Genetic characterization of 32 X-InDels in a population sample from São Paulo State (Brazil)

Martinez, Juliana; Polverari, Fernanda Silva; Silva, Flávia Alves de Jesus; Braganholi, Danilo Faustino; Ferraz, Joyce Aparecida Martins Lopes; Gusmão, Leonor; Cicarelli, Regina Maria Barretto

doi:10.1007/s00414-018-01988-w

Cited by 8 publications

(6 citation statements)

References 26 publications

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“…Apart from the associations already discussed for X‐STRs on the LGs, significant values for LD were found between pairs of X‐Indels at distances of 0.204 cM and smaller (Table S6). For these marker pairs, significant p ‐values for LD were previously observed in other populations from different continents (Caputo et al, 2017; Edelmann et al, 2016; Ferragut et al, 2017; Freitas et al, 2010; Ibarra et al, 2014; Martinez et al, 2019; Pereira, Pereira, et al, 2012; Pereira, Pillips, et al, 2012; Pinto et al, 2015; see Table S6). A significant association was also observed between indels MID3754 and MID3722, which were separated by 1.433 cM and not detected in previously studied populations.…”

Section: Resultsmentioning

confidence: 53%

“…Multidimensional scaling analysis (MDS) based on F ST genetic distances calculated for (a) 32 X‐Indels (Stress = 0.0678) and (b) 12 X‐STRs (Stress = 0.0308). (a) Data used were retrieved from The 1000 Genomes Project Consortium (2015) (Africa, Colombia, Peru, and Mexico), Ibarra et al (2014) (Colombia), and Martinez et al (2019) (Brazil). Only a subset of 23 X‐Indels was used in this analysis, since no data are available for the remaining 9 X‐Indels in the samples from the 1000 Genomes Project.…”

Section: Resultsmentioning

confidence: 99%

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Investigating genetic diversity in admixed populations from Ecuador

Flores-Espinoza

Paz-Cruz²,

Ruiz-Pozo³

et al. 2021

American J Phys Anthropol

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Objectives According to demographic history, Ecuador has experienced shifts in its Native American populations caused by European colonization and the African slave trade. The continuous admixture events among Europeans, Native Americans, and Africans occurred differently in each region of the country, producing a stratified population. Thus, the aim of this study was to investigate the level of genetic substructure in the Ecuadorian Mestizo population. Materials and methods A total of 377 male and 209 female samples were genotyped for two sets of X‐chromosomal markers (32 X‐Indels and 12 X‐STRs). Population analyses performed included Hardy–Weinberg equilibrium tests, LD analysis, PCA, pairwise FSTs, and AMOVA. Results Significant levels of LD were observed between markers separated by distances of less than 1 cM, as well as between markers separated by distances varying from 10.891 to 163.53 cM. Among Ecuadorian regions, Amazonia showed the highest average R2 value. Discussion When X‐chromosomal and autosomal differentiation values were compared, a sex‐biased admixture between European men and Native American and African women was revealed, as well as between African men and Native American women. Moreover, a distinct Native American ancestry was discernible in the Amazonian population, in addition to sex‐biased gene flow between Amazonia and the Andes and Pacific coast regions. Overall, these results underline the importance of integrating X chromosome information to achieve a more comprehensive view of the genetic and demographic histories of South American admixed populations.

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Section: Resultsmentioning

confidence: 53%

Section: Resultsmentioning

confidence: 99%

Investigating genetic diversity in admixed populations from Ecuador

Flores-Espinoza

Paz-Cruz²,

Ruiz-Pozo³

et al. 2021

American J Phys Anthropol

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“…In theory, alleles of InDel show difference in amplified fragments length that makes it easy to be typed on the CE platform without artificial peaks such as stutter peaks. It is with characteristic above‐mentioned that InDels have played an essential role in forensic DNA analysis practice, such as individual identification [4, 5], degraded samples detection [6], and biogeographic ancestry inference [7, 8].…”

