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

An All-Feline Retroviral Packaging System for Transduction of Human Cells

Doty et al. in this technical report generate and characterize a helper-free, packaging system composed entirely of feline leukemia virus subgroup C (FeLV-C) components. Using this new packaging system, the authors demonstrate that they can produce higher titer vectors than existing gammaretroviral packaging systems

Patterns of diversity and abundance of fungus-growing ants (Formicidae: Attini) in areas of the Brazilian Cerrado Padrões de diversidade e abundância de formigas cultivadoras de fungo (Formicidade: Attini) em áreas do Cerrado Brasileiro

Fungus-growing ants (tribe Attini) are characteristic elements of the New World fauna. However, there is little information on the patterns of diversity, abundance, and distribution of attine species in their native ecosystems, especially for the so-called "lower" genera of the tribe. A survey of attine ant nests (excluding Atta Fabricus, 1804 and Acromyrmex Mayr, 1865) was conducted in a variety of savanna and forest habitats of the Cerrado biome near Uberlândia, Brazil. In total, 314 nests from 21 species of nine genera were found. Trachymyrmex Forel, 1893 was the most diverse genus with 10 species. Eighteen species were found in the savannas, including Mycetagroicus cerradensis Brandão & Mayhé-Nunes, 2001, a species from a recently-described genus of Attini, whereas in the forests only 12 species were found. Forest and savannas support relatively distinct faunas, each with a number of unique species; the species present in the forest habitats did not represent a nested subset of the species found in the savannas. Furthermore, although many species were common to both types of vegetation, their abundances were quite different. The density of attine nests is relatively high at some sites, exceeding an estimated 4,000 nests per hectare. In this sense, attine ants can be regarded as prevalent invertebrate taxa in the Brazilian Cerrado.<br>As formigas cultivadoras de fungos (tribo Attini) são exclusivas da fauna do Novo Mundo. Entretanto, existem poucas informações sobre os padrões de diversidade, abundância e distribuição das espécies de Attini em seus ecossistemas nativos, em especial para os gêneros menos derivados desta tribo. Um levantamento de ninhos de Attini (excluindo Atta Fabricius, 1804 e Acromyrmex Mayr, 1865) foi realizado em diversos ambientes savânicos e de floresta do bioma Cerrado próximos à Uberlândia, Brasil. Encontramos 314 ninhos de 21 espécies pertencentes a nove gêneros da tribo. Trachymyrmex Forel, 1893 foi o gênero mais diverso, com 10 espécies. Encontramos 18 espécies na savana, incluindo Mycetagroicus cerradensis Brandão & Mayhé-Nunes, 2001, uma espécie de um gênero de Attini recentemente descrito, enquanto que nas áreas de floresta registramos somente 12 espécies. As savanas e florestas apresentaram faunas relativamente distintas, com espécies exclusivas de cada tipo de vegetação; as espécies presentes nas florestas não representaram um subconjunto das espécies encontradas nas savanas. Além disso, apesar de muitas espécies terem sido comuns a ambos os tipos de vegetação, suas abundâncias foram muito diferentes. A densidade estimada de ninhos de Attini foi relativamente alta em alguns locais, ultrapassando 4.000 ninhos por hectare. Neste sentido, as formigas da tribo Attini podem ser consideradas como invertebrados predominantes no Cerrado brasileiro