Kayser:Q:Baldness? A:early-onset is considered 'disease'; 8 genes known (main one on the X-chrom) #IWT14
8:35am September 15th 2014 via Hootsuite
Kayser: A limitation is no longer the technology, it is the biology that is the lmitation #IWT14
8:33am September 15th 2014 via Hootsuite
Kayser: Simultaneous extraction, STR via PGM corresponds to commercial Sanger kits; can do tissue ID via AmpliSeq RNA #IWT14
8:32am September 15th 2014 via Hootsuite
Kayser: 3rd example, combining STR with RNA for tissue ID, indel for sex determination #IWT14
8:31am September 15th 2014 via Hootsuite
Kayser: Second example - using the human microbiome and using 16S rDNA. Used HMP extraction and primers #IWT14
8:30am September 15th 2014 via Hootsuite
Kayser: Now looking at 539 Y-SNPs, analyzed using AmpliSeq and Ion PGM #IWT14
8:28am September 15th 2014 via Hootsuite
Kayser: Also can estimate time of day, melatonin level differences (jet-lag effect); vary over time and can be measured #IWT14
8:25am September 15th 2014 via Hootsuite
Kayser: mRNA multi-plex tests based on cell/tissue type - 2012 publication: http://t.co/ax0i2wxTWY #IWT14
8:23am September 15th 2014 via Hootsuite
Kayser: Facial shape is 'far away' (meaning not anytime soon) due to genetic complexity #IWT14
8:22am September 15th 2014 via Hootsuite
Kayser: Skin color, hair morphology, height variation (but only 10% var determined to-date); hair-loss; facial shapes (first 5 genes) #IWT14
8:21am September 15th 2014 via Hootsuite
Kayser: Now showing chronological age from DNA using CpG data on real-time PCR, work in-progress. #IWT14
8:20am September 15th 2014 via Hootsuite
Kayser: Now hair and eye color publication 2011 http://t.co/w0topK0FAf #IWT14
Kayser: Blue/brown predictable; IrisPlex develped with 6-SNPs, 2011 paper here: http://t.co/0GZ5HCK7pe #IWT14
8:19am September 15th 2014 via Hootsuite
Kayser: Predicting eye color - figure from 2009 Liu et al paper http://t.co/Dg6YGtVIjK #IWT14
8:17am September 15th 2014 via Hootsuite
Kayser: Looking at distribution of the Y-chrom. worldwide, can determine easily with >600K SNPs. AmpliSeq comes in here #IWT14
8:16am September 15th 2014 via Hootsuite
Kayser: How to find unknown perpetrators? A new field called 'forensic DNA phenotyping': externally identifiable phenotypes #IWT14
8:13am September 15th 2014 via Hootsuite
Kayser: 13 STRs current system; (background here on Behind the Bench blog: http://t.co/Cbkm3bCZ29 ) #IWT14
8:12am September 15th 2014 via Hootsuite
Kayser: STR's - profile matches have to have matches at a 1:1, look for a complete identical match. #IWT14
8:11am September 15th 2014 via Hootsuite
Kayser: How forensics all started: Sir Alec Jeffreys in 1984 "Sept 10, DNA fingerprinting was born" #IWT14
8:09am September 15th 2014 via Hootsuite
Manfred Kayser (Erasmus Univ Rotterdam): "Ion Torrent PGM in Forensic Genetics" #IWT14
8:07am September 15th 2014 via Hootsuite
Certa: Can determine pathway-based direct responses of novel cmpds to determine mech. of action. Timepoints, concentrations... #IWT14
8:03am September 15th 2014 via Hootsuite
Certa: Feels that 1K genes can be interrogated with AmpliSeq RNA at 100 samples per PI run #IWT14
7:58am September 15th 2014 via Hootsuite
Certa: Indicates modulated pathways as a short-hand for the genome-wide work #IWT14
7:57am September 15th 2014 via Hootsuite
Certa: Some examples of pathway development in hepato-toxicity, up & down regulation of genes on a microarray-wide scale... #IWT14
7:56am September 15th 2014 via Hootsuite
Certa: Instead of 48K genes on a microarray, same result from 917 AmpliSeq RNA genes #IWT14
7:52am September 15th 2014 via Hootsuite
Certa: Calculated 96 pathways for their model, and determined from AmpliSeq RNA data exactly 96 pathways from PCA analysis #IWT14
