Genomes and Genes
Experts and Doctors on haplotypes in Los Angeles, California, United States
Locale: Los Angeles, California, United States
- Aung T, Ozaki M, Lee M, Schlötzer Schrehardt U, Thorleifsson G, Mizoguchi T, et al. Genetic association study of exfoliation syndrome identifies a protective rare variant at LOXL1 and five new susceptibility loci. Nat Genet. 2017;49:993-1004 pubmed publisher..3 (TMEM136), 6p21 (AGPAT1), 3p24 (RBMS3) and 5q23 (near SEMA6A). These findings provide biological insights into the pathology of XFS and highlight a potential role for naturally occurring rare LOXL1 variants in disease biology. ..
- Jones M, Mathur R, Cui J, Guo X, Azziz R, Goodarzi M. Independent confirmation of association between metabolic phenotypes of polycystic ovary syndrome and variation in the type 6 17beta-hydroxysteroid dehydrogenase gene. J Clin Endocrinol Metab. 2009;94:5034-8 pubmed publisher..These replication data suggest a role for HSD17B6 in PCOS. How HSD17B6, an enzyme involved in steroid metabolism, may influence BMI and insulin resistance in PCOS remains to be determined. ..
- Platt A, Horton M, Huang Y, Li Y, Anastasio A, Mulyati N, et al. The scale of population structure in Arabidopsis thaliana. PLoS Genet. 2010;6:e1000843 pubmed publisher..Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales. ..
- Aldave A, Rosenwasser G, Yellore V, Papp J, Sobel E, Pham M, et al. Linkage of posterior amorphous corneal dystrophy to chromosome 12q21.33 and exclusion of coding region mutations in KERA, LUM, DCN, and EPYC. Invest Ophthalmol Vis Sci. 2010;51:4006-12 pubmed publisher..Linkage and haplotype analyses identified 12q21.33 as a locus for PACD. However, no mutations were identified in the candidate genes (KERA, LUM, DCN, EPYC) within this region. ..
- Qin J, Richardson L, Jasin M, Handel M, Arnheim N. Mouse strains with an active H2-Ea meiotic recombination hot spot exhibit increased levels of H2-Ea-specific DNA breaks in testicular germ cells. Mol Cell Biol. 2004;24:1655-66 pubmed..The recombination-related breaks in the hot spot likely reflect SPO11-induced double-strand breaks and/or recombination intermediates containing free 3' hydroxyl groups. ..
- Sakurai D, Zhao J, Deng Y, Kelly J, Brown E, Harley J, et al. Preferential binding to Elk-1 by SLE-associated IL10 risk allele upregulates IL10 expression. PLoS Genet. 2013;9:e1003870 pubmed publisher..Taken together, our data suggest that preferential binding of activated Elk-1 to the IL10 rs3122605-G allele upregulates IL10 expression and confers increased risk for SLE in European Americans. ..
- Mishra D, Wu Y, Sarkissyan M, Sarkissyan S, Chen Z, Shang X, et al. Vitamin D receptor gene polymorphisms and prognosis of breast cancer among African-American and Hispanic women. PLoS ONE. 2013;8:e57967 pubmed publisher..VDR haplotypes are associated with breast cancer in African-Americans, but not in Hispanic/Latinas. The VDR-FokI FF genotype is linked with poor prognosis in African-American women with breast cancer. ..
- McGovern D, Taylor K, Landers C, Derkowski C, Dutridge D, Dubinsky M, et al. MAGI2 genetic variation and inflammatory bowel disease. Inflamm Bowel Dis. 2009;15:75-83 pubmed publisher..007). Quantitative antibody levels were also associated with variants in intron 4 (anti-IgA ASCA, P = 0.0003 and anti-IgG ASCA, P = 0.0002). These findings support the significance of the epithelial barrier in IBD pathogenesis. ..
