Biomedical subjects

M V Lareu

Publications and source records attributed to M V Lareu.

At least 19 recordsLinked to original sources

PubMed2006

The genetic male legacy from El Salvador.

Allele frequencies and haplotype and haplogroup analysis have been performed for 16 Y-chromosome binary markers and 8 Y-chromosome STRs (DYS19, DYS385I and II, DYS389I and II, DYS390, DYS391, DYS392, DYS393). Data was obtained from a general sample of 93 unrelated individuals living in metropolitan areas from El Salvador, and 67 individuals from different historical ethnic groups, Conchagua, San Alejo, Panchimalco, Izalco and finally Nueva Concepción with white people. Levels of admixture among metropolitan and rural areas were evaluated and population substructure measured. A total of 13 haplogroups and 136 different haplotypes were found. The most frequent haplogroup in the general metropolitan population was the European R1b, while in the Indigenous samples considered as a whole the most frequent was the Amerindian haplogroup Q3.

Chromosomes, Human, Y↗

PubMed2004

Y-chromosome haplotype analysis in Antioquia (Colombia).

Allele frequencies and haplotype analysis have been performed for eight Y-chromosome STRs (DYS19, DYS385 I and II, DYS389 I and II, DYS390, DYS391, DYS392, DYS393). Population data was obtained from a sample of 400 unrelated individuals living in Antioquia (Colombia). A total of 270 different haplotypes were found, and the haplotype diversity was 0.989. The first and second most frequent haplotypes where shared by 8 and 6% of the individuals, respectively.

Chromosomes, Human, Y↗

PubMed2004

Hierarchical analysis of 30 Y-chromosome SNPs in European populations.

Analysis of Y-chromosome haplogroups defined by binary polymorphisms, has became a standard approach for studying the origin of modern human populations and for measuring the variability between them. Furthermore, the simplicity and population specificity of binary polymorphisms allows inferences to be drawn about the population origin of any male sample of interest for forensic purposes. From the 245 binary polymorphisms that can be analysed by PCR described in the Y Chromosome Consortium tree, we have selected 30 markers. The set of 30 has been grouped into 4 multiplexes in order to determine the most frequent haplogroups in Europe, using only 1 or 2 multiplexes. In this way, we avoid typing unnecessary SNPs to define the final haplogroup saving effort and cost, since we only need to type 9 SNPs in the best case and in the worst case, no more than 17 SNPs to define the haplogroup. The selected method for allele discrimination was a single base extension reaction using the SNaPshot multiplex kit. A total of 292 samples from 8 different districts of Galicia (northwest Spain) were analysed with this strategy. No significant differences were detected among the different districts, except for the population from Marina Lucense, which showed a distant haplogroup frequency but not higher Phi(st) values.

Base Sequence↗

PubMed2004

Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing.

The development of new methodologies for high-throughput SNP analysis is one of the most stimulating areas in genetic research. Here, we describe a rapid and robust assay to simultaneously genotype 17 mitochondrial DNA (mtDNA) coding region SNPs by minisequencing using SNaPshot. SNaPshot is a methodology based on a single base extension of an unlabeled oligonucleotide with labeled dideoxy terminators. The set of SNPs implemented in this multiplexed SNaPshot reaction allow us to allocate common mitochondrial West Eurasian haplotypes into their corresponding branch in the mtDNA skeleton, with special focus on those haplogroups lacking unambiguous diagnostic positions in the first and second hypervariable regions (HVS-I/II; by far, the most common segments analyzed by sequencing). Particularly interesting is the set of SNPs that subdivide haplogroup H; the most frequent haplogroup in Europe (40-50%) and one of the most poorly characterized phylogenetically in the HVS-I/II region. In addition, the polymorphic positions selected for this multiplex reaction increase considerably the discrimination power of current mitochondrial analysis in the forensic field and can also be used as a rapid screening tool prior to full sequencing analysis. The method has been validated in a sample of 266 individuals and shows high accuracy and robustness avoiding both the use of alternative time-consuming classical strategies (i.e. RFLP typing) and the need for high quantities of DNA template.

DNA Primers↗

PubMed2004

Results of a collaborative study of the EDNAP group regarding mitochondrial DNA heteroplasmy and segregation in hair shafts.

