Increasing the reference populations for the 55 AISNP panel: the need and benefits

Pakstis, Andrew J.; Kang, Longli; Liu, Lijun; Zhang, Zhiying; Jin, Tianbo; Grigorenko, Elena L.; Wendt, Frank R.; Budowle, Bruce; Hadi, Sibte; Qahtani, Mariam Salam Al; Morling, Niels; Mogensen, Helle Smidt; Themudo, Gonçalo Espregueira; Soundararajan, Usha; Rajeevan, Haseena; Kidd, Judith R.; Kídd, Kenneth K.

doi:10.1007/s00414-016-1524-z

Cited by 40 publications

(43 citation statements)

References 12 publications

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“…Panels of individual SNPs have been studied by many researchers (cf. [3]) and some are capable of biogeographic ancestry inference of up to 8 to 10 distinct global regions [4,5]. While those panels of SNPs can provide very small random match probabilities (RMP) as low as or lower than the standard STR markers, they are poor at identifying mixtures and the added ancestry information has not been of high enough value in forensic practice to overcome the absence of the offender databases that exist for the STR markers.…”

Section: Introductionmentioning

confidence: 99%

Evaluating 130 microhaplotypes across a global set of 83 populations

Kídd

Speed

Pakstis

et al. 2017

Forensic Science International: Genetics

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106

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Today the primary DNA markers used in forensics are short tandem repeat (STR) polymorphisms (STRPs), initially selected because they are highly polymorphic. However, the increasingly common need to deal with samples with a mixture of DNA from two or more individuals sometimes is complicated by the inherent stutter involved with PCR amplification, especially in strongly unbalanced mixtures when the minor component coincides with the stutter range of the major component. Also, the STRPs in use provide little evidence of ancestry of a single source sample beyond broad "continental" resolution. Methodologies for analyzing DNA have become much more powerful in recent years. Massively parallel sequencing (MPS) is a new method being considered for routine use in forensics. Primarily to aid in mixture deconvolution and avoid the issue of stutter, we have begun to investigate a new type of forensic marker, microhaplotype loci, that will provide useful information on mixtures of DNA and on ancestry when typed using massively parallel sequencing (MPS). We have identified 130 loci and estimated their haplotype (allele) frequencies in 83 different population samples. Many of these loci are shown to be highly informative for individual identification and for mixture identification and deconvolution.

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Section: Introductionmentioning

confidence: 99%

Evaluating 130 microhaplotypes across a global set of 83 populations

Kídd

Speed

Pakstis

et al. 2017

Forensic Science International: Genetics

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106

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“…Bu AISNPs panellerinden en geniş kapsamlı olanı Kidd ve ark. (19,27,28) tarafından geliştirilen 55 AISNPs paneli olup, bu panel tüm dünya popülasyonlarını en az on farklı popülasyon grubuna ayırabilmektedir. Bu panel güncel haliyle ülkemiz popülasyonu da dahil olmak üzere 164 dünya popülasyonunda çalışılmıştır (27)(28)(29).…”

Section: Biyocoğrafik Soy Kavramı Ve Soy Snp Markırları (Aisnps-ancesunclassified

“…(19,27,28) tarafından geliştirilen 55 AISNPs paneli olup, bu panel tüm dünya popülasyonlarını en az on farklı popülasyon grubuna ayırabilmektedir. Bu panel güncel haliyle ülkemiz popülasyonu da dahil olmak üzere 164 dünya popülasyonunda çalışılmıştır (27)(28)(29). Türkiye'de AISNPs çalışmaları, SNP seçimi ve panel geliştirilmesi üzerine çeşitli araştırmalar bulunmaktadır (29)(30)(31).…”

Section: Biyocoğrafik Soy Kavramı Ve Soy Snp Markırları (Aisnps-ancesunclassified

Biyocoğrafik Soy Tahmini ve Adli Bilimlerde Kullanımı

Bülbül

Filoğlu

2019

Bull Leg Med

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Adli bilimlerde SNP (Single nucleotide polymorphism, tek nükleotid polimorfizm) markırları kimliklendirmede, fenotip belirlemede, nesep ve soy tayininde kullanılmaktadır. Biyocoğrafik soy tahmininde farklı coğrafik bölgelerde bulunan popülasyonlar arasındaki farklılıkları gösteren soy SNP markırları (AISNPs, Ancestry Informative SNP Markers) kullanılmaktadır. AISNP markırları ile bir kişinin biyocoğrafik orijini ve her biyocoğrafik bölgeden alınan genetik soy yüzdesi tespit edilebilir. Bu bilgiler adli bilimlerde bilinmeyen bir şüphelinin, felaket kurbanlarının veya kayıp kişilerin kimliklendirilmesinde kullanılabilir. Bu makalede biyocoğrafik soy kavramı, biyocoğrafik soy tahmininde kullanılan AISNPs panelleri, uygulama yöntemleri, kullanılan istatistiksel yöntemler ve güncel adli uygulamalar tartışılmıştır.

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“…Consequently, AIMs do not overlap across studies. Of the 21 AIM datasets, reviewed by Pakstis et al [26], only 1397 AIMs appeared in at least two sets. Finally, studies typically show that AIMs can separate populations or broadly classify individuals into subcontinental populations rather than showing that AIMs can capture the population structure of the complete SNP set or allow fine-population mapping.…”

Section: The Use Of Ancestry Informative Markers (Aims) In Geneticsmentioning

confidence: 99%

Ancient ancestry informative markers for identifying fine-scale ancient population structure in Eurasians

Esposito

Das

Pirooznia

et al. 2018

Preprint

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The rapid accumulation of ancient human genomes from various areas and time periods potentially allows the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations known to misrepresent the population structure. Past studies addressed these problems using ancestry informative markers (AIMs). However, it is unclear whether AIMs derived from contemporary human genomes can capture ancient population structure and whether AIM finding methods are applicable to ancient DNA (aDNA) provided that the high missingness rates in ancient, oftentimes haploid, DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperforms all competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of population microarrays and the interpretation of aDNA results.

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Increasing the reference populations for the 55 AISNP panel: the need and benefits

Cited by 40 publications

References 12 publications

Evaluating 130 microhaplotypes across a global set of 83 populations

Evaluating 130 microhaplotypes across a global set of 83 populations

Biyocoğrafik Soy Tahmini ve Adli Bilimlerde Kullanımı

Ancient ancestry informative markers for identifying fine-scale ancient population structure in Eurasians

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