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Cymbron T, Mendes P, Ramos A, Raposo M, Kazachkova N, Medeiros AM, Bruges-Armas J, Bourbon M, Lima M. Familial hypercholesterolemia: Molecular characterization of possible cases from the Azores Islands (Portugal). Meta Gene 2014; 2:638-45. [PMID: 25606447 PMCID: PMC4287853 DOI: 10.1016/j.mgene.2014.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/30/2014] [Accepted: 08/15/2014] [Indexed: 01/17/2023] Open
Abstract
Familial hypercholesterolemia (FH) is an autosomal dominant disorder of the cholesterol metabolism, which constitutes a risk factor for coronary arterial disease (CAD). In the Azores Islands (Portugal), where mortality from CAD doubles its rate comparatively to the rest of the country and where a high frequency of dyslipidemia has been reported, the prevalence and distribution of FH remain unknown. The molecular characterization of a group of 33 possible cases of FH of Azorean background was undertaken in this study. A DNA array was initially used to search mutations in the LDLR, APOB and PCSK9 loci in 10 unrelated possible cases of FH. No mutations were detected in the array; after sequencing the full LDLR gene, 18 variants were identified, corresponding to two missense (c.806G > A; c.1171G > A) and sixteen synonymous alterations. Six of the synonymous variants which are consistently described in the literature as associated with altered cholesterol levels were used to build haplotypes. The most frequent haplotype corresponded to TTCGCC (45%), a “risk” haplotype, formed exclusively by alleles that were reported to increase cholesterol levels. Some of the variants detected in the full sequencing of the LDLR gene fell within the ligand-binding domain of this gene, defined by exons 2 to 6. To add information as to the role of such variants, these exons were sequenced in the remaining 23 possible FH cases. Two missense alterations (c.185C > T; c.806G > A) were found in this subset of possible FH cases. The missense alteration c.185C > T, identified in one individual, is novel for the Portuguese population. In silico analysis was not conclusive for this alteration, whose role will have to be further investigated. This study represents the first approach to the establishment of the mutational profile of FH in the Azores Islands.
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Affiliation(s)
- Teresa Cymbron
- Centre of Research in Natural Resources (CIRN), Department of Biology, University of the Azores, 9501-801 Ponta Delgada, Azores, Portugal ; Institute for Molecular and Cell Biology (IBMC), University of Porto, 4150-180 Porto, Portugal
| | - Patrícia Mendes
- The Azores School of New Technologies (ENTA), 9504-540 Ponta Delgada, Azores, Portugal
| | - Amanda Ramos
- Centre of Research in Natural Resources (CIRN), Department of Biology, University of the Azores, 9501-801 Ponta Delgada, Azores, Portugal ; Institute for Molecular and Cell Biology (IBMC), University of Porto, 4150-180 Porto, Portugal
| | - Mafalda Raposo
- Centre of Research in Natural Resources (CIRN), Department of Biology, University of the Azores, 9501-801 Ponta Delgada, Azores, Portugal ; Institute for Molecular and Cell Biology (IBMC), University of Porto, 4150-180 Porto, Portugal
| | - Nadiya Kazachkova
- Centre of Research in Natural Resources (CIRN), Department of Biology, University of the Azores, 9501-801 Ponta Delgada, Azores, Portugal ; Institute for Molecular and Cell Biology (IBMC), University of Porto, 4150-180 Porto, Portugal
| | - Ana Margarida Medeiros
- Grupo de Investigação Cardiovascular, Unidade I&D, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Dr. Ricardo Jorge, 1649-040 Lisboa, Portugal ; Centre for Biodiversity, Functional and Integrative Genomics (BioFIG), Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Jácome Bruges-Armas
- Institute for Molecular and Cell Biology (IBMC), University of Porto, 4150-180 Porto, Portugal ; Specialized Service of Epidemiology and Molecular Biology (SEEBMO), Hospital of Santo Espírito, 9700-049 Angra do Heroísmo, Azores, Portugal
| | - Mafalda Bourbon
- Grupo de Investigação Cardiovascular, Unidade I&D, Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Dr. Ricardo Jorge, 1649-040 Lisboa, Portugal ; Centre for Biodiversity, Functional and Integrative Genomics (BioFIG), Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Manuela Lima
- Centre of Research in Natural Resources (CIRN), Department of Biology, University of the Azores, 9501-801 Ponta Delgada, Azores, Portugal ; Institute for Molecular and Cell Biology (IBMC), University of Porto, 4150-180 Porto, Portugal
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Pacheco PR, Branco CC, Gomes CT, Cabral R, Mota-Vieira L. HLA Class I and II profiles in São Miguel Island (Azores): genetic diversity and linkage disequilibrium. BMC Res Notes 2010; 3:134. [PMID: 20462405 PMCID: PMC2883542 DOI: 10.1186/1756-0500-3-134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 05/12/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human leukocyte antigen (HLA) genes are characterized by high levels of polymorphism and linkage disequilibrium (LD), important characteristics to study the genetic background of human populations and their genetic structure. Here, we analyse the allele distribution and LD extent of HLA class I and II in São Miguel Island population (Azores archipelago, Portugal). FINDINGS The sample set was composed of 106 healthy blood donors living in São Miguel Island obtained from the anonymized Azorean DNA bank. HLA class I (-A, -B and -Cw) and class II (-DRB1, -DQB1, -DPA1 and -DPB1) genotyping was performed by PCR-SSP Olerup SSP (GenoVision Inc.), according to the manufacturer's instructions.Genetic diversity values, based on the 7 loci, ranged from 0.821 both for HLA-DPA1 and -DQB1 to 0.934 for HLA-B, with a mean value of 0.846. Analysis of 5 HLA-A-Cw-B-DRB1-DQB1 haplotypes revealed that A*01-Cw*07-B*08-DRB1*03-DQB1*02 is the most frequent in São Miguel (7.9%) followed by A*24-B*08-Cw*07-DRB1*03-DQB1*02 (3.8%). In addition, even though the reports of high LD for HLA markers in worldwide populations, São Miguel islanders do not have extensive LD (average D' = 0.285). CONCLUSIONS In summary, the results demonstrate high variability of HLA in São Miguel Island population as well as absence of genetic structure and extensive LD. The data here presented suggest that in São Miguel islanders autoimmune diseases studies will necessarily encompass a more focused analysis of HLA extended haplotypes as well as the evaluation of other non-HLA candidate genes.