A collaborative exercise was carried out by the European DNA Profiling Group (EDNAP) in order to evaluate the distribution of mitochondrial DNA (mtDNA) heteroplasmy amongst the hairs of an individual who displays point heteroplasmy in blood and buccal cells. A second aim of the exercise was to study reproducibility of mtDNA sequencing of hairs between laboratories using differing chemistries, further to the first mtDNA reproducibility study carried out by the EDNAP group. Laboratories were asked to type 2 sections from each of 10 hairs, such that each hair was typed by at least two laboratories. Ten laboratories participated in the study, and a total of 55 hairs were typed. The results showed that the C/T point heteroplasmy observed in blood and buccal cells at position 16234 segregated differentially between hairs, such that some hairs showed only C, others only T and the remainder, C/T heteroplasmy at varying ratios. Additionally, differential segregation of heteroplasmic variants was confirmed in independent extracts at positions 16093 and the poly(C) tract at 302-309, whilst a complete A-G transition was confirmed at position 16129 in one hair. Heteroplasmy was observed at position 16195 on both strands of a single extract from one hair segment, but was not observed in the extracts from any other segment of the same hair. Similarly, heteroplasmy at position 16304 was observed on both strands of a single extract from one hair. Additional variants at positions 73, 249 and the HVII poly(C) region were reported by one laboratory; as these were not confirmed in independent extracts, the possibility of contamination cannot be excluded. Additionally, the electrophoresis and detection equipment used by this laboratory was different to those of the other laboratories, and the discrepancies at position 249 and the HVII poly(C) region appear to be due to reading errors that may be associated with this technology. The results, and their implications for forensic mtDNA typing, are discussed in the light of the biology of hair formation.

DNA, Mitochondrial↗

PubMed2003

Insights into Iberian population origins through the construction of highly informative Y-chromosome haplotypes using biallelic markers, STRs, and the MSY1 minisatellite.

To investigate the diversity of Y chromosomes in the Iberian Peninsula and the North African population of Maghreb, we constructed superhaplotypes on the basis of 10 biallelic markers, 7 microsatellites, and 1 minisatellite located in the nonrecombining portion of the human Y chromosome. The analysis of extremely high MSY1 variability was performed by reducing the MVR-codes to modular structures. Y-STRs and MSY1 data provide information about the relationship between closely related populations such as those of Iberia. Analysis of biallelic markers allowed us to identify 7 of 12 haplogroups defined by those polymorphisms. The haplogroup background showed clear differences between Iberian populations and the North African one. The use of differently mutating Y-chromosome markers allowed us to infer different population events at different time scales: the Paleolithic background of the Iberian Peninsula, the Neolithic fingerprint on Y-chromosome lineages, and the Iron Age influence in the populations of Iberia. Implications of our results for the highly debated origin of Basques are also discussed.

Black People↗

PubMed2001

Fluorescent SSCP of overlapping fragments (FSSCP-OF): a highly sensitive method for the screening of mitochondrial DNA variation.

The mtDNA analysis (mtDNA) is increasingly being demanded for forensic purposes due to the fact that many times the use of standard nuclear marker fails to analyze degraded samples (such as bones) and specially for the analysis of hair shafts (a common sample in the crime scene). However, analysis of mtDNA sequencing implies a great lab effort when a high number of samples must be analyzed. The present work introduces a novel and reliable method for the screening of mtDNA variation in the first and second hypervariables (HV1 and HV2) regions which we have denominated fluorescent single strand conformation polymorphism (SSCP) of overlapping fragments (FSSCP-OF). FSSCP-OF is based on the basic theory of SSCP analysis and combines two complementary strategies: the use of PCR amplified overlapping fragments and fluorescent detection technology. The overlap region contains a high percentage (50%) of the d-loop mtDNA variation and for this reason, the probability to detect a polymorphic position by SSCP analysis is clearly increased in comparison to conventional SSCP methods due to the fact that the same polymorphic position is usually placed in a different "relative" position in the two overlapped fragments. The use of multicolor fluorescent technology allows also the multiplex amplification of overlapping fragment and its subsequent analysis in an automatic sequencer. We have analyzed 50 samples of unrelated individuals through the FSSCP-OF technique and we have found that using this methodology the probability to distinguish two samples with different sequences is close to 100%. FSSCP-OF has other important advantages with respect to previous screening methods, such as the automation and standardization of the protocols, which is of special interest for the forensic routine.

Base Sequence↗

PubMed2001

STR data for the AmpFlSTR profiler plus loci from Macau (China).

Allele frequencies for the nine STRs included in the AmpFlSTR profiler plus kit (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) were estimated from a sample of 87 unrelated individuals living in the region of Macau, a territory located in the southeastern coast of China.

