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Biomedical subjects

A Carracedo

Publications and source records attributed to A Carracedo.

At least 55 records · Page 3Linked to original sources
PubMed2001

The R71G BRCA1 is a founder Spanish mutation and leads to aberrant splicing of the transcript.

In a BRCA1 screening in familial breast cancer carried out in different centres in Spain, France, and United Kingdom, a missense mutation 330A>G which results in a Arg to Gly change at codon 71 (R71G) was independently identified in 6 families, all of them with Spanish ancestors. This residue coincides with the -2 position of the exon 5 donor splice site. We further investigated the effect of this base substitution on the splicing of BRCA1 mRNA. The sequence analysis of the cDNA indicated that 22 bp of exon 5 were deleted, creating with the first bases of exon 6 a termination codon at position 64, which results in a truncated protein. The BRCA1 haplotype of the R71G carrier patients and Spanish controls was analysed by use of six microsatellites located within or near BRCA1. Our results are consistent with the possibility that these families shared a common ancestry with BRCA1 R71G being a founder mutation of Spanish origin.

Age of Onset↗
PubMed2001

Mutation analysis of the adenomatous polyposis coli (APC) gene in northwest Spanish patients with familial adenomatous polyposis (FAP) and sporadic colorectal cancer.

Germline mutations in the tumor-suppresor APC gene are associated with hereditary familial adenomatous polyposis (FAP) and somatic mutations are common in sporadic colorectal cancer. In this study, we report the identification of three novel germline mutations: 1682-1683insA, 3252-3253insAT, 3544A>T and a new somatic mutation 4130-4131delTT, all giving rise to truncated APC proteins. The majority of the mutations we found originate a truncated APC protein and cause the FAP phenotype. However, special attention must be given to the missense mutations Asp1822Val and Ser2621Cys since their segregation with the FAP phenotype is questionable. In our FAP families we did not find any genetical alterations at codon 1309, being this mutation the most frequent reported in APC. Differences in the recurrence of pathological mutations in APC could exist among populations. However, epidemiological studies must be performed to confirm this hypothesis.

Adenomatous Polyposis Coli↗
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↗
PubMed2001

DNA commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs.

During the past few years the DNA commission of the International Society of Forensic Genetics has published a series of documents providing guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. This latest report addresses a relatively new area, namely Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). This report addresses nomenclature, use of allelic ladders, population genetics and reporting methods.

Alleles↗
PubMed2001

Length variability and interspersion patterns of the HRAS1 minisatellite: a new approach for the reconstruction of human population relationships.

During recent years the HRAS1 minisatellite has been analysed by several authors because of its putative association with cancer susceptibility. The aim of this report is to test the usefulness of this minisatellite in investigating human population relationships. We have studied 370 chromosomes from two well-differentiated populations: Galicia (North-west Iberia) and South-east Africa, as well as available data on allele length gene frequencies. The fragment analysis results show a strong tendency to differentiate between non-African and African populations. In spite of the usefulness of fragment analysis, the minisatellite variant repeat (MVR) approach of the HRAS1 minisatellite appears to be a more powerful method for use in human population studies, due to the high level of diversity of its interspersion pattern structures. In addition, this approach has allowed us to define some new structural characteristics of this minisatellite. Four different major groups of human HRAS1 minisatellite alleles could be distinguished following a structural criterion based on the MVR code. Furthermore, the characterisation of the HRAS1 minisatellite in chimpanzees revealed clear differences when compared to humans, not only with respect to the allele size but also to the internal structure.

Africa, Southern↗
PubMed2001

Identification of Mycobacterium marinum in sea-urchin granulomas.

