Proficiency of 38 HID-INDELS in kinship analysis and forensic parameters in a Mexican population / Eficiencia de 38 HID-INDELS en análisis de parentesco y parámetros forenses en una población mexicana

Introduction: Insertion–deletions for human identification (HID-INDELs) allow solving peculiar forensic situations when autosomal STRs are insufficient. Although limitations were predicted since the forensic implementation of biallelic markers, formal evaluation of these restrictions is scarce. Particularly, to define the informativity provided by HID-INDELs in kinship analysis is useful to avoid wasting work, resources, and –finally– disappointments.Material and methods: For this reason, we analyzed the 38-plex HID-INDEL system in 25 Mexican families including father, daughter, and mother, whose kinship was previously established with 22 autosomal STRs.Results and discussion: From genotypes of unrelated individuals, we updated allele frequencies and forensic parameters of the Jalisco state (West, Mexico), by increasing the population sample size from 62 to 112. Among the forensic a priori parameters, the Typical paternity index (PI) of the 38plex HID-INDEL system showed important differences regarding the PI and probability of paternity (W) estimated herein from real paternity cases, generally undervaluing the observed informativity of these 38-plex HID-INDEL system. Conversely, the studied HID-INDEL loci offered confident kinship conclusions based on the paternity index (PI ≥10,000) and probability of paternity (W ≥ 99.99%) in 68% of the standard trio cases (18/25), and only 12% of duo paternity cases (6/50) (motherless and fatherless). In fact, 14% of duo paternity cases (7/50) did not reach minimum requirements to stablish paternity (IP < 100; W < 99%).Conclusions: We updated a Mexican population database for 38 HID-INDEL loci, and we described their proficiency from real paternity cases, detailing some limitations non-previously specified. (AU)

Introducción: Las inserciones-deleciones para identificación humana (HID-INDEL), permiten resolver situaciones forenses peculiares cuando los STR autosómicos son insuficientes. Aunque se predijeron sus limitaciones desde la implementación forense de marcadores bialélicos, la evaluación formal de estas restricciones es escasa. Particularmente es útil definir su informatividad en el análisis de parentesco, para evitar desperdiciar trabajo, recursos y –finalmente– decepciones.Material y Métodos: Por este motivo, analizamos el sistema de 38plex HID-INDELs en 25 familias mexicanas entre padre, hija y madre, cuyo parentesco se estableció previamente con 22 STR autosómicos. A partir de los individuos no emparentados, actualizamos las frecuencias alélicas y los parámetros forenses del estado de Jalisco (Oeste, México), aumentando el tamaño de la muestra poblacional de 62 a 112.Resultados y discusión: Entre los parámetros forenses a priori, el índice de paternidad típico (IPT) del sistema 38plex HID-INDEL mostró diferencias importantes con respecto al IP y la probabilidad de paternidad (W) derivados de casos reales de paternidad, generalmente subestimando la informatividad observada de ese sistema. Sin embargo, los 38 HID-INDELs ofrecieron conclusiones de parentesco confiables basadas en el índice de paternidad (IP ≥ 10,000) y la probabilidad de paternidad (W ≥ 99,99%) sólo en el 68% de los casos tríos estándar (18/25), y el 12% de casos de paternidad dúo (6/50) (sin madre y sin padre). De hecho, el 14% de los casos de paternidad dúo (7/50) no alcanzó los requisitos mínimos para establecer la paternidad (IP <100; W < 99%).Conclusiones: En este trabajo actualizamos una base de datos de población mexicana para 38 HID-INDELs y describimos su eficiencia en casos reales de paternidad, detallando algunas limitaciones no especificadas previamente. (AU)

"Distribution of paternal lineages in Mestizo populations throughout Mexico: an in silico study based on Y-STR haplotypes".

The Mexican-Mestizo population arose following European contact with the Americas due to the admixture of principally Spaniards, Native Americans, and Africans around 500 years ago. Because the paternal lineage distribution of the Mexican population has been poorly investigated, this study inferred the haplogroups of ten populations based on 1859 haplotypes (Y-STR data) using two haplogroup predictor programs. In the Mexican population sample, we found predominantly European ancestry (50.1%), followed by Native American (32.5%), Eurasian (13.4%), African (2.1%), East African-South Eurasian (1.3%), and Asian (0.6%) ancestries. In general, our results support a contrary north-to-south gradient throughout the Mexican territory of European and Native-American ancestries, respectively. Moreover, the presence of West-European R1b and Sub-Saharan African E1b1a haplogroups agrees with historical and genetic data of gene flow during the European conquest. This study represents the effort to analyze these paternal lineages on a large scale by taking advantage of Y-STR haplotype data to determine the distribution and ancestry proportions in this country.

Forensic parameters of 15 autosomal STRs (Identifiler™ kit) in three Mayan groups and one Mestizo population from Guatemala.

