September 2014

Lenze: Their Sanger dropout rate is 10%; tested extraction (went from Q to Promega); library PCR got 3/4 products, good PGM data #IWT14

3:33am September 16th 2014 via Hootsuite

Lenze: Important points: amplifiability of DNA: they do a QC PCR for every sample, a four-plex test. Poor library PCR -> poor PGM seq #IW

3:32am September 16th 2014 via Hootsuite

Lenze: Now they apply 5% MAF minimum, 500x coverage of amplicons. 30 samples/week with one PGM. #IWT14

3:30am September 16th 2014 via Hootsuite

Lenze: Using titrated dilutions, mixtures got even to the lowest 1% MAF at 25x coverage. 'No false positives' #IWT14

3:30am September 16th 2014 via Hootsuite

Lenze: 49 comparison samples chosen, already Sanger sequenced. Also incl. complex deletion, all tested accurately on PGM #IWT14

3:29am September 16th 2014 via Hootsuite

Lenze: First it was 1 hotspot in 1 gene, now 6 hotspots in 2 genes. Ion PGM as suitable for FFPE due to low input, standard panels #IWT14

3:27am September 16th 2014 via Hootsuite

Next: Dido Lenze (Charité Pathology, Berlin) “Moving from Sanger to NGS” #IWT14

3:25am September 16th 2014 via Hootsuite

Trujillano: Upcoming work submitted in J Mol Diag, 75 prev. not described #IWT14

3:24am September 16th 2014 via Hootsuite

Trujillano: Since their pipeline was originally designed around WES, a different subset of tools used. #IWT14

3:16am September 16th 2014 via Hootsuite

Trujillano: Used Torrent Suite to obtain var calling and VCF output. They apply functional annotation and prioritization #IWT14

3:15am September 16th 2014 via Hootsuite

Trujillano: Another 95 samples with unk mutations were the challenge group. At 2000x depth, 99.99% of target at 20x (!) #IWT14

3:13am September 16th 2014 via Hootsuite

Trujillano: For hereditary breast and ovarian Ca; tested 150 samples previously sequenced on Sanger #IWT14

3:13am September 16th 2014 via Hootsuite

Trujillano: Decided to try AmpliSeq BRCA1/2 (see here http://t.co/QvbdgF7bnG ) Due to size of gene with Sanger, many missed var's #IWT14

3:10am September 16th 2014 via Hootsuite

Trujillano: Their unique CentoMD database; they est. only 50% of the deleterious var's are in the public domain #IWT14

3:08am September 16th 2014 via Hootsuite

Trujillano: WES at Centogene (CentoXome) is 120x, >95% at >20x, turnaround time is 1 mo. #IWT14

3:07am September 16th 2014 via Hootsuite

Trujillano: Emph of their Centogene is rare diseases. >350M people affected worldwide. #IWT14

3:05am September 16th 2014 via Hootsuite

Daniel Trujillano (Centogene AG, Rostock) NGS analysis of BRCA1 and BRCA2 genes #IWT14

3:04am September 16th 2014 via Hootsuite

Tyrelle:Q: Can pools of amplicons be analyzed as a group in Reporter? A: Can be done, if pool information is in the design file #IWT14

2:59am September 16th 2014 via Hootsuite

Tyrelle:Q: Use of informatic tools from other platforms? A:For annotation from VCF's, yes. Trio workflow requires variant caller, no #IWT14

2:57am September 16th 2014 via Hootsuite

Tyrelle: (HiQ con't): Still early with HiQ, will be of interest to see performance of HiQ on Proton #IWT14

2:56am September 16th 2014 via Hootsuite

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

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