Evaluating methods to correct for population stratification when estimating paternity indexes.

The statistical interpretation of the forensic genetic evidence requires the use of allelic frequency estimates in the reference population for the studied markers. Differences in the genetic make up of the populations can be reflected in statistically different allelic frequency distributions. One can easily figure out that collecting such information for any given population is not always possible. Therefore, alternative approaches are needed in these cases in order to compensate for the lack of information. A number of statistics have been proposed to control for population stratification in paternity testing and forensic casework, Fst correction being the only one recommended by the forensic community. In this study we aimed to evaluate the performance of Fst to correct for population stratification in forensics. By way of simulations, we first tested the dependence of Fst on the relative sizes of the sub-populations, and second, we measured the effect of the Fst corrections on the Paternity Index (PI) values compared to the ones obtained when using the local reference database. The results provide clear-cut evidence that (i) Fst values are strongly dependent on the sampling scheme, and therefore, for most situations it would be almost impossible to estimate real values of Fst; and (ii) Fst corrections might unfairly correct PI values for stratification, suggesting the use of local databases whenever possible to estimate the frequencies of genetic profiles and PI values.

Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations.

The human leucocyte antigen (HLA) system shows extensive variation in the number and function of loci and the number of alleles present at any one locus. Allele distribution has been analysed in many populations through the course of several decades, and the implementation of molecular typing has significantly increased the level of diversity revealing that many serotypes have multiple functional variants. While the degree of diversity in many populations is equivalent and may result from functional polymorphism(s) in peptide presentation, homogeneous and heterogeneous populations present contrasting numbers of alleles and lineages at the loci with high-density expression products. In spite of these differences, the homozygosity levels are comparable in almost all of them. The balanced distribution of HLA alleles is consistent with overdominant selection. The genetic distances between outbred populations correlate with their geographical locations; the formal genetic distance measurements are larger than expected between inbred populations in the same region. The latter present many unique alleles grouped in a few lineages consistent with limited founder polymorphism in which any novel allele may have been positively selected to enlarge the communal peptide-binding repertoire of a given population. On the other hand, it has been observed that some alleles are found in multiple populations with distinctive haplotypic associations suggesting that convergent evolution events may have taken place as well. It appears that the HLA system has been under strong selection, probably owing to its fundamental role in varying immune responses. Therefore, allelic diversity in HLA should be analysed in conjunction with other genetic markers to accurately track the migrations of modern humans.

Male lineages in South American native groups: evidence of M19 traveling south.

With this study, we aimed to determine the different male ancestral components of two Native American communities from Argentina, namely Toba and Colla. The analysis of 27 Y-chromosome SNPs allowed us to identify seven different haplogroups in both samples. Chromosomes carrying the M3 mutation, which typically defines the Native American haplogroup Q1a3a, were seen most frequently in the Toba community (90%). Conversely, Q1a3a was represented in 34% of the Colla Y-chromosomes, whereas haplogroup R1b1, the main representative of western European populations, exhibited the highest frequency in this population (41%). Different M3 sublineages in the Toba community could be identified by observing point mutations at both DYS385 and M19 loci. A microvariant at DYS385, named 16.1, has been characterized, which helps to further subdivide Q1a3a. It is the first time the M19 mutated allele is described in a population from Argentina. This finding supports the old age of the lineages carrying the M19 mutation, but it contradicts the previous hypothesis that the M19 mutated allele is confined to only two Equatorial-Tucano population groups from the north region of South America. The detection of M19 further south than previously thought allows questioning of the hypothesis that this lineage serves as an example of isolation after colonization. This observation also affirms the strong genetic drift to which Native Americans have been subjected. Moreover, our study illustrates a heterogeneous contribution of Europeans to these populations and supports previous studies showing that most Native American groups were subjected to European admixture that primarily involved immigrant men.

Population stratification in Argentina strongly influences likelihood ratio estimates in paternity testing as revealed by a simulation-based approach.

A simulation-based analysis was carried out to investigate the potential effects of population substructure in paternity testing in Argentina. The study was performed by evaluating paternity indexes (PI) calculated from different simulated pedigree scenarios and using 15 autosomal short tandem repeats (STRs) from eight Argentinean databases. The results show important statistically significant differences between PI values depending on the dataset employed. These differences are more dramatic when considering Native American versus urban populations. This study also indicates that the use of Fst to correct for the effect of population stratification on PI might be inappropriate because it cannot account for the particularities of single paternity cases.