Section: Introductionmentioning

confidence: 99%

A targeted ancestry informative InDels panel on capillary electrophoresis for ancestry inference in Asian populations

et al. 2021

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CE is the primary methodology used in forensic DNA typing. Alleles of commonly used types of genetic markers could be separated and detected via CE based on dye color and migration time. Insertion/deletion (InDel) is an ideal genetic marker for forensic DNA analysis due to their abundance in the human genome, low mutation rate, availability of their allele types via CE, and elimination of stutter peaks. Moreover, InDels could be used as ancestry informative markers since allele frequencies of InDels is different among geographically separated populations. Several ancestry informative insertion/deletion panels have been established based on CE platform to achieve the intercontinental populations distinction. However, improvements to differentiate intracontinental populations is few. In this study, 21 InDels with fixation index (FST) > 0.15 were selected and assembled into one ancestry informative insertion/deletion panel. Using well‐designed primers, those 21 InDels could be amplified successfully and genotyped on the CE platform accurately and completely. The panel showed a large FST distance distinction among the ten Asian populations. Using clustering analysis, ten Asian populations were classified into three subgroups: East Asian, Southeast Asian, and South Asian subgroups. To evaluate the panel's capability in ancestry inference, a validation experiment was undertaken with 319 individuals from four geographically separated populations in China. Four Chinese populations were classified into different ancestry subgroups and 81.8% test individuals’ ancestry could be inferred correctly. Our result showed that development of high ancestry informative InDels panel based on CE platform is a potential for individual ancestry inference among intracontinental populations.

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“…In South Asian and African groups, the block 1 (rs3859989 - rs61260787) and block 3 (rs3216913 - rs10699224) were detected as well, but no significant association was observed between InDels rs36094418 and rs79829945 (block 2). This discrepancy could be explained by other factors than linkage, such as admixture and population substructure ( Martinez et al, 2019 ). Drawing on the methods described by Ferragut et al (2017) we retained all the associated loci in the subsequent genetic analysis.…”

Section: Resultsmentioning

confidence: 99%

Genetic Structure and Forensic Feature of 38 X-Chromosome InDels in the Henan Han Chinese Population

Zhang

Zhu

et al. 2022

Front. Genet.

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Insertion/deletion (InDel) polymorphisms, as ideal forensic markers, show useful characteristics of both SNPs and STRs, such as low mutation rate, short amplicon size and general applicability of genotyping platform, and have been used in human identification, population genetics and biogeographic research in recent years. X-chromosome genetic markers are significant in population genetic studies and indispensable complements in some complex forensic cases. However, the population genetic studies of X-chromosome InDel polymorphisms (X-InDels) still need to be explored. In this study, the forensic utility of a novel panel including 38 X-InDel markers was evaluated in a sample of Han population from Henan province in China. It is observed that the heterozygosities ranged from 0.0054 to 0.6133, and the combined discrimination power was 1–9.18 × 10−17 for males and 1–7.22 × 10−12 for females respectively. The mean exclusion chance in trios and duos were 0.999999319 and 0.999802969 respectively. Multiple biostatistics methods, such as principal component analysis, genetic distances analysis, phylogenetic reconstruction, and structure analysis was used to reveal the genetic relationships among the studied Henan Han group and other 26 reference groups from 1,000 Genomes Project. As expected, the Henan Han population was clustered with East Asian populations, and the most intimate genetic relationships existed in three Han Chinese populations from Henan, Beijing and South China, and showed significant differences compared with other continental groups. These results confirmed the suitability of the 38 X-InDel markers both in individual identification and parentage testing in Han Chinese population, and simultaneously showed the potential application in population genetics.

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Genetic characterization of 32 X-InDels in a population sample from São Paulo State (Brazil)

Cited by 8 publications

References 26 publications

Investigating genetic diversity in admixed populations from Ecuador

Investigating genetic diversity in admixed populations from Ecuador

A targeted ancestry informative InDels panel on capillary electrophoresis for ancestry inference in Asian populations

Genetic Structure and Forensic Feature of 38 X-Chromosome InDels in the Henan Han Chinese Population

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