Regional Association-based Fine-mapping for Sodium-Lithium Countertransport on Chromosome 10

Morrison, Alanna C.; Boerwinkle, Eric; Turner, Stephen T.; Ferrell, Robert E.

doi:10.1038/ajh.2007.17

Cited by 5 publications

(3 citation statements)

References 26 publications

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“…Here, we note that the top 20 SNPs with the highest “informativeness” (Infocalc I_n scores) in the current analyses included those correlated with heart rate response to β-blockers ( rs11931264 ; Shahin et al. 2018 ), high blood pressure ( rs225555 ; Morrison et al. 2008 ), and blood glucose levels ( rs1516510 ; Liu et al.…”

Section: Discussionmentioning

confidence: 99%

An Ancestry Informative Marker Set Which Recapitulates the Known Fine Structure of Populations in South Asia

Das

Upadhyai

2018

Genome Biology and Evolution

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The inference of genomic ancestry using ancestry informative markers (AIMs) can be useful for a range of studies in evolutionary genetics, biomedical research, and forensic analyses. However, the determination of AIMs for highly admixed populations with complex ancestries has remained a formidable challenge. Given the immense genetic heterogeneity and unique population structure of the Indian subcontinent, here we sought to derive AIMs that would yield a cohesive and faithful understanding of South Asian genetic origins. To discern the most optimal strategy for extracting AIMs for South Asians we compared three commonly used AIMs-determining methods namely, Infocalc, FST, and Smart Principal Component Analysis with ADMIXTURE, using previously published whole genome data from the Indian subcontinent. Our findings suggest that the Infocalc approach is likely most suitable for delineation of South Asian AIMs. In particular, Infocalc-2,000 (N = 2,000) appeared as the most informative South Asian AIMs panel that recapitulated the finer structure within South Asian genomes with high degree of sensitivity and precision, whereas a negative control with an equivalent number of randomly selected markers when used to interrogate the South Asian populations, failed to do so. We discuss the utility of all approaches under evaluation for AIMs derivation and interpreting South Asian genomic ancestries. Notably, this is the first report of an AIMs panel for South Asian ancestry inference. Overall these findings may aid in developing cost-effective resources for large-scale demographic analyses and foster expansion of our knowledge of human origins and disease, in the South Asian context.

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Section: Discussionmentioning

confidence: 99%

An Ancestry Informative Marker Set Which Recapitulates the Known Fine Structure of Populations in South Asia

Das

Upadhyai

2018

Genome Biology and Evolution

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“…Several studies on diseases other than TB have revealed that rs930507 was associated with an increased risk of invasive pneumococcal disease (IPD) in African Americans [27] and otitis media in children younger than 2 years of age [28]. Moreover, it was also shown to be associated with sodium-lithium countertransport (SLC) and systolic blood pressure [29]. Previous studies have found no association between rs2099902 and recurrent vulvovaginal infections risk [30] or severe dengue [31]; however, another study performed by Zanetti et al suggested that rs2099902 was associated with increased risk of colon cancer in African Americans [32].…”

Section: Discussionmentioning

confidence: 99%

Mannose-binding lectin 2 gene polymorphisms and their association with tuberculosis in a Chinese population

et al. 2020

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Background: Immune-and inflammation-related genes (IIRGs) play an important role in the pathogenesis of tuberculosis (TB). However, the relationship between IIRG polymorphisms and TB risk remains unknown. In this study, the gene polymorphisms and their association with tuberculosis were determined in a Chinese population. Methods: We performed a case-control study involving 1016 patients with TB and 507 healthy controls of Han Chinese origin. Sixty-four single-nucleotide polymorphisms (SNPs) belonging to 18 IIRGs were genotyped by the PCR-MassArray assay, and the obtained data was analyzed with χ 2-test, Bonferroni correction, and unconditional logistic regression analysis. Results: We observed significant differences in the allele frequency of LTA rs2229094*C (P = 0.015), MBL2 rs2099902*C (P = 0.001), MBL2 rs930507*G (P = 0.004), MBL2 rs10824793*G (P = 0.004), and IL12RB1 rs2305740*G (P = 0.040) between the TB and healthy groups. Increased TB risk was identified in the rs930507 G/G genotype (P adjusted = 0.027) under a codominant genetic model as well as in the rs2099902

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“…This approach could not be realized without the advancement of next-generation sequencing and genotyping technologies, as well as the massive efforts spent in the annotation of the structural and functional properties of the human genome (HapMap and ENCODE projects) [10] , [11] . Moreover, attempts to identify the causal genes or gene subnetworks for a disease-linked genomic region have employed large-scale candidate gene association analyses [12] – [15] , linkage disequilibrium (LD) fine mapping [16] , and more recently, reversely engineered molecular network methods [17] .…”

Section: Introductionmentioning

confidence: 99%

Association and Haplotype Analyses of Positional Candidate Genes in Five Genomic Regions Linked to Scrotal Hernia in Commercial Pig Lines

Xiao

Vukasinovic³

et al. 2009

PLoS ONE

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Scrotal hernia in pigs is a complex trait likely affected by genetic and environmental factors. A large-scale association analysis of positional and functional candidate genes was conducted in four previously identified genomic regions linked to hernia susceptibility on Sus scrofa chromosomes 2 and 12, as well as the fifth region around 67 cM on chromosome 2, respectively. In total, 151 out of 416 SNPs discovered were genotyped successfully. Using a family-based analysis we found that four regions surrounding ELF5, KIF18A, COL23A1 on chromosome 2, and NPTX1 on chromosome 12, respectively, may contain the genetic variants important for the development of the scrotal hernia in pigs. These findings were replicated in another case-control dataset. The SNPs around the ELF5 region were in high linkage disequilibrium with each other, and a haplotype containing SNPs from ELF5 and CAT was highly significantly associated with hernia development. Extensive re-sequencing work focused on the KIF18A gene did not detect any further SNPs with extensive association signals. These genes may be involved in the estrogen receptor signaling pathway (KIF18A and NPTX1), the epithelial-mesenchymal transition (ELF5) and the collagen metabolism pathway (COL23A1), which are associated with the important molecular characteristics of hernia pathophysiology. Further investigation on the molecular mechanisms of these genes may provide more molecular clues on hernia development in pigs.

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Regional Association-based Fine-mapping for Sodium-Lithium Countertransport on Chromosome 10

Abstract: This fine-mapping survey of genetic variation in a linkage region of interest provides overall support for association-mapping for SLC on chromosome 10. Genes significantly associated with systolic blood pressure and/or SLC in these families will be prioritized for future studies.

Cited by 5 publications

References 26 publications

An Ancestry Informative Marker Set Which Recapitulates the Known Fine Structure of Populations in South Asia

An Ancestry Informative Marker Set Which Recapitulates the Known Fine Structure of Populations in South Asia

Mannose-binding lectin 2 gene polymorphisms and their association with tuberculosis in a Chinese population

Association and Haplotype Analyses of Positional Candidate Genes in Five Genomic Regions Linked to Scrotal Hernia in Commercial Pig Lines

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