PS: When to use mRNA for forensics? In special cases - can do saliva as it works reliably; skin can be but depends on age #HIDS15
7:29am March 11th 2015 via Twitter Web Client
PS: mRNA forensics 2014 ref http://t.co/bRYc1726vc Showing results across sample types #HIDS15
PS: Exploring RNA analysis for forensics: labile, mRNA levels vary, mRNA expression enriched but not restricted; FP/FN dangers #HIDS15
PS: 2014 Claes et al PLOS Genet http://t.co/L2NJu0Fycq Facial recognition from genotypes just starting #HIDS15
PS: But for height and facial characteristics - polygenic, very difficult to determine, need many more samples & genotypes #HIDS15
PS:The external phenotypic traits: eye/skin/hair color; hair morphology; male baldness; body height; facial char's #HIDS15
7:28am March 11th 2015 via Twitter Web Client
PS: Needs: improve db workflow, harmonize legislation. Shows chart down to 25pg input of 'no calls' and dropout; publ. under rev #HIDS15
PS: Charts of DNA db's in EU: As of 2013, 1.4M unsolved crime cases: an unknown criminal w/a known DNA profile. #HIDS15
PS: CSI Effect may have contributed to decrease in funding: "everything is perfect" "just like on TV" #HIDS15
PS: The 'CSI Effect' can lead to confirmation bias - correctly observed DNA profiles resulting in wrongful conclusions #HIDS15
PS: Starts with 'The CSI Effect': propagating a false idea that 'everything has been solved in forensic DNA typing' #HIDS15
PS: Part of a 15-member EUROFORGEN Ref http://t.co/O6cnxwohQL #HIDS15
Peter Schneider (Institute of Legal Medicine, Cologne, Germany) Forensic genetics: meeting the challenges of biological evidence #HIDS15
RD:"Pleased to see that in the @iontorrent Ion Chef there was no contamination in the negative control" #HIDS15
7:27am March 11th 2015 via Twitter Web Client
RD: Performance is 'impressive' - sensitivity down to 0.5 to 1ng. Automated library & template prep must be considered. #HIDS15
RD:Reviews 3 examples of admixture via AmpliSeq Admixture panel - and self-reported results. 'High accuracy for continental groups' #HIDS15
RD:Part 2 - AmpliSeq HID Ancestry Panel http://t.co/og8gxhOnu6 1ng input, >97% at >300x, need 600x coverage #HIDS15
RD: Conclude '@iontorrent chemistry is sufficiently optimized'. Used established PCR protocol where possible #HIDS15
RD: 9947A, 1 hu sample; 0.05, 0.1 and 0.5ng input. Platinum Taq coverage lower. Evidence of primer-dimer carryover affects perf. #HIDS15
7:26am March 11th 2015 via Twitter Web Client
RD: Wanted to check new purification (Nucleospin), and reduce PCR cycles; also try replacing AmpliTaq Gold w/Platinum Taq #HIDS15
RD:Showed coverage at 0.1, 0.2 and 0.3 ng input. Did show lower coverage for smaller amplicons. #HIDS15
RD: <3% missing data; >98% reprod, >98% accuracy. Robust given it was crude: no balance amplicons between & w/in assays #HIDS15
RD:135 amplicons (just reported by Chris Phillips) w/Eurasiaplex etc. Used QIAquick 100bp cutoff, pooled & sequenced #HIDS15
Runa Daniel Victoria Police Forensic Services Dept, Australia Effects of Taq and PCR purification on Ion Torrent genotyping #HIDS15
CP: A forensic ancestry panel Phillips ref http://t.co/O6cnxwohQL Custom AmpliSeq panel for 128 SNPs #HIDS15
7:25am March 11th 2015 via Twitter Web Client
CP: Limited low-level DNA expt's suggests 'very high sens.' 81/169 gave >100x from aDNA sample #HIDS15
CP: "99.8% concordance is best of any SNP test comparisons made at USC" #HIDS15
CP:@lifetech worked really hard to reduce amplicon size. Kinds of outliers ID'd: 3% 'should remove', 5% 'outlying chars' #HIDS15
CP: Bauer ref for aDNA: http://t.co/IyfbVuPQZK Quality of top SNPs 'very very good' #HIDS15
CP:Mixtures' data easy to detect. Sensitivity:at optimum 1-3 SNPs no-calls or dropout. Low-input: 8-12 fail. aDNA 450 pg #HIDS15
CP:Strand-bias plot did have 9 SNPs that were outliers, visuallized in IGV. 3 SNPs unidirectional, not explainable - affects call #HIDS15
7:24am March 11th 2015 via Twitter Web Client
CP: 'Very low rate of @iontorrent misincorporation'. 0.25% overall rate - applicable to nearly all SNPs. 34 bases from >2M #HIDS15
CP: Lowest performing samples - <100pg, degraded, too many samples/run. #HIDS15
CP:Coverage plotted as coverage per sample and coverage per SNP as a heatmap. #HIDS15
CP: Used 007 & 9947a w/12th century aDNA (0.45ng). Parameters: coverage, allele read freq, base misincorporation, strand bias #HIDS15
CP: NIST validation framework described. Also added 6 TGP genomic controls from Coriell. #HIDS15
CP: Also the Human Identification Ancestry Panel http://t.co/og8gxhOnu6 #HIDS15
7:23am March 11th 2015 via Twitter Web Client
CP: Desc the Human Identity SNP AmpliSeq http://t.co/UZ31pTGL1B #HIDS15
CP: Genotyping concordance 'quite good' (98.5%) but illus. problems w/SNaPshot. 3% discordance; 1.5% discordant w/Sanger #HIDS15
CP: Input template insensitive to coverage. Allelic balance 'okay but not ideal' 10-30% and 70-90% difficult to interpret #HIDS15
CP: Five forensic SNaPshot PCRs - 52 ID, 27 Eurasia, 28 Pacifiplex, 6 Irisplex, 34-plex. From 0.2ng wide var in coverage #HIDS15
CP: Another study w/LT forensic ID panel. 3rd w/ 128 ancestry markers they designed from scratch. #HIDS15
CP: SNPs are binary but what about mixtures? Need to examine allelic balance. Combined 5 SNaPshot PCRs for 136 amplicon pool #HIDS15
CP: Balancing coverage, multiplexing SNPs, barcoding samples. What are coverage outliers? What min coverage to use? #HIDS15
CP: What happens w/low-level or mixed DNA is in the input? Alignment adds another layer of complexity if indels/homopol's near SNP #HIDS15
7:22am March 11th 2015 via Twitter Web Client
CP: Asking about good/poor performers in a SNP panel, and what dependence there is w/low level DNA #HIDS15
CP: Shares this PDF from Nature http://t.co/CS2TVDw5hl and the role SOLiD and @iontorrent had to play in it #HIDS15
Christopher Phillips University of Santiago de Compostela Spain: Validation of identity and ancestry SNP Panels #HIDS15
SH: 'This meeting has reinforced for me the suitableness of this technology for us' (the forensic community) #HIDS15
7:17am March 11th 2015 via Twitter Web Client
SH: From here she expects a 3-5 year transition over to NGS for all casework. Working on microbial genetics, identical twins #HIDS15
