Ancestry informative markers: Inference of ancestry in aged bone samples using an autosomal AIM-Indel multiplex

Romanini, Carola; Romero, Magdalena; Puerto, Mercedes Salado; Catelli, Laura; Pereira, Rui; Gusmão, Leonor; Vullo, Carlos

doi:10.1016/j.fsigen.2014.11.025

Cited by 26 publications

(14 citation statements)

References 26 publications

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“…InDel is suitable for population analysis, since the allele distributions show significant differences in different geographic regions4041. Studies based on simple InDels have proved its great potential in ancestry inference researches374243. F ST and I n are commonly used to measure the ancestral information of AIMs.…”

Section: Resultsmentioning

confidence: 99%

“…A fair amount of Ancestry Information Markers (AIMs) have been proposed for various purposes including detecting stratification in biomedical studies12 and determining an individual’s ancestry from a forensic context34567891011121314. In the genotype-phenotype studies, such as the popular genome-wide association studies (GWAS), the presence of uncontrolled population structure may lead to false-positive or false-negative results1516171819.…”

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confidence: 99%

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Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

Sun

Luò

et al. 2016

Sci Rep

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Ancestry inference is of great interest in diverse areas of scientific researches, including the forensic biology, medical genetics and anthropology. Various methods have been published for distinguishing populations. However, few reports refer to sub-populations (like ethnic groups) within Asian populations for the limitation of markers. Several InDel loci located very tightly in physical positions were treated as one marker by us, which is multi-InDel. The multi-InDel shows potential as Ancestry Inference Marker (AIM). In this study, we performed a genome-wide scan for multi-InDels as AIM. After examining the FST distributions in the 1000 Genomes Database, 12 candidates were selected and validated for eastern Asian populations. A multiplexed assay was developed as a panel to genotype 12 multi-InDel markers simultaneously. Ancestry component analysis with STRUCTURE and principal component analysis (PCA) were employed to estimate its capability for ancestry inference. Furthermore, ancestry assignments of trial individuals were conducted. It proved to be very effective when 210 samples from Han and Tibetan individuals in China were tested. The panel consisting of multi-InDel markers exhibited considerable potency in ancestry inference, and was suggested to be applied in forensic practices and genetic population studies.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

Sun

Luò

et al. 2016

Sci Rep

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“…These markers were selected due to their high allele frequency divergence between different ancestral or geographically distant populations, including more than 1,000 individuals from 40 reference populations from the Human Genome Diversity Project (HGDP)-Centre d/Etude du Polymorphisme (CEPH), plus individuals from Angola, Portugal, Taiwan, and indigenous Brazilian, which allowed to establish the ancestral proportions in high admixture individuals and populations, like the Brazilian one (14). Moreover, they were assembled in a simple multiplex reaction following a short amplicon strategy, adequate for challenging samples such as FFPE (15,26,27). The primer sequences and PCR conditions were according to Giolo et al (14).…”

Section: Genetic Ancestry Determinationmentioning

confidence: 99%

Role of Genetic Ancestry in 1,002 Brazilian Colorectal Cancer Patients From Barretos Cancer Hospital

et al. 2020

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Background: Colorectal cancer (CRC) is the third most frequent and the second deadliest cancer worldwide. The ethnic structure of the population has been gaining prominence as a cancer player. The purpose of this study was to determine the genetic ancestry of Brazilian CRC patients. Moreover, we intended to interrogate its impact on patients' clinicopathological features.Methods: Retrospective observational cohort study with 1,002 patients with CRC admitted from 2000 to 2014 at Barretos Cancer Hospital. Following tumor DNA isolation, genetic ancestry was assessed using a specific panel of 46 ancestry informative markers. Survival rates were obtained by the Kaplan-Meier method, and the log-rank test was used to compare the survival curves. Multivariable Cox proportional regression models were used to estimate hazard ratios (HRs). Results:We observed considerable admixture in the genetic composition, with the following average proportions: European 74.2%, African 12.7%, Asian 6.5%, and Amerindian 6.6%. The multivariate analysis for cancer-specific survival showed that clinical stage, lymphovascular invasion, and the presence of recurrence were associated with an increased relative risk of death from cancer (p < 0.05). High African proportion was associated with younger age at diagnosis, while high Amerindian proportion was associated with the mucinous histological subtype.Conclusions: This represents the larger assessment of genetic ancestry in a population of Brazilian patients with CRC. Brazilian CRC patients exhibited similar clinicopathological features as described in Western countries.Impact: Genetic ancestry components corroborated the significant admixture, and importantly, patients with high African proportion develop cancer at a younger age.

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“…However, there were some potential limitations of STRs in forensic applications because of its relatively high mutation rate, long amplicon size, and the deficiency in the analysis of highly degraded DNA samples and complex kinship cases. In recent years, a novel genetic marker: insertion and deletion polymorphisms (InDels) dispersing through the human genome showed some advantages, such as short amplicon size, low mutation rate, and practicability of being genotyped in the present forensic DNA lab platforms678, which were useful for forensic DNA applications (Supplementary method for STR applications), population genetics9101112, and biogeographic ancestry analysis131415. Population genetic and forensic validation studies have been performed using the Qiagen Investigator DIPplex ® reagent including 30 autosomal InDel loci plus amelogenin locus, and population data of Chinese Han, Tibetan, Uigur, Kazak, She, Xibe and Yi populations have been reported in previous studies910161718.…”

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A 30-InDel Assay for Genetic Variation and Population Structure Analysis of Chinese Tujia Group

Shen

Zhu

Yao

et al. 2016

Sci Rep

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In the present study, thirty autosomal insertion and deletion polymorphic loci were simultaneously amplified and genotyped in a multiplex system, and their allelic frequencies as well as several forensic parameters were obtained in a sample of 236 unrelated healthy Tujia individuals. All the loci were in Hardy-Weinberg equilibrium after applying a Bonferroni correction and all pair-wise loci showed no significant linkage disequilibrium. These loci were observed to be relatively informative and discriminating, quite efficient for forensic applications. Allelic frequencies of 30 loci were compared between the Tujia group and other reference populations, and the results of analysis of molecular variance indicated the Tujia group showed the least significant differences with the Shanghai Han at one locus, and the most with Central Spanish population at 22 loci. We analyzed the population genetic structure by the principal component analysis, the clustering of STRUCTURE program and a Neighbor-Joining tree, and then evaluated the genetic relationships among Tujia and other 15 populations.

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Ancestry informative markers: Inference of ancestry in aged bone samples using an autosomal AIM-Indel multiplex

Cited by 26 publications

References 26 publications

Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

Role of Genetic Ancestry in 1,002 Brazilian Colorectal Cancer Patients From Barretos Cancer Hospital

A 30-InDel Assay for Genetic Variation and Population Structure Analysis of Chinese Tujia Group

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