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Noah Zaitlen, Alkes Price and colleagues report a new approach to estimate the narrow-sense heritability of complex traits from unrelated individuals in a recently admixed population. They apply this approach to estimate the heritability for 13 quantitative or case-control phenotypes in 21,497 African-American individuals and suggest the inflation of family-based h2 estimates.
Peter Sorger, Mohammed AlQuraishi and colleagues present a statistical framework for integrating biophysical and genomic data to predict the consequences of cancer-related mutations on protein-protein interactions. They apply their framework to the SH2 phosphoprotein network using publicly available data from The Cancer Genome Atlas.
David Jaffe and colleagues report a new algorithm, DISCOVAR, for variant calling and de novo genome assembly. They test the algorithm on a new reference variant call set and demonstrate improved variant calling, particularly in challenging regions of the genome.
Frank Steemers and colleagues report a new method for genome-wide haplotyping based on contiguity-preserving transposition and combinatorial indexing. They apply this method to assemble over 95% of the heterozygous variants in a human genome into long, accurate haplotype blocks.
Gerton Lunter and colleagues report Platypus software, which combines a haplotype-based multi-sample variant caller with local sequence assembly in a Bayesian statistical framework. They demonstrate applications to exome and whole-genome data sets, to the identification de novo mutations in parent-offspring trios and to the genotyping of HLA loci.
Stephan Schiffels and Richard Durbin report the multiple sequentially Markovian coalescent (MSMC) method for inferring human population size and separation history from multiple genome sequences. Their application to the whole-genome sequences of 34 individuals from 9 populations allows inferences about events in human population history as recent as 2,000 years ago.
Gonçalo Abecasis, Chaolong Wang and colleagues report a new statistical method, implemented in a publicly available software program LASER, to estimate an individual's genetic ancestry directly from off-target sequence reads from targeted sequencing experiments, making use of a reference panel. Their simulations and testing on real data sets show accurate inference of worldwide continental ancestry with whole-genome shotgun coverage as low as 0.001× and of fine-scale ancestry within Europe with coverage as low as 0.1×.
Jay Shendure, Greg Cooper and colleagues report a framework for annotation of genetic variation, Combined Annotation–Dependent Depletion (CADD), integrating diverse annotations into a single C score. They show that C scores correlate with annotations of functionality, pathogenicity and experimentally measured regulatory effects.
Douglas Higgs and colleagues report a high-throughput approach, called Capture-C, to analyze interactions between cis regulatory elements. Using Capture-C, the authors interrogated hundreds of specific interactions at high resolution in a single experiment.