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 (> or =1 in 5 x 10(5)) and females (> or =1 in 3 x 10(9)), as well as high mean exclusion chance in father/daughter duos (> or =99.953%) and in father/mother/daughter trios (> or =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.

Y chromosome microsatellite genetic variation in two Native American populations from Argentina: population stratification and mutation data.

Two Native American populations from North and northwest regions of Argentina (Toba and Colla) were analyzed for 17 Y chromosome short tandem repeat loci (Y-STRs), namely, DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1. Over 357 allele transfers, two one-step mutations could be detected at DYS456 and GATA H4.1 loci. A new 16.1 'micro-variant' allele was observed for DYS385, characterized by an insertion at the fifth GAAA repeat. We also observed two alleles at the DYS448 locus in three samples (two from Toba and one from Colla). A total of 34 and 16 different haplotypes were detected for Toba and Colla, respectively, the former with a haplotype diversity value of 0.9769+/-0.01, whereas 0.9497+/-0.02 for the latter. Significant population differences were observed between Colla and Toba, at least in part, due to a more prevalent European input in the Colla. In agreement with this observation is the fact that the genetic distances between Colla and Iberian populations are lower than those observed between Iberian and any other Native American population. The results of multiscaling dimensional analysis and genetic distances (Rst) among Native American population samples also reflect this fact. The data show the existence of clear population stratification in the Argentina, a fact that should be taken into account in forensic casework.

Association of DRB1 and DQB1 HLA class II polymorphisms in high-grade and neoplastic cervical lesions of women from Argentina.

OBJECTIVES: To investigate associations between HLA-DRB1 and HLA-DQB1 polymorphisms with low- and high-grade cervical lesions in Argentine population and the role human papillomavirus status in these associations. MATERIALS AND METHODS: Cervical biopsies and peripheral blood samples were taken from 32 patients with cervical intraepithelial neoplasia grade 1 (CIN 1) and 44 patients with cervical CIN 3 or invasive squamous cell carcinomas. Cervical cells and peripheral blood samples from 40 healthy women were included as control group. Human papillomavirus detection and typing were done by polymerase chain reaction (PCR) MY09, 11-restriction fragment length polymorphisms, or PCR 5+, 6+ dot-blot hybridization, and HLA DR/DQ typing by the PCR-sequence-specific oligonucleotide probes method. RESULTS: HLA-DRB1*04 and HLA-DQB1*0302 were found to be positive associated with the CIN 3/invasive squamous cell carcinomas subgroup, whereas HLA-DRB1*13 and HLA-DQB1*02 were negatively associated with the same group, when comparing to the control group. CONCLUSIONS: The data support the hypothesis that HLA-DRB1*04 and HLA-DQB1*0302 may be considered risk factors for malignant progression, whereas HLA-DRB1*13 and HLA-DQB1*02 may have a protective role. Further studies with a larger group are needed to confirm these susceptibility and protective roles in disease progression in Argentine population.

Testing for genetic structure in different urban Argentinian populations.

Fifteen autosomal short tandem repeat (STR) markers (D3S1358, HUMTH01, D21S11, D18S51, PENTA E, D5S818, D13S317, D7S820, D16S539, CSF1PO, PENTA D, HUMvWA, D8S1179, HUMTPOX, FGA) were analyzed in 1734 individuals living in urban areas of cities from six different Argentinian provinces (Buenos Aires, Neuquén, Tucumán, La Pampa, San Luis, Santa Cruz) in order to determine if a common urban database could be used in Argentina for forensic purposes. Frequencies estimates, Hardy-Weinberg equilibrium (HWE), and other parameters of forensic interest were computed. Comparisons between the six populations, and with published data from one Native American population from Argentina and other urban populations from Argentina and Europe were also performed. Our results reveal evidences for population structure, both when testing for genetic differentiation and when comparing frequencies distributions between different pairs of populations. Therefore, caution should be taken when using a common pooled database with general forensic purposes in Argentina.

