Accounting for multiple comparisons in a genome-wide association study (GWAS).

Background: As we enter an era when testing millions of SNPs in a single gene association study will become the standard, consideration of multiple comparisons is an essential part of determining statistical significance. Bonferroni adjustments can be made but are conservative due to the preponderance of linkage disequilibrium (LD) between genetic markers, and permutation testing is not always a viable option. Three major classes of corrections have been proposed to correct the dependent nature of genetic data in Bonferroni adjustments: permutation testing and related alternatives, principal components analysis (PCA), and analysis of blocks of LD across the genome.

Multistage genomewide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS.

Background: A mean of 9-10 years of human immunodeficiency virus type 1 (HIV-1) infection elapse before clinical AIDS develops in untreated persons, but this rate of disease progression varies substantially among individuals. To investigate host genetic determinants of the rate of progression to clinical AIDS, we performed a multistage genomewide association study.

Methods: The discovery stage comprised 156 individuals from the Multicenter AIDS Cohort Study, enriched with rapid and long-term nonprogressors to increase statistical power.

A high-density admixture map for disease gene discovery in african americans.

Admixture mapping (also known as "mapping by admixture linkage disequilibrium," or MALD) provides a way of localizing genes that cause disease, in admixed ethnic groups such as African Americans, with approximately 100 times fewer markers than are required for whole-genome haplotype scans. However, it has not been possible to perform powerful scans with admixture mapping because the method requires a dense map of validated markers known to have large frequency differences between Europeans and Africans. To create such a map, we screened through databases containing approximately 450000 single-nucleotide polymorphisms (SNPs) for which frequencies had been estimated in African and European population samples.

Phylogeny and development of marine model species: strongylocentrotid sea urchins.

The phylogenetic relationships of ten strongy-locentrotid sea urchin species were determined using mitochondrial DNA sequences. This phylogeny provides a backdrop for the evolutionary history of one of the most studied groups of sea urchins. Our phylogeny indicates that a major revision of this group is in order.

POPULATION BIOLOGY OF THE TRANS-ARCTIC EXCHANGE: MtDNA SEQUENCE SIMILARITY BETWEEN PACIFIC AND ATLANTIC SEA URCHINS.

MtDNAs from 2 protein coding regions comprising 576 base pairs were sequenced from 17 individual sea urchins of the species Strongylocentrotus pallidus collected from the north Pacific and north Atlantic oceans. Twelve of 17 individual sequences were identical. Two of these were further sequenced in a third, 441 base pair region, and were also found to be identical.