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

Lexical and semantic binding in verbal short-term memory

Semantic dementia patients make numerous phoneme migration errors in their immediate serial recall of poorly comprehended words. In this study, similar errors were induced in the word recall of healthy participants by presenting unpredictable mixed lists of words and nonwords. This technique revealed that lexicality, word frequency, imageability, and the ratio of words to nonwords all influence the stability of the phonological trace. These factors affected phoneme migrations and phoneme identity errors for both the words themselves and the nonwords they were presented with. Therefore, lexical/semantic knowledge encourages the phonological segments of familiar words to emerge together in immediate serial recall. In the absence of such knowledge, the elements of a particular item are more likely to recombine with the phonemes of other list items. These findings demonstrate the importance of lexical and semantic binding in verbal short-term memory

Phonological short term memory and single word reading

Period of award: 01/06/00 to 31/07/01. Includes bibliographical referencesAvailable from British Library Document Supply Centre- DSC:3739. 0605(000223026) / BLDSC - British Library Document Supply CentreSIGLEGBUnited Kingdo