Month: May 2017


[PMID:28557980] [Nature Methods]

E-scape: interactive visualization of single-cell phylogenetics and cancer evolution

“E-scape consists of three visualization tools deployed as R html widgets: (i) TimeScape for time series analysis; (ii) MapScape for spatial distribution analysis; and (iii) CellScape for single-cell analysis, including analysis of the phylogenetic and population dynamics of cancer.”


[PMID:28416821] [Nature Genetics]

Pathogenic variants that alter protein code often disrupt splicing

“We discovered that the alleles causing splicing defects cluster in disease-associated genes (for example, haploinsufficient genes). We analyzed 4,964 published disease-causing exonic mutations using a massively parallel splicing assay (MaPSy), which showed an 81% concordance rate with splicing in patient tissue. Approximately 10% of exonic mutations altered splicing, mostly by disrupting multiple stages of spliceosome assembly.”


[PMID:28530675] [Nature Genetics]

Reevaluation of SNP heritability in complex human traits

“SNP heritability, the proportion of phenotypic variance explained by SNPs, has been reported for many hundreds of traits. Its estimation requires strong prior assumptions about the distribution of heritability across the genome, but current assumptions have not been thoroughly tested. By analyzing imputed data for a large number of human traits, we empirically derive a model that more accurately describes how heritability varies with minor allele frequency (MAF), linkage disequilibrium (LD) and genotype certainty. Across 19 traits, our improved model leads to estimates of common SNP heritability on average 43% (s.d. 3%) higher than those obtained from the widely used software GCTA and 25% (s.d. 2%) higher than those from the recently proposed extension GCTA-LDMS.”


[PMID:28506277] [Genome Biology]

Quantifying the mapping precision of genome-wide association studies using whole-genome sequencing data

“Using simulations based on whole-genome sequencing (WGS) data from 3642 unrelated individuals of European descent, we show that the association signals at rare causal variants (minor allele frequency ≤ 0.01) are very unlikely to be mapped to common variants in GWAS using either WGS data or imputed data and vice versa. We predict that at least 80% of the common variants identified from published GWAS using imputed data are within 33.5 Kbp of the causal variants, a resolution that is comparable with that using WGS data. Mapping precision at these loci will improve with increasing sample sizes of GWAS in the future. For rare variants, the mapping precision of GWAS using WGS data is extremely high, suggesting WGS is an efficient strategy to detect and fine-map rare variants simultaneously.” Work from Jian Yang.


[PMID:28502612] [American Journal of Human Genetics]

MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome

“MARRVEL (model organism aggregated resources for rare variant exploration) is a publicly available website that integrates information from six human genetic databases and seven model organism databases. For any given variant or gene, MARRVEL displays information from OMIM, ExAC, ClinVar, Geno2MP, DGV, and DECIPHER.”