Variabilidad genética en 17 microsatélites del Cromosoma Y en dos poblaciones nativas de Argentina (Tobas, Collas) / Genetic Variability in 17 Y-STR loci of a native population from Argentine (Tobas, Collas)

Se analizan 17 marcadores microsatélites del cromosoma Y del tipo Short Tandem Repeats (STRs) (DYS19,DYS3891, DYS38911, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, y GATA H4)en dos poblaciones nativas de las regiones Norte y Noroeste de la Argentina (Tobas y Collas)

Variabilidad genética en 17 microsatélites del Cromosoma Y en dos poblaciones nativas de Argentina (Tobas, Collas) / Genetic Variability in 17 Y-STR loci of a native population from Argentine (Tobas, Collas)

Se analizan 17 marcadores microsatélites del cromosoma Y del tipo Short Tandem Repeats (STRs) (DYS19,DYS3891, DYS38911, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, y GATA H4)en dos poblaciones nativas de las regiones Norte y Noroeste de la Argentina (Tobas y Collas)(AU)

Results of the 2003-2004 GEP-ISFG collaborative study on mitochondrial DNA: focus on the mtDNA profile of a mixed semen-saliva stain.

We report here a review of the seventh mitochondrial DNA (mtDNA) exercise undertaken by the Spanish and Portuguese working group (GEP) of the International Society for Forensic Genetics (ISFG) corresponding to the period 2003-2004. Five reference bloodstains from five donors (M1-M5), a mixed stain of saliva and semen (M6), and a hair sample (M7) were submitted to each participating laboratory for nuclear DNA (nDNA; autosomal STR and Y-STR) and mtDNA analysis. Laboratories were asked to investigate the contributors of samples M6 and M7 among the reference donors (M1-M5). A total of 34 laboratories reported total or partial mtDNA sequence data from both, the reference bloodstains (M1-M5) and the hair sample (M7) concluding a match between mtDNA profiles of M5 and M7. Autosomal STR and Y-STR profiling was the preferred strategy to investigate the contributors of the semen/saliva mixture (M6). Nuclear DNA profiles were consistent with a mixture of saliva from the donor (female) of M4 and semen from donor M5, being the semen (XY) profile the dominant component of the mixture. Strikingly, and in contradiction to the nuclear DNA analysis, mtDNA sequencing results yield a more simple result: only the saliva contribution (M4) was detected, either after preferential lysis or after complete DNA digestion. Some labs provided with several explanations for this finding and carried out additional experiments to explain this apparent contradictory result. The results pointed to the existence of different relative amounts of nuclear and mtDNAs in saliva and semen. We conclude that this circumstance could strongly influence the interpretation of the mtDNA evidence in unbalanced mixtures and in consequence lead to false exclusions. During the GEP-ISFG annual conference a validation study was planned to progress in the interpretation of mtDNA from different mixtures.

Determinación del polimorfismo de los genes KIR en la población argentina normal / Determination of the polymorphism of kir genes in a normal argentine population

The "Natural Killer" cells play an important roll in the immune response to tumoral cells and viral infections, and also they particpate in the rejection processes in allogeneic bone marrow transplantation. The interaction of natural killer cells and their receptors, with special reference to human diversity in killer cell inhibitory receptor genes, are described in this article with consideration to a normal Argentine population

Determinación del polimorfismo de los genes KIR en la población argentina normal / Determination of the polymorphism of kir genes in a normal argentine population

The "Natural Killer" cells play an important roll in the immune response to tumoral cells and viral infections, and also they particpate in the rejection processes in allogeneic bone marrow transplantation. The interaction of natural killer cells and their receptors, with special reference to human diversity in killer cell inhibitory receptor genes, are described in this article with consideration to a normal Argentine population

Results of the GEP-ISFG collaborative study on the Y chromosome STRs GATA A10, GATA C4, GATA H4, DYS437, DYS438, DYS439, DYS460 and DYS461: population data.

The Spanish and Portuguese ISFG Working Group (GEP-ISFG) carried out a collaborative exercise in order to asses the performance of two Y chromosome STR tetraplexes, which include the loci DYS461, GATA C4, DYS437 and DYS438 (GEPY I), and DYS460, GATA A10, GATA H4 and DYS439 (GEPY II). The groups that reported correct results in all the systems were also asked to analyse a population sample in order to evaluate the informative content of these STRs in different populations. A total of 1020 males out of 13 population samples from Argentina, Brazil, Costa Rica, Macao, Mozambique, Portugal and Spain were analysed for all the loci included in the present study. Haplotype and allele frequencies of these eight Y-STRs were estimated in all samples. The lowest haplotype diversity was found in the Lara (Argentina) population (95.44%) and the highest (99.90%) in Macao (China). Pairwise haplotype analysis showed the relative homogeneity of the Iberian origin samples, in accordance with what was previously found in the European populations for other Y-STR haplotypes (http://www.ystr.org). As expected, the four non-Caucasian samples, Macao (Chinese), Mozambique (Africans), Costa Rica (Africans) and Argentina (Lara, Amerindians), show highly significant Phist values in the pairwise comparisons with all the Caucasian samples.

