SH: Many options on the doing it yourself analysis (BWA, GATK, IGV, Bowtie, GenomeMapper, Galaxy) #HIDS15
7:17am March 11th 2015 via Twitter Web Client
SH: Be careful of introduction of bias at many process steps; big management problem is what to do w/the data, how long to keep #HIDS15
SH: Method select. need to balance performance; commercial kits vs. custom-designed; subset of DNA markers or more comprehensive #HIDS15
SH: Lab guidelines at http://t.co/eCSKFMTftj tech note 37. Different skill sets needed (bifx); public outreach for awareness #HIDS15
SH:66% and 90% full concord.; 4% and 7% no results respectively. Showed uneven representation of reads cp to electopherograms #HIDS15
7:16am March 11th 2015 via Twitter Web Client
SH:They setup their own pipeline for informatics; align w/Bowtie2 and STRaitRazor 2 ref: http://t.co/6rTA0NUY9C #HIDS15
SH: Objectives: transform routine STR typing to genomics. Evaluate pre-amplified Identifiler & PPY samples, sequence on PGM #HIDS15
SH: Want new tech that is supported by the forensic community, compatible w/existing db; fast turnaround, cost-neutral, more data #HIDS15
SH: National laboratory, the sole provider to NZ Police. Agree that existing platforms are sensitive & well-characterized #HIDS15
SallyAnn Harbison (Institute of Environmental Science and Research New Zealand) Integrating the Ion PGM™ into your forensic lab #HIDS15
7:15am March 11th 2015 via Twitter Web Client
MK:Q:Some concern for multiplexing? A:Well-est concept outside forensics; benefits of throughput & cost effectiveness #HIDS15
MK: Allows to combine some of these major forensic questions: who did what and when. #HIDS15
7:13am March 11th 2015 via Twitter Web Client
MK: Highly promising results from degraded DNA - correct haplogroup inference possible from all samples used #HIDS15
MK:Tiling-path approach - detect NUMTs - long-range 8kb PCR, of 5 samples 1 had difference in 2 positions #HIDS15
MK: 2 indel represent true PGM artifacts (not seen w/Sanger). Calculated as 6x10^-6 (!) (Used Hi-Q enzyme + N=only 20) #HIDS15
MK:Addressing PGM @iontorrent accuracy - compared mtDNA to Sanger: 'almost all homopol errors not called as true consensus seq' #HIDS15
7:12am March 11th 2015 via Twitter Web Client
MK: Chart of 20 samples: alignment 7-96%; coverage >1300 to 3500. #HIDS15
MK: 3rd project - entire mtDNA genome in single run. 161bp (small) amplicons. Tested w/ 20 global samples Sanger seq'd #HIDS15
MK: Wet and dry pipelines available here: http://t.co/gbuOUMHHHH #HIDS15
7:11am March 11th 2015 via Twitter Web Client
MK: Major haplogroups and paternal ancestry charted for 21 samples. Able to determine major geography where haplogroups occur #HIDS15
MK: Tested against 21 global samples, large chart of statistics, 73-89% aligned to Y-chr. 295K-720K reads/sample #HIDS15
MK: Ralf ref http://t.co/FKRMz7CDlZ Now have the entire tree http://t.co/PQokn0DNA2 #HIDS15
MK: 2nd example: higher-resolution Y-haplotype 530 Y-SNPs on 446 amplicons for 432 Y-haplogroups #HIDS15
MK: Amplicon size for RNA designed smaller (150bp) #HIDS15
MK:RNA tissue ID with hum ID STR's, n=7 fully matched. 8 DNA/8 RNA in one 318 v2 run; only 1ng template (likely can go lower) #HIDS15
MK: Pilot from dried tissue - skin, blood, vag. secretion, saliva, semen, mens. blood. #HIDS15
MK: AmpliSeq 9 STRs + AMELY/X, 14 mRNAs (2 ref + 12 tissue-spec RNAs). Zubakov et al. under review #HIDS15
MK: In principle - targeted D/RNA sequencing. Did 3 pilots w/@iontorrent - first was individ and tissue ID (via RNA) #HIDS15
7:10am March 11th 2015 via Twitter Web Client
MK: 'And at the end you want to do it all'. A tech that starts to do this for multiplexing. DNA, RNA, human, non-human... #HIDS15
MK: Age of deposition - RNA markers or metabolites. Microbial forensics. Showed chart: STR, mt lineage, age, ancestry, appearance #HIDS15
MK:Can age be traced? (Open question.) Ancestry testing w/detail, need 100's if not 1000's of SNPs. Tissue types? #HIDS15
MK: Uni-parental lineage chart by geography - need large number of markers #HIDS15
MK: (Profiled here on Behind the Bench: http://t.co/RD87b18cV1 ) #HIDS15
Manfred Kayser (Erasmus U) Towards multi-purpose forensic D/RNA analysis via targeted NGS #HIDS15
NM: Individ w/Kidd and Seldin AIM SNPs; hair and eye color clustering shown. #HIDS15
7:06am March 11th 2015 via Twitter Web Client
NM: Reviewing SNPs, showed results w/AmpliSeq Human ID panel, down to 100pg input. Recent publ http://t.co/ADHhPAdjTZ #HIDS15
NM: Multiple platforms, lots of training involved. Wishes easier data analysis, more laboratory automation #HIDS15
NM: Showed how the 10 STRs from the LT AmpliSeq panel would be reported. Following prior strategies for tech adoption #HIDS15
NM: Have suggestions for nomenclature for STRs: from 2014 Gelardi ref http://t.co/x0qfmPjddv Ongoing work for std format #HIDS15
NM: Works down to 100pg in our hands. Showed data from mixtures 1:1 & 1:20. Onto challenging material, FFPE #HIDS15
7:05am March 11th 2015 via Twitter Web Client
NM: Can find stutter and artifact. Lost or gain of a NT 47/50 most freq errors. '100% concordance with AmpFlstr in 10 samples' #HIDS15
NM:Adjusting STR primers, make the size distribution conform to readout Fordyce 2015 ref http://t.co/CpceCgZjeK #HIDS15
NM: LT STR-10plex, using @iontorrent AmpliSeq; amplicons 75-170bp; used an HID STR plug-in. 'Often take data out for other analysis' #HIDS15
NM: Lessons from 454 Gelardi et al ref http://t.co/x0qfmPjddv 30% of one-allele types from PCR-CE were from heterozygotes #HIDS15
RT @NatGeo: Elephant poachers "will not have the last word in Kenya." http://t.co/EhNjL0XUCk
7:05am March 11th 2015 via Hootsuite
NM: Showing D12S391 w/errors and stutters. Another CSF1PO allele illustration: able to sep stutters and artifacts #HIDS15
NM: Fordyce et al 2011 ref http://t.co/H6YcIA7bKN for STR via barcoded NGS (via 454) #HIDS15
NM:PGM using both the HID indentity and ancestry panels. Illustrates readlength-dependance on picking up repeat regions #HIDS15
NM: Using NGS for a lot of molecular pathology (i.e. heart disease); has all three 454 GS Jr, MiSeq and PGM benchtop systems #HIDS15
7:04am March 11th 2015 via Twitter Web Client
Niels Morling (Univ Copenhagen) SNP and STR analysis using NGS #HIDS15
