Forensic parameters and admixture in Mestizos from five geographic regions of Mexico based on 20 autosomal STRs (Powerplex 21 system)

Choice between DNA primer sets (A or B) of the ForenSeq kit: forensic evaluation in a Mexican admixed population sample

Massively parallel sequencing (MPS) overcomes many PCR-CE limitations to analyze STRs and allow simultaneous inclusion of SNPs in forensic cases. By MPS, the ForenSeq™ DNA Signature Prep kit analyzes 27 aSTRs, 7 X-STRs, 24Y-STRs, and 94 identity-informative SNPs (iiSNPs) with the DNA Primer Set-A (DPS-A). Optionally, the DNA Primer Set-B (DPS-B) adds to the analysis 56 ancestry-informative SNPs (aiSNPs) and 24 phenotype-informative SNPs (piSNPs), but diminishes from 96 to 32 the number of samples per sequencing run. We assessed the forensic informativity provided by the loci analyzed by these two DPS in admixed individuals from Mexico City (Center, Mexico). For STRs, we report length-based (LB) and sequence-based (SB) allele frequencies and forensic parameters of the 152 identity informative markers (DPS-A). For aSTRs, the combined PD of SB genotypes (PD ~ 100%) was ~ 2949 times larger than that from LB. Conversely, the observed phenotype distribution offered low PD levels (PD = 6.6% and 10.4%), whereas piSNPs predicted accurately only the modal brown eye and dark hair colors, respectively. Similarly, aiSNPs detected a large prevalence of admixed individuals (97.3%; PD = 5.4%). Although few individuals were inferred as Europeans and Native Americans (1.37% each), they were self-declared as admixed, which result confusing for HID purposes. In brief, SB genotypes increased significantly the informativity of STRs to solve complex cases (DPS-A), whereas aiSNPs and piSNPs added mostly irrelevant information (DPS-B). We provide useful cost-benefit criteria in one Latin American population to choose DPS-A (96 samples) instead of DPS-B (32 samples) of the Forenseq kit.

Genetic Diversity and Forensic Parameters of 27 Y-STRs in Two Mestizo Populations from Western Mexico

BACKGROUND

Analyzing Y-chromosome short tandem repeats (Y-STRs) is essential in forensic genetics and population studies. The Yfiler™ Plus kit, which includes 27 Y-STR markers, enhances the discrimination power for forensic and kinship applications. However, this genetic system has not been analyzed in Mexican populations, which limits its application and representativeness in international databases.

OBJECTIVES

We wished to examine the genetic diversity and forensic parameters of the 27 Y-STRs included in the YFiler™ Plus kit in two populations from Western Mexico (Jalisco and Michoacán).

METHODS

Male DNA samples were amplified using the Yfiler™ Plus kit, followed by a fragment analysis via capillary electrophoresis (CE). The haplotype frequencies and forensic parameters were calculated. The haplogroups of all samples were predicted, and the distribution and percentages of ancestries were determined. The Rst genetic distances, including reference populations, were calculated and graphically represented in a multidimensional scaling (MDS) plot.

RESULTS

A total of 224 haplotypes were identified in all of the samples, of which 98.66% corresponded to unique haplotypes. Bi- and tri-allelic patterns were observed in both populations. The observed discriminatory capacity was 98.4% for Jalisco and 98.9% for Michoacán, while the haplotype diversity values were 0.9998 and 0.9997, respectively. The most frequent haplogroup was R1b, followed by Q, representing the European and Native American ancestries, in both populations.

CONCLUSIONS

This study is the first to report the haplotype diversity and forensic parameters of the 27 Y-STRs included in the Yfiler™ Plus kit in Mexican populations. These findings confirm the forensic utility of these markers for human identification, biological relationship testing, and criminal investigations, reinforcing their applicability in forensic casework.

Population expansion, larger, and more homogeneous native American ancestry among Mexican mestizo populations based on 10 X-chromosome STR loci (X-STR decaplex system)

OBJECTIVE

To evaluate the genetic diversity, admixture, genetic relationships, and sex-biased demographic processes in Mexican Mestizo (admixed) populations based on 10 X-chromosome STRs (X-STRs).

METHODS

We analyzed the X-STRs Decaplex system in 104 Mexican Native Americans to obtain the ancestral reference needed to complete the demographic analyses above mentioned. We included reported Iberian and Latin American (admixed) populations from Central and South America, as well as datasets from Mexican Mestizos based on Y-linked STRs (Y-STRs), autosomal STRs (A-STRs), and mtDNA.

RESULTS

Higher X-linked Native American ancestry was observed among Latin American populations regarding that reported from A-STRs and Y-STRs. The interpopulation differentiation based on ancestry among Mexican Mestizos diminished according to the inheritance pattern: Y-STRs (highest), A-STRs, X-STRs, and mtDNA (lowest). This finding is related to the peculiar admixture process that occurred during and after the Spanish Conquest of Mexico (and most of Latin America), involving a large number of Spanish men (Y-chromosomes) with a lesser proportion of X-chromosomes than autosomes; besides to the limited number of Spanish women (XX) arrived in the Americas in subsequent and shorter periods. Population expansion was detected in Mexican Mestizos from all the country, except those from the southeast region characterized by elevated indigenous ancestry, marginalization, and poorness.

