WP:A2:Rel low penetrance of PHP due to this bottleneck effect. Distinguish true PHP from artifacts in alignment & contam. #HIDS15
7:04am March 11th 2015 via Twitter Web Client
WP:Q:Hypoth. for origin of PHP? A:Relatively poorly understood; a bottleneck phase where mut's can increase. Diff tissues segregate #HIDS15
WP: PEC (primer extension) used in aDNA but new to forensics; for PHP (point heteroplasmy) be careful of phylogenetic interpretation #HIDS15
WP: # of coding region 'point heteroplasmy only observed once' close to 100% across studies; outlier may be artifact in anlysis #HIDS15
WP: Literature review (Just et al under review) - detection threshold chart (MAF 10%, 2%, 1% and <1%) across 9 studies #HIDS15
WP: 2014 TGP PNAS ref http://t.co/b6q31Wt489 Correlation between subst rates and heteroplasmy rates #HIDS15
7:03am March 11th 2015 via Twitter Web Client
WP: From 1000 Genomes project - 90% indiv's carry at least 1 heteroplasmy (>1% MAF). #HIDS15
WP: Full 588 mtGenomes: Just et al ref http://t.co/oaQPILBPYj #HIDS15
WP:mtDNA heteroplasmy: do our MPS findings align w/Sanger data? Reports data from 2009: 6% control region het rate, max 3/indiv #HIDS15
WP: Currently doing aDNA mtDNA analysis on tooth samples from 1700BC. #HIDS15
WP: Of samples w/o any Sanger data - how to confirm? 7mtGE/uL [51bp]; 2 mtGE/ul [57bp] full match in overlapping GeneBank seq's #HIDS15
WP: (PEC is Primer Extension Capture: Paabo 2009 ref http://t.co/pDz8dIFBpi ) #HIDS15
WP: Showed pileup map of reads - looked at medieval samples, some w/Sanger, shows nice concordance w/ PEC approach #HIDS15
WP: Mentions this Paabo Science http://t.co/ZJ8iLgO830 for mtDNA of Neanderthals as a place to start. 14 ctrl region primers #HIDS15
WP: mtDNA from hair shaft ref http://t.co/Mn3JsDVP1h #HIDS15
7:02am March 11th 2015 via Twitter Web Client
WP: Uses degradation sensitive qPCR to measure 51bp, 57bp and 143bp fragments. #HIDS15
WP: But couldn't get much more. Can they understand qty vs quality? Shows chart of mtDNA gen equiv/uL vs DNAse treatment #HIDS15
WP: Shows this Reuter's story: http://t.co/91U4i7wWsv Burned, exposed to water, and got lucky http://t.co/9eaUx2xXy9 #HIDS15
Walther Parson (Innsbruck Austria) "Massively parallel sequencing in forensic genetics" #HIDS15
BB: Showed this 2010 PNAS paper from Knight's group http://t.co/VhHEBOljln for skin microbiome and forensic ID #HIDS15
6:57am March 11th 2015 via Twitter Web Client
BB: Identical twins - WGS done by EuroFins, sorting out who is who. Also - microbiome to Human ID #HIDS15
BB: Looking back - grandmother in Asia, father western Africa; child looks like 'Middle East' a mistake #HIDS15
BB: Can ID relationships w/blinded samples via ancestry SNPs. "Biogeography doesn't equal bioancestry" #HIDS15
BB: South Dakota city called 'Deadwood': Ingleside cemetary (1876-78) Doing phenotyping http://t.co/arOL0AAYAo #HIDS15
BB: Found four length variants. Sanger vs MPS - same results; small amplicons across entire mtGenome (for degraded samples) #HIDS15
BB: Variation across the mtGenome: ~75% of variation is in coding regions. #HIDS15
BB: Can see mtDNA length heteroplasmy. King 2014 mitoSave ref http://t.co/Bky3SzZERK #HIDS15
BB:mtDNA is a tool - a lot of value in most challenging cases. And expensive too - $1K-$3K #HIDS15
BB: Can lead to mixture interpretation; can quant 11,12 allele from stutter. Increasing discrimination including stutter data #HIDS15
6:56am March 11th 2015 via Twitter Web Client
BB: Shows bar-chart of allele and stutter distribution for D3S1358 het. #HIDS15
BB: Loci w/intra-repeat var (n=24) - 13-32 repeats in 5 loci, and freq #'s chart. Affected by efficiency of PCR #HIDS15
BB: Even after alignment: allele calls, strand bias, threshold for calling... One tool Warshauer http://t.co/kglZ4uCBEz #HIDS15
BB: Illus w/5,000 bases on a page. How many is 3.2GB at 6x? Forty boxes/pallet x 16 pallets. Shredded and reassembled? How? #HIDS15
BB: Bioinformatics 'a science in itself'. Merging biology, computer science, and information tech. "There won't be one in every lab' #HIDS15
BB: @iontorrent has a lot of nice features - rapid, 'ingenious b/c there aren't optics and dyes' https://t.co/Fr8mG5MRsH #HIDS15
BB: MPS is 'just another detector' - more power, but no fundamental change in the way we think about things. #HIDS15
BB:Not so different than what we do now; no 'paradigm shift' here - it's all based on the same workflow; extraction & ampl. #HIDS15
BB: Core markers plus more for STRs. Also SNPs: indiv ID, ancestry, lineage, phenotype #HIDS15
6:55am March 11th 2015 via Twitter Web Client
BB:'Size no longer matters': CE markers needed to have differentiation in size for resolution. Now w/MPS: size no longer matters #HIDS15
BB: All the markers we have now - don't need to be thrown out. 99.99% can be converted. Size-differences translated #HIDS15
BB:'I don't like the term 'next-generation' b/c everything is next-generation' #HIDS15
BB: 'Markers provide no add'l lead w/o a suspect or db hit'. Female victim fingernails - first should be Y-STRs. Better decisions #HIDS15
BB:Areas of interest - STRs, mtDNA, SNPs. Almost all dev countries have DB's. A kit w/core markers 'no matter the case' #HIDS15
BB: Many potential applications - enforcement, military, borders, victim ID. True microfluidic tech can change our future #HIDS15
BB: Cost-effective (cp to building a lab). Netbio, integenX, etc. 'Anyone can do it' (photo of himself doing it). #HIDS15
BB:Rapid DNA - is it fast, or rather mobile? Std approach of direct amplification - fast, yes. But a single field device? #HIDS15
6:54am March 11th 2015 via Twitter Web Client
BB:What is effective validation for drop-out and drop-in errors? #HIDS15
BB:Issues for LCN (low-copy) typing: do models reflect reality? Does dividing sample into 3 a sound method? #HIDS15
BB: From a binary model to semi continuous model. Allele dropout statistics, frequency. Balding 2009 ref: http://t.co/lEbkj3vJ2B #HIDS15
BB: Shows slide comparing 1ng w/ 33pg - pointing out dropouts, stutter. Now hypothesis-driven methods: mtDNA 'led the way' #HIDS15
