Tang: Illus. meiosis of human oocytes, 1st polar body (2N); then 2nd polar body (1N). Looking for euploidy from polar bodies #AGBT14
11:40am February 15th 2014 via Hootsuite
Tang: Major Q is what det. early cell fate? Early embryos in dev. - uses MALBEC for WGS, others. Science PDF: http://t.co/dQUv9NtGOg #AGBT14
11:39am February 15th 2014 via Hootsuite
Up next: Fuchou Tang, Peking Univ.: The Transcriptome and DNA Methylome Landscapes of Human Preimplantation Embryos and ESC's #AGBT14
11:35am February 15th 2014 via Hootsuite
OMG the US beat Russia in the hockey game in a 3-2 shootout. Back to live-tweeting a scientific meeting.
11:32am February 15th 2014 via Hootsuite
Burton: 1K rhododendron spp., only 660MB but near-perfect 10kb repeats. Was able to isolate intact rhododen. nuclei #AGBT14
11:30am February 15th 2014 via Hootsuite
Burton:Hi-C has mainly been done in cell lines; now looking at new world monkeys, hops, and rhododendron (next) #AGBT14
11:29am February 15th 2014 via Hootsuite
Burton:Test of how small a short contig size does the method fail? ~ 50kb #AGBT14
11:28am February 15th 2014 via Hootsuite
Burton: Review of Lachesis software method published in 2013 Nature Biotech http://t.co/8WVXrWhpLy #AGBT14
11:24am February 15th 2014 via Hootsuite
Burton: Hi-C and refers to Lieberman-Aiden's work in 2009 http://t.co/NBRlmFPEuc #AGBT14 (Note - a hero to me- see http://t.co/oPankrrbOS )
11:23am February 15th 2014 via Hootsuite
Burton: Incomplete as there are no BACs, no genetic & physical maps to build on as with the HGP #AGBT14
11:21am February 15th 2014 via Hootsuite
Burton: De novo solely from short reads: cheap de novo assy's lack chromosome-scale assy -Hard to align/compare; gene model incompl #AGBT14
11:20am February 15th 2014 via Hootsuite
Next up: Joshua Burton, Univ. WA: Chromosome-Scale Scaffolding of de novo Genome Assemblies Based on Chromatin Interactions #AGBT14
11:17am February 15th 2014 via Hootsuite
Listening to Carlos reminds me of how entertaining and informative an excellent presenter can be. #AGBT14
11:16am February 15th 2014 via Hootsuite
Bustamante: Concl: Goal is a WGS of an ancient genome at only 2-3x the cost of a modern human. #AGBT14
11:15am February 15th 2014 via Hootsuite
Bustamante: Bias? 92%-96% correlation; all the correct spp. taxonomy per location #AGBT14
Ehrich: Looking at different env. samples (saliva, cheek swab, human soil): 50-70% microbial, enriched to 70-97% #AGBT14
11:13am February 15th 2014 via Hootsuite
Bustamante: 43k pre-capture ILMN lib. SNPs, 400K variable sites on Proton, the PCA looks much better. Several 2012 papers #AGBT14
11:11am February 15th 2014 via Hootsuite
Bustamante: Otzi 'iceman' story: the PCA with Sardinians - 5.3k y.o. border of Italy, was he on vacation in the Alps when he died? #AGBT14
11:10am February 15th 2014 via Hootsuite
Bustamante: Proton data allows them to find ground-truth data for ancient samples. DNA damage evidence toward beg. and end #AGBT14
11:09am February 15th 2014 via Hootsuite
Bustamante: Showed some @IonTorrent Proton data, in collaboration with T Harkins. Pointed out the help of orthogonal technology #AGBT14
11:08am February 15th 2014 via Hootsuite
Bustamante: Get 15-60% of reads to map to the human genome; AJHG 2013 paper #AGBT14
Bustamante: Use biotinylated RNA baits to pulldown whole-genome human 1% from an environmental paleo sample #AGBT14
11:02am February 15th 2014 via Hootsuite
Ehrich: Q: Is there latitude for consent? A: Existing regulations - OK for QC, also specialized consent post-test #AGBT14
10:30am February 15th 2014 via Hootsuite
Ehrich: Q: Perturbations - systemic change to reagents? A: Chem versions is a big deal, several $MM. All the revalidation... #AGBT14
10:29am February 15th 2014 via Hootsuite
Ehrich: Q: Neutrophil extracellular traps of cell-free DNA? A: No, b/c of QC in-place. No a priori exclusion criteria. >4% fetal: OK #AGB
10:28am February 15th 2014 via Hootsuite
Ehrich: Q: How to detect bal tranloc? A: Map into the read. Unperfect matches can have a linear model applied #AGBT14
10:27am February 15th 2014 via Hootsuite
Ehrich: Conclude: How do we relay info back? 4M preg's/y (US); 3-5% of these have a genetic condition. More genetic counseling too #AGBT14
10:26am February 15th 2014 via Hootsuite
Ehrich: Have identified balanced translocations - 'but no one other than us seem to care'. Their algorithm is single-base resolution #AGBT14
10:22am February 15th 2014 via Hootsuite
Ehrich: Can find 'outside prenatal' - ID 'uterine ploemorphic leiomyosarcoma'; some will have disease DNA in the sample #AGBT14
10:21am February 15th 2014 via Hootsuite
Ehrich: Can find down to 3-6MB, but only 60-85% sens, still >99% spec. Better at >7MB #AGBT14
10:19am February 15th 2014 via Hootsuite
Ehrich: Ability to detect depends on: size of indel; counts; fetal fx.; sequence noise. Plan to work with existing reads / process #AGBT14
10:18am February 15th 2014 via Hootsuite
Ehrich: Now looking at sub-chromosomal rearrangements. Now a signal-to-noise deviation problem, with subsampled reads #AGBT14
10:17am February 15th 2014 via Hootsuite
Ehrich: Have found instances of confined placental mosaicism; co-twin demise; fetal mosaicism; maternal mosaicism or malignancy #AGBT14
10:15am February 15th 2014 via Hootsuite
Ehrich: Only offered to high-risk pts.; 2.14% positive rate identical to expected incidence rate #AGBT14
10:14am February 15th 2014 via Hootsuite
Ehrich: 'no result' in 0.8% (insuff. DNA); 'no result' 0.3% (technical) Ave gestational age 14w 6d TA 4d 3.7 multi-fetal rate #AGBT14
10:13am February 15th 2014 via Hootsuite
Ehrich: Trisomy 21 (T21) test lists several 2011 - 2013 clinical validation data publications. >200K samples tested; 150k in '13 #AGBT14
10:12am February 15th 2014 via Hootsuite
Ehrich: NGS use is only chromosomal copy number of fetal origin, 36-bp. #AGBT14
10:05am February 15th 2014 via Hootsuite
Ehrich: 90% of free DNA is from mother. Amt of Chr21 is only 1.35% of the fetal genome. #AGBT14
10:04am February 15th 2014 via Hootsuite
Ehrich: 97.7% of amniocentesis cases are normal. Lo discovery in 1997 (Lancet) of cell-free fetal DNA http://t.co/1QKqUhiC9T #AGBT14
10:03am February 15th 2014 via Hootsuite
Up next: Mathias Ehrich, Sequenom. “Non Invasive Prenatal Testing: A Showcase of High Volume Next Generation” #AGBT14
9:59am February 15th 2014 via Hootsuite
Blainey: Q: When for sale? A: We have no interest in commercializing. #AGBT14
Blainey: Q: For metagenomics, lysis can be a challenge to get 100% DNA downstream A: Acknowl. the problem, not easy to solve #AGBT14
9:58am February 15th 2014 via Hootsuite
Blainey: A: (con't) They are doing short-read libraries, using Tn5-based fragmentation, all integrated but hasn't been done yet #AGBT14
9:57am February 15th 2014 via Hootsuite
Blainey: Q: How will it handle 200kb DNA? A: Believes it will work well. Low Reynolds number. #AGBT14
9:56am February 15th 2014 via Hootsuite
Blainey: Cost calcs: 128/run, $5K controller, reagents list is $0.94. FWIW $0.01/sample for the amortized cost of a pipettor. Hmm. #AGBT14
9:54am February 15th 2014 via Hootsuite
Blainey: Showing quality and contam. levels, a continuous flow device, 'libraries/hour'. 1 chip = 1k libraries/day (theoretical) #AGBT14
9:53am February 15th 2014 via Hootsuite
Blainey: Not sure if this is the Quake ref from 2005 for library prep purpose, but here you go. http://t.co/lYmO62BWTt #AGBT14
9:52am February 15th 2014 via Hootsuite
Blainey: 'Chips have a productive lifetetime of months' #AGBT14
9:49am February 15th 2014 via Hootsuite
Blainey: Tech called 'sieve valve' from Stephen Quake 2005, Tan et al PLoS Ref http://t.co/xWmcvhI8yV #AGBT14
9:48am February 15th 2014 via Hootsuite
Blainey: Micron-scale particles for capture, solid-phase reversible immob. tech (ChargeSwitch anyone?) elute, flush, mix. #AGBT14
9:46am February 15th 2014 via Hootsuite