CONCLUSIONS

Population growth was detected in most Mexican Mestizos, besides more homogeneous and larger Native American ancestry based on X-linked inheritance than that based on autosomal STRs and Y-STRs.

Analysis of 26 STR loci (PowerPlex® Fusion 6C System) in a mestizo population from Mexico city

BACKGROUND

Short tandem repeats (STRs) are the most widely used genetic markers in forensic genetics. Therefore, it is essential to document genetic population data of new kits designed for human identification purposes to enable laboratories to use these genetic systems to interpret and solve forensic casework. However, in Mexico, there are no studies with the PowerPlex Fusion 6C System, which includes 26 STRs (23 autosomal STRs and 3 Y-STRs).

METHODS AND RESULTS

600 DNA samples from Mexico City were subjected to genotyping using the PowerPlex Fusion 6C System. For autosomal STRs, 312 different alleles were observed. Combined PE and PD were 99.999999809866% and 99.99999999999999999999999818795%, respectively. Genetic distances and AMOVA test showed low but significant differentiation between Mexican populations.

CONCLUSIONS

The results reported in this work demonstrate the efficacy of this system for human identification purposes in the population studied and justify its possible application in other Mexican Mestizo populations.

STAT4 Gene Variant rs7574865 Is Associated with Rheumatoid Arthritis Activity and Anti-CCP Levels in the Western but Not in the Southern Population of Mexico

Rheumatoid Arthritis (RA) is a multifactorial autoimmune disease. Currently, several genes play an important role in the development of the disease. The objective was to evaluate the association of the STAT4 rs7574865 and rs897200 gene variants with RA susceptibility, DAS28, RF, and anti-CCP in Western and Southern Mexico populations. Genotyping was performed on 476 samples (cases = 240; controls = 236) using the Taqman® system and qPCR probes. Disease activity was assessed using DAS28 and HAQ DI. CRP, ESR, RF, and anti-CCP were determined for clinical assessment. Our study showed there is a statistically significant association with susceptibility to RA for the rs7574865 variant in the Western population for the GT and TT genotypes. The same genotypes also showed a moderate-to-high activity according to DAS28 and positive anti-CCP compared to the control group. This association was not found in the Southern population. This work confirms the association of the rs7574865 variant with RA, as well as a moderate-to-high activity and positive anti-CCP in the Western population but not in the Southern population. No association of the rs897200 variant was found in any of the studied populations.

Forensic parameters and population structure based on 21 autosomal STRs with the investigator 24plex QS in mestizos from the Mexico City population

Allele frequencies and forensic parameters for 21 STR autosomal markers (CSF1PO, D10S1248, D12S391, D13S317,D16S539, D18S51, D19S433, D1S1656,D21S11, D22S1045, D2S1338, D2S441, D3S1358, D5S818, D7S820, D8S1179, FGA, SE33, TH01, TPOX and vWA) were reported in 289 unrelated individuals from Mexico City, Mexico. In addition, an interpopulation analysis was performed including other world populations. In brief, the established population database of 21 autosomal STR markers in the present work is adequate for human identification purposes.

Accuracy of Eye and Hair Color Prediction in Mexican Mestizos from Monterrey City Based on ForenSeqTM DNA Signature Prep

Forensic genomic systems allow simultaneously analyzing identity informative (iiSNPs), ancestry informative (aiSNPs), and phenotype informative (piSNPs) genetic markers. Among these kits, the ForenSeq DNA Signature prep (Verogen) analyzes identity STRs and SNPs as well as 24 piSNPs from the HIrisPlex system to predict the hair and eye color. We report herein these 24 piSNPs in 88 samples from Monterrey City (Northeast, Mexico) based on the ForenSeq DNA Signature prep. Phenotypes were predicted by genotype results with both Universal Analysis Software (UAS) and the web tool of the Erasmus Medical Center (EMC). We observed predominantly brown eyes (96.5%) and black hair (75%) phenotypes, whereas blue eyes, and blond and red hair were not observed. Both UAS and EMC showed high performance in eye color prediction (p ≥ 96.6%), but a lower accuracy was observed for hair color prediction. Overall, UAS hair color predictions showed better performance and robustness than those obtained with the EMC web tool (when hair shade is excluded). Although we employed a threshold (p > 70%), we suggest using the EMC enhanced approach to avoid the exclusion of a high number of samples. Finally, although our results are helpful to employ these genomic tools to predict eye color, caution is suggested for hair color prediction in Latin American (admixed) populations such as those studied herein, principally when no black color is predicted.

Characterization of 58 STRs and 94 SNPs with the ForenSeq™ DNA signature prep kit in Mexican-Mestizos from the Monterrey city (Northeast, Mexico)

BACKGROUND

STR allele frequency databases from populations are necessary to take full advantage of the increased power of discrimination offered by massively parallel sequencing (MPS) platforms.

