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

Information retrieved from specimens at Natural History Collections can improve the quality of field-based ecological networks

Numerous studies analyze the interactions between plants and their pollinators in ecological communities using a network approach. However, field studies rarely record all the interactions occurring in the field. In this sense Natural History Collections (NHCs) can provide information on interactions that may have been missed by field sampling. In this study we compare a network based on field sampling with a network based on data retrieved from specimens at NHCs, and we assess the degree to which these two sources of data are complementary. For this we used data available from a bee biodiversity study conducted in Southern Argentina for the South American bee genus Corynura (Halictidae: Augochlorini). Data on the floral associations of the specimens at NHCs were retrieved from the specimens’ labels, as the name of the plant species on which a given bee was captured is often recorded for many specimens at NHCs. Although field sampling recorded an unusually high number of insect-plant interactions, it misses some unique interactions present in the NHCs networks. Some structural properties of these networks are briefly analyzed, and usefulness and limitations of using NHCs data are discussed. We conclude that the information about insect-plant interactions extracted from NHCs could complement field-based data, especially in poorly sampled communities.Fil: González Vaquero, Rocío Ana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaFil: Gravel, A. I.. York University; CanadáFil: Devoto, Mariano. Universidad de Buenos Aires. Facultad de Agronomía; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin