GA: Ph I: finished '12; >38.5M SNPs, 1.5M indels ftp://ftp.1000genomes.ebi.ac.uk/ #ASHG14
11:03am October 21st 2014 via Hootsuite
GA:TGP's goal: >95% accessible var's >1% AF, pilot completed '10 - 2 trio's, 179 low-coverage, 8,820 exons in 697 indiv's. 15M SNPs #A
11:02am October 21st 2014 via Hootsuite
First #ASHG14 Plenary: Goncalo Abecasis (U Mich) Completion of The 1000 Genomes Project: Results, Lessons Learned and Open Questions #ASHG14
11:00am October 21st 2014 via Hootsuite
With @josetb: "With so many #ASHG14 concurrent tracks, @erlichya's 4th rule is that they are optimized for content, not happiness"
10:43am October 21st 2014 via Hootsuite
A @BBC_Future piece on the internet in 2040 http://t.co/vMTZHySMSX HT @kapoorsanjay_
10:21am October 21st 2014 via Hootsuite
RT @iontorrent: Come and take a look at the new Ion PGM Dx at #ASHG14 Booth 513 http://t.co/zHQa8aN38z
10:08am October 21st 2014 via Hootsuite
Work by Stan Nelson (UCLA) on exome sequencing for rare Mendelian disorders | Science Daily http://t.co/U07StUAXtP @GRDO_IRELAND
9:37am October 21st 2014 via Hootsuite
.@CaptainFuture__ @iontorrent Since the poster belongs to $SQNM you will need to request it from the author.
8:32am October 21st 2014 via Hootsuite in reply to
RT @conradhackett: Trust in news source CNN 54% ABC, NBC 50% CBS 46% Fox 44% Daily Show 16% Rush 12% Buzzfeed 2% http://t.co/g6b7SrKMs2
8:25am October 21st 2014 via Hootsuite
RT @mashable: Headed to a conference? 7 tips for getting the most out of it with social media http://t.co/FXeRSPVZO6 via @dailymuse
8:18am October 21st 2014 via Hootsuite
RT @iontorrent: The Ion Torrent Transcriptome Profiling Grant- apply & tell us about your clinical research project. http://t.co/ysBRLQH
7:40am October 21st 2014 via Hootsuite
RT @iontorrent: Keep up with #ASHG14 from the comfort of your own home & Download posters from the show: http://t.co/pXnfb4ABbq
6:40am October 21st 2014 via Hootsuite
MT @girlscientist: Resilience project: 600k indivs, 14 "final unexpected hero candidates" w/fully penetrant mutns but still healthy. #ASHG14
11:45pm October 20th 2014 via Hootsuite
PW: Looking at t(12;21), 25% of ALL subtypes, pediatric. Primary tumors (BM biopsy), 2013 publ: http://t.co/2uKIthhFKZ #ASHG14
9:20pm October 20th 2014 via Hootsuite
Per Wahlberg (Uppsala Univ) Whole genome bisulfite sequencing of acute lymphoblastic leukemia cells #ASHG14
9:17pm October 20th 2014 via Hootsuite
EO:MWAS and GWAS become unrelated due to environmental effects #ASHG14
9:15pm October 20th 2014 via Hootsuite
EO: Comparing MWAS to GWAS: some overlap. Can get locus refinement due to methylation data. ID top 3 genes SDCCAG8, CREB1, ATXN7 #ASHG14
9:08pm October 20th 2014 via Hootsuite
EO:'very cost-efficient' for MWAS (methylome-wide association). Blood and brain: post-mortem not many, so look at both blood&brain #ASHG
9:06pm October 20th 2014 via Hootsuite
EO: MBD <> MeDIPs; likes the @LifeTech MethylMiner, low salt elution. Single-end libraries, very cost-efficient. #ASHG14
9:05pm October 20th 2014 via Hootsuite
EO: MBD-Seq, blood, N=1500; Brain N=75. GWAS w/1K imputation. Replication via targeted pyroseq #ASHG14
9:03pm October 20th 2014 via Hootsuite
Edwin Van den Oord (VCU): Joint methylome- and GWAS in blood and brain identifies new disease mechanisms for schizophrenia #ASHG14
9:02pm October 20th 2014 via Hootsuite
DH: Data from 2010 PLOS Genet pub: http://t.co/wkIqqzu1Co Tested against 150 EUR from TGP, four add'l SNPs in same region #ASHG14
8:56pm October 20th 2014 via Hootsuite
DH:Focus on 80 SNPs, 9 CpG probes. Mapped cis-meQTL in prefrontal cortex. After Bonferroni - ~8 SNPs with CHRNA5 #ASHG14
8:54pm October 20th 2014 via Hootsuite
DH: Chr15q25 region of association w/ nicotine dep. One missense alters CHRNA5, nicotine acetocholine recp pathway #ASHG14
8:51pm October 20th 2014 via Hootsuite
Dana Hancock Res Triangle Inst Cis-methylation QTL mapping of chromosome 15q25.1 in human brain & novel ass'n w/nicotine dependence #ASH
8:50pm October 20th 2014 via Hootsuite