MATERIAL AND METHODS

For this reason, we sequenced 58 STRs (aSTRs, X-STRs, and Y-STRs) and 94 identity informative SNPs (iiSNPs) on 105 Mestizo (admixed) individuals from Monterrey City (Northeast, Mexico), with the Primer Set-A of the ForenSeq™ DNA Signature Prep Kit.

RESULTS

Most of the STR markers were in Hardy Weinberg equilibrium, with a few exceptions. We found 346 different length-based alleles for these 58 STRs; nevertheless, they became 528 alleles when the sequence was assessed. The combined power of discrimination from autosomal STRs (aSTRs) was -virtually- 100% in both length and sequence-based alleles, while the power of exclusion was 99.9999999976065 and 99.9999999999494%, respectively. Haplotypes based on X-STRs and Y-STRs showed 100% of discriminatory capacity.

CONCLUSIONS

These results provide -for the first time- forensic genomic population data from Mexico necessary for interpretation in kinship and criminal analyses.

Use of Investigator 24plex GO! to analyse allele frequencies of 21 autosomal STRs in the population of Veracruz state, Mexico

BackgroundMexican population databases for autosomal STRs are scarce, and no previous studies have been performed with the Qiagen Investigator 24plex GO! Aim: To analyse the frequency of 21 autosomal short tandem repeat (STR) loci and forensic parameters in individuals from Veracruz state, Mexico. Subjects and methods: A total of 234 unrelated individuals were analysed with the Investigator 24plex GO! Kit, which includes the following autosomal STRs: TH01, D3S1358, vWA, D21S11, TPOX, D1S1656, D12S391, SE33, D10S1248, D22S1045, D19S433, D8S133879, D2S1338, D2S441, D18S51, FGA, D16S539, CSF1PO, D13S317, D5S818, and D7S820. Allele frequencies, forensic parameters, and relationships with neighbouring Mexican populations were estimated. Results: The STRs analysed were in Hardy-Weinberg Equilibrium (HWE). The combined matching probability and combined PE were 1.5266 E-24 and 0.999999988711, respectively. The D18S51 and SE33 loci presented the highest Ho (0.8974 and 0.8932) and PE (0.7902 and 0.7815), respectively. The highest PIC (0.9337) and PD (0.9894) values corresponded to SE33. Conversely, D22S1045 had the lowest PIC and PE (0.5533 y 0.3546, respectively). A population cluster among southern Mexican populations, which included non-differentiation between Guerrero and Veracruz states was detected. Conclusion: The forensic efficacy of the 21 STRs analysed by the Investigator 24plex GO! Kit was evaluated in the Veracruz state. Moreover, new population clusters that have not been yet been described and are related to geographic regions were identified, and these are in agreement with previously reported ancestral differences.

Paternal lineages and forensic parameters based on 23 Y-STRs (Powerplex® Y23) in Mestizo males from Mexico City

We analyzed 307 Mexican-Mestizo (admixed) males from Mexico City with the Powerplex® Y23 system. The complete list of Y-STR haplotypes was uploaded into the YHRD database (accession number YA004275). The discriminatory capacity (98.70 %) and gene diversity (D = 99.99 %) were calculated, improving the haplotype diversity regarding previous studies in Mexico based on 17 Y-STRs and 12 Y-STRs. Haplogroup distribution assignment was inferred by means of two different online-available algorithms. The Native American Q* haplogroup was the most frequent (66.2 %), followed by the European R1b lineage (19.5 %). In addition, eight Eurasian (3.9%) and two African (6.6%) haplogroups were observed in this population sample from Mexico City. Interestingly, AMOVA test showed a low but significant differentiation among Mexican-Mestizos (Fst = 1.52%; p = 0.0000), suggesting that four population clusters allow to explain their genetic structure according to geographic criteria: north, west, center, and south.

Haplotype block 1 variant (HB-1v) of the NKG2 family of receptors

The natural killer group 2 (NKG2) family of receptors, encoded within the NK complex gene region (NKC), modulate the cytotoxic activity of NK cells. Two haplotype blocks throughout the NKC, hb-1 and hb-2 have been associated with different levels of overall natural cytotoxicity. Here, we evaluated allelic and genotype frequencies at rs1049174, rs2617160, rs2617170, rs2617171, rs1983526 (hb-1 haplotype), and rs2255336 and rs2246809 (hb-2 haplotype) in 928 subjects examined from Mexico City. The most frequent alleles and genotypes were as follows: C, CG to rs1049174; G, GG to rs2255336; T, AT to rs2617160; G, GG to rs2246809; C, CT to rs2617170; G, CG to rs2617171; and G, CG to rs1983526. Linkage disequilibrium analysis revealed that rs1049174, rs2617160, rs2617170, and rs2617171 constituted the haplotype block-1 variant (hb-1v) (r² ≥ 0.89). Two predominant haplotypes of hb-1v were identified based on the allele content and included CTCG and GATC. This study is the first to evaluate the allelic and genotype frequency distribution of rs1049174, rs2255336, rs2617160, rs2246809, rs2617170, rs2617171, and rs1983526 in the population of Mexico City.