Alleles↗

PubMed2001

Sequence structure of 12 novel Y chromosome microsatellites and PCR amplification strategies.

In this work, we present sequencing data for 12 recently reported Y STR loci (DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, GATA A10, GATA 7.1, GATA 7.2, GATA C4, GATA H4, GATA A4), as well as the PCR multiplex strategies we implemented for their detection. Sequenced allelic ladders were constructed and a nomenclature for these new systems is proposed based on the sequence structure and following ISFG recommendations.GATA A4 and DYS439 are likely the same STR. They have the same STR structure and the alleles are always the same in the same individuals.Sequence polymorphisms were observed in the GATA C4 and DYS437 STRs. The variation in DYS437 was associated with a specific population group and is very interesting not only for forensic genetics but also for anthropological studies.

Alleles↗

PubMed2001

Heteroplasmy in mtDNA and the weight of evidence in forensic mtDNA analysis: a case report.

Mitochondrial DNA (mtDNA) sequencing has been validated as a useful tool for forensic analysis. However, there are several aspects of the analysis which need to be considered in order to evaluate the value of the evidence. One of these aspects is related to heteroplasmy which is the state when two or more mtDNA populations occur in a single individual, cell or mitochondrion. In this report a case is described where the mtDNA profile of the blood sample of a raped woman was compared with the mtDNA profile of a single hair found in the suspect's car. The results obtained show differences in sequence between different portions of the hair and the victim's sequence. These differences are related to various heteroplasmy events. The concordance between the hair sample and the potential source (victim) of this sample is questionable and the strength of the evidence depends on how the sequence information is interpreted by the expert. The discussion of the results emphasises the necessity to evaluate heteroplasmic events in routine forensic work.

DNA, Mitochondrial↗

PubMed2001

Autosomal STR genetic variation in negroid Chocó and Bogotá populations.

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.

Alleles↗

PubMed2000

Alternative primers for DYS391 typing: advantages of their application to forensic genetics.

The amplification of the STR DYS391, using the primers described in the Genome Data Base (GDB: G00-365-251), shows not only an additional band to the Y-specific one in males with a size range of 26 bp less than those of DYS391 locus alleles, but also a polymorphic pattern in females in the same size range as the additional band observed in males. The DYS391 pattern in families reflects a Y-specific linked locus and also a polymorphic X locus with an X-linked pattern of inheritance. A first screening in the X homologous locus allowed the identification of five different alleles. Allele frequencies were explored in different population groups for both the Y locus and the homologous locus in the X chromosome showing a similar allele distribution pattern in the X and Y homologous loci. An alternative reverse primer was designed to amplify the Y-chromosome specific STR in order to improve the specificity and applicability of this system to forensic genetics. Comparative results of the amplification with the new and the previously described primers proved that with this new primer there is a substantial increase in the specificity of the amplification. Moreover, a smaller fragment is amplified with a size out of the range of the alleles of the other Y-STRs usually used in forensic applications, therefore simplifying its inclusion in multiplex systems.

Alleles↗

PubMed2000

Distribution of Y-chromosome STR defined haplotypes in Iberia.

Seven Y-specific STR loci (DYS19, DYS389I, DY5389II, DYS390, DYS391, DYS392 and DYS393) were studied in five populations from the Iberian Peninsula: Andalusia, Valencia, Basque Country, Galicia and Northern Portugal. Haplotype and allele frequencies of these seven Y-chromosome STRs were estimated. Observed haplotype diversities are in a range between 0.96 (Basque Country) and 0.99 (Valencia and Andalusia). Significant population differentiation was registered between Basques and all the other Iberian populations and also between Valencia and Northern Portugal.

Alleles↗

PubMed2000

Sequence variation of two hypervariable short tandem repeats at the D22S683 and D6S477 loci.

For two short tandem repeats at the D22S683 and D6S477 loci, 30 and 22 selected alleles, respectively were sequenced. A total of 20 different alleles were found for the D22S683 locus and 12 alleles for the D6S477 locus. In both systems the alleles were designated according to the total number of repeats. D22S683 is a hypervariable STR consisting of blocks of (TATC) repeats with a basic sequence structure (TATATC)n (TATC)n (ATC)0-1 (TATC)n. The D6S477 locus consists of blocks of (TCTA) repeats with a basic sequence structure (TCTA)n (TA)1 (TCTA)0-2 (TA)0-1 (TCTA)n. Population data showed a heterozygosity of 0.89 for D22S683 and 0.75 for D6S477. These STRs are promising markers for forensic genetics as they are robust and can be easily included in multiplexes.

