J.J. Builes

A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations

In a collaborative work carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG), a polymerase chain reaction multiplex was optimized in order to type ten X-chromosome short tandem repeats (STRs) in a single reaction, including: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08, and DXS7423. Using this X-decaplex, each 17 of the participating laboratories typed a population sample of approximately 200 unrelated individuals (100 males and 100 females). In this work, we report the allele frequencies for the ten X-STRs in 15 samples from Argentina (Buenos Aires, Córdoba, Río Negro, Entre Ríos, and Misiones), Brazil (São Paulo, Rio de Janeiro, Paraná, and Mato Grosso do Sul), Colombia (Antioquia), Costa Rica, Portugal (Northern and Central regions), and Spain (Galicia and Cantabria). Gene diversities were calculated for the ten markers in each population and all values were above 56%. The average diversity per locus varied between 66%, for DXS7133, and 82%, for DXS6809. For this set of STRs, a high discrimination power was obtained in all populations, both in males (≥1 in 5 × 105) and females (≥1 in 3 × 109), as well as high mean exclusion chance in father/daughter duos (≥99.953%) and in father/mother/daughter trios (≥99.999%). Genetic distance analysis showed no significant differences between northern and central Portugal or between the two Spanish samples from Galicia and Cantabria. Inside Brazil, significant differences were found between Rio de Janeiro and the other three populations, as well as between São Paulo and Paraná. For the five Argentinean samples, significant distances were only observed when comparing Misiones with Entre Ríos and with Río Negro, the only two samples that do not differ significantly from Costa Rica. Antioquia differed from all other samples, except the one from Río Negro.

Continent-Wide Decoupling of Y-Chromosomal Genetic Variation from Language and Geography in Native South Americans

Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans.

Autosomal STR genetic variation in negroid Chocó and Bogotá populations.

Abstract Genetic data for eight autosomal STRs were obtained from two different population samples from Colombia: the European Mestizo population of Bogotá and the African descent population of the Chocó region. The STRs were analysed in a multiplex system that includes the STR markers CSF1PO, TPOX, TH01, VWA, D13S317, D7S820, D16S539 and D5S818. Separation of the fragments and fluorescent detection was carried out in an ABI 310 DNA sequencer and the typing was made by comparison with sequenced allelic ladders. Exact tests were used for testing linkage between the loci and for Hardy-Weinberg equilibrium. Significant differences were found between both populations for all the loci.

Admixture and Genetic Diversity Distribution Patterns of Non-Recombining Lineages of Native American Ancestry in Colombian Populations

Genetic diversity of present American populations results from very complex demographic events involving different types and degrees of admixture. Through the analysis of lineage markers such as mtDNA and Y chromosome it is possible to recover the original Native American haplotypes, which remained identical since the admixture events due to the absence of recombination. However, the decrease in the effective population sizes and the consequent genetic drift effects suffered by these populations during the European colonization resulted in the loss or under-representation of a substantial fraction of the Native American lineages. In this study, we aim to clarify how the diversity and distribution of uniparental lineages vary with the different demographic characteristics (size, degree of isolation) and the different levels of admixture of extant Native groups in Colombia. We present new data resulting from the analyses of mtDNA whole control region, Y chromosome SNP haplogroups and STR haplotypes, and autosomal ancestry informative insertion-deletion polymorphisms in Colombian individuals from different ethnic and linguistic groups. The results demonstrate that populations presenting a high proportion of non-Native American ancestry have preserved nevertheless a substantial diversity of Native American lineages, for both mtDNA and Y chromosome. We suggest that, by maintaining the effective population sizes high, admixture allowed for a decrease in the effects of genetic drift due to Native population size reduction and thus resulting in an effective preservation of the Native American non-recombining lineages.

Discrimination index of Y-chromosomal haplotypes in an Antioquia (Colombia) population sample

Abstract Y-chromosome STR haplotypes (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393) in a sample of 507 healthy male blood donors from Antioquia (Colombia) were studied. 323 different haplotypes were found, 256 of them being unique. Gene diversity ranged between 0.3640 at DYS393 and 0.8900 at DYS385. The haplotype diversity value (power of discrimination (PD) and power of exclusion (PE)) calculated from all eight loci combined was 0.9946, which is informative. This study provides further information on the Y-chromosome polymorphisms commonly used in paternity testing, forensic genetics and in the population genetic studies of complex patterns of sex differential racial admixture.

Multiple sclerosis: association to HLA DQalpha in a tropical population.

Studies performed in subtropical populations have found significant association between the phenotype multiple sclerosis (MS) and the major histocompatibility complex (MHC). We present the results of a case-control study conducted on a tropical population (Antioquia, Colombia) in order to detect a possible association between MS and HLA DQα (HLA DQA1*) alleles. Forty chromosomes belonging to MS patients were compared to two sets of controls (40 and 910 chromosomes, respectively). The HLA DQA1*0101 and DQA1*0102 alleles were found in a significantly higher proportion among the cases than among the controls, whereas the HLA DQA1*0103 allele was found in a significantly lower proportion of the cases. These results suggest that the association of HLA DQA1*0101, DQA1*0102 and DQA1*0103 to the MS phenotype found in Caucasian subtropical populations remains in individuals with MS inhabiting the tropics. This finding could mean that the major genetic component associated to the MHC in subtropical populations is the same in the tropics.

