Patterns of genetic diversity in Colombia for 38 indels used in human identification

Ossa, Humberto; Posada, Y.; Trujillo, Nathalia; Martínez, Beatriz; Loiola, S.; Simão, Filipa; Ossa, Rafael H.; Castillo, A.; Ibarra, A.; Marrugo, Javier; Carvalho, E.F.; Vargas, Clara Inés; Pereira, Rui; Gusmão, Leonor

doi:10.1016/j.fsigen.2021.102495

Cited by 6 publications

(4 citation statements)

References 15 publications

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“…Li et al also showed that Colombian was clustered with European populations and other American populations were dispersedly distributed in MDS plot ( Li et al, 2019 ). For historical reasons, most of the Puerto Rican and Colombian from the four American populations are European or European-Indian mixed-race population ( Via et al, 2011 ; Ossa et al, 2021 ), which could be the reason that American populations clustered not obviously.…”

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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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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“…Two commercial InDel kit exist: (1) Investigator DIPlex (QIAGEN, Hilden, Germany) with 30 InDels [ [527] , [528] , [529] , [530] , [531] ] and (2) InnoTyper 21 (InnoGenomics, New Orleans, Louisiana, USA) with 21 autosomal insertion-null (INNUL) markers [ [532] , [533] , [534] , [535] ]. In addition, a number of InDel assays have been published including a 32plex [ 536 ], a 35plex [ 537 ], a 38plex [ 538 ], a 39plex with AIMs [ 539 ], a 43plex [ 540 ], a 57plex [ 541 ], a 60plex with 57 autosomal InDels, 2 Y-chromosome InDels, and amelogenin [ 542 ], a 32plex with X-chromosome InDels [ 543 ], and a 21plex with AIMs [ 544 ].…”

Section: Emerging Technologies Research Studies and Other Topicsmentioning

confidence: 99%

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

Butler

2023

Forensic Science International: Synergy

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“…The Colombian population has a complex and diverse genetic structure as a result of migrations of different human groups separated by origin, time, and space [ 8 , 9 ]. Cultural, geographical, and climatic characteristics delimit the country in six regions, Andean, Pacific, Caribbean, Orinoquia, Amazonian and Insular.…”

Section: Introductionmentioning

confidence: 99%

Recombination events drives the emergence of Colombian Helicobacter pylori subpopulations with self-identity ancestry

et al. 2022

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Helicobacter pylori have coevolved with mankind since its origins, adapting to different human groups. In America, H. pylori has evolved into several subpopulations. We analysed the genome of 154 Colombian strains along with 1,091 strains from worldwide populations to discern the ancestry and adaption to Colombian people. Population structure and ancestry was inferred with FineStructure and ChromoPainter. Phylogenetic relationship and the relative effect of recombination were analysing the core SNPs. Also, a Fst index was calculated to identify the gene variants with the strongest fixation in the Colombian subpopulations compared to their parent population hspSWEurope . FineStructure allowed the identification of two Colombian subpopulations, the previously described hspSWEuropeColombia and a novel subpopulation named hspColombia , that included three subgroups following their geographic origin. Colombian subpopulations represent an admixture of European, African and Indigenous ancestry; although some genomes showed a high proportion of self identity, suggesting an advanced adaption to these mestizo Colombian groups. We found that recombination is more important that punctual mutations in H. pylori genome diversity, 13.9 more important in hspSWEurope , 12.5 in hspSWEColombia and 10.5 in hspColombia , reflecting the divergence of these subpopulations. Fst analysis identified 82 SNPs fixed in 26 genes of the hspColombia subpopulation that encode for outer membrane and central metabolism proteins. Strongest fixation indexes were identified in genes encoding HofC, HopE, FrpB-4 and Sialidase A. These findings demonstrate that H. pylori has evolved in Colombia to give rise to subpopulations with a self identity ancestry, reflected in allele changes on genes encoding for outer membrane proteins.

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Patterns of genetic diversity in Colombia for 38 indels used in human identification

Cited by 6 publications

References 15 publications

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

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

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

Recombination events drives the emergence of Colombian Helicobacter pylori subpopulations with self-identity ancestry

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