Inferring bio-geographical ancestry with 35 microhaplotypes

Huang, Shuainan; Sheng, Mingchen; Li, Zheng; Li, Kai; Chen, Ji; Wu, Jiayi; Wang, Kang; Shi, Changling; Ding, Hao; Zhou, Hongwei; Ma, Lingmin; Yang, Jiawen; Pu, Yan; Yu, Youjia; Chen, Feng; Chen, Peng

doi:10.1016/j.forsciint.2022.111509

Cited by 8 publications

(2 citation statements)

References 40 publications

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“…The outcome of this population genetics evaluation further corroborates the robustness and reliability of this STR dataset. Despite all the applications already addressed in the beginning of this section, the most important contribution of this open access genotype dataset probably lies in the fact that it may be used to estimate and establish additional population genetics parameters that may be taken as direct references in many studies that are using the 1000 Genomes Project dataset to retrieve new sets of SNPs, indels and microhaplotypes in various efforts to maximize intelligence from DNA evidence [ 27 , 47 , 48 , 49 , 50 ].…”

Section: Discussionmentioning

confidence: 99%

Open-Access Worldwide Population STR Database Constructed Using High-Coverage Massively Parallel Sequencing Data Obtained from the 1000 Genomes Project

Frontanilla

Valle-Silva

Ayala

et al. 2022

Genes

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Achieving accurate STR genotyping by using next-generation sequencing data has been challenging. To provide the forensic genetics community with a reliable open-access STR database, we conducted a comprehensive genotyping analysis of a set of STRs of broad forensic interest obtained from 1000 Genome populations. We analyzed 22 STR markers using files of the high-coverage dataset of Phase 3 of the 1000 Genomes Project. We used HipSTR to call genotypes from 2504 samples obtained from 26 populations. We were not able to detect the D21S11 marker. The Hardy-Weinberg equilibrium analysis coupled with a comprehensive analysis of allele frequencies revealed that HipSTR was not able to identify longer alleles, which resulted in heterozygote deficiency. Nevertheless, AMOVA, a clustering analysis that uses STRUCTURE, and a Principal Coordinates Analysis showed a clear-cut separation between the four major ancestries sampled by the 1000 Genomes Consortium. Except for larger Penta D and Penta E alleles, and two very small Penta D alleles (2.2 and 3.2) usually observed in African populations, our analyses revealed that allele frequencies and genotypes offered as an open-access database are consistent and reliable.

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Section: Discussionmentioning

confidence: 99%

Open-Access Worldwide Population STR Database Constructed Using High-Coverage Massively Parallel Sequencing Data Obtained from the 1000 Genomes Project

Frontanilla

Valle-Silva

Ayala

et al. 2022

Genes

View full text Add to dashboard Cite

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Section: Resultsmentioning

confidence: 99%

Diversidade genética de populações globais inferida por STRs autossômicos utilizados para identificação humana genotipados a partir de genomas completos

Recalde¹

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A Deus, por ter me dado a possibilidade de seguir meus sonhos, e a capacidade para descobri-los.À minha família, pelo apoio incondicional. Especialmente ao meu marido por ter me apoiado em tudo sempre, por ter confiando em mim, me ensinado com tanta paciência todos os conceitos de bioinformática e por ser um pilar fundamental na minha vida. Também a meus pais, Mirian e Narciso, por me apoiarem, sem dúvidas, em todos os meus sonhos e projetos. E, um carinho especial aos meus tios, Maria Lucia e Álvaro por terem me dado uma casa no Brasil, muito carinho e apoio sempre.Ao meu amigo e parceiro de pesquisas Guilherme Valle Silva. Com certeza não teria conseguido esses resultados sem o apoio incondicional dele, o ensino e as tardes de trabalho, risadas e pesquisa.Ao meu orientador, o Prof. Dr. Celso Teixeira Mendes Junior a quem admiro, e respeito muito. Obrigada pela confiança, paciência, oportunidades profissionais, motivação e por contribuir de maneira inigualável na minha formação profissional.

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Feasibility study of a single‐primer extension‐based microhaplotype NGS system

Zhu,

Shu,

Wang

et al. 2024

Electrophoresis

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DNA degradation has been a thorny problem in forensic science. Shortening the amplicon length of the genetic markers improves the analysis of degraded DNA effectively. Microhaplotype (MH) has been proposed as a potential genetic marker that can be used for degraded DNA analysis. In the present study, a 146‐plex MH‐next‐generation sequencing (NGS) system with an average Ae of 6.876 was constructed. Unlike other MH studies, a single‐primer extension (SPE)‐based NGS library preparation method was used to improve the detection of MH markers for degraded DNA. SPE employs a locus‐specific and universal primer to amplify target fragments, reducing the necessity for complete fragment sequences. SPE might effectively mitigate the impact of degradation on amplification. However, SPE produces amplicons of varying lengths, posing challenges in allele calling for SPE‐NGS data. To address this issue, this study proposed a flexible allele‐calling strategy to improve amplicon detection. In addition, this study evaluated the forensic efficacy of the system using 12 low‐template samples (from 1 ng to 7.8 pg), 10 mock‐degraded DNA with various degrees of degradation, and 8 forensic casework samples. When the template is as low as 7.8 pg, our system can accurately detect at least 37 loci and achieves a random match probability (RMP) of 10−30 using the complete allele‐calling strategy. Eighty‐two loci can be detected, and RMP can reach 10−54 using a flexible allele‐calling strategy. After 150 min of 98°C treatment, 36 loci can still be detected, and an RMP of 10−5 can be obtained using the flexible allele‐calling strategy. Furthermore, the number of single nucleotide polymorphism detected at different DNA amounts and degradation levels suggests that the SPE method combined with a flexible allele‐calling strategy is effective.

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Inferring bio-geographical ancestry with 35 microhaplotypes

Cited by 8 publications

References 40 publications

Open-Access Worldwide Population STR Database Constructed Using High-Coverage Massively Parallel Sequencing Data Obtained from the 1000 Genomes Project

Open-Access Worldwide Population STR Database Constructed Using High-Coverage Massively Parallel Sequencing Data Obtained from the 1000 Genomes Project

Diversidade genética de populações globais inferida por STRs autossômicos utilizados para identificação humana genotipados a partir de genomas completos

Feasibility study of a single‐primer extension‐based microhaplotype NGS system

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