Alleles↗

PubMed2000

Genetic variability at nine STR loci in the Chueta (Majorcan Jews) and the Balearic populations investigated by a single multiplex reaction.

A study of the genetic variability in the Chueta (Majorcan Jews) and the Balearic (Majorca and Minorca Islands) populations was carried out using a multiplex system containing the nine tetrameric STRs D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820. The Chueta population has remained isolated because intermarriage with non-Jews did not take place until the middle of this century, which has resulted in it being a small inbred community. The results indicate the existence of HW equilibrium for the Chueta and Balearic populations. No pair-wise correlation was observed between the nine markers. Consequently, they seem to comprise a suitable group of markers for population genetics purposes and for paternity and forensic testing.

DNA↗

PubMed2000

Genetic diversity of nine STRs in two northwest Iberian populations: Galicia and northern Portugal.

The genotyping of two population samples from Galicia and northern Portugal was performed for nine STR loci using a single multiplex reaction with the AmpF/STR Profiler Plus PCR amplification kit which co-amplifies the systems D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820 and the XY homologous gene amelogenin. Allele frequencies for these nine tetranucleotide repeat markers were calculated and no significant differences were observed when comparing these two populations. Conformity with Hardy-Weinberg equilibrium proportions was good for all systems in both samples. The combined power of exclusion was 99.981% and 99.980% in Galicia and northern Portugal, respectively and the combined power of discrimination was greater than 99.999%. Segregation analysis of all loci detected two incompatibilities, one in D3S1358 (out of 112 meioses) and another in D7S820 (out of 104 meioses). Both could be explained by single-step mutations. In general co-amplification was good except for some relatively degraded samples in which poor amplification was observed for the largest STRs. Nevertheless the system is technically robust even when small amounts of template DNA are used and in the addition is highly informative and time-saving. However, caution should be taken in the interpretation of profiles in degraded samples and the apparently high mutation rate of D3S1358 and D7S820 should also be kept in mind.

Adult↗

PubMed2000

Ethical-legal problems of DNA databases in criminal investigation.

Advances in DNA technology and the discovery of DNA polymorphisms have permitted the creation of DNA databases of individuals for the purpose of criminal investigation. Many ethical and legal problems arise in the preparation of a DNA database, and these problems are especially important when one analyses the legal regulations on the subject. In this paper three main groups of possibilities, three systems, are analysed in relation to databases. The first system is based on a general analysis of the population; the second one is based on the taking of samples for a particular list of crimes, and a third is based only on the specific analysis of each case. The advantages and disadvantages of each system are compared and controversial issues are then examined. We found the second system to be the best choice for Spain and other European countries with a similar tradition when we weighed the rights of an individual against the public's interest in the prosecution of a crime.

Civil Rights↗

PubMed2000

[Retinitis pigmentosa: results of rhodopsin gene analysis in the Galician population].

PURPOSE: Retinitis pigmentosa (RP) is the most prevalent inherited degeneration in the retina. The clinical manifestations are variable in terms of severity, age of onset and progression. The clinical variation is paralleled by genetic heterogeneity (more than 20 different loci have been described to date). The aim of this work was to identify mutations in rhodopsin gene and to determine the frequencies of the different genetic forms of RP in the Galician population. METHODS: 47 previously diagnosed RP patients and their relatives were studied. Genetic forms of RP were identified by recording full family history and clinical examination. DNA samples from patients with RP and control individuals were screened for point mutations in the rhodopsin gene by using PCR SSCPs (Single Strand Conformation Polymorphisms) and direct sequencing in 36 unrelated nonsyndromic RP patients. RESULTS: We report the frequency distribution of the different genetic RP forms. In the SSCPs analysis of rhodopsin gene we found different mobility shifts: one variant in the 5'-untranslated region of the gen and one variant in the third intron. Direct sequencing revealed an A269-->G and an C3982-->T transitions, respectively. Additionally, we observed a single base change in codon 160 (C-->A) of this gene. CONCLUSIONS: Polymorphisms are commom findings in the exon 1 and 3 of rhodopsin gene. They are neutral variations and do not represent a change in the protein. No significant differences in the frecuencies of A269-->G and C3982-->T polymorphisms among the three groups of RP patients (ADRP, ARRP, Esporadic RP) and normal individuals were found. There was no significant deviation from Hardy-Weinberg's equilibrium in each genotype in any group.

Adolescent↗