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Using well-calibrated statistical methods the authors jointly analyze Undiagnosed Diseases Network genomes, identifying known and novel disease genes. Software is publicly available to support future cross-cohort rare disease discovery efforts.

Michael Bamshad, Jay Shendure and colleagues report the first application of exome resequencing to identify the cause of a mendelian disorder. They sequenced the exomes of four individuals with Miller syndrome in three independent families and identify mutations in DHODH, a key enzyme in the pyrimidine de novo biosynthesis pathway, as causal for the disorder.

Michael Bamshad and colleagues report an exome sequencing study of extreme phenotypes to identify genetic variants that modify the risk for chronic Pseudomonas aeruginosa airway infection in individuals with cystic fibrosis.

Inherited alterations of the 8q24 genomic locus are linked to cancer etiology. Here, the authors investigate hereditary prostate cancer to reveal ancestral risk-altering haplotypes, the sentinel genetic variants optimally predicting risk, and causal mutation candidates.

The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) aims to better understand population genetics of the African diaspora. Here, it uses deeply sequenced whole-genomes to describe the impact of admixture and potential disease burden of deleterious variants.

Short tandem repeat mutations in a primate Alu element on chromosome 15q cause activation of a thyroid-specific enhancer, upregulating MIR7-2/MIR1179. This results in defective thyroid proliferation and thyrotropin resistance.

Deep whole-genome sequencing of 300 individuals from 142 diverse populations provides insights into key population genetic parameters, shows that all modern human ancestry outside of Africa including in Australasians is consistent with descending from a single founding population, and suggests a higher rate of accumulation of mutations in non-Africans compared to Africans since divergence.

Resequencing of genes from individuals of European and African American ancestry indicates that approximately 73% of all protein-coding SNVs and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000–10,000 years, and that European Americans carry an excess of deleterious variants in essential and Mendelian disease genes compared to African Americans.

Jay Shendure and colleagues report exome sequencing of ten individuals with Kabuki syndrome. They identify mutations in MLL2, encoding a Trithorax-group histone methyltransferase, as causal for this rare autosomal dominant malformation disorder.

Neurodevelopmental disorders (NDDs) are a heterogeneous group of diseases for which the genetic basis is still unknown in more than half of the cases. Here, the authors report a NDD associated with disruptive variants in the TANC2 gene and show that rols, the TANC2 homolog in flies, is required for synapse growth and function.

Acheiropodia is associated with homozygous deletions in the LMBR1 gene around ZRS, an enhancer regulating SHH during limb development, but how these deletions lead to this phenotype is unknown. Here the authors use whole-genome sequencing, ChIP-seq, 4C-seq and DNA FISH to show that alterations in CTCF motifs are responsible via altered enhancer–promoter interactions.

Mutations in genes affecting intraflagellar transport account for some but not all cases of short rib polydactyly syndromes. Here Taylor et al. use whole exome sequencing and in vivo cell line assays to identify novel disease associated mutations in DYNC2LI1.

Simultaneous profiling of the genome, methylome, epigenome and transcriptome using single-molecule chromatin fiber sequencing and multiplexed arrays isoform sequencing identifies the genetic and molecular basis of an undiagnosed Mendelian disease case with an X;13-balanced translocation.

Personalized medicine requires accurate and ethnicity-optimized reference genome panels. Here, the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) evaluates typical variant filters and existing genome databases against newly sequenced African-ancestry populations.

Exome sequencing is a powerful approach for accelerating the discovery of the genes underlying Mendelian disorders and, increasingly, of genes underlying complex traits. This Review describes the experimental and analytical options for applying exome sequencing and the key challenges in using this approach.

Richard Thompson, Melissa Sambrotta and colleagues show that biallelic mutations in TJP2 cause severe cholestatic liver disease. Their findings suggest that loss of TJP2 protein disrupts the structural integrity of tight junctions in liver tissue, resulting in progressive liver damage.

Although DNA sequencing costs have fallen dramatically, they are still too high for whole genome sequencing to be used to routinely identify rare and novel variants in large cohorts. The targeted capture and massively parallel sequencing of the exomes of 12 humans is now reported. Freeman–Sheldon syndrome is used as a proof-of-concept that candidate genes for monogenic disorders can be identified by exome sequencing of a small number of unrelated, affected individuals.

Exome sequence analysis of nearly 10,000 people was carried out to identify alleles associated with early-onset myocardial infarction; mutations in low-density lipoprotein receptor (LDLR) or apolipoprotein A-V (APOA5) were associated with disease risk, identifying the key roles of low-density lipoprotein cholesterol and metabolism of triglyceride-rich lipoproteins.

Regie Lyn Santos-Cortez and colleagues identify a duplication variant within A2ML1 that cosegregates with otitis media in an indigenous Filipino pedigree. They also identify seven additional A2ML1 variants in otitis-prone children.

Silvère van der Maarel, Stephen Tapscott, Daniel Miller and colleagues show that digenic inheritance of a mutation in SMCHD1 and a chromosome 4 haplotype permissive for DUX4 mRNA polyadenylation causes fascioscapulohumeral dystrophy type 2.