- Li Y, Gauderman W, Conti D, Lin P, Avol E, Gilliland F. Glutathione S-transferase P1, maternal smoking, and asthma in children: a haplotype-based analysis. Environ Health Perspect. 2008;116:409-15 pubmed publisher..Variants in both the promoter and coding regions of the GSTP1 locus may contribute to the occurrence of childhood asthma and wheezing and may increase susceptibility to adverse effects of tobacco-smoke exposure. ..
- Antoine H, Pall M, Trader B, Chen Y, Azziz R, Goodarzi M. Genetic variants in peroxisome proliferator-activated receptor gamma influence insulin resistance and testosterone levels in normal women, but not those with polycystic ovary syndrome. Fertil Steril. 2007;87:862-9 pubmed..In controls, however, the His447His T-allele may be in linkage disequilibrium with a functional variant that influences insulin resistance and T production. ..
- Goodarzi M, Guo X, Taylor K, Quiñones M, Samayoa C, Yang H, et al. Determination and use of haplotypes: ethnic comparison and association of the lipoprotein lipase gene and coronary artery disease in Mexican-Americans. Genet Med. 2003;5:322-7 pubmed..91). This study outlines the haplotype structure of the LPL gene, illustrates the utility of haplotype-based analysis in association studies, and demonstrates the importance of defining haplotype frequencies for different ethnic groups. ..
- Aldave A, Yellore V, Thonar E, Udar N, Warren J, Yoon M, et al. Novel mutations in the carbohydrate sulfotransferase gene (CHST6) in American patients with macular corneal dystrophy. Am J Ophthalmol. 2004;137:465-73 pubmed..To further characterize the mutations within the CHST6 gene responsible for causing macular corneal dystrophy in a cohort of affected patients from the United States...
- Goodarzi M, Taylor K, Guo X, Quiñones M, Cui J, Li Y, et al. Association of the diabetes gene calpain-10 with subclinical atherosclerosis: the Mexican-American Coronary Artery Disease Study. Diabetes. 2005;54:1228-32 pubmed..The fact that the diabetes gene CAPN10 also influences the risk for atherosclerosis shows that inherited factors may underlie the frequent co-occurrence of these two conditions. ..
- Kang C, Marjoram P. A sample selection strategy for next-generation sequencing. Genet Epidemiol. 2012;36:696-709 pubmed publisher..We then describe a variation on our algorithm that is more focused on detecting rarer variants. We demonstrate the performance of our algorithm using simulated data and data from the 1000 Genomes Project. ..
- Wegmann D, Kessner D, Veeramah K, Mathias R, Nicolae D, Yanek L, et al. Recombination rates in admixed individuals identified by ancestry-based inference. Nat Genet. 2011;43:847-53 pubmed publisher..These results suggest that outside of structurally variable regions, admixture does not substantially disrupt the factors controlling recombination rates in humans. ..
- Goodarzi M, Wong H, Quiñones M, Taylor K, Guo X, Castellani L, et al. The 3' untranslated region of the lipoprotein lipase gene: haplotype structure and association with post-heparin plasma lipase activity. J Clin Endocrinol Metab. 2005;90:4816-23 pubmed
- Padhukasahasram B, Wall J, Marjoram P, Nordborg M. Estimating recombination rates from single-nucleotide polymorphisms using summary statistics. Genetics. 2006;174:1517-28 pubmed..We used our method to analyze a human data set recently genotyped by Perlegen Sciences. ..
- VonHoldt B, Pollinger J, Lohmueller K, Han E, Parker H, Quignon P, et al. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature. 2010;464:898-902 pubmed publisher..More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity...
- Goodarzi M, Antoine H, Azziz R. Genes for enzymes regulating dehydroepiandrosterone sulfonation are associated with levels of dehydroepiandrosterone sulfate in polycystic ovary syndrome. J Clin Endocrinol Metab. 2007;92:2659-64 pubmed..Variants within STS were not associated with DHEAS level. No associations were observed in control women. This study presents genetic evidence suggesting a potential role of SULT2A1, but not STS, in the inherited AA excess of PCOS. ..
- Goodarzi M, Jones M, Antoine H, Pall M, Chen Y, Azziz R. Nonreplication of the type 5 17beta-hydroxysteroid dehydrogenase gene association with polycystic ovary syndrome. J Clin Endocrinol Metab. 2008;93:300-3 pubmed..These data suggest that polymorphisms in the HSD17B5 gene are not associated with PCOS risk or elevated testosterone as previously reported. ..
- Bodnar J, Chatterjee A, Castellani L, Ross D, Ohmen J, Cavalcoli J, et al. Positional cloning of the combined hyperlipidemia gene Hyplip1. Nat Genet. 2002;30:110-6 pubmed..These results reveal a new pathway of potential clinical significance that contributes to plasma lipid metabolism. ..
- Breton C, Vora H, Salam M, Islam T, Wenten M, Gauderman W, et al. Variation in the GST mu locus and tobacco smoke exposure as determinants of childhood lung function. Am J Respir Crit Care Med. 2009;179:601-7 pubmed publisher..Genetic variation across the GST mu locus is associated with 8-year lung function growth. Children of mothers who smoked during pregnancy and had variation in GSTM2 had lower lung function growth. ..
- Saruta M, Targan S, Mei L, Ippoliti A, Taylor K, Rotter J. High-frequency haplotypes in the X chromosome locus TLR8 are associated with both CD and UC in females. Inflamm Bowel Dis. 2009;15:321-7 pubmed publisher..These associations further emphasize the importance of genetic variation in innate immunity as determinants, not only of CD, but of UC as well. ..
- Goodarzi M, Jones M, Chen Y, Azziz R. First evidence of genetic association between AKT2 and polycystic ovary syndrome. Diabetes Care. 2008;31:2284-7 pubmed publisher..1, P = 0.005). These data suggest that polymorphisms in two components of the insulin signaling pathway, AKT2 and GSK3B, are associated with PCOS. The presence of multiple lesions in a single pathway may confer increased risk. ..
- Lurje G, Zhang W, Yang D, Groshen S, Hendifar A, Husain H, et al. Thymidylate synthase haplotype is associated with tumor recurrence in stage II and stage III colon cancer. Pharmacogenet Genomics. 2008;18:161-8 pubmed publisher..Larger, independent, prospective studies are, however, needed to confirm and validate our preliminary findings. ..
- Danciger M, Hendrickson J, Lyon J, Toomes C, McHale J, Fishman G, et al. CORD9 a new locus for arCRD: mapping to 8p11, estimation of frequency, evaluation of a candidate gene. Invest Ophthalmol Vis Sci. 2001;42:2458-65 pubmed..However, only 2 loci for arCRD have been documented. This is the report of a third. ..
- Sarkissyan M, Wu Y, Chen Z, Mishra D, Sarkissyan S, Giannikopoulos I, et al. Vitamin D receptor FokI gene polymorphisms may be associated with colorectal cancer among African American and Hispanic participants. Cancer. 2014;120:1387-93 pubmed publisher..The results from this study suggest that genetic variation of the VDR-FokI SNPs may influence CRC risk, particularly in African American cohorts. ..
- Visapää I, Fellman V, Lanyi L, Peltonen L. ABCB6 (MTABC3) excluded as the causative gene for the growth retardation syndrome with aminoaciduria, cholestasis, iron overload, and lactacidosis. Am J Med Genet. 2002;109:202-5 pubmed..Haplotype analysis of the critical DNA region provided evidence for positional exclusion also. Based on these data, ABCB6 is not the causative gene for GRACILE syndrome...
- Michelsen K, Thomas L, Taylor K, Yu Q, Mei L, Landers C, et al. IBD-associated TL1A gene (TNFSF15) haplotypes determine increased expression of TL1A protein. PLoS ONE. 2009;4:e4719 pubmed publisher..Thus, TL1A may provide an important target for therapeutic intervention in this subgroup of IBD patients. ..