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

Categorization in Hybrid Search: A Study Using Eye Movement Registration

Categorization is the process by which objects are combined according to a certain principle, which provides more efficient and cost-effective information processing. One of the topical areas of research in this field is the study of the categorical effect in perceptual tasks, for example in the task visual search task. The present study investigated the effect of the role of category (basic or superordinate) on the time of guidance - the search for a target stimulus and verification - the time of identification of a target stimulus in a hybrid search task. Subjects had to find certain objects on the screen, which could be specified either as basic-level categories (e.g., cars) or superordinate-level categories (e.g., transport vehicles). An eye-tracking method was used to separate the entire hybrid search process into a guidance and a verification. A significant effect of category level was found on the rate of guidance, but not on the rate of verification.</p

Characterization of volatile and semivolatilecompounds in green and fermented leaves of Bergenia crassifolia L. by gas chromatography-mass spectrometry and ID-CUBE direct analysis in real time-high resolution mass spectrometry

Chemical compositions of volatile and semi-volatile components in green and fermented leaves of Bergenia crassifolia L. were studied. Leaf components were identified using gas chromatography with low resolution mass spectrometry and direct analysis in real time (DART) high resolution mass spectrometry with an ID-CUBE ion source. Phytol, nerolidol, geraniol, linalool, α-bisabolol, α-bisabololoxide B, α-cadinol, δ-cadinene, α-terpineol and several other marker compounds of special interest were defined, for which the process of fermentation significantly changed their content in the leaves. Low resolution EI GC-MS and ID-CUBE DART-HRMS were found to be complementary methods, as they provide different information, helpful to increase the confidence of identification. © IM Publications LLP 2014