STK39 polymorphisms and blood pressure: an association study in British Caucasians and assessment of cis-acting influences on gene expression

<p>Abstract</p> <p>Background</p> <p>Blood pressure (BP) has significant heritability, but the genes responsible remain largely unknown. Single nucleotide polymorphisms (SNPs) at the <it>STK39 </it>locus were recently associated with hypertension by genome-wide association in an Amish population; <it>in vitro </it>data from transient transfection experiments using reporter constructs suggested that altered <it>STK39 </it>expression might mediate the effect. However, other large studies have not implicated <it>STK39 </it>in hypertension. We determined whether reported SNPs influenced <it>STK39 </it>expression <it>in vivo</it>, or were associated with BP in a large British Caucasian cohort.</p> <p>Methods</p> <p>1372 members of 247 Caucasian families ascertained through a hypertensive proband were genotyped for reported risk variants in <it>STK39 </it>(rs6749447, rs3754777, rs35929607) using Sequenom technology. MERLIN software was used for family-based association testing. <it>Cis</it>-acting influences on expression were assessed <it>in vivo </it>using allelic expression ratios in cDNA from peripheral blood cells in 35 South African individuals heterozygous for a transcribed SNP in <it>STK39 </it>(rs1061471) and quantified by mass spectrometry (Sequenom).</p> <p>Results</p> <p>No significant association was seen between the SNPs tested and systolic or diastolic BP in clinic or ambulatory measurements (all p > 0.05). The tested SNPs were all associated with allelic expression differences in peripheral blood cells (p < 0.05), with the most significant association for the intronic SNP rs6749447 (P = 9.9 × 10^-4). In individuals who were heterozygous for this SNP, on average the G allele showed 13% overexpression compared to the T allele.</p> <p>Conclusions</p> <p><it>STK39 </it>expression is modified by polymorphisms acting in <it>cis </it>and the typed SNPs are associated with allelic expression of this gene, but there is no evidence for an association with BP in a British Caucasian cohort.</p

Frequency of rare recessive mutations in unexplained late onset cerebellar ataxia.

Sporadic late onset cerebellar ataxia is a well-described clinical presentation with a broad differential diagnosis that adult neurologists should be familiar with. However, despite extensive clinical investigations, an acquired cause is identified in only a minority of cases. Thereafter, an underlying genetic basis is often considered, even in those without a family history. Here we apply whole exome sequencing to a cohort of 12 patients with late onset cerebellar ataxia. We show that 33% of 'idiopathic' cases harbor compound heterozygous mutations in known ataxia genes, including genes not included on multi-gene panels, or primarily associated with an ataxic presentation

Atl1 Regulates Choice between Global Genome and Transcription-Coupled Repair of O6-Alkylguanines

Nucleotide excision repair (NER) has long been known to remove DNA lesions induced by chemical carcinogens, and the molecular mechanism has been partially elucidated. Here we demonstrate that in Schizosaccharomyces pombe a DNA recognition protein, alkyltransferase-like 1 (Atl1), can play a pivotal role in selecting a specific NER pathway, depending on the nature of the DNA modification. The relative ease of dissociation of Atl1 from DNA containing small O6-alkylguanines allows accurate completion of global genome repair (GGR), whereas strong Atl1 binding to bulky O6-alkylguanines blocks GGR, stalls the transcription machinery, and diverts the damage to transcription-coupled repair. Our findings redraw the initial stages of the NER process in those organisms that express an alkyltransferase-like gene and raise the question of whether or not O6-alkylguanine lesions that are poor substrates for the alkyltransferase proteins in higher eukaryotes might, by analogy, signal such lesions for repair by NER

Identification of Heterozygous Single- and Multi-exon Deletions in IL7R by Whole Exome Sequencing

PURPOSE: We aimed to achieve a retrospective molecular diagnosis by applying state-of-the-art genomic sequencing methods to past patients with T-B+NK+ severe combined immunodeficiency (SCID). We included identification of copy number variations (CNVs) by whole exome sequencing (WES) using the CNV calling method ExomeDepth to detect gene alterations for which routine Sanger sequencing analysis is not suitable, such as large heterozygous deletions. METHODS: Of a total of 12 undiagnosed patients with T-B+NK+ SCID, we analyzed eight probands by WES, using GATK to detect single nucleotide variants (SNVs) and small insertions and deletions (INDELs) and ExomeDepth to detect CNVs. RESULTS: We found heterozygous single- or multi-exon deletions in IL7R, a known disease gene for autosomal recessive T-B+NK+ SCID, in four families (seven patients). In three families (five patients), these deletions coexisted with a heterozygous splice site or nonsense mutation elsewhere in the same gene, consistent with compound heterozygosity. In our cohort, about a quarter of T-B+NK+ SCID patients (26%) had such compound heterozygous IL7R deletions. CONCLUSIONS: We show that heterozygous IL7R exon deletions are common in T-B+NK+ SCID and are detectable by WES. They should be considered if Sanger sequencing fails to detect homozygous or compound heterozygous IL7R SNVs or INDELs

Allelic expression analysis of the osteoarthritis susceptibility locus that maps to MICAL3

<p>Abstract</p> <p>Background</p> <p>A genome-wide association scan with subsequent replication study that involved over 67,000 individuals of European ancestry has produced evidence of association of single nucleotide polymorphism rs2277831 to primary osteoarthritis (OA) with a P-value of 2.9 × 10^-5. rs2277831, an A/G transition, is located in an intron of <it>MICAL3</it>. This gene is located on chromosome 22q11.21 and the association signal encompasses two additional genes, <it>BCL2L13 </it>and <it>BID</it>. It is becoming increasingly apparent that many common complex traits are mediated by <it>cis</it>-acting regulatory polymorphisms that influence, in a tissue-specific manner, gene expression or transcript stability.</p> <p>Methods</p> <p>We used total and allelic expression analysis to assess whether the OA association to rs2277831 is mediated by an influence on MICAL3, BCL2L13 or BID expression. Using RNA extracted from joint tissues of 60 patients who had undergone elective joint replacement surgery, we assessed whether rs2277831 correlated with allelic expression of either of the three genes by: 1) measuring the expression of each gene by quantitative PCR and then stratifying the data by genotype at rs2277831 and 2) accurately discriminating and quantifying the mRNA synthesised from the alleles of OA patients using allelic-quantitative PCR.</p> <p>Results</p> <p>We found no evidence for a correlation between gene expression and genotype at rs2277831, with P-values of 0.09 for <it>BCL2L13</it>, 0.07 for <it>BID </it>and 0.33 for <it>MICAL3</it>. In the allelic expression analysis we observed several examples of significant (p < 0.05) allelic imbalances, with an allelic expression ratio of 2.82 observed in <it>BCL2L13 </it>(P = 0.004), 2.09 at <it>BID </it>(P = 0.001) and the most extreme case being at <it>MICAL3</it>, with an allelic expression ratio of 5.47 (P = 0.001). However, there was no correlation observed between the pattern of allelic expression and the genotype at rs2277831.</p> <p>Conclusions</p> <p>In the tissues that we have studied, our data do not support our hypothesis that the association between rs2277831 and OA is due to the effect this SNP has on <it>MICAL3, BCL2L13 </it>or <it>BID </it>gene expression. Instead, our data point towards other functional effects accounting for the OA associated signal.</p