Scharer: Size-selection results after 19-cycle PCR. Then chose optimum levels, did replicates, and sequenced. #ASHG15
7:30pm October 8th 2015 via Hootsuite
Scharer:Uses melt curve analysis for complexity of post-ligation step. Higher conc = much better. But - almost all dimers. #ASHG15
7:27pm October 8th 2015 via Hootsuite
Scharer: thus for 10^4 cells, only 10pg input. Played with driving adapter ligation with higher molar concentrations. (to 80K:1) #ASHG15
7:26pm October 8th 2015 via Hootsuite
Scharer: Single-tube end-repair, adapter ligation, then SPRI. Currently >1ng input. Did work with H3K4me3. 10^7 cells is 30ng #ASHG15
7:24pm October 8th 2015 via Hootsuite
Chris Scharer (Emory): Low-input ChIP-Seq. Explains general workflow. Typically M's of cells, they wanted 10's of thousands #ASHG15
7:23pm October 8th 2015 via Hootsuite
Barwick: Studies LPS activation of b-cells; cp to plasmablast, plasma cells. Showed mouse cells isolated by cell division cycle #ASHG15
7:21pm October 8th 2015 via Hootsuite
Barwick: Shows reprod between 10ng and 500ng libraries. Validated via methyl-sens qPCR. PhiX data down to 100pg #ASHG15
7:19pm October 8th 2015 via Hootsuite
Barwick: Kapa's enzyme is dUTP-friendly. Showed nice 5 to 15 cycle quant data to get precise target concentration #ASHG15
7:18pm October 8th 2015 via Hootsuite
Barwick: Methylated barcoded adapters, as a universal. Can go down to 10ng input library. Use QIAGEN Epitect for conversion #ASHG15
7:17pm October 8th 2015 via Hootsuite
Barwick: Differential MspI and TaqI sensitive to methylation status; use unmeth lambda as spike-in. Kapa Hyperprep #ASHG15
7:16pm October 8th 2015 via Hootsuite
Barwick: DNMT + SAM->SAH; Nice chart comparing methods; 450K array, MeDIP, WGBS, and RBBS #ASHG15
7:14pm October 8th 2015 via Hootsuite
At the @kapabiosystems workshop, Benjam Barwick (Emory) describing his work for low-input ChIP and methylation assays #ASHG15
7:11pm October 8th 2015 via Hootsuite
Coban-Akdemir: Of 66 families, dx rate of 38%. Describes details of genes for individual cases. Ex: PURA http://t.co/K1fPlLXH9r #ASHG15
7:00pm October 8th 2015 via Hootsuite
Coban-Akdemir: Their var's: known? function? relatedness? var freq? Others? http://t.co/kG1z85ViTC then functional protein domains #ASHG15
6:55pm October 8th 2015 via Hootsuite
Coban-Akdemir: Describes their pipeline at Baylor for homozyg. and cmpd hets; has a de-novo var pipeline; a third for CNV #ASHG15
6:53pm October 8th 2015 via Hootsuite
Coban-Akdemir: Clinical WES started in 2013; 380 enrolled, 142 families; 1,600 families waiting #ASHG15
6:51pm October 8th 2015 via Hootsuite
Zeynep Coban-Akdemir (Baylor) Improving dx and furthering gene discovery through recruitment of clinical WES cases into research #ASHG15
6:50pm October 8th 2015 via Hootsuite
Nesbitt: Found a FB site on p3 of Google. Mother was looking for a KAT6A match. Similar; soon others found http://t.co/9Wi8uGZW6A #ASHG15
6:49pm October 8th 2015 via Hootsuite
Nesbitt: Social media: 9yo MZ twins, KAT6A (Lysine acetyltransferase); mouse model had cleft palate. Google said... #ASHG15
6:47pm October 8th 2015 via Hootsuite
Nesbitt: Another case, Spectrin beta-IV (SPTBN4), KO mouse model has similar features - motor neuropathy, brainstem response #ASHG15
6:46pm October 8th 2015 via Hootsuite
Nesbitt: One case: CAMK2A de novo missense mutation, part of Ras pathway. #ASHG15
6:44pm October 8th 2015 via Hootsuite
Nesbitt: Candidate genes' evidence - animal models, pathways, segregation, ID add'l patients #ASHG15
6:43pm October 8th 2015 via Hootsuite
Nesbitt: Their dx yield is about 25%. Often rare, being left with VUS. She goes through their process, from 400 var to 12 to 0 or 1 #ASHG15
6:42pm October 8th 2015 via Hootsuite
Adi Nesbitt (CHOP) Utilization of social media, model organisms, and pathway analysis in pediatric exome sequencing #ASHG15
