Tyrelle:Q:Var calling and HiQ? A:HiQ data looks much nicer; but calling stats don't improve as the error model is well tuned already #IWT14
2:56am September 16th 2014 via Hootsuite
Tyrelle: Level of data: from DAT to Wells to BAM to aligned BAM to VCF. Archive is offloading; backup is making a copy #IWT14
2:52am September 16th 2014 via Hootsuite
Tyrelle: Review of project tracking fn's in Ion Reporter, new heat map of deleterious mutations (ability to compare across samples) #IWT14
2:50am September 16th 2014 via Hootsuite
First up: Greg Tyrelle (Thermo Fisher Scientific): “Bioinformatics: reporting out, tracking audit, storage, backup & archiving” #IWT14
2:49am September 16th 2014 via Hootsuite
RT @mashable: "It's not about the money. It's about my sanity." -Minecraft creator @notch, on Microsoft acquis. http://t.co/4XSW5EQaBt
11:00pm September 15th 2014 via Hootsuite
Study: Male scientists want to be involved dads, but few are | Washington Post http://t.co/uRQLslnH6f
8:01pm September 15th 2014 via Hootsuite
RT @nickwingfield: Why Notch sold Mojang for $2.5B to Microsoft: "The pressure of owning Minecraft became too much" http://t.co/1nDCtDv5zG
7:00pm September 15th 2014 via Hootsuite
Wisdom in the Age of Information and the Importance of Storytelling | Brain Pickings http://t.co/TjY79zPAdo
6:01pm September 15th 2014 via Hootsuite
RT @TheEconomist: A fossil discovery in Morocco represents the first firm evidence of a semi-aquatic dinosaur http://t.co/1AYOMChDQv
5:00pm September 15th 2014 via Hootsuite
RT @dinisguarda: 16 Traits Of The World's Most #Successful People http://t.co/fpFjFHDZ2Z
4:00pm September 15th 2014 via Hootsuite
MT @GenomeNathan: Sins of fathers, not genomes...or public libraries: Fear-mongering exceptionalism re. DNA testing http://t.co/T6Arb93nHh
3:02pm September 15th 2014 via Hootsuite
Major study from 43K cases MT @DrKhouryCDC: Meta-analysis identifies 23 new SNPs for prostate cancer w/total 100 http://t.co/iH1m4BRU2S
2:00pm September 15th 2014 via Hootsuite
RT @NatureNews: New device inspired by the spleen can quickly clean blood of everything from E. coli to Ebola http://t.co/ZeIn1iZFuY
1:01pm September 15th 2014 via Hootsuite
RT @mnt: Cycling or walking to work ‘improves psychological health’ http://t.co/uWpBY6DJFv #commuting #psychology
12:03pm September 15th 2014 via Hootsuite in reply to
RT @washingtonpost: The anti-standardized testing movement is growing, and it’s finding success around country http://t.co/Onlb09DCfG
11:01am September 15th 2014 via Hootsuite in reply to
Pfarr:Q:fixation artifacts? A:Some are called; need inspection, about 5-10% freq, sample-dep #IWT14
10:28am September 15th 2014 via Hootsuite
Pfarr:Q:With low amt of DNA? Amplification? A:Sometimes will do direct amplification #IWT14
10:24am September 15th 2014 via Hootsuite
Pfarr:Q:Many software for analysis? A:To assist with confirmation #IWT14
10:23am September 15th 2014 via Hootsuite
Pfarr: Laid out eight standard and custom panels for their work, all FFPE compatible (<150bp amplicons) #IWT14
10:14am September 15th 2014 via Hootsuite
Pfarr: Their rate of sample failure is 7.7% (in line with comment from IWT Manchester presenter) on FFPE samples #IWT14
10:11am September 15th 2014 via Hootsuite
Pfarr: 70K samples/yr; FFPE can have low yield, C:G>T:A due to fixation artifacts. #IWT14
10:07am September 15th 2014 via Hootsuite
Nicole Pfarr (Univ Hosp Heidelberg) "Analysis of FFPE tumor samples" #IWT14
10:01am September 15th 2014 via Hootsuite
Farinelli:Q:Proton capacity sufficient for exome? A:Yes due to evenness of coverage. Turnaround time is very fast #IWT14
9:59am September 15th 2014 via Hootsuite
Farinelli:Q:Thought about pre-implantation? A:Yes. #IWT14
9:57am September 15th 2014 via Hootsuite
Farinelli: Also developed liquid handling automation for library prep, did 150 samples from Proton order to data delivery 2 months #IWT14
9:49am September 15th 2014 via Hootsuite
Farinelli: They took 9 mos to develop their test Feb 2013; on Proton, did 3 runs per init ('unsupported'); showed verification 2 mos #IWT14
9:47am September 15th 2014 via Hootsuite
Farinelli: Gave a history of Down Syndrome; trisomy is detecting a 10% compared to 15% of a normal background #IWT14
9:43am September 15th 2014 via Hootsuite
Farinelli: Showed quality, evenness of coverage, visualization of both exome and cancer panel #IWT14
9:39am September 15th 2014 via Hootsuite
Farinelli: They have a lot of experience with AmpliSeq Exome; a CSP for @Lifetechcorp http://t.co/JEi9qZ5DR9 #IWT14
9:38am September 15th 2014 via Hootsuite
Next up: Laurent Farinelli, Fasteris (Geneva) "Experience with clinical research applications and Ion AmpliSeq on Ion Proton" #IWT14
9:32am September 15th 2014 via Hootsuite
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