TT:Q:Reprod. of single-cell data? A:Data noisy 'for sure'. Took steps to reduce false-positives #ASHG14
8:48pm October 20th 2014 via Hootsuite
TT:Inferring phase, confirmed previous finding. "Points toward wide diversity in escape" - types of approaches to extend #ASHG14
8:46pm October 20th 2014 via Hootsuite
TT: Found 17 het sites in 16 genes with biallelic expression. Not enough expression in single cells. W/o parental genotypes though...#ASHG14
8:45pm October 20th 2014 via Hootsuite
TT:Single-cell: 192 cells from blood, 1 Asian female, look for X-chr biallelic exp. Found 102 het sites in 67 genes. #ASHG14
8:44pm October 20th 2014 via Hootsuite
TT:Escape genes have consistent effect direction, larger fold change acc. to sex (but still <1-fold). Found male-biased genes also #ASHG1
8:42pm October 20th 2014 via Hootsuite
TT:At pop level, used GTEx, 39 tissue types, 72-361 indivs. 66 escape genes, 49 var, 313 inactivated genes. Next- focus on sex bias #ASHG14
8:40pm October 20th 2014 via Hootsuite
TT: Single-cell RNA-seq can go direcly to escape genes biallelically expressed. But req heterozygous sites, limited # of sites #ASHG14
8:39pm October 20th 2014 via Hootsuite
TT: Reviews random X-chrom inactivation by XIST. Some genes escape inactivation. 15% escape, from 2005 Carrel http://t.co/0mkRlMrNr1 #ASHG14
8:37pm October 20th 2014 via Hootsuite
Taru Tukiainen (MGH): Population-scale and single-cell RNA sequencing provides insight into X chromosome inactivation #ASHG14
8:35pm October 20th 2014 via Hootsuite
TL: Next steps: ~8500 GTEx samples, many more tissues, and large family datasets #ASHG14
8:33pm October 20th 2014 via Hootsuite
TL:All evol. theories of imprinting 'have both supporting and contradictory evidence' - perhaps a combination is true? #ASHG14
TL:Difference in imprinted allele between tissues; IGF2 is maternally imprinted, but in brain is paternal (!) It flips. #ASHG14
8:32pm October 20th 2014 via Hootsuite
TL: Showing tissue differential paternal imprinting differences. Also inter-individual variation #ASHG14
8:30pm October 20th 2014 via Hootsuite
@Massgenomics Of course! (Tell whoever that Dale Yuzuki said so!)
8:27pm October 20th 2014 via Hootsuite
TL: Across 47 genes: no global correlation between mat/pat imprinting and female/male differential expression #ASHG14
8:26pm October 20th 2014 via Hootsuite
TL: FP can be caused by list of technical noise (i.e. random sampling error, phasing error, strong eQTLs, RNA-Seq mapping error) #ASHG14
8:24pm October 20th 2014 via Hootsuite
TL: Also used GEUVADIS and Gencord data. Used online catalog http://t.co/ZTMctTGamh Look again for monoallelic exp in RNA-Seq #ASHG14
8:23pm October 20th 2014 via Hootsuite
TL: Imprinting in ~100 genes; but why? 30-70 pat/mat. Evol. causes unknown. Use GTEx; 175 post-mortem donors x 1-30 tissues #ASHG14
8:22pm October 20th 2014 via Hootsuite
Tuuli Lappalainen @tuliel Tissue-specific patterns of imprinting revealed by analysis of monoallelic expression in human populations #ASHG14
8:20pm October 20th 2014 via Hootsuite
CW:Q:Any earlier placenta data? A:No, not yet #ASHG14
8:17pm October 20th 2014 via Hootsuite
CW:Concl: maternal genotype data showed 90% validation; 18 novel imprinted genes; est. there are ~122 imprinted genes in total #ASHG14
8:16pm October 20th 2014 via Hootsuite
CW:Another ex: CPXM2, affects fetal growth, paternally imprinted. 25 genes and their allelic ratios: monoallelic to incomplete #ASHG14
8:14pm October 20th 2014 via Hootsuite
CW: 79% paternally expressed; 21 maternal. A few examples: THSD7A, paternal; RASA1, maternal. Function makes sense on angiogenesis #ASHG14
8:12pm October 20th 2014 via Hootsuite
CW:Manh. plot overlay: all top hits have evidence of maternal bias. 90% showed monoallelic exp of same parental allele; 18 new genes #ASHG14
8:11pm October 20th 2014 via Hootsuite
CW:More detail: defined as imprinted loci, 31 mother-placenta pairs, genotyping, imputation to 2.4M SNPs, can assign parent-of-orig #ASHG14
8:10pm October 20th 2014 via Hootsuite
