Validation of a microRNA target site polymorphism in <i>H3F3B</i> that is potentially associated with a broad schizophrenia phenotype

<div><p>Despite much progress, few genetic findings for schizophrenia have been assessed by functional validation experiments at the molecular level. We previously reported evidence for genetic linkage of broadly defined schizophrenia to chromosome 17q25 in a sample of 24 multiplex families. 2,002 SNPs under this linkage peak were analyzed for evidence of linkage disequilibrium using the posterior probability of linkage (PPL) framework. SNP rs1060120 produced the strongest evidence for association, with a PPLD|L score of 0.21. This SNP is located within the 3'UTR of the histone gene <i>H3F3B</i> and colocalizes with potential gene target miR-616. A custom miRNA target prediction program predicted that the binding of miR-616 to <i>H3F3B</i> transcripts would be altered by the allelic variants of rs1060120. We used dual luciferase assays to experimentally validate this interaction. The rs1060120 A allele significantly reduced luciferase expression, indicating a stronger interaction with miR-616 than the G allele (p = 0.000412). These results provide functional validation that this SNP could alter schizophrenia epigenetic mechanisms thereby contributing to schizophrenia-related disease risk.</p></div

Linkage disequilibrium between 1,544 SNPs and broad schizophrenia spectrum phenotype.

<p>PPLD|L values for 1,544 SNPs, including five MirSNPs (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194233#pone.0194233.t001" target="_blank">Table 1</a>), from chr17: 74,684,647 to 83,257,441 (GRCh38), were calculated using KELVIN v2.4.0 and plotted vs physical distance. The MirSNP rs1060120 in <i>H3F3B</i> produced a PPLD|L of 0.21, notably higher than the remaining SNPs.</p

Predicted MirSNPs from the chromosome 17q25 region of association/linkage to broadly defined schizophrenia.

<p>Predicted MirSNPs from the chromosome 17q25 region of association/linkage to broadly defined schizophrenia.</p

Whole-genome sequencing suggests mechanisms for 22q11.2 deletion-associated Parkinson’s disease

<div><p>Objectives</p><p>To investigate disease risk mechanisms of early-onset Parkinson’s disease (PD) associated with the recurrent 22q11.2 deletion, a genetic risk factor for early-onset PD.</p><p>Methods</p><p>In a proof-of-principle study, we used whole-genome sequencing (WGS) to investigate sequence variants in nine adults with 22q11.2DS, three with neuropathologically confirmed early-onset PD and six without PD. Adopting an approach used recently to study schizophrenia in 22q11.2DS, here we tested candidate gene-sets relevant to PD.</p><p>Results</p><p>No mutations common to the cases with PD were found in the intact 22q11.2 region. While all were negative for rare mutations in a gene-set comprising PD disease-causing and risk genes, another candidate gene-set of 1000 genes functionally relevant to PD presented a nominally significant (<i>P</i> = 0.03) enrichment of rare putatively damaging missense variants in the PD cases. Polygenic score results, based on common variants associated with PD risk, were non-significantly greater in those with PD.</p><p>Conclusions</p><p>The results of this first-ever pilot study of WGS in PD suggest that the cumulative burden of genome-wide sequence variants may contribute to expression of early-onset PD in the presence of threshold-lowering dosage effects of a 22q11.2 deletion. We found no evidence that expression of PD in 22q11.2DS is mediated by a recessive locus on the intact 22q11.2 chromosome or mutations in known PD genes. These findings offer initial evidence of the potential effects of multiple within-individual rare variants on the expression of PD and the utility of next generation sequencing for studying the etiology of PD.</p></div

Clinical and 22q11.2 deletion-related characteristics of individuals with 22q11.2 deletion syndrome of European Ancestry with whole-genome sequencing results.

