-
[show abstract]
[hide abstract]
ABSTRACT: The characterization of Y chromosome haplogroups is currently done by genotyping SNPs and a few InDels. However, InDels are increasingly gaining importance, so the aim of this work was to create an InDel PCR multiplex allowing a fast, simple and straightforward characterization of the main Y-haplogroups. For this, we have selected the InDels already accepted by the Y Chromosome Consortium. However, due to their position in the Y chromosome phylogenetic tree, they only allow classifying chromosomes from 6 of the 20 main Y haplogroups. Thus, we have extended the search to already described and validated InDels in dbSNP and MGS. All 154 InDels retrieved from that search were subjected to multiple screenings and just 10 were found to be new, potentially polymorphic and Y specific. Their typing in samples for 13 distinct haplogroups confirmed only 2 polymorphisms (named M2 and M14). M2 is polymorphic in R haplogroup but it also shows a reversion within the R1b1b2 sub-haplogroup. Therefore, it is not recommended for the characterization and distinction between R and the other haplogroups. M14 shows variation in R and Q and so it can be used to identify samples belonging to the paragroup P, which was not possible before using the InDels in the phylogenetic tree of the Y Chromosome Consortium. The detailed analysis of all the available information allowed us to conclude that the creation of the aimed multiplex will only be possible with the detection and phylogenetic characterization of new InDels.
24th International ISFG Congress; 12/2011
-
Ana Peixoto,
Catarina Santos,
Manuela Pinheiro,
Pedro Pinto,
Maria José Soares,
Patrícia Rocha, Leonor Gusmão,
António Amorim,
Annemarie van der Hout,
Anne-Marie Gerdes, [......],
Alberto Gulino,
Maria I Achatz,
Dirce M Carraro,
Brigitte Bressac de Paillerets,
Audrey Remenieras,
Cindy Benson,
Silvia Casadei,
Mary-Claire King,
Erik Teugels,
Manuel R Teixeira
[show abstract]
[hide abstract]
ABSTRACT: The c.156_157insAlu BRCA2 mutation has so far only been reported in hereditary breast/ovarian cancer (HBOC) families of Portuguese origin. Since this mutation is not detectable using the commonly used screening methodologies and must be specifically sought, we screened for this rearrangement in a total of 5,443 suspected HBOC families from several countries. Whereas the c.156_157insAlu BRCA2 mutation was detected in 11 of 149 suspected HBOC families from Portugal, representing 37.9% of all deleterious mutations, in other countries it was detected only in one proband living in France and in four individuals requesting predictive testing living in France and in the USA, all being Portuguese immigrants. After performing an extensive haplotype study in carrier families, we estimate that this founder mutation occurred 558 ± 215 years ago. We further demonstrate significant quantitative differences regarding the production of the BRCA2 full length RNA and the transcript lacking exon 3 in c.156_157insAlu BRCA2 mutation carriers and in controls. The cumulative incidence of breast cancer in carriers did not differ from that of other BRCA2 and BRCA1 pathogenic mutations. We recommend that all suspected HBOC families from Portugal or with Portuguese ancestry are specifically tested for this rearrangement.
Breast Cancer Research and Treatment 06/2011; 127(3):671-9. · 4.43 Impact Factor
-
Ana Peixoto,
Catarina Santos,
Patrícia Rocha,
Manuela Pinheiro,
Sofia Príncipe,
Deolinda Pereira,
Helena Rodrigues,
Fernando Castro,
Joaquim Abreu, Leonor Gusmão,
António Amorim,
Manuel R Teixeira
[show abstract]
[hide abstract]
ABSTRACT: We evaluated the contribution of an Alu insertion in BRCA2 exon 3 (c.156_157insAlu) to inherited predisposition to breast/ovarian cancer in 208 families originated mostly from northern/central Portugal. We identified the c.156_157insAlu BRCA2 mutation in 14 families and showed that it accounts for more that one-fourth of deleterious BRCA1/BRCA2 mutations in breast/ovarian cancer families originated from this part of the country. This mutation originates BRCA2 exon 3 skipping and we demonstrated its pathogenic effect by showing that the BRCA2 full length transcript is derived only from the wild type allele in carriers, that it is absent in 262 chromosomes from healthy blood donors, and that it co-segregates with the disease. Polymorphic microsatellite markers were used for haplotype analysis in three informative families. In two of the three families one haplotype was shared for all but two markers, whereas in the third family all markers telomeric to BRCA2 differed from that observed in the other two. Although the c.156_157insAlu BRCA2 mutation has so far only been identified in Portuguese breast/ovarian cancer families, screening of this rearrangement in other populations will allow evaluation of whether or not it is a population-specific founder mutation and a more accurate estimation of its distribution and age.
