AM: Of 16 indivs w/var: T2D 7x increased risk #AGBT15
8:03pm February 27th 2015 via Hootsuite
AM:PPAR-gamma from 20K T2D cases/controls: 2014 PNAS ref http://t.co/8k6YsRHBh2 Most var's fn as WT; 9 novel PPARg cause loss-of-fn #AGBT15
8:02pm February 27th 2015 via Hootsuite
AM: Now application of MITE-Seq ot PPARg in human fat cells: a master reglator of adipocyte diff and antidiabetic drug target #AGBT15
8:01pm February 27th 2015 via Hootsuite
AM: Engineered synthetic var's found 2000x difference in specificities to antibiotics #AGBT15
8:00pm February 27th 2015 via Hootsuite
AM:ID of spec-determining residues. Positions tolerated or depleted under paromycin selection #AGBT15
7:59pm February 27th 2015 via Hootsuite
AM: (These tweets dedicated to Keith R of @omicsomicsblog) #AGBT15
7:58pm February 27th 2015 via Hootsuite
AM: Dec [kana] -> fewer mutations. Showed structure of predicted changes. More tolerance for mut's outside the core #AGBT15
AM: MITE library, selection in liquid carbinicellin w/diff conc of aminoglycoside. Showed map of kanamycin conc-dep sequence act map #AGBT15
7:57pm February 27th 2015 via Hootsuite
AM: APH(3')II bacterial enzyme; 6 aminoglycoside antibiotics w/diff structures / potencies. Synth 4997 single aa subst across enz #AGBT15
7:56pm February 27th 2015 via Hootsuite
AM:Deep mut scanning; 1000's of mutated protein-coding var's; select for fn via cell-based assay; char seq http://t.co/ElLnEvEJ6i #AGBT14
7:55pm February 27th 2015 via Hootsuite
#AGBT15: Ion AmpliSeq Transcriptome poster interview (Video) http://t.co/9VbYPk0KTy Behind the Bench Blog
Alexandre Melnikov, The Broad Inst "Comprehensive Mutational Scanning of Bacterial and Human Proteins Using MITE-Seq” #AGBT15
7:53pm February 27th 2015 via Hootsuite
#AGBT15: Ion AmpliSeq Automation (Video) http://t.co/h2uN5ABHrT Behind the Bench blog
7:50pm February 27th 2015 via Hootsuite
.@froggleston And I can reveal that ERCC controls are handy for single cell transcriptomics Behind the Bench http://t.co/tmN74Tk3e3 #AGBT
7:48pm February 27th 2015 via Hootsuite in reply to
RT @splon: Donna Muzny #AGBT15 Lightning exome for clinical diagnosis, make all the library steps and hybridization efficient. Turnaround 3…
7:46pm February 27th 2015 via Twitter Web Client
#AGBT15: The Avalanche of NGS Data http://t.co/lYJNyGiAuu Behind the Bench blog
7:39pm February 27th 2015 via Hootsuite
Nice work on Single Cell sequencing - too bad tweeps!
7:38pm February 27th 2015 via Hootsuite
While discussing natural human knockouts w/a new friend at #ASHG15 I was told to thank my paralogues. So there it is.
5:41pm February 27th 2015 via Hootsuite
Worth a look! MT @gsaldanha: Here's the @10xgenomics video #AGBT15 http://t.co/gsvkHNx2P0
5:01pm February 27th 2015 via Hootsuite
BH:Announces instrument - $75K cost, $500/sample, Q2 availability #AGBT15
5:00pm February 27th 2015 via Hootsuite
BH: Quotes Jay Shendure (UW Mendelian genetics center), "high quality exomes from 1ng!" #AGBT15
4:59pm February 27th 2015 via Hootsuite
BH: Showed slide from David Jaffe's talk last night - 'behaves like 100kb accurate read'. #AGBT15
4:58pm February 27th 2015 via Hootsuite
BH: Shows strong PPV and sensitivity data with a fraction of input for WES. #AGBT15
4:57pm February 27th 2015 via Hootsuite
.@milospm1206 Yes it is remarkable technology; we've been hearing at #AGBT15 how impt large structural variation is.
