Chinnappa Kodira (GE Global Research) In situ genome-wide expression profiling of individual cell types #ASHG14
9:02pm October 21st 2014 via Hootsuite
RT @claritas4kids: #ASHG14 BP: diagnostic lists as high as 521 for ID and autism, others much smaller
8:57pm October 21st 2014 via Hootsuite
MC: STRs are heavily biased toward insertion; 387 STR insertions >1kb, 14>5kb. Worried that extreme expansion an artifact #ASHG14
8:55pm October 21st 2014 via Hootsuite
MC: 100% validated, and 32 add'l complex inversions detected. #ASHG14
8:54pm October 21st 2014 via Hootsuite
MC: 34 inversions detected, ave 7.1kb; inverted dupl flank 23 events (1.6kb, 95% identity) diff. to detect via other methods #ASHG14
8:53pm October 21st 2014 via Hootsuite
MC: Raw acc. ~85%; ave length 5.8kb. About 26K ins/del >50bp. Points out Alu and L1 elements. Balanced indel rates shown #ASHG14
8:51pm October 21st 2014 via Hootsuite
MC:Hydatidiform mole is naturally haploid - fertilization of an enucleated egg. 40x seq provided. 243 SMRTcells, P5C3 @PacBio chem #ASHG14
8:49pm October 21st 2014 via Hootsuite
MC:From karyotyping, to aCGH, to NGS. All different scales. Focus on small-scale structural var (50bp - 10's of KB) #ASHG14
8:48pm October 21st 2014 via Hootsuite
Mark Chaisson (UW) Increased complexity of the human genome revealed by single-molecule sequencing #ASHG14
8:47pm October 21st 2014 via Hootsuite
XZ:Q:How many validated? A:Difficult to do, b/c only single-end primer. Q:See polyA? A:Somatic signal weak. Need Sanger full-length #ASHG14
8:46pm October 21st 2014 via Hootsuite
XZ:Q:Majority of insertions not tissue-spec? A:Yes, consistent. #ASHG14
8:45pm October 21st 2014 via Hootsuite
XZ: Using droplet digital PCR to validate tissue-spec TE insertions; TE junction abundance shown; ability to validate tissue-spec #ASHG14
8:41pm October 21st 2014 via Hootsuite
RT @claritas4kids: #ASHG14 MH: medical exome project founded by Emory, CHOP, and Harvard/Partners
8:38pm October 21st 2014 via Hootsuite
XZ: Modified this 2012 method: http://t.co/V6LCz2voe2 getting high- and low-confidence calls for Alu and L1 in tissues #ASHG14
8:37pm October 21st 2014 via Hootsuite
XZ:2 methods for somatic: capture microarray, also L1-IP. In somatic brain: mosaic. Two individs, 3 tissues. 60-90x WGS #ASHG14
8:35pm October 21st 2014 via Hootsuite
XZ: Somatic tranposition can be causative for # of neurological disorders (Rett syndrome) In brain: debatable http://t.co/a954X3Seag #ASHG14
8:34pm October 21st 2014 via Hootsuite
XZ:50% are transposable elements; 17.5% LINE1, 9.2% LTR Tn. L1 retrotransposition 1/140; Alu retro-Tn 1/20 in germline #ASHG14
8:32pm October 21st 2014 via Hootsuite
Xiaowei Zhu (Stanford) Deep WGS-based analysis of mosaic transposable mobile element insertions in adult human tissue #ASHG14
8:31pm October 21st 2014 via Hootsuite
JB:Q:Chimeric reads in assy? A:Always a risk, but chimeras are at the end of reads #ASHG14
8:30pm October 21st 2014 via Hootsuite
JB:Q:How compared to Sanger for rarity? A:NGS affordable, in theory Sanger is stronger for assembly Q:Source? A:Vag. swabs #ASHG14
8:29pm October 21st 2014 via Hootsuite
JB:Q:Links betw. spp.? Horiz gene transfer? A:Can be artifacts of several types, incl. shared ancestry #ASHG14
8:28pm October 21st 2014 via Hootsuite
JB:Q:Applied to human gut microbiome? A:Well-studied, working on it #ASHG14
8:27pm October 21st 2014 via Hootsuite
JB: Most clusters match BV spp. Cluster 9 blank - b/c it was BVAB1 (novel) was able to get de novo assembly (1.5MB, 35 scaffolds) #ASHG14
8:26pm October 21st 2014 via Hootsuite
JB: 25 spp. ID'd from sample; clear separation, including BVAB1 at 55%; Prevotella 13% etc. #ASHG14
8:24pm October 21st 2014 via Hootsuite
JB:Applied to vaginal microbiome w/bacterial vaginosis (known novel strains, with unculturable BVAB1 spp. dominant) #ASHG14
8:23pm October 21st 2014 via Hootsuite
JB:Cross-link before cell lysis. Developed tool MetaPhase deconvoluting synthetic mix of yeast 2014 G3 ref: http://t.co/4xFvNWqNGd #ASHG14
8:22pm October 21st 2014 via Hootsuite
JB:Doing Hi-C for metagenome assembly:clsuter, order contigs. 2013 Nature Biotech ref: http://t.co/CrhUGp1jcK #ASHG14
8:20pm October 21st 2014 via Hootsuite
JB:3rd:Metagenome shotgun assembly, a set of contigs. But no spp. info; no genome of any one spp. Just many puzzle pieces. #ASHG14
8:18pm October 21st 2014 via Hootsuite
JB: Hard to tell what is 'in' a microbial community. Can be cultured & char.; can be sequenced via 16S rRNA (but what about novel?) #ASH
8:17pm October 21st 2014 via Hootsuite
Joshua Burton (UW) Metagenomic deconvolution and species discovery in microbiomes using contact probability maps #ASHG14
8:15pm October 21st 2014 via Hootsuite
GF:Q:How in a nc region? A:Need to select phenotype by expression. Maybe FACS, or enough hnRNA #ASHG14
8:12pm October 21st 2014 via Hootsuite
GF: Ongoing: non-coding region assays; tile across entire genes; improve efficiency of editing #ASHG14
8:11pm October 21st 2014 via Hootsuite
GF: Plot of sequence-function map of DBR1 by nt; missense, nonsense, splice, synonymous. Strong pref. for wt a.a. at active site #ASHG14
8:10pm October 21st 2014 via Hootsuite
GF: Now looking at cellular fitness. Use Hap1 cells (haploid), and DBR1 enzyme cleaves intron lariats. DBR1 edits, view growth phen. #ASHG14
8:09pm October 21st 2014 via Hootsuite
GF:Looking at effect on splicing and transcripts. 2014 Nature paper: http://t.co/z1WodpxrXP Next look at effect of SNVs #ASHG14
8:07pm October 21st 2014 via Hootsuite
GF:Cells grown 5d, then 'selective PCR' - pick out only edited cells, sequence pools of gDNA and cDNA and count hexamers #ASHG14
8:06pm October 21st 2014 via Hootsuite
GF:HDR is 4,096 NNNNNN sequences (random hexamers), integrates at spec site, fixed edited spot as a marker. Now a heterogeneous mix #ASHG14
8:05pm October 21st 2014 via Hootsuite
GF:Measure function of 'every permutation at a single locus'. HEK293 cells, transfect CRISPR-Cas9 target BRCA1 exon 18; also HDR lib #ASHG14
8:04pm October 21st 2014 via Hootsuite
GF:Use genome editing for permanent changes; after double-stranded break. But programmed edits singly. Goal: thousands #ASHG14
8:03pm October 21st 2014 via Hootsuite
GF:VUS are common outcomes; even with BRCA1/2 after 1M samples, still VUS's exist #ASHG14
8:01pm October 21st 2014 via Hootsuite
Gregory Findlay (UW): Saturation Genome Editing by Multiplex Homologous Donor Repair #ASHG14
8:00pm October 21st 2014 via Hootsuite
MM:Q:Amt of cells? A:A million to a few million #ASHG14
7:59pm October 21st 2014 via Hootsuite
MM:Q:Can a diploid de novo assy be done w/what coverage? A:Not a tool developed yet, can use different restriction enzymes #ASHG14
7:58pm October 21st 2014 via Hootsuite
MM: For transgene sequence - primer pairs spec to the trans-gene, showed many examples. Looked at fusions in MLL 90kb in 2 chr #ASHG14
7:56pm October 21st 2014 via Hootsuite
MT @claritas4kids: #ASHG14 SM: look at indivs who have ext clinical diagnosis over lifetime, correlate seq results with clinical phenotype
7:54pm October 21st 2014 via Hootsuite
MM:Able to get HLA haplotypes across region. Can design primers specific per each allele. Showed IGV plot. #ASHG14
7:53pm October 21st 2014 via Hootsuite
MM:PE reads - same circle, same copy of the locus, same allele. BRCA1 gene illust: get separate alleles, across large distances #ASHG14
MM:Each copy of a locus closer will be sequenced more often; further away less so. Irrespective of sequence, indels, fusions #ASHG14
7:51pm October 21st 2014 via Hootsuite
MM: Proximity=from the same locus; circles ~2kb in size, just an inverse PCR amplicons. Starts with millions of cells #ASHG14
7:50pm October 21st 2014 via Hootsuite
MM: Refers to this recent Nature Biotech paper http://t.co/tIc6eyYrtB Illustrating how it works - after cross-linking via proximity #ASHG14
7:49pm October 21st 2014 via Hootsuite