Results of the GEP-ISFG collaborative study on two Y-STRs tetraplexes: GEPY I (DYS461, GATA C4, DYS437 and DYS438) and GEPY II (DYS460, GATA A10, GATA H4 and DYS439).

A collaborative exercise was carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG) in order to evaluate the performance of two Y-chromosome STR PCR tetraplexes, which include the loci DYS461, GATA C4, DYS437 and DYS438 (GEPY I), and DYS460, GATA A10, GATA H4 and DYS439 (GEPY II). The participating laboratories were asked to type three samples for the eight markers, using a specific amplification protocol. In addition, two control samples, with known haplotypes, were provided. The results obtained by the 13 different participating laboratories were identical, except for two laboratories that failed to type correctly the same two samples for GATA C4. By sequence analyses, two different GATA C4 allele structures were found. One control sample (allele 21) and two questioned samples (allele 22, correctly typed by all the laboratories, and allele 25) presented the following repeat structure: (TCTA)4(TGTA)2(TCTA)2(TGTA)2(TCTA)n, but different from the one found for allele 26 in one sample included in this exercise, as well as in the second control sample (allele 23), namely (TCTA)4(TGTA)2(TCTA)2(TGTA)2(TCTA)2(TGTA)2(TCTA)n. The collaborative exercise results proved that both Y-tetraplexes produce good amplification results, with the advantage of being efficiently typed using different separation and detection methodologies. However, since GATA C4 repeat presents a complex structure, with alleles differing in sequence structure, efficient denaturing conditions should be followed in order to avoid typing errors due to sizing problems.

STR data for PowerPlex 16 System from Neuquen population, SW Argentina.

Allele frequencies for the 15 autosomic STR loci included in the PowerPlex 16 System kit (Promega) were estimated from a sample of 111 unrelated individuals living in Neuquen province, southwest of Argentina. Population showed to be in HWE.

STR data for PowerPlex 16 System from Buenos Aires population, Argentina.

Allele frequencies for the 15 autosomic STR loci included in the PowerPlex 16 System kit (Promega Corp.) were estimated from a sample of 143 unrelated individuals living in Capital Federal and in Buenos Aires Metropolitan Area, Argentina. Population showed to be in HWE.

Historia natural de la hepatitis C: experiencia multidisciplinaria en Argentina / Natural history of the hepatitis C: multidisciplinary experience in Argentina

O’Brien es un pueblo rural de la Prov. de Buenos Aires con 2300 habitantes. Durante la última década, los profesionales de O’Brien notaron una inusual frecuencia de elevación de transaminasas en análisis obtenidos por rutina y un número creciente de pacientes con diagnóstico de hepatitis C, incluyendo 4 casos que requirieron trasplante hepático por cirrosis avanzada. El objetivo de este trabajo fue investigar la prevalencia de infección y hepatitis por HCV en O’Brien. En 1832 de los 2300 habitantes (80 por ciento) se investigó la presencia de anti-HCV por un EIE de 3ª generación. La prevalencia de infección por HCV en O’Brien fue de 5.6 por ciento (102/1832), 0.56 por ciento en los individuos 40 años (p<0.001) con un pico máximo de 23.4 por ciento entre la 6ª y 7ª década. La edad mediana de los 102 pacientes infectados (52 mujeres y 50 hombres) fue de 60 años con un rango de 7 a 81 años. El 89 por ciento de los sueros reactivos por EIE fueron confirmados por RIBA-3. Once pacientes fueron RIBA-indeterminados y ninguno RIBA-negativo. El internvalo estimado entre la infección y el diagnóstico fue de 36ñ8 años. A pesar de la prolongada duración de la infección, el 81 por ciento de los pacientes (83/102) presentaron HCV RNA detectable en suero por PCR y el 59 por ciento (60/102) elevación de transaminasas. La presencia de viremia se asoció significativamente con la positividad del RIBA (99 por ciento, p<0.001) y con la elevación de AST/ALT (72 por ciento, p<0.001). El genotipo de HCV, determinado por la técnica de RFLP, fue 1b en el 100 por ciento de los pacientes virémicos, hallazgo que diferencia a este estudio de todas las series publicadas... (TRUNCADO)