4:57pm February 27th 2015 via Hootsuite in reply to
BH: Large-scale structural rearrangements LUMPY ref: http://t.co/A6oSyLqPnN showed nice reduction of errors #AGBT15
4:56pm February 27th 2015 via Hootsuite
BH: Across HLA-DPA1, HLA-DPB1, HLA-DPB2. Not their focus but can give a glimpse of potential #AGBT15
4:54pm February 27th 2015 via Hootsuite
BH: Can go in and pull out only the exome, at 139x, can get 95% SNPs phased; 96% of genes #AGBT15
4:53pm February 27th 2015 via Hootsuite
BH: (That video actually got applause. Nicely done!) #AGBT15
4:52pm February 27th 2015 via Hootsuite
BH: Built Loupe, a haplotype-aware browser. Animation from NA12878: nothing like a cool video with a waltz. 'Who's your daddy?' #AGBT15
4:51pm February 27th 2015 via Hootsuite
BH:Software based on std tools (BWA, GATK), linux-based, 'open-platform for high-throughput NGS' #AGBT15
4:49pm February 27th 2015 via Hootsuite
BH: Recycling - going back to the template with additional adapter priming/extension rounds. Then finish ends w/PCR #AGBT15
4:48pm February 27th 2015 via Hootsuite
BH: <10fg / partition; 0.3% of genome per GEM; 90% gel bead fill rate. #AGBT15
4:47pm February 27th 2015 via Hootsuite
BH:Gelbead dissolves, releasing thousands of barcodes into the bubble. So 1ng DNA now has >100K barcoded partitions #AGBT15
4:46pm February 27th 2015 via Hootsuite
BH: 54um bead, movie looks just like RainDance with emulsifying in oil. >100K reactions/5min. Gelbead in emulsion ("GEM") #AGBT15
4:45pm February 27th 2015 via Hootsuite
BH: GemCode system. 750K reagents in 1 tube; a 14bp barcode with a gelbead; highly uniform; built-in seq adapter & primer #AGBT15
4:44pm February 27th 2015 via Hootsuite
BH:Why not done at scale before? 384 partitions, Now >100K. Barcodes 384 vs. 750K. Input 100ng vs 1ng #AGBT15
4:43pm February 27th 2015 via Hootsuite
BH: Instead of nanopore, individual partitioning and molecular barcode. For both WGS and targeted; simple workflow #AGBT15
4:42pm February 27th 2015 via Hootsuite
BH: With linked reads: Accurate SNPs, haplotyping, precise counting, critical content (HLA), de novo, structural var's #AGBT15
4:41pm February 27th 2015 via Hootsuite
BH: 'This is the first technical presentation on 10X ever.' #AGBT15
4:40pm February 27th 2015 via Hootsuite
Ben Hindson 10X Genomics “Long Range Applications With Short Read Sequencing” #AGBT15
JS: Used BAC-based approach to get closure of Chr20 gap. #AGBT15
1:37pm February 27th 2015 via Hootsuite
JS: 'We discovered a large number of large struct var's in genes that are disease related' #AGBT15
1:33pm February 27th 2015 via Hootsuite
JS: For struct var, used Symap, UCSC tools, then a script to compare to GRCh38. Est total in AK1 ~21K 130kb ins 79kb del #AGBT15
JS: Used optical maps (Bionano) to fill gaps, also SMRT subreads. Of 604 total, 250 closed, 180 extended, 174 still open Total 5.4Mb #AGBT15
1:27pm February 27th 2015 via Hootsuite
JS: AK1, used 215GB ~72x on PacBio; ave RL 13.4kb. FALCON + Daligner made it fast - 4-5d. N50 7.3Mb, 2.8Gb length. 91% coverage #AGBT15
1:25pm February 27th 2015 via Hootsuite
JS: Mongolian project (GENDISCAN), Kazakshstan Genome project, Korean BAC Clone project (2001) #AGBT15
1:23pm February 27th 2015 via Hootsuite
Jeong-Sun Seo (Seoul Nat'l Univ, MacroGen) "De novo assembly of an asian diploid genome using SMRT sequencing" #AGBT15
1:21pm February 27th 2015 via Hootsuite
DC: Can do 1st and 2nd-pass alignments in GRCh37 and compare to GRCh38; beware of misassembly of 37 that appears as missing in 38 #AGBT15
1:15pm February 27th 2015 via Hootsuite
RT @drgitlin: DC: alternate loci contain genes! If you’re not using them in your analyses you’re missing important information. #AGBT15
1:12pm February 27th 2015 via Hootsuite
RT @AndyLarrea: Fear the Franken alleles #agbt15 @deannachurch http://t.co/G6k9KCvaQK
