Development of a SNP panel for predicting biogeographical ancestry and phenotype using massively parallel sequencing

Abstract

Inferring ancestry and physical characteristics of an unknown individual can contribute to the direction of the investigation and to clarify the event for unknown contributors, cold cases or identification of missing persons and disaster victims. The objective of this study is to develop a custom SNP panel on massively parallel sequencing devices for predicting the biogeographic ancestry and phenotype of an individual. We focused on a two-tier approach to enhance ancestry. Our MPS panel contains two ancestry informative SNP (AISNPs) panels (i.e., Kidd 55 and SWA panel) to differentiate Southwest Asia from Europe and other continental regions. Then we integrated the set of phenotype informative SNPs into a set of AISNPs. The final set of 156 SNPs was evaluated on the following: sensitivity, genotype concordance, mixtures, ancestry assignment, and phenotype prediction. SNP rs6599400 had consistently poor performance and was removed from further analyses. The extreme mixture (1:10) was difficult to interpret for minor contributor. Ancestry assignment and phenotype predictions (for eye, hair and skin) were accurate for samples' population origin. The results show that the developed panel provides high coverage data that can be used for inferring ancestry and predicting eye, hair, and skin color from the intermediate population regions.

Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples

“…Forensic genetics currently stands in front of a new era of DNA analysis as Massively Parallel Sequencing (MPS) is becoming a more commonly used tool for DNA analysis. The enhanced multiplexing capabilities of MPS technology coupled with the ability to analyze a variety of marker types has led to increased research and use of single nucleotide polymorphisms (SNPs) to predict externally visible characteristics (EVCs) and biogeographical ancestry (BGA) from a DNA sample [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15]. To implement the new capabilities in DNA testing, legal changes are obligatory for SNP analysis by MPS to be applied in new cases.…”

Biyocoğrafik Soy Tahmini ve Adli Bilimlerde Kullanımı

“…Her iki ticari MPS panelinde de (Thermo Fisher Scientific ve The Illumina ® ) biyocoğrafik soy paneli olarak Kidd 55 ve Seldin 128 AISNP panelleri bulunmaktadır. Aynı zamanda ticari olmayan ve araştırıcılar tarafından geliştirilen SNP panelleri de bulunmaktadır (25,26,38,45). EUROFORGEN Global AIM-SNP paneli bu panellerden biri olup, bir Avrupa Birliği projesi çerçevesinde geliştirilmiştir.…”

“…Global AIM-SNP panelinde pek çok SNP panelinden seçilmiş 128 SNP'den oluşan, beş kıtasal popülasyonun ayrımında kullanılmak üzere tasarlanmıştır (25). MPS sistemi ile ülkemizde yapılan bir çalışmada ise biyocoğrafik soy ve fenotip SNP markırlarından oluşan yeni bir panel (moleküler görgü tanıklığı) geliştirilmiştir (38). Bu çalışmada Kidd 55, 86 AISNPs ve göz, saç ve ten rengi PISNPs markırlarını içeren 186 SNP den oluşan bir panel geliştirilmiştir (38).…”

“…MPS sistemi ile ülkemizde yapılan bir çalışmada ise biyocoğrafik soy ve fenotip SNP markırlarından oluşan yeni bir panel (moleküler görgü tanıklığı) geliştirilmiştir (38). Bu çalışmada Kidd 55, 86 AISNPs ve göz, saç ve ten rengi PISNPs markırlarını içeren 186 SNP den oluşan bir panel geliştirilmiştir (38). Bu panel ile Türkiye'de faile ulaşılamayan ve aydınlatılamayan adli vakalarda delilden suçluya giderken adli sürecin daha hızlı işlemesine ve olguların çözümüne büyük katkı sağlayacağı düşünülmektedir.…”

A set of novel multi‐allelic SNPs for forensic application developed through massively parallel sequencing and its examples of population genetic studies

“…Besides, genotyping on the basis of sequence depth and particular analysis software also help to analyze mixed samples [21,22]. Numerous MPS-based forensic scientific researches have been conducted, such as customized SNP panels for the biogeographic ancestry and phenotype predictions [23], revealing the sequence variations within STR alleles [24], as well as the RNA biomarkers expression profiles for body fluid identification [25,26]. MPS technology satisfy the detection requirements of more complex cases and massive samples in forensic practices.…”