Breast Cancer Research and Treatment 04/2008; 114(1):31-8. · 4.43 Impact Factor
-
Ana Peixoto,
Catarina Santos,
Manuela Pinheiro,
Pedro Pinto,
Maria José Soares,
Patrícia Rocha, Leonor Gusmão,
António Amorim,
Annemarie Van Der Hout,
Anne-Marie Gerdes, [......],
Alberto Gulino,
Maria I Achatz,
Dirce M Carraro,
Brigitte Bressac-De Paillerets,
Audrey Remenieras,
Cindy Benson,
Silvia Casadei,
Mary-Claire King,
Erik Teugels,
Manuel R Teixeira
-
[show abstract]
[hide abstract]
ABSTRACT: Canine genotyping is demanded in a vast range of situations that more commonly include pedigree verification, parentage and forensic investigations, and population structure, genetic origin and diversity studies. We developed a PCR multiplex that performs consistently up to the standards required for forensic and population analysis. Primers were designed for co-amplification of 9 tetra-nucleotide STR loci in an optimized PCR reaction for fragment size detection in automated capillary electrophoresis. The system includes FH3210, FH3241, FH2004, FH2658, FH4012, REN214L11, FH2010, FH2361 loci (on chromosomes 2, 8, 11, 14, 15, 16, 24 and 33, respectively) and a newly described locus on chromosome 38. Forensic parameters were calculated based on genotyping results obtained in a case-study population. This PCR multiplex for canine genotyping presented robustness and reproducibility of results.
Forensic Science International Genetics Supplement Series 1(1):628-629.
-
[show abstract]
[hide abstract]
ABSTRACT: Microbial community profiling is an important issue for microbial forensics. Some works support a large-scale dispersion of microbes and weak or absent biogeography, while others report the existence of endemic strains. Fungi have recently been used for soil discriminatory and definition of specific ecosystems. The advent of large-scale genotyping studies on fungal populations may provide a unique opportunity to compare genetic diversity within and among populations.In this work, we studied the pathogenic mould Aspergillus fumigatus that is frequently associated to several human disorders. A set of clinical and environmental isolates of A. fumigatus from Hospital S. João (Porto, Portugal) was tested, in addition to another group from other Portuguese and American Hospitals. A. fumigatus isolates were genotyped using a microsatellite-based single-multiplex PCR with eight short tandem repeat markers and a single nucleotide polymorphism (SNP).This SNP could split A. fumigatus population in two groups: 357 isolates with an additional nucleotide A and 55 isolates without this base insertion. The smallest group, comprising 27 genotypes, contained exclusively strains from Hospital S. João. The occurrence of microvariation events (strains differing in a single marker) was very common among environmental isolates. A larger study including more strains from diverse locations may improve the categorisation of local/regional strains. Additionally, the inclusion of more SNPs for A. fumigatus genotyping will improve the characterisation of A. fumigatus population.
Forensic Science International Genetics Supplement Series 2(1):297-299.
-
[show abstract]
[hide abstract]
ABSTRACT: Sickle cell anemia (HBB*S) and glucose-6-phosphatedehydrogenase (G6PD) deficiency, present a clinal distribution in Portugal, being more frequent in the South and showing foci of high prevalence in some places from Alentejo such as Coruche and Pias. Since the reconstruction of the evolutionary history of G6PD deficiency alleles and HBB*S lead to conclude that Sub-Saharan Africa was the place of origin of many of them, it is likely that at least some were introduced in Alentejo by Sub-Saharan individuals whose presence in the region is known to have had considerable demographic impact. To evaluate the male mediated Sub-Saharan influence in present-day populations from Coruche and Pias, we have performed a high resolution analysis of 16 Y-STRs and 23 Y-SNPs in 91 males from Coruche and 54 from Pias. The results showed the absence of haplogroups of Sub-Saharan origin and a Y-chromosome composition basically not differing from those previously reported for other Portuguese mainland regions. Therefore, from the forensic point of view the studied populations can be dealt without special concerns.
Forensic Science International Genetics Supplement Series 1(1):208-209.