Certa: Key pathway reporter genes shown: TNF, Wnt, Nitric Oxide, TGF - comparing microarray vs. AmpliSeq RNA signals #IWT14
7:51am September 15th 2014 via Hootsuite
Certa: (Work published recently here in BMC Genomics http://t.co/QRIPsBF3dT using AmpliSeq RNA) #IWT14
7:50am September 15th 2014 via Hootsuite
Certa: Showing 50 low-expressors completely missed on the microarray. Moderate- or high-expressors very linear #IWT14
7:49am September 15th 2014 via Hootsuite
Certa: Signal intensities (microarray) - sigmoid curves are similar, r=0.78 RNA-Seq: r=0.87 (likely due to mapping of RNA-Seq) #IWT14
7:48am September 15th 2014 via Hootsuite
Certa: No mis-matches - b/c the amplicons are matched. One read corresponds to one molecule, RPKM values shown #IWT14
7:47am September 15th 2014 via Hootsuite
Certa: We like the speed - 30 minutes later we have an excel sheet for analysis" #IWT14
7:46am September 15th 2014 via Hootsuite
Certa: Reverse transcription to DNA - still use PolyA primed, kit for making full-length cDNA, 96 samples per Proton PI run #IWT14
7:45am September 15th 2014 via Hootsuite
Certa: 917 target transcripts with 4 species: human, mouse, Cynomolgus monkey (pharma important), minipig (custom) #IWT14
7:44am September 15th 2014 via Hootsuite
Certa: Pathways include everything - immune responses, toxicology, etc. Will publish soon in silico database - 917 'response genres' #IWT14
7:42am September 15th 2014 via Hootsuite
Certa: Can use different activators / compounds to look at primary molecular response based upon gene exp signatures #IWT14
7:41am September 15th 2014 via Hootsuite
Certa: Pathway diagram with reporter gene readouts; cover spectrum of cell types and cover each with all reporter genes #IWT14
7:40am September 15th 2014 via Hootsuite
Certa: Molecular phenotyping: 152 signalling pathways ID'd, 917 response genres; modularized signalling cascades in diff cell types #IWT14
7:38am September 15th 2014 via Hootsuite
Certa: Applied AmpliSeq RNA and compared to microarray as well as RNA-Seq on Ion Proton #IWT14
7:37am September 15th 2014 via Hootsuite
Certa: SC-specific, switch genes (Yamanaka factors), cardiomyocyte-spec gene regulation: model well-characterized #IWT14
7:36am September 15th 2014 via Hootsuite
Certa: They monitor diff. to the molecular level. First work on microarray gene expression; stem cell to myocytes big change #IWT14
7:35am September 15th 2014 via Hootsuite
Certa: Reviewed iPS cell differentiation; most popular starting point is cardiomyocytes as you can visualize them #IWT14
7:34am September 15th 2014 via Hootsuite
Next: Ulrich Certa (Roche): "Highly sensitive amplicon-based transcript quantification by Ion Proton™ sequencing" #IWT14
7:32am September 15th 2014 via Hootsuite
Affourtit: AmpliSeq transcriptome accessing FFPE - much simpler analysis compared to regular RNA-Seq #IWT14
6:26am September 15th 2014 via Hootsuite
Affourtit: Highlights custom panel made available to anyone, first one on hearing loss http://t.co/5XOcMBO3Og #IWT14
6:22am September 15th 2014 via Hootsuite
Affourtit: Reviewing AmpliSeq Human Exome RDY; 58MB footprint, 50ng input; dry primers for better uniformity / ease of use #IWT14
6:18am September 15th 2014 via Hootsuite
Jason Affourtit (Thermo Fisher Scientific): "Ion AmpliSeq™ Gene Panels—DNA and RNA, latest and how to use in your research" #IWT14
6:14am September 15th 2014 via Hootsuite
Dowds: In Ion Reporter, showing multi-sample visualization: under new 'variant impact' tab; mouseover shows rich data #IWT14
6:09am September 15th 2014 via Hootsuite
Dowds: Aneuploidy in Ion Reporter: now doing mtDNA copy number ratio, based on recent research of how impt it is to monitor #IWT14
6:05am September 15th 2014 via Hootsuite
Dowds: AmpliSeq RNA fusion analysis in Ion Reporter allows visual inspection #IWT14
6:04am September 15th 2014 via Hootsuite
