An integrated map of structural variation in 2,504 human genomes

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association. © 2015 Macmillan Publishers Limited. All rights reserved

Hot deformation behavior and processing maps of diamond/Cu composites

The hot deformation behaviors of 50 vol pct uncoated and Cr-coated diamond/Cu composites were investigated using hot isothermal compression tests under the temperature and strain rate ranging from 1073 K to 1273 K (800 C to 1000 C) and from 0.001 to 5 s1, respectively. Dynamic recrystallization was determined to be the primary restoration mechanism during deformation. The Cr3C2 coating enhanced the interfacial bonding and resulted in a larger flow stress for the Cr-coated diamond/Cu composites. Moreover, the enhanced interfacial affinity led to a higher activation energy for the Cr-coated diamond/Cu composites (238 kJ/mol) than for their uncoated counterparts (205 kJ/mol). The strain-rate-dependent constitutive equations of the diamond/Cu composites were derived based on the Arrhenius model, and a high correlation (R = 0.99) was observed between the calculated flow stresses and experimental data. With the help of processing maps, hot extrusions were realized at 1123 K/0.01 s1 and 1153 K/0.01 s1 (850 C/0.01 s1 and 880 C/0.01 s1) for the uncoated and coated diamond/Cu composites, respectively. The combination of interface optimization and hot extrusion led to increases of the density and thermal conductivity, thereby providing a promising route for the fabrication of diamond/Cu composites

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 integrated encyclopedia of DNA elements in the human genome.

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research