Milos: Majority of variation are single nucleotide polymorphisms. Well over 90% total overall sensitivity. #ionworld2013
4:25pm October 21st 2013 via Hootsuite
Milos:Subst. errors - 94%. Indels is a struggle - 42% and 41% (1 or 2/run) #ionworld2013
4:24pm October 21st 2013 via Hootsuite
Milos: 1 exome/run: 94% of the available variants are seen and called; 2 samples/run is 92% #ionworld2013
4:23pm October 21st 2013 via Hootsuite
Milos: 167x 1 sample/run; 93x 2 samples/run.92% coverage with 2 samples/run. 97% of the targets at 20x; 92% at 20x with 2 /run #ionworld2013
Milos: Readlength 142nt, 80M reads/Proton P1 run; 10.4Gb/run. #ionworld2013
4:22pm October 21st 2013 via Hootsuite
Milos: Their comparison was with TargetSeq and SureSelect (Agilent). Used HapMap samples as 'truth' sample. #ionworld2013
4:21pm October 21st 2013 via Hootsuite
Milos: 'It is amazing to do a 5h run and get data'. We spend a lot of time with annotation, automation is under dev. #ionworld2013
4:20pm October 21st 2013 via Hootsuite
Milos: They compared AmpliSeq Exome to bait capture. 'The beauty is the simplicity of the workflow.' Taking a SOP and apply it #ionworld2013
4:19pm October 21st 2013 via Hootsuite
Milos: AmpliSeq Exome - their criteria is fast, accurate, scalable and economical. #ionworld2013
4:18pm October 21st 2013 via Hootsuite
Milos: Nils Homer has done the work at Claritas - presenting tomorrow. #ionworld2013
Milos: NGS-based tests include: gene panels and CNV detection. Neuromuscular disorder panel, gene list from BCH 110kb seq #ionworld2013
4:16pm October 21st 2013 via Hootsuite
Milos: DMD= developmental delays; focused on Autism, microarray-based, >10K pts. #ionworld2013
4:15pm October 21st 2013 via Hootsuite
Milos: Has a menu of 110 tests, incl NGS panel for DMD, a proprietary microarray CNV optimized for autism, dev. clin. exomes #ionworld2013
4:12pm October 21st 2013 via Hootsuite
Milos: Claritias: Boston Children's Hosp., LifeTech (investor), Medical Info co., a combination of supporters #ionworld2013
4:10pm October 21st 2013 via Hootsuite
Milos: Two reports in Science - lentiviral hematopoetic stem gene therapy in children 'perhaps a glimpse of the future' #ionworld2013
4:09pm October 21st 2013 via Hootsuite
Milos: Claritas - 'We have a very bold vision: to become the leading provider of next-generation pediatric diagnostics' #ionworld2013
4:07pm October 21st 2013 via Hootsuite
Next up: Patrice Milos, Claritas Genomics "Future clinical applications of exome sequencing using the Ion Proton system" #ionworld2013
4:03pm October 21st 2013 via Hootsuite
Photo of Christian Marshall of The Hospital of Sick Children #ionworld2013 http://t.co/kGPYSriecM
4:02pm October 21st 2013 via Hootsuite
Marshall: It wasn't Adams-Oliver, it was FOP. 'Often IDs variants that can only be interpreted by going back to the phenotype' #ionworld2013
4:01pm October 21st 2013 via Hootsuite
Marshall: ACVR1 Sanger validated; ass'd with 'Fibrodysplasia ossificans progressiva'; returning to phenotype, it overlaps AOS #ionworld2013
4:00pm October 21st 2013 via Hootsuite
Marshall: Assumed new dominant mut.; discovered 12 variants, 1 of which was 'really interesting' ACVR1 bone receptor #ionworld2013
3:59pm October 21st 2013 via Hootsuite
Marshall: Could be wrong dx; unk. inh. pattern; decided to seq trio with AmpliSeq Exome and Ion Reporter 4 with trio analysis. #ionworld2013
3:58pm October 21st 2013 via Hootsuite
Marshall: Some exons had low coverage; Sanger backfilled 85 targets in 3 known genes. Then new gene EOGT published; neg still #ionworld2013
3:57pm October 21st 2013 via Hootsuite
Marshall: Adams-Oliver syndrome P1 chip, 8.8Gb, 130bp readlength, whole-exome. All allele freq >20%, neg for known genes #ionworld2013
3:54pm October 21st 2013 via Hootsuite