The population of Guatemala includes Mestizos (admixed) and different Mayan groups (Native Americans), which have been poorly studied in regards to short tandem repeat (STR) loci used for human identification (HID) purposes. Therefore, 483 unrelated Guatemalan volunteers from one Mestizo and three Mayan populations (Poqomchi, Ixil, and Achi) were analyzed with an AmpFlSTR Identifiler™ kit. Allele frequencies and forensic parameters were obtained for 15 autosomal STRs in these populations. Hardy-Weinberg equilibrium by locus and equilibrium linkage between pair of loci were demonstrated by exact tests in all the studied populations. Larger genetic differentiation probably due to genetic drift effects was observed among the studied Guatemalan Mayan groups than the neighboring Mexican Mayas. In brief, our results validate to use the Identifiler™ kit for HID in three non-previously studied Mayan groups, and one Mestizo population from Guatemala.

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

We analyzed Mestizo (admixed) population samples from different geographic regions of Mexico (n = 1283) with 20 autosomal STRs (PowerPlex® 21, Promega Corp.). Allele frequencies and forensic parameters from the Northwest, Northeast, West, Center, and Southeast regions are reported, as well as from the pooled Mexican population sample. The combined PD and PE for this 20 STR system were > 0.9999999999 and > 0.99999996593% in all five population samples, respectively. Analysis of molecular variance (AMOVA) of these Mexican population samples, plus Monterrey (Northeast) and Mexico (Center) Cities, showed low but significant differences among Mexican-Mestizos from the seven populations (Fst = 0.20%; p = 0.0000). Structure analysis showed the highest proportion of Native American ancestry in Mexico City, Center, and Southeast regions, respectively, which was in agreement with the estimated genetic distances represented in a MDS plot and a NJ tree. The best fit of population clusters (K = 4) obtained with the Structure software indicates that Mexican-Mestizos are mainly composed by European, African, and two Native American ancestries. The European and Native American ancestries displayed a contrary gradient, increasing toward the North-West and South-Southeast, respectively. These 20 autosomal STR loci improved the admixture estimation regarding previous studies with the 13 CODIS-STRs, as supported by the higher similarity with previous estimates based on genome-wide SNP. In brief, this study validates the confident use of the PowerPlex® 21 system for human identification purposes in Mestizo populations throughout the Mexican territory.

Evaluation of the contribution of D9S1120 to anthropological studies in Native American populations.

The D9S1120 locus exhibits a population-specific allele of 9 repeats (9RA) in all Native American and two Siberian populations currently studied, but it is absent in other worldwide populations. Although this feature has been used in anthropological genetic studies, its impact on the evaluation of the structure and genetic relations among Native American populations has been scarcely assessed. Consequently, the aim of this study was to evaluate the anthropological impact of D9S1120 when it was added to STR population datasets in Mexican Native American groups. We analyzed D9S1120 by PCR and capillary electrophoresis (CE) in 1117 unrelated individuals from 13 native groups from the north and west of Mexico. Additional worldwide populations previously studied with D9S1120 and/or 15 autosomal STRs (Identifier kit) were included for interpopulation analyses. We report statistical results of forensic importance for D9S1120. On average, the modal alleles were the Native American-specific allele 9RA (0.3254) and 16 (0.3362). Genetic distances between Native American and worldwide populations were estimated. When D9S1120 was included in the 15 STR population dataset, we observed improvements for admixture estimation in Mestizo populations and for representing congruent genetic relationships in dendrograms. Analysis of molecular variance (AMOVA) based on D9S1120 confirms that most of the genetic variability in the Mexican population is attributable to their Native American backgrounds, and allows the detection of significant intercontinental differentiation attributed to the exclusive presence of 9RA in America. Our findings demonstrate the contribution of D9S1120 to a better understanding of the genetic relationships and structure among Mexican Native groups.

Population data of 23 STR loci (PowerPlex® Fusion System) in Mexican Mestizos from the West Region.

We analyzed 238 unrelated Mestizo (admixed) individuals from the West region of Mexico with the PowerPlex® Fusion System (Promega Corp.). Allele frequencies and forensic parameters were estimated for the 23 STRs included in this kit. Hardy-Weinberg equilibrium by locus and non-association between pair of loci were demonstrated by exact tests in this population. The combined PE and PD offered by this HID kit were ≥0.9999999986, representing a substantial improvement with respect to those previously offered by 15 STR systems. Interpopulation comparison by AMOVA tests demonstrated low but significant differences among Mexican Mestizos from West, Center, and Northeast regions (Fst = 0.01558; p = 0.0000), similar to the observed among three main ethnic groups from USA (Fst = 0.02048; p = 0.0000). This finding is consistent with the contrary clines of European and Amerindian ancestries described throughout the Mexican territory for Mestizos, the largest population (~90 %) in this country.