 2.18 NA12878 Genome in a Bottle (http://t.co/t9s5wLIKUC) Also put into low-complexity domains affecting stats #AGBT15
BS:Seen strong improvements in moving to Hi-Q chemistry. 4% improvement in sensitivity, 5% increase in PPV. 'Impressive'. #AGBT15
BS: And 90.2% uniformity. 12-plex gives them 200-250x coverage. 'Pretty sweet data for such a highly multiplexed assay' #AGBT15
BS: 275bp inserts along with 100bp peaks - they wanted full-length exons as well as hotspots, bimodal distribution. 96.2% on-target #AGBT15
BS:'On-target and uniformity remains high despite panel diversity' - the 'performance has been amazing for us'. #AGBT15
6:33pm March 3rd 2015 via Twitter Web Client
BS: Their 13 number they are confident about. Now they need to recruit samples; e-consent process w/at-home collection kit #AGBT15
BS:Retrospective view: of 600K samples w/exome datasets, found 13 potential resilient samples. But poor data quality a problem #AGBT15
BS:Has pie-chart of types of conditions (cardiovascular, cancer, PGx, Mendelian...) Project homepage: http://t.co/H8wjvD8Htd #AGBT15
BS: Individuals w/mutation w/o symptoms - naturally resilient, could give impt clues into researching disease #AGBT15
BS: Developed a 25K AmpliSeq panel, for 750 disease-related genes; >4K disease-ass'd genomics hotspots; total 4.4MB target #AGBT15
BS: @icahninstitute take integrated DNA and RNA seq approach; 10 Protons, 3 PGMs, other platforms incl microarray #AGBT15
Next: Bobby Selva Mt Sinai with Resilience Project #AGBT15
6:32pm March 3rd 2015 via Twitter Web Client
More about Isothermal Amplification - interview here: http://t.co/L0nVWg04ov #AGBT15
AW:Reporting sensitivity >99%; 1% limit of detection enabled on Ion Reporter v.4.4 (available now) #AGBT15
AW: Also on http://t.co/6puEapf9xO 140bp designs for cfDNA. New Ion Reporter for 1% variant detection #AGBT15
AW:New LiquidBiopsy platform, getting germline DNA, CTC DNA and cfDNA. All 3 from 1 sample #AGBT15
AW:20-cell input for AmpliSeq, shows very high uniformity, high on-target coverage #AGBT15
AW: Direct AmpliSeq out of blood or buccal swabs; shows Cancer Hotspot v2 coverage data #AGBT15
AW: Other things: putting AmpliSeq library prep on an Ion Chef instrument; nearly automated from sample prep through sequencing #AGBT15
AW:10h template prep now cut in half with Isothermal Amp; >500K reads at >99% accuracy #AGBT15
6:31pm March 3rd 2015 via Twitter Web Client
AW:Isothermal amplification: Ion Chef, partnering with HLA typing org, >600bp readlengths. >200Mb on 314 chip #AGBT15
AW:Data from 30x WGS on PI w/400bp reads: 3.6M SNVs, 1.693 het/hom ratio; Tx/Tv ratio 2.06, 97.4% concordance w/dbSNP (chr1) #AGBT15
AW:Tech access expected 2nd half of 2015, 20G at 400bp goal at launch #AGBT15
AW:Now about PI: pushing readlength and accuracy - 30GB total bases; 400bp modal readlength; 99% accuracy. 3 PI chips = 30x WGS #AGBT15
AW: Did PII w/120bp insert, cell-free DNA analysis on PII, with 21 barcodes separated nicely, nice even coverage #AGBT15
AW:Cp rocket-plots of PI vs PII, for both fresh-frozen and FFPE samples. (Note: AmpliSeq Transcriptome works well for FFPE) #AGBT15
#AGBT15: 12 hour Single-Cell Aneuploid Detection http://t.co/e4Y9moGDVW
6:25pm March 3rd 2015 via Hootsuite
#AGBT15: Sequencing Over 100 Exomes per day http://t.co/a4MFeMYvZb
6:02pm March 3rd 2015 via Hootsuite
RT @noahWG: Wild panda numbers may be rising, but questions on this latest “census” remain http://t.co/7h2UckAHid http://t.co/qS93E7iTcI
5:35pm March 3rd 2015 via Hootsuite
I should frame this @appliedbio Twitter notification. http://t.co/4gKk6HkgNf
5:28pm March 3rd 2015 via Hootsuite
.@kirkenglehardt Really cool! Thanks for sharing. (Ex-musician here.)
5:02pm March 3rd 2015 via Hootsuite in reply to
RT @sjin_lee: PacBio AGBT 2015 Live Workshop: http://t.co/D6WoFgHaNo via @YouTube
4:31pm March 3rd 2015 via Hootsuite in reply to
RT @kirkenglehardt: Another nice Storify on public engagement from the @AAAS conference - http://t.co/xXZ31zIvLH @thegeoffhunt #scicomm
3:25pm March 3rd 2015 via Hootsuite in reply to
RT @m_m_campbell: The X factor. Laser 3D-imaging of virus opens possibility of live cell X-rays. http://t.co/jQWeL9V6xH
2:31pm March 3rd 2015 via Hootsuite in reply to
RT @DailyNewsGW: Qiagen: $114.2M price tag for Enyzmatics acquisition. Contingent cash payments could total $25.5M. http://t.co/TO29A4HY2U
1:45pm March 3rd 2015 via Hootsuite
RT @dynarski: Outsourcing the hard work of being nice. http://t.co/jjhFKiRTQ5… http://t.co/aKI7eE9NWe
12:40pm March 3rd 2015 via Hootsuite
Genetically speaking, mammals are more like their fathers - ScienceDaily http://t.co/DonlYvIUk1 HT @labspaces
11:36am March 3rd 2015 via Hootsuite
RT @illumina: Insightful #AGBT15-inspired post via @h2so4hurts: http://t.co/eQAkRmCNSI
11:35am March 3rd 2015 via Hootsuite
.@GholsonLyon You are welcome. IMHO blog posts can be a nice way to practice writing, say on the way to putting together a book.
10:53am March 3rd 2015 via Hootsuite in reply to
Yes this is a blog post about blog posts: 6 Great Medium Posts About Social Media - Hootsuite Blog http://t.co/2a0LRH0PqK
10:30am March 3rd 2015 via Hootsuite
A few observations from #AGBT15 http://t.co/UX2Ij2ixyC
9:40am March 3rd 2015 via Hootsuite
RT @LeeMurphyCRF: 7900HT replaced with shiny new QuantStudio 12K flex http://t.co/F3Hj9qNfl1
8:30am March 3rd 2015 via Hootsuite
Today on @human_id I'll be live-tweeting #HIDS15 - the latest in forensic analysis from @lifetech and @servingscience http://t.co/MNXHaOOJk1
2:10am March 3rd 2015 via Hootsuite
RainDance Files for IPO Targeting $60M | GenomeWeb http://t.co/iL0pJUz6wM
6:25pm March 2nd 2015 via Hootsuite
New post at Behind the Bench: Mate-Pair bacterial sequencing http://t.co/pJw21Kuxh7
5:38pm March 2nd 2015 via Hootsuite