<p>Clinical and 22q11.2 deletion-related characteristics of individuals with 22q11.2 deletion syndrome of European Ancestry with whole-genome sequencing results.</p

() and () QuantiSNP is able to detect as many as 3–4 SNPs in simulated 5 SNP aberration region but only if we accept false calls rates of around 10 in 100 000 SNPs

<p><b>Copyright information:</b></p><p>Taken from "QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data"</p><p></p><p>Nucleic Acids Research 2007;35(6):2013-2025.</p><p>Published online 6 Mar 2007</p><p>PMCID:PMC1874617.</p><p>© 2007 The Author(s)</p> However, in () and (), when the length of the event increases to 10 SNPs, QuantiSNP successfully detects nearly all affected SNPs in the deletion and duplication events even at very stringent false call rates of less than 1 in 100 000 SNPs. In all cases, the localization of the true boundary is good, with less than one extra SNP called outside of the true aberrant region

Rare nonsynonymous variants in 22q11.2 deletion-associated early-onset Parkinson’s disease (22q11.2ds-pd) patients compared with 22q11.2 deletion patients with no Parkinson’s disease (22q11.2DS-NPD).

<p>Rare nonsynonymous variants in 22q11.2 deletion-associated early-onset Parkinson’s disease (22q11.2ds-pd) patients compared with 22q11.2 deletion patients with no Parkinson’s disease (22q11.2DS-NPD).</p

Rare CNV burden in 340 unrelated adults with tetralogy of Fallot and/or pulmonary atresia.

a<p>Rare autosomal CNVs>10 kb and <6.5 Mb in size in individuals of European ancestry. Inclusion of three subjects with anomalies >6.5 Mb in a secondary analysis did not change the overall results (data not shown). Note that the above results also do not include 49 subjects of European ancestry with typical 1.5 to 3 Mb 22q11.2 deletions in the TOF group (all syndromic); see text for details on the results if these subjects had been included.</p>b<p>Fisher's exact test.</p

Rare large CNVs (>500 kb) in 43 of 433 unrelated adults with tetralogy of Fallot.

<p>Case, subjects from discovery sample (n = 433) with TOF; Locus, cytogenetic location of CNV; CNV start, hg18 (NCBI Build 36.1, March 2006); CNV size, in base pairs; CN, type of copy number aberration; Very rare, not found in 2,773 controls (•), see text for details; Confirmed, by qPCR and/or FISH (•) or not done (ND); Origin, <i>de novo</i> or inherited (where known); # of genes, number of known genes overlapped by a CNV as annotated in the Database of Genomic Variants (<a href="http://projects.tcag.ca/variation/" target="_blank">http://projects.tcag.ca/variation/</a>; September 2011); Candidate gene(s), selected based on reported cardiovascular system involvement; References derived from systematic searches of human (e.g., Online Mendelian Inheritance in Man; <a href="http://www.omim.org/" target="_blank">http://www.omim.org/</a>) and model organism (e.g., Mouse Genome Informatics; <a href="http://www.informatics.jax.org/" target="_blank">http://www.informatics.jax.org/</a>) databases presented in Table 4 in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002843#pgen.1002843.s001" target="_blank">Supporting Information S1</a>.</p>a<p><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002843#pgen-1002843-g002" target="_blank">Figure 2</a> in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002843#pgen.1002843.s001" target="_blank">Supporting Information S1</a>.</p>b<p><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002843#pgen-1002843-t003" target="_blank">Table 3</a>.</p>c<p>Neighbor of a top disease gene (GATA4, NKX2-5, TBX5), as identified in the pathway analysis (Table 11 in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002843#pgen.1002843.s001" target="_blank">Supporting Information S1</a>).</p>d<p>Non-European ancestry.</p>f<p>Previously reported by our group <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002843#pgen.1002843-Costain1" target="_blank">[21]</a>.</p>g<p>Figure 3 in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002843#pgen.1002843.s001" target="_blank">Supporting Information S1</a>.</p

Functional clusters of candidate genes for tetralogy of Fallot.

<p>Diagram of results of pathway analyses comparing rare CNVs in cases and controls. Five overlapping functional clusters involved 19 gene-sets; functional neighbors of three known candidate genes identified another cluster (circle size indicates relative number of cases involved).</p