Genetic admixture estimates by Alu elements in Afro-Colombian and Mestizo populations from Antioquia, Colombia

Abstract Aim: This work was intended to gain insights into the admixture processes occurring in Latin American populations by examining the genetic profiles of two ethnic groups from Antioquia (Colombia). Subjects and methods: To analyse the genetic variability, eight Alu insertions were typed in 64 Afro-Colombians and a reference group of 34 Hispanics (Mestizos). Admixture proportions were estimated using the Weighted Least Squares and the Gene Identity methods. The usefulness of the Alu elements as Ancestry Informative Markers (AIMs) was evaluated through differences in weighted allelic frequencies (δ values) and by hierarchical analysis of the molecular variance (AMOVA). Results: The Afro-Colombian gene pool was largely determined by the African component (88.5–88.8%), but the most prominent feature was the null contribution of European genes. Mestizos were characterized by a major European component (60.0–63.8%) and a comparatively low proportion of Amerindian (19.2–20.7%) and African (17.0–19.3%) genes. Five of the Alu loci examined (ACE, APO, FXIIIB, PV92 and TPA25) showed an adequate resolving power to differentiate between continental groups, as indicated by δ values and AMOVA results. Conclusions: The peculiarity of the Afro-Colombian gene pool seems to be associated with intense genetic drift episodes that occurred in isolated communities founded by small groups of runaway slaves. ACE, APO, FXIIIB, PV92 and TPA25 could be efficiently utilized in studies dealing with demographic history and biogeographical ancestry in human populations.

Population genetics of eight new Y-chromosomal STR haplotypes in three Colombian populations: Antioquia, Chocó and Cartagena

Abstract In this study, eight new Y-chromosomal (GATA-C4, DYS438, DYS437, DYS461, GATA-H4, DYS439, GATA-A10 and DYS460) short tandem repeat (STR) polymorphic systems were typed by two PCR quadruplex reactions in three Colombian populations: Antioquia, Choco and Cartagena. GATA-C4 showed the highest gene diversity in the three populations. In the Antioquia population sample, a total of 123 different haplotypes were observed among which 85 were unique and 38 were found at least two times; in the Choco population sample: 55 different haplotypes, 47 unique and 8 at least two times; in the Cartagena population sample: 82 different haplotypes, 77 unique and 5 at least two times. The highest average gene diversity was found in Cartagena and the lowest was in Choco. The haplotype diversity for the eight Y-chromosomal STR loci in the Antioquia, Choco and Cartagena population samples were calculated to be 0.9949, 0.9959 and 0.9940, respectively.

Development of a new highly efficient 17 X‐STR multiplex for forensic purposes

Currently, two of the most widely used X‐chromosome STR (X‐STR) multiplexes are composed by ten (GHEP‐ISFG decaplex) and 12 markers (Investigator Argus X‐12 Kit). The number of markers included is a drawback for complex relative testing cases, likewise the large size of some amplicons difficult their application to degraded samples. Here, we present a new multiplex of 17 X‐STRs with the aim of increasing both the resolution power and forensic applicability. This newly proposed set includes the X‐STRs of the GHEP‐ISFG decaplex, four X‐STRs from the Investigator Argus X‐12 Kit, three of them also included in the decaplex, and six additional more. In order to ensure the allele designation, an allelic ladder was developed. The validation of the present multiplex was carried out according to the revised guidelines by the SWGDAM (Scientific Working Group on DNA Analysis Methods). A total of 488 unrelated individuals from four different continents were analyzed. The forensic efficiency evaluation showed high values of combined power of discrimination in males (≥0.999999996) and females (≥0.999999999999995) as well as combined paternity exclusion probabilities in trios (≥0.99999998) and duos (≥0.999996). The results presented herein have demonstrated that the new 17 X‐STR set constitutes a high‐resolution alternative to the current X‐STR multiplexes.

I-DNASE21 system: development and SWGDAM validation of a new STR 21-plex reaction.

I-DNASE21 is a new STR multiplex system that amplifies 21 STR autosomal loci, plus the amelogenin locus in one reaction. This system has been designed to analyze all the STR loci included in the Combined DNA Index System (CODIS), Interpol Standard Set of Loci (ISSL), Extended European Standard Set (ESS-Extended), UK National Criminal Intelligence DNA Database (NDNAD) and German Core loci (GCL). This manuscript presents the validation of the I-DNASE21 system according to the revised guidelines issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM). The results of this validation, added to the extremely high discriminatory power showed, suggest that I-DNASE21 could be a potentially helpful tool for identification and kinship determination even in complex paternity cases.