Sen: If a disease gene, should be found at site of discovery. Autopsy section of CAC, significant TREML4 expression. Macrophages #AGBT14
8:26pm February 14th 2014 via Hootsuite
Sen: Westerns & Flow cytometry: an atypical aa sequence, glycosialated but validated the protein (took 6 mos) #AGBT14
8:25pm February 14th 2014 via Hootsuite
Sen: Needed to go back to northerns for TREML4 transcript validation; not a gene actively studied. #AGBT14
8:23pm February 14th 2014 via Hootsuite
Sen: Looked at relative risk for CAC score for rs2803496, nice correlation. 'RNA-seq made my life more complicated cp to microarray" #AGBT14
8:21pm February 14th 2014 via Hootsuite
Sen: Then went back and looked for an eQTL using genomic data; found a SNP rs2803496 upstream of TREML4. #AGBT14
8:19pm February 14th 2014 via Hootsuite
Sen: RNA-Seq of periph. blood; not clear. Went to Framingham heart study (1000 samples) Found increased TREML5 expression in CAC. #AGBT14
Sen: ClinSeq to use, using RNA-Seq, genome, proteome, deep clinical phenotyping. 8 cases / 8 controls. #AGBT14
8:17pm February 14th 2014 via Hootsuite
Sen: CAC was studied via GWAS; ODonnell an example Manhattan plot with 100's of thousands samples Ref. http://t.co/npxsra6NwI #AGBT14
8:15pm February 14th 2014 via Hootsuite
Sen: Part of ClinSeq, Les Biesecker et al at NHLBI looking at coronary artery calcification. ClinSeq ref: http://t.co/JlmSHsUtkw #AGBT14
8:14pm February 14th 2014 via Hootsuite
Up next: Shurjo Sen, NHGRI. "Increased TREML4 Expression and rs2803496 Genotypes are Associated with Coronary Artery Calcification" #AGBT14
8:12pm February 14th 2014 via Hootsuite
Mullikin:Q: Add'l platforms? A: Had 454 data on top of it #AGBT14
8:11pm February 14th 2014 via Hootsuite
Mullikin:Q: Do you get the PacBio reads? Any error artifacts? A: they handed us finished data, v. high quality. Cons. washes errors #AGBT14
Mullikin: Found in a sink drain - where a biofilm is resistant to even bleach. #AGBT14
8:06pm February 14th 2014 via Hootsuite
Mullikin: But evidence for horiz gene transfer from patient to environment (!) #AGBT14
Mullikin: Full genome seq ruled out patient to patient plasmid transfer. Targeted could have given erroneous results #AGBT14
8:04pm February 14th 2014 via Hootsuite
Mullikin: Looking now for horizontal gene transfer, and tracing it how it traveled in the hosp environment. #AGBT14
8:03pm February 14th 2014 via Hootsuite
Mullikin: SND = single nucl difference, DID = deletion insertion differences; very high accuracy #AGBT14
Mullikin: PacBio seq; delivered 4 indiv plasmids; 10 isolate with OpGen maps, 454 and MiSeq for QC, all 10 genomes, SND or DID #AGBT14
8:02pm February 14th 2014 via Hootsuite
Mullikin: KPC (resistant form), problem was with resistance-carrying plasmids De novo assy from 454 #AGBT14
8:00pm February 14th 2014 via Hootsuite
Mullikin: K. pneumoniae - normal gut, skin flora; 1/7 bloodstream ICU infections. Carbapenum = last line of defense. 1985 approved #AGBT14
7:56pm February 14th 2014 via Hootsuite
Mullikin: 2011 outbreak: K. pneumoniae, carbapenem-res. 18 indiv's colonized, 6 deaths, 5 deaths add'l from underlying disease #AGBT14
7:54pm February 14th 2014 via Hootsuite
Mullikin: 2M affected/y in US, 99K deaths/y, at a cost of $30B: all health-care assoc'd infections #AGBT14
7:53pm February 14th 2014 via Hootsuite
Mullikin: With Julie Segre, working on determining an outbreak in the NIH Clinical Center #AGBT14
Up next: Jim Mullikin (NIH): Sequence analysis of plasmid diversity amongst hospital-assoc'd carbapenem-resistant Enterobactericeae #AGBT14
7:52pm February 14th 2014 via Hootsuite
Interesting technology at #AGBT14 was Gen Cell Biosystem's CLiC HTP NGS library system. http://t.co/DVpwrswyVk Lanai #283 Droplet in oil^2
7:51pm February 14th 2014 via Hootsuite
Auvinen: Did 16S sequencing & compared samples at depths, Venn diagrams of OTU's. #AGBT14