6:38pm October 8th 2015 via Hootsuite
I think it's about that time at #ASHG15 for this. http://t.co/ZnD4AU29x8
6:34pm October 8th 2015 via Hootsuite
Acuna-Hidalgo: These DNM's were de-novos as mosaics in blood, at ratios of 20-32%.Modelled 80x; <5% allelic ratio 20% detected #ASHG15
6:32pm October 8th 2015 via Hootsuite
Acuna-Hidalgo: Derived a Z-score from WGS, amplicons, and Sanger. Cp with heterozygotes, found 9 outliers, then 7/107 were mosaics #ASHG15
6:31pm October 8th 2015 via Hootsuite
Acuna-Hidalgo: After CGI 80x; they validated with Ion AmpliSeq, Sanger, and single-molecule MIP #ASHG15
6:26pm October 8th 2015 via Hootsuite
Acuna-Hidalgo: Higher level mosaicism can be confused with a heterozygote. 50 trios w/intellectual disability - ID'd 4,081 DNMs #ASHG15
6:25pm October 8th 2015 via Hootsuite
Acuna-Hidalgo: Looking at allelic ratio imbalance; but technical limitations of low-level detection. #ASHG15
6:24pm October 8th 2015 via Hootsuite
Acuna-Hidalgo: DNM (de novo mutations) known to occur post-zygote. Thus mosaicism has role in disease, and also for recurrence #ASHG15
6:23pm October 8th 2015 via Hootsuite
Rocio Acuna-Hidalgo (Radboud) Post-zygotic point mutations are an underrecognized source of novel genomic variation #ASHG15
6:22pm October 8th 2015 via Hootsuite
Lyons:Q:Which cancers in cats? A:Lymphomas (older), and mammary (younger) cats, and another lymphoma. Not as good as dog for cancer #ASHG15
6:21pm October 8th 2015 via Hootsuite
Lyons: Cats have been cloned, made transgenic. Ends with 'Cats rule, Dogs drool' #ASHG15
6:18pm October 8th 2015 via Hootsuite
Lyons: A cat trio against the reference (Cinnamon) - WGS with 18M var's. '15 myopathy ref http://t.co/XFM7OcDNGg #ASHG15
6:16pm October 8th 2015 via Hootsuite
Lyons: Cat genome project underway, a public effort, same coverage and technology, working with Maverix for informatics #ASHG15
6:13pm October 8th 2015 via Hootsuite
RT @MollyGasp: learning about Cinnamon the reference genome cat, and inbred cats #ASHG15 http://t.co/Ic8xZZ8QAY
6:11pm October 8th 2015 via Hootsuite
.@ksamocha The 'in-bread' cat photos were classic. (The cats were probably hers!) #ASHG15
6:11pm October 8th 2015 via Hootsuite in reply to ksamocha
Lyons: "Inbred cats" hilarious! #ASHG15
6:10pm October 8th 2015 via Hootsuite
RT @aaronjtowers: Cat-loving geneticists heads are exploding at Lyons talk #ASHG15
6:09pm October 8th 2015 via Hootsuite
Lyons: Discussion of breeds from this '13 ref http://t.co/mev5k47HN8 Polycystic Kidney Disease affects felines #ASHG15
Lyons: Shows figure from this '09 ref http://t.co/MTI2rfJEjk with breed diversity #ASHG15
6:07pm October 8th 2015 via Hootsuite
Lyons: Cats only domesticated for 10K-15K years, to catch mice. 100K. Some feral cat work: 38 STRs, 148 SNPs. 10-12 'racial poplns' #ASHG15
6:06pm October 8th 2015 via Hootsuite
L Lyons (Univ MO) 99 Lives Cat Genome Sequencing Initiative: Discovery of feline models for human diseases #ASHG15
6:05pm October 8th 2015 via Hootsuite
Posey: Looked at their dual dx cases - 5.7% of them, and re-examined for phenotype via HPO for blended vs composite phenotypes #ASHG15
6:01pm October 8th 2015 via Hootsuite
Posey: 5,651 sequential cases for proband WES. 25.6% diagnoses. 82 cases w/ >=2 diagnoses. Autosomal dom most common #ASHG15
5:56pm October 8th 2015 via Hootsuite
Posey:Dual diagnoses: do 2 genes have distinct phenotypes, or do they overlap? #ASHG15
5:54pm October 8th 2015 via Hootsuite
Posey: Aggregated rare var's: mutational load or burden. Dual mendelian dx: '13 NEJM ref http://t.co/GUZQsx3lA2 #ASHG15
Jennifer Posey Baylor: Indiv clin var, beyond monogenic disease: The aggregation of pathogenic variant alleles in a personal genome #ASHG15
5:52pm October 8th 2015 via Hootsuite
Tayoun:Has contributing labs (Ambry, Athena, GeneDx, Greenwood, invites others to participate) #ASHG15
5:50pm October 8th 2015 via Hootsuite
