Haplotype tagging efficiency and tagSNP sets portability in worldwide populations in NAT2 gene
Genetic polymorphism in the NAT2 gene is responsible for pronounced interindividual differences in the acetylation activity of the N-acetyltransferase 2 (NAT2) enzyme, which plays a crucial role in the metabolism of many clinically useful drugs and exogenous chemicals. Up to now, most association st...
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| Format: | Article |
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Société d'Anthropologie de Paris
2007-12-01
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| Series: | Bulletins et Mémoires de la Société d’Anthropologie de Paris |
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| Online Access: | https://journals.openedition.org/bmsap/5223 |
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| author | Audrey Sabbagh Pierre Darlu André Langaney Estella S. Poloni |
| author_facet | Audrey Sabbagh Pierre Darlu André Langaney Estella S. Poloni |
| author_sort | Audrey Sabbagh |
| collection | DOAJ |
| description | Genetic polymorphism in the NAT2 gene is responsible for pronounced interindividual differences in the acetylation activity of the N-acetyltransferase 2 (NAT2) enzyme, which plays a crucial role in the metabolism of many clinically useful drugs and exogenous chemicals. Up to now, most association studies that have attempted to relate the acetylation phenotype in NAT2 to a variety of complex human disorders have led to contradictory results in different populations. Some of these inconsistencies may result from a poor knowledge of linkage patterns at NAT2 and their geographic variation. Using data from an extensive survey of the literature, we investigated the worldwide haplotype diversity and linkage disequilibrium structure of NAT2. For 28 population samples (including 3,994 individuals) from four continental regions (Africa, Europe, Asia, America), we evaluated haplotype tagging efficiency at NAT2 and defined population-specific sets of haplotype tagging SNPs (htSNPs) to be used for future association studies. Tagging common haplotypes yielded 2- to 3-fold savings in European and East Asian samples, while no gains from tagging were observed in samples of African ancestry, which displayed high haplotype diversity at NAT2. htSNPs sets appeared to be portable among populations from a same continent, provided that the continent-specific htSNPs sets were selected with a stringent criterion. A “cosmopolitan” htSNPs set suitable for all human populations could not be identified for the NAT2 gene, but a single four-htSNP set proved to perform successfully in all the non-African populations investigated. |
| format | Article |
| id | doaj-art-3188148305054cb5b8b153f64f06de33 |
| institution | Kabale University |
| issn | 1777-5469 |
| language | English |
| publishDate | 2007-12-01 |
| publisher | Société d'Anthropologie de Paris |
| record_format | Article |
| series | Bulletins et Mémoires de la Société d’Anthropologie de Paris |
| spelling | doaj-art-3188148305054cb5b8b153f64f06de332025-01-30T11:27:40ZengSociété d'Anthropologie de ParisBulletins et Mémoires de la Société d’Anthropologie de Paris1777-54692007-12-0119423324110.4000/bmsap.5223Haplotype tagging efficiency and tagSNP sets portability in worldwide populations in NAT2 geneAudrey SabbaghPierre DarluAndré LanganeyEstella S. PoloniGenetic polymorphism in the NAT2 gene is responsible for pronounced interindividual differences in the acetylation activity of the N-acetyltransferase 2 (NAT2) enzyme, which plays a crucial role in the metabolism of many clinically useful drugs and exogenous chemicals. Up to now, most association studies that have attempted to relate the acetylation phenotype in NAT2 to a variety of complex human disorders have led to contradictory results in different populations. Some of these inconsistencies may result from a poor knowledge of linkage patterns at NAT2 and their geographic variation. Using data from an extensive survey of the literature, we investigated the worldwide haplotype diversity and linkage disequilibrium structure of NAT2. For 28 population samples (including 3,994 individuals) from four continental regions (Africa, Europe, Asia, America), we evaluated haplotype tagging efficiency at NAT2 and defined population-specific sets of haplotype tagging SNPs (htSNPs) to be used for future association studies. Tagging common haplotypes yielded 2- to 3-fold savings in European and East Asian samples, while no gains from tagging were observed in samples of African ancestry, which displayed high haplotype diversity at NAT2. htSNPs sets appeared to be portable among populations from a same continent, provided that the continent-specific htSNPs sets were selected with a stringent criterion. A “cosmopolitan” htSNPs set suitable for all human populations could not be identified for the NAT2 gene, but a single four-htSNP set proved to perform successfully in all the non-African populations investigated.https://journals.openedition.org/bmsap/5223association studieslinkage disequilibriumhaplotype taggingpopulation geneticsNAT2 |
| spellingShingle | Audrey Sabbagh Pierre Darlu André Langaney Estella S. Poloni Haplotype tagging efficiency and tagSNP sets portability in worldwide populations in NAT2 gene Bulletins et Mémoires de la Société d’Anthropologie de Paris association studies linkage disequilibrium haplotype tagging population genetics NAT2 |
| title | Haplotype tagging efficiency and tagSNP sets portability in worldwide populations in NAT2 gene |
| title_full | Haplotype tagging efficiency and tagSNP sets portability in worldwide populations in NAT2 gene |
| title_fullStr | Haplotype tagging efficiency and tagSNP sets portability in worldwide populations in NAT2 gene |
| title_full_unstemmed | Haplotype tagging efficiency and tagSNP sets portability in worldwide populations in NAT2 gene |
| title_short | Haplotype tagging efficiency and tagSNP sets portability in worldwide populations in NAT2 gene |
| title_sort | haplotype tagging efficiency and tagsnp sets portability in worldwide populations in nat2 gene |
| topic | association studies linkage disequilibrium haplotype tagging population genetics NAT2 |
| url | https://journals.openedition.org/bmsap/5223 |
| work_keys_str_mv | AT audreysabbagh haplotypetaggingefficiencyandtagsnpsetsportabilityinworldwidepopulationsinnat2gene AT pierredarlu haplotypetaggingefficiencyandtagsnpsetsportabilityinworldwidepopulationsinnat2gene AT andrelanganey haplotypetaggingefficiencyandtagsnpsetsportabilityinworldwidepopulationsinnat2gene AT estellaspoloni haplotypetaggingefficiencyandtagsnpsetsportabilityinworldwidepopulationsinnat2gene |