Marshall: Now talking about a subject with prior dx of Adams Oliver Syndrome, 3 known genes, 2 dom, 1 reces., test not avail. #ionworld2013
Marshall: Ion Proton seq metrics getting 9-10 GB / run of mapped data #ionworld2013
3:49pm October 21st 2013 via Hootsuite
Up next: Christian Marshall, The Hospital for Sick Children Toronto #ionworld2013
Nelen: Showed Sanger validation of the 3 mutations from the trio data #IonWorld2013
2:56pm October 21st 2013 via Hootsuite
Nelen: SOLiD 4 found 2 mutations; GNOM detected 3; Ion Proton 3 exomes on 1 chip detected 15 candidates. 12 indels, 3 are real #IonWorld2013
Nelen: De novo mutations look very much like false positive variants. So they sent in to Life Tech a well-known sample #IonWorld2013
2:54pm October 21st 2013 via Hootsuite
Nelen: Exome sequencing using Ion Proton and AmpliSeq Exome: looking for de novo mutations for neurodev. disease #IonWorld2013
2:53pm October 21st 2013 via Hootsuite
Nelen: "Semiconductor sequencing on an Ion PGM System is as good as the gold standard" #IonWorld2013
2:50pm October 21st 2013 via Hootsuite
Nelen: E.g,: Sample A Gene A plus Sample B and Gene B doesn't need a barcode. #IonWorld2013
Nelen: How to automate all of this? Efficient use of barcoding. "You need to use unique amplicons, unique genes per barcode" #IonWorld2013
2:48pm October 21st 2013 via Hootsuite
Nelen: Calculated sens. & specificity: 283MB, sens of 99.6%, spec 99.98%. #IonWorld2013
2:47pm October 21st 2013 via Hootsuite
Nelen: Looking at a minor number of FP due to identical tandem repeated genomic regions. #IonWorld2013
2:44pm October 21st 2013 via Hootsuite
Marcel Nelen presenting their clinical research work from Radboud Univ Nijmegen Netherlands #IonWorld2013 http://t.co/SuwRvXb18m
2:39pm October 21st 2013 via Hootsuite
Nelen: They do 25K DNA isolations, 400K amplicons, 800K Sanger reactions annually - all fully automated for CE. #IonWorld2013
2:38pm October 21st 2013 via Hootsuite
Nelen: 800 genes on CE, 10K amplicons, can they all convert at the same sensitivity and specificity? #IonWorld2013
2:37pm October 21st 2013 via Hootsuite
Nelen: A large gene RYR1 (106 exons) redesigned amplicons to 100bp, now routine on Ion PGM #IonWorld2013
2:35pm October 21st 2013 via Hootsuite
Nelen: Mitochip can detect ~9% heteroplasmy. NGS on Ion PGM gave a reliable 5% detection. #IonWorld2013
Nelen: BRCA1/2 started at first - to see how it works in clinical research. To date 155 pathogenic mutations sequenced #IonWorld2013
2:33pm October 21st 2013 via Hootsuite
Nelen: "I'm old enough to know how laborious it was to generate these data" (showing a slab gel and the colors of C.E.) #IonWorld2013
2:32pm October 21st 2013 via Hootsuite
Next up: Marcel Nelen of Radboud Univ Nijmegen Netherlands on BRCA, RYR1 and mtDNA #IonWorld2013
2:30pm October 21st 2013 via Hootsuite
Reynolds: Presented data for Plavix CYP2C19 and distribution of phenotypes among populations #IonWorld2013
2:23pm October 21st 2013 via Hootsuite
Photo of Tom Reynolds of AIBiotech on stage #IonWorld2013 http://t.co/Q7LTjwaXA6
2:22pm October 21st 2013 via Hootsuite
Reynolds: "We see the biggest benefit of Ion Chef is getting turnaround time decrease by 24 hours" (early access) #IonWorld2013
2:19pm October 21st 2013 via Hootsuite
Reynolds: "There is a steep learning curve with any technology but low-level technicians easily learned the workflow." #IonWorld2013
2:18pm October 21st 2013 via Hootsuite
Reynolds: To date: 30K samples, 1K samples/day capacity. Surprising: "QNS" values very low (unable to get a result) #IonWorld2013
Reynolds: 'The sequencing part has always been easy for us' 'The LifeTech's built-in variant caller has made our lives easier' #IonWorld2013
2:16pm October 21st 2013 via Hootsuite
