The revolution in next-generation sequencing has made obtaining both common and rare high-quality sequence variants across the entire genome feasible. Because researchers are now faced with the analytical challenges of handling a massive amount of genetic variant information from sequencing studies, numerous methods have been developed to assess the impact of both common and rare variants on di...

Human brucellosis is considered to be an important but typically under-diagnosed cause of febrile illness in many low and middle-income countries. In Kenya, and throughout East Africa, laboratory diagnosis for the disease is based primarily on the febrile antigen Brucella agglutination test (FBAT), yet few studies of the diagnostic accuracy of this test exist. Assessment of the performance of t...

BACKGROUND Advances in whole genome sequencing have enabled the investigation of rare variants, which could explain some of the missing heritability that genome-wide association studies are unable to detect. Most methods to detect associations with rare variants are developed for unrelated individuals; however, several methods exist that utilize family studies and could have better power to det...

This simulation-based report compares the performance of five methods of association analysis in the presence of linkage using extended sibships: the Family-Based Association Test (FBAT), Empirical Variance FBAT (EV-FBAT), Conditional Logistic Regression (CLR), Robust CLR (R-CLR) and Sibship Disequilibrium Test (SDT). The two tests accounting for residual familial correlation (EV-FBAT and R-CLR...

With the advent of sequencing technology opening up a new era of personal genome sequencing, huge amounts of rare variant data have suddenly become available to researchers seeking genetic variants related to human complex disorders. There is an urgent need for the development of novel statistical methods to analyze rare variants in a statistically powerful manner. While a number of statistical...

BACKGROUND Type 1 diabetes (T1D) is a multifactorial autoimmune disorder where interaction and integration of immune response genes along with environmental factors play a role in autoimmune destruction of the insulin producing Pancreatic Beta cells. METHODOLOGY/PRINCIPAL FINDINGS We have studied four single nucleotide polymorphisms (FokI site in Exon 2, BsmI and ApaI sites in Intron 8 and Ta...

The vitamin D receptor (VDR) gene has been associated with prostate cancer, although previous results are somewhat equivocal. To further study this, we did a family-based case-control study (N = 918) of the association between prostate cancer and six common VDR variants: Cdx2, FokI, BsmI, ApaI, TaqI, and the poly-A microsatellite. Looking at each variant alone, only FokI and ApaI were associate...

Most currently available family based association tests are designed to account only for nuclear families with complete genotypes for parents as well as offspring. Due to the availability of increasingly less expensive generation of whole genome sequencing information, genetic studies are able to collect data for more families and from large family cohorts with the goal of improving statistical...