7:45pm February 14th 2014 via Hootsuite
Great to meet @CRIgenomics - and he was wearing QuantStudio 3D cufflinks! http://t.co/2OIzTiw0qj #AGBT14 #digitalpcr
7:43pm February 14th 2014 via Hootsuite
Auvinen: Metagenomics - precautions taken, takes days to put down / pull up (days) over 2km deep. 2B years old, Sampled at depths #AGBT14
7:40pm February 14th 2014 via Hootsuite
Auvinen: 2500m borehole in Outokumpu Finland; 22cm diameter. Bedrock described here Itavaara ref http://t.co/YlMeKKUnx8 #AGBT14
7:37pm February 14th 2014 via Hootsuite
Auvinen: title: "..diverse microbial communities in deep crystalline rocks of the Fennoscandian Shield" #AGBT14
7:34pm February 14th 2014 via Hootsuite
First up in "Medical, Animal and Microbial Genomics" track: Petri Aurvinen, Univ Helsinki "Taxonomically and functionally... (cont) #AGBT14
7:33pm February 14th 2014 via Hootsuite
Unger: Implications: all the RNA, all the gDNA from a single cells. Single cells at 1000x conc. than single bulk tube. #AGBT14
4:59pm February 14th 2014 via Hootsuite
Unger: Roadmap: expect WGA targeted reseq this Q, WGA WGS in Q2, WGA Exome in Q3 this year. Working protein, also open up platform #AGBT14
Unger: Real-world - blast cells segregated; original cell with translocation to clone 1 (10 mut) clone 2 (11 mut). #AGBT14
4:56pm February 14th 2014 via Hootsuite
Unger: A cell line data - showing subpopulation present as homozygotes across cells at specific het loci #AGBT14
4:55pm February 14th 2014 via Hootsuite
Unger: Clustering het alleles across 369 cells are variably distributed. Interesting - subpopulations of cells that are not het! #AGBT14
Unger: Targeted using AccessArray Oncogene panel, also map >95%. Reviewed different types of dropout, SNV and allelic dropout rates #AGBT
4:54pm February 14th 2014 via Hootsuite
Unger: #AWGS - coverage was ~75% at 10x; mapping >95%; l plot of fx of reads / fx of genome is 'as good as one can get' #AGBT14
4:52pm February 14th 2014 via Hootsuite
Unger: Using phi29 MDA WGA, implemented on the chip, export to WGS, WES, or targeted. Analyze via 'SINGuLAR' #AGBT14
4:50pm February 14th 2014 via Hootsuite
Unger: Highlight of Nature Methods 'method of the year' in 2013 #AGBT14
4:49pm February 14th 2014 via Hootsuite
Unger: 358 single cells, 16 cell groups, PCA: found groups by type. 200K reads/cell enough to get exact clustering as high-depth #AGBT14
4:48pm February 14th 2014 via Hootsuite
Unger: C1 information here http://t.co/2C8kLWCzHX Additive fluidics - capture, lyse, RT, pre-Amp #AGBT14
4:46pm February 14th 2014 via Hootsuite
Unger: Illustrates the average of a bimodal distribution. Bulk vs. individual variation: mutations may group / segregate differently #AGBT14
4:44pm February 14th 2014 via Hootsuite
.@notSoJunkDNA You are welcome. I grew up in Santa Monica, the beach is always there. Presentations have been uniformly GREAT.
4:43pm February 14th 2014 via Hootsuite in reply to
Next up: Fluidigm Corp., Marc Unger: New Insight in System Biology Through Single-Cell Sequencing #AGBT14
4:42pm February 14th 2014 via Hootsuite
Beecham: Able to monitor proteins from FNAs; can do 60 SNPs, 100 genes, several proteins on the same platform. #AGBT14
4:41pm February 14th 2014 via Hootsuite
Beecham: Publication shows protein detection with Ab. Down to single-cell. Science Trans Med reference http://t.co/mIUSjFWn4B #AGBT14
4:40pm February 14th 2014 via Hootsuite
Beecham: Detection of DNA fusions. "From research publication to LDT in <1y" #AGBT14
4:38pm February 14th 2014 via Hootsuite
Beecham: FFPE samples had low RIN numbers; didn't matter. Noise of 1-3%, upcoming publication #AGBT14
4:35pm February 14th 2014 via Hootsuite
Beecham: Named Prosignia, FFPE samples, 50 gene-based CodeSet, software output a pt report. 2634 samples in 2 clinical tests #AGBT14
4:34pm February 14th 2014 via Hootsuite
