Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants

Somatic mosaicism for a PDHA1 mutation in a female with pyruvate dehydrogenase deficiency

Somatic mosaicism for a mutation in the X-linked PDHA1 gene was found in a girl who presented with manifestations of pyruvate dehydrogenase deficiency. Mutation in the PDHA1 gene was suggested by a mosaic pattern of E1α subunit immunostaining; however, initial screening of cDNA and the exons and intro-exon boundaries yielded only normal sequence, apart from a heterozygous 4 bp insertion in intron 10. This was considered to be a polymorphism as it is also present in her unaffected mother who has normal enzyme activity and uniform E1α immunostaining in fibroblasts. Detailed genetic analysis, which included isolation of cloned fibroblasts expressing the mutant X chromosome, resulted in the identification of a base substitution in the acceptor splice site of intron 9 which leads to activation of a cryptic unstream splice site. The proportion of cells expressing the mutation was then determined by direct analysis of the X-inactivation pattern. Genetic diagnosis in this unique case of PDHA1 somatic mosaicism was complicated by the absence of an abnormal transcript in primary fibroblasts, the presence of three different alleles and an X-inactivation pattern favouring expression of the normal, paternal, X chromosome. Although the mutation was only present in a proportion of cells, and only expressed in a subset of these due to random X-inactivation, the resulting enzyme defect was sufficient to be clinically apparent

Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity

Obesity is a genetically heterogeneous disorder. Using targeted and whole-exome sequencing, we studied 32 human and 87 rodent obesity genes in 2,548 severely obese children and 1,117 controls. We identified 52 variants contributing to obesity in 2% of cases including multiple novel variants in GNAS, which were sometimes found with accelerated growth rather than short stature as describedw previously. Nominally significant associations were found for rare functional variants in BBS1, BBS9, GNAS, MKKS, CLOCK and ANGPTL6. The p.S284X variant in ANGPTL6 drives the association signal (rs201622589, MAF∼0.1%, odds ratio = 10.13, p-value = 0.042) and results in complete loss of secretion in cells. Further analysis including additional case-control studies and population controls (N = 260,642) did not support association of this variant with obesity (odds ratio = 2.34, p-value = 2.59 × 10-3), highlighting the challenges of testing rare variant associations and the need for very large sample sizes. Further validation in cohorts with severe obesity and engineering the variants in model organisms will be needed to explore whether human variants in ANGPTL6 and other genes that lead to obesity when deleted in mice, do contribute to obesity. Such studies may yield druggable targets for weight loss therapies