Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Summer and fall habitat of North Atlantic right whales (Eubalaena glacialis) inferred from satellite telemetry

Author Posting. © National Research Council Canada, 2005. This article is posted here by permission of National Research Council Canada for personal use, not for redistribution. The definitive version was published in Canadian Journal of Fisheries and Aquatic Sciences 62 (2005): 527-543, doi:10.1139/F04-238.Satellite-monitored radio tags were attached to North Atlantic right whales (Eubalaena glacialis) in Grand Manan Basin of the lower Bay of Fundy during the summer and early fall seasons of 1989–1991 and 2000. Monte Carlo tests were used to examine the distribution of the tagged whales in space and time and with respect to a variety of environmental variables to characterize right whale habitat on their northern feeding grounds. These environmental variables included depth, depth gradient, climatological surface and bottom hydrographic properties, and remotely sensed surface temperature, chlorophyll concentration, and their respective horizontal gradients. Site fidelity in the Bay of Fundy was very low during 1989–1991 and high during 2000. When the tagged animals left the Bay, they did not frequently visit the deep basins of the Gulf of Maine and Scotian Shelf, where abundances of their primary copepod prey, Calanus finmarchicus, are thought to be high. Instead, right whales visited areas characterized by low bottom water temperatures, high surface salinity, and high surface stratification. No evidence was found that the tagged right whales associated with oceanic fronts or regions with high standing stocks of phytoplankton.This study was supported by the Office of Naval Research, National Marine Fisheries Service, Oregon State University Marine Mammal Endowment, and the Space Grant and Earth System Science fellowship programs of the National Aeronautics and Space Administration