Dataset Information

Next-generation linkage and association methods applied to hypertension: a multifaceted approach to the analysis of sequence data.

ABSTRACT: To realize the full potential of next-generation sequencing, it is important to consider multiple sources of genetic information, including inheritance, association, and bioinformatics. To illustrate the promise of such an approach, we applied our next-generation linkage and association (NGLA) methods to the sequence data of a large 57-member Mexican American family with hypertension. Our results show that OSBPL10--a disease susceptibility gene for dyslipidemia--may also influence systolic blood pressure (SBP). In particular, our NGLA dense single-nucleotide polymorphism (SNP) analysis identified a 2.5-megabase (Mb) region that strongly cosegregates with low SBP (maximum posterior probability of linkage [PPL] = 68%). Furthermore, using the posterior probability of linkage disequilibrium (PPLD), we fine-mapped this region and identified 12 SBP-associated variants (PPLD ranging between 4% and 14%) that comprise a rare, 4-site haplotype. This haplotype extends into the candidate gene, OSBPL10 (oxysterol-binding protein-like 10). In contrast to our NGLA methods, a commonly used filter-based approach identified 23 variants with little evidence for spatial clustering around any particular gene or region of interest.

SUBMITTER: Stewart WC

PROVIDER: S-EPMC4143636 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Next-generation linkage and association methods applied to hypertension: a multifaceted approach to the analysis of sequence data.

Stewart William Cl WC Huang Yungui Y Greenberg David A DA Vieland Veronica J VJ

BMC proceedings 20140617 Suppl 1 Genetic Analysis Workshop 18Vanessa Olmo

To realize the full potential of next-generation sequencing, it is important to consider multiple sources of genetic information, including inheritance, association, and bioinformatics. To illustrate the promise of such an approach, we applied our next-generation linkage and association (NGLA) methods to the sequence data of a large 57-member Mexican American family with hypertension. Our results show that OSBPL10--a disease susceptibility gene for dyslipidemia--may also influence systolic blood ...[more]

PMID: 25519364

Similar Datasets

Project description:As multiple species of bats are currently experiencing dramatic declines in populations due to white-nose syndrome (WNS) and other factors, conservation managers have an urgent need for data on the ecology and overall status of populations of once-common bat species. Standard approaches to obtain data on bat populations often involve capture and handling, requiring extensive expertise and unavoidably resulting in stress to the bats. New methods to rapidly obtain critical data are needed that minimize both the stress on bats and the spread of WNS. Guano provides a noninvasive source of DNA that includes information from the bat, but also dietary items, parasites, and pathogens. DNA metabarcoding is a high-throughput, DNA-based identification technique to assess the biodiversity of environmental or fecal samples. We investigated the use of multifaceted DNA metabarcoding (MDM), a technique combining next-generation DNA sequencing (NGS), DNA barcodes, and bioinformatic analysis, to simultaneously collect data on multiple parameters of interest (bat species composition, individual genotype, sex ratios, diet, parasites, and presence of WNS) from fecal samples using a single NGS run. We tested the accuracy of each MDM assay using samples in which these parameters were previously determined using conventional approaches. We found that assays for bat species identification, insect diet, parasite diversity, and genotype were both sensitive and accurate, the assay to detect WNS was highly sensitive but requires careful sample processing steps to ensure the reliability of results, while assays for nectivorous diet and sex showed lower sensitivity. MDM was able to quantify multiple data classes from fecal samples simultaneously, and results were consistent whether we included assays for a single data class or multiple data classes. Overall, MDM is a useful approach that employs noninvasive sampling and a customizable suite of assays to gain important and largely accurate information on bat ecology and population dynamics.

Dataset Information

Next-generation linkage and association methods applied to hypertension: a multifaceted approach to the analysis of sequence data.

Publications

Next-generation linkage and association methods applied to hypertension: a multifaceted approach to the analysis of sequence data.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets