Clinical and genetic profile of WBS patient cohorts.

<p><b><i>Key:</i></b> +ve = deleted for ELN/LIMK1 FISH probe; −ve = not deleted for ELN/LIMK1 FISH probe. Bc refers to the centromeric breakpoint and Bm to the medial breakpoint.</p>#<p>approximate size due to the breakpoints residing in LCR duplicon regions. FD = facial dysmorphology; C = cardiac abnormality; SS = short stature; Hca = hypercalcaemia; HA = Hyperacusis; HS = hypersociability; Anx = Anxiety; Fear = Fears or Phobias; DD = developmental delay.</p

Williams-Beuren syndrome region on chromosome 7q11.23.

<p>Black lines represent the regions deleted in WBS patients. A: common ∼1.5/1.6 Mb deletion; B: ∼1.8 Mb deletion; C: patient WBS245; D: patient WBS023I; E: partial deletion patients with only isolated SVAS and associated cardiac pathologies<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047457#pone.0047457-Tassabehji1" target="_blank">[22]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047457#pone.0047457-Tassabehji2" target="_blank">[23]</a>. Shaded boxes represent the B-block flanking duplicons containing the deletion breakpoints (Bc = centromeric; Bm = medial; Bt = telomeric). Not to scale.</p

Cognitive similarities and differences between WBS patient cohorts and atypical partial deletion cases.

<p>Graphs showing the performance of WBS patients in Groups 1 or 2 (∼1.5/1.6 Mb or 1.8 Mb deletion respectively), patients with atypical deletions, and MA matched and CA matched controls. Differences occur between WBS patient subgroups on spatial perception. Atypical patients show impairments on emotion recognition and spatial perception relative to controls. Error bars represent standard error; * = significant difference at p<.01, ^○ = marginal difference at p<.05.</p

Descriptive statistics for the WBS patient cohorts and for the atypical partial deletion cases (WBS425 and WBS023I).

<p><i>Note</i>: Mean (standard deviation) and range are reported for chronological age, IQ, and Socio-Economic Status. Chronological age and mental age are in years. Mean (standard deviation) are provided for WJ-R COG Factor Scores. Standard scores are represented. Standard scores have a mean of 100 and a standard deviation of 15. Scores below 80 are impaired compared to typically developing chronological age matched controls.</p

Characterisation of Genetic Variation in <i>ST8SIA2</i> and Its Interaction Region in NCAM1 in Patients with Bipolar Disorder

<div><p>Alpha-2,8-sialyltransferase 2 (ST8SIA2) is an enzyme responsible for the transfer of polysialic acid (PSA) to glycoproteins, principally the neuronal cell adhesion molecule (NCAM1), and is involved in neuronal plasticity. Variants within <i>ST8SIA2</i> have previously shown association with bipolar disorder, schizophrenia and autism. In addition, altered PSA-NCAM expression in brains of patients with schizophrenia or bipolar disorder indicates a functional dysregulation of glycosylation in mental illness. To explore the role of sequence variation affecting PSA-NCAM formation, we conducted a targeted re-sequencing study of a ∼100 kb region – including the entire ST8SIA2 gene and its region of interaction with NCAM1 – in 48 Caucasian cases with bipolar disorder using the Roche 454 platform. We identified over 400 DNA variants, including 47 putative novel variants not described in dbSNP. Validation of a subset of variants via Sequenom showed high reliability of Roche 454 genotype calls (97% genotype concordance, with 80% of novel variants independently verified). We did not observe major loss-of-function mutations that would affect PSA-NCAM formation, either by ablating ST8SIA2 function or by affecting the ability of NCAM1 to be glycosylated. However, we identified 13 SNPs in the UTRs of <i>ST8SIA2</i>, a synonymous coding SNP in exon 5 (rs2305561, P207P) and many additional non-coding variants that may influence splicing or regulation of <i>ST8SIA2</i> expression. We calculated nucleotide diversity within <i>ST8SIA2</i> on specific haplotypes, finding that the diversity on the specific “risk” and “protective” haplotypes was lower than other non-disease-associated haplotypes, suggesting that putative functional variation may have arisen on a spectrum of haplotypes. We have identified common and novel variants (rs11074064, rs722645, 15∶92961050) that exist on a spectrum of haplotypes, yet are plausible candidates for conferring the effect of risk and protective haplotypes via multiple enhancer elements. A Galaxy workflow/pipeline for sequence analysis used herein is available at: <a href="https://main.g2.bx.psu.edu/u/a-shaw-neura/p/next-generation-resources" target="_blank">https://main.g2.bx.psu.edu/u/a-shaw-neura/p/next-generation-resources</a>.</p></div

Cognitive similarities and differences between WBS patient cohorts and atypical partial deletion cases.

<p>Performance of WBS patients in Groups 1 or 2 (∼1.5/1.6 Mb or 1.8 Mb deletion respectively), patients with atypical deletions, and MA matched and CA matched controls. Differences are seen between WBS patient subgroups on cognitive flexibility. Atypical patients also show impairments on cognitive flexibility relative to controls. Error bars represent standard error; * = significant difference at p<.01, ^○ = marginal difference at p<.05.</p

Haplotype phasing of all detected nucleotide variants in <i>ST8SIA2</i> gene region.

<p>The gene structure is shown above, with the minor allele frequency of each SNP detected shown by the histogram immediately below the gene (red represents frequency of alternate allele). The red, green and yellow bars on the left indicate the haplotype on which the detected variation resides (risk  =  red; protective  =  green; other haplotypes  =  yellow). Detected variation with respect to the specific haplotype on which it resides is shown to the right of haplotype bars, where non-reference alleles are coloured in light blue (homozygous) and dark blue (heterozygous). The locations of the six SNP markers that were used to define the haplotypes are shown below the variation. The location of the PreSTIGE enhancer elements within the 454 sequenced region from human skeletal muscle myoblasts (HSMM) are indicated in orange, and from neuronal precursor cells (NPC) are indicated in purple. PreSTIGE enhancer locations were obtained from <a href="http://genetics.case.edu/prestige/" target="_blank">http://genetics.case.edu/prestige/</a>).</p

Genotype concordance between 454-generated genotype calls and those directly genotyped via Illumina GoldenGate or Illumina 660 W.

<p>Genotype calls are divided into two categories: all calls; or confident genotype calls based on Genotype Quality (GQ) ≥ 10. Call accuracy gives the concordance between the SNP genotype derived from 454 data and Illumina-generated data across all samples excluding missing data, and the call rate incorporates missing data on an individual basis. These are calculated for all genotypes, and heterozygous (het) calls only.</p

Comparison of SNP detection methods from 454 data, and identification of bona fide SNPs for functional analysis.

<p>The number of SNPs (n) which were detected individually by Refmapper and GATK are shown. The SNPs that were called by both algorithms (and passed filtering) are given in the intersection, and the union represents SNPs that were called by at least one package. SNPs detected in the 5.3 kb region sequenced via Sanger sequencing are also listed.</p

Comparison of detected SNP variants with all SNPs detected in 1 kG data.

<p>The minor allele frequency (MAF) of all SNPs identified in the sequenced region from 174 Caucasian Europeans from phase I of the 1 kG project (n = 519) and 48 bipolar disorder cases (n = 412) were compared. SNPs found in bipolar individuals only (yellow) and 1 kG individuals only (light blue) were predominantly rare alleles whereas those found in both sets (green) were predominantly common.</p