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Affiliation(s)
- Paula R Pacheco
- Molecular Genetics and Pathology Unit, Hospital of Divino Espírito Santo of Ponta Delgada, EPE, São Miguel Island, Azores, Portugal.
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Branco CC, Pacheco PR, Cabrol E, Cabral R, Vicente AM, Mota-Vieira L. Linkage disequilibrium and diversity for three genomic regions in Azoreans and mainland Portuguese. Genet Mol Biol 2009; 32:220-6. [PMID: 21637671 PMCID: PMC3036928 DOI: 10.1590/s1415-47572009000200003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 01/02/2009] [Indexed: 11/22/2022] Open
Abstract
Studies on linkage disequilibrium (LD) across the genome and populations have been used in recent years with the main objective of improving gene mapping of complex traits. Here, we characterize the patterns of genetic diversity of HLA loci and evaluate LD (D') extent in three genomic regions: Xq13.3, NRY and HLA. In addition, we examine the distribution of DXS1225-DXS8082 haplotype diversity in Azoreans and mainland Portuguese. Allele distribution has demonstrated that the São Miguel population is genetically very diverse; haplotype analysis revealed 100% discriminatory power for X- and Y-markers and 94.3% for HLA markers. Standardized multiallelic D' in these three genomic regions shows values lower than 0.33, thereby suggesting there is no extensive LD in the São Miguel population. Data regarding the distribution of DXS1225-DXS8082 haplotypes indicate that there are no significant differences among all the populations studied, (Azorean geographical groups, the Azores archipelago and mainland Portugal). Moreover, in these as well as in other European populations, the most frequent DXS1225-DXS8082 haplotype is 210-219. Even though São Miguel islanders and Azoreans do not constitute isolated populations and show LD for only very short physical distances, certain characteristics, such as the absence of genetic structure, the same environment and the possibility of constructing extensive pedigrees through church and civil records, offer an opportunity for dissecting the genetic background of complex diseases in these populations.
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Affiliation(s)
- Claudia C Branco
- Molecular Genetics and Pathology Unit, Hospital of Divino Espírito Santo of Ponta Delgada, São Miguel Island, Azores Portugal
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Guerreiro-Junior V, Bisso-Machado R, Marrero A, Hünemeier T, Salzano FM, Bortolini MC. Genetic signatures of parental contribution in black and white populations in Brazil. Genet Mol Biol 2009; 32:1-11. [PMID: 21637639 PMCID: PMC3032968 DOI: 10.1590/s1415-47572009005000001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 05/14/2008] [Indexed: 12/02/2022] Open
Abstract
Two hundred and three individuals classified as white were tested for 11 single nucleotide polymorphisms plus two insertion/deletions in their Y-chromosomes. A subset of these individuals (n = 172) was also screened for sequences in the first hypervariable segment of their mitochondrial DNA (mtDNA). In addition, complementary studies were done for 11 of the 13 markers indicated above in 54 of 107 black subjects previously investigated in this southern Brazilian population. The prevalence of Y-chromosome haplogroups among whites was similar to that found in the Azores (Portugal) or Spain, but not to that of other European countries. About half of the European or African mtDNA haplogroups of these individuals were related to their places of origin, but not their Amerindian counterparts. Persons classified in these two categories of skin color and related morphological traits showed distinct genomic ancestries through the country. These findings emphasize the need to consider in Brazil, despite some general trends, a notable heterogeneity in the pattern of admixture dynamics within and between populations/groups.
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Affiliation(s)
- Vanderlei Guerreiro-Junior
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS Brazil
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