Association of the C-type lectin-like domain family-16A (CLEC16A) gene polymorphisms with acute coronary syndrome in Mexican patients

Vargas‐Alarcón, Gilberto; Ramírez‐Bello, Julián; Angeles-Martínez, Javier; Rodrı́guez-Pérez, José Manuel; Pérez-Hernández, Nonanzit; Posadas‐Romero, Carlos; Jorge‐Galarza, Esteban; Ocampo-Arcos, Wendy Angélica; Obil-Chavarria, Claudia; Fragoso, José Manuel

doi:10.1016/j.imlet.2014.10.003

Cited by 1 publication

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“…SNP rs6498115 lies within prominent H3Kme1 and H3K27Ac marks defined by seven ENCODE cell lines (http://genome.ucsc.edu; last accessed October 16, 2016) and in four of the seven, these marks lie in regions predicted to have strong enhancement (53/125 cell lines also demonstrate DNase hypersensitivity). As shown in supplementary figure S3, Supplementary Material online, two SNPs in the NHGRI genome-wide association study catalog fall within this interval (Welter et al 2014), rs4781011 within the CIITA gene, from a secondary analysis in a case–control association study of ulcerative colitis in Europeans (McGovern et al 2010), and rs6498142 within the neighboring CLEC16A gene, from a case–control association analysis of acute coronary syndrome in Mexican Americans (Vargas-Alarcon et al 2014). The other SNPs in table 4 within the CIITA linkage disequilibrium region were rs35346036 (within 100 kb of CIITA ); rs45601437 ( CIITA intron); rs77979769 (within 10 kb 3′ of SOCS1 ); rs2021760 (within 10 kb 3′ of SOCS1 ); rs8054781 (within 10 kb 3′ of PRM1 ).…”

Section: Resultsmentioning

confidence: 99%

Genome-wide Analysis in Brazilians Reveals Highly Differentiated Native American Genome Regions

et al. 2017

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Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental admixture in 1,538 North-Eastern Brazilians to estimate individual ancestry and ancestral allele frequencies, we computed 400,000 genome-wide locus-specific branch length (LSBL) Fst statistics of Brazilian Amerindian ancestry compared to European and African; and a similar set of differentiation statistics for their Amerindian component compared with the closest Asian 1000 Genomes population (surprisingly, Bengalis in Bangladesh). After ranking SNPs by these statistics, we identified the top 10 highly differentiated SNPs in five genome regions in the LSBL tests of Brazilian Amerindian ancestry compared to European and African; and the top 10 SNPs in eight regions comparing their Amerindian component to the closest Asian 1000 Genomes population. We found SNPs within or proximal to the genes CIITA (rs6498115), SMC6 (rs1834619), and KLHL29 (rs2288697) were most differentiated in the Amerindian-specific branch, while SNPs in the genes ADAMTS9 (rs7631391), DOCK2 (rs77594147), SLC28A1 (rs28649017), ARHGAP5 (rs7151991), and CIITA (rs45601437) were most highly differentiated in the Asian comparison. These genes are known to influence immune function, metabolic and anthropometry traits, and embryonic development. These analyses have identified candidate genes for selection within Amerindian ancestry, and by comparison of the two analyses, those for which the differentiation may have arisen during the migration from Asia to the Americas.

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Section: Resultsmentioning

confidence: 99%