BACKGROUND: Sea-urchin granuloma is a chronic granulomatous reaction arising after injury with sea-urchin spines. Classified as an allergic foreign-body type of granuloma, it is believed to be a delayed-type reaction to an as yet unidentified antigen. In a clinicopathological study, 50 biopsy specimens from 35 patients diagnosed as having sea-urchin granuloma caused by Paracentrotus lividus, we found different inflammatory patterns that in some cases suggested a mycobacterial infection. OBJECTIVES: To investigate and identify mycobacterial DNA in formalin-fixed and paraffin-embedded skin biopsy specimens diagnosed as sea-urchin granulomas. METHODS: A search combining polymerase chain reaction amplification using Mycobacterium genus-specific primers, and subsequent restriction enzyme analysis enabling identification to the species level, was performed in 41 samples. RESULTS: Amplification of a 924-bp DNA fragment encoding mycobacterial 16S rRNA gene was positive in eight biopsy specimens from seven patients (21%). M. marinum-specific restriction patterns were identified in three samples. CONCLUSIONS: Although further controlled studies are necessary, from these data it would appear that mycobacteria may play a pathogenic role in some cases of sea-urchin granuloma.

Adolescent↗
PubMed2000

The 1998-1999 collaborative exercises and proficiency testing program on DNA typing of the Spanish and Portuguese Working Group of the International Society for Forensic Genetics (GEP-ISFG).

A total of 28 laboratories (labs) submitted results for the 1998 collaborative exercise and the proficiency testing program of the Spanish and Portuguese Working Group of the International Society for Forensic Genetics (GEP-ISFG) group. This number increased to 46 labs in 1999. Six bloodstains were submitted, each one with 200 microl soaked in cotton except the sample no. 6 submitted for DNA quantification which had 2 microl. One of the samples was a mixed stain. A paternity testing case and a criminal case in the 1998 trial (GEP'98) and two paternity testing cases in 1999 (GEP'99) were included and the statistical evaluation of the evidence was requested in both cases. In the GEP'99 trial, a theoretical paternity testing case was included. A total of 52 DNA genetic markers were used by the participants in the GEP'98 trial, which increased to 101 in GEP'99. Despite this increasing number of participating labs, results remained quite satisfactory. All the labs used PCR-based DNA polymorphisms with an increasing number of markers, obtaining good results. SLPs were used by a decreasing number of labs but the results indicated a good level of expertise despite the different protocols used. Good results were also obtained for mtDNA despite the difficulties presented by the samples due to the presence of length heteroplasmy in some samples in both trials. The detection of heteroplasmy should, however, be improved. Similar conclusions were reached for both, the paternity and the criminal case by all the labs. Common methodologies for the statistical evaluation of the paternity case were used and the paternity index and the probability of paternity (with an a priori value of 0.5) reported by most of the labs. Also, a great uniformity was found in the evaluation of the criminal case despite the lack of a specific hypothesis in the design of the exercise. Some errors in statistical programs or in calculations were detected in a theoretical paternity case included in the GEP'99 trial for statistical analysis.

Clinical Laboratory Techniques↗
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

Assessing microsatellite instability with semiautomated fluorescent technology: application to the analysis of primary brain tumors.

The replication error phenotype, revealed by the observation of widespread microsatellite instability (MIN), has been identified as a new mechanism of cancer susceptibility, and the comparison of the allele sizes of polymorphic microsatellite repeats between normal and tumor DNA is now frequently undertaken in colorectal and other human neoplasias. The lack of precise characterization of the electrophoretic profiles of microsatellites is one of the main sources of discord between the rate of MIN reported for the same type of tumor by different investigators. The recent introduction of fluorescent-based semiautomated microsatellite analysis allows a more accurate size comparison, but one or more artificial peaks, generated during polymerase chain reaction (PCR) and/or electrophoresis, are frequently detected along with the true allele peaks. The aim of this study was to characterize the most frequent artificial extra peaks in the short tandem repeats (STRs) used by us to assess MIN in human cancers. We analyzed eight microsatellite loci in 113 primary brain tumors. HumFibra/FGA exhibited the most frequent extra peak formation. For each microsatellite there is a characteristic pattern of artifact formation which must be recognized to avoid a false-positive diagnosis of MIN.

Automation↗
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↗