Identification of NCAN as a candidate gene for developmental dyslexia

A whole-genome linkage analysis in a Finnish pedigree of eight cases with developmental dyslexia (DD) revealed several regions shared by the affected individuals. Analysis of coding variants from two affected individuals identified rs146011974G >A (Ala1039Thr), a rare variant within the NCAN gene co-segregating with DD in the pedigree. This variant prompted us to consider this gene as a putative candidate for DD. The RNA expression pattern of the NCAN gene in human tissues was highly correlated (R > 0.8) with that of the previously suggested DD susceptibility genes KIAA0319, CTNND2, CNTNAP2 and GRIN2B. We investigated the association of common variation in NCAN to brain structures in two data sets: young adults (Brainchild study, Sweden) and infants (FinnBrain study, Finland). In young adults, we found associations between a common genetic variant in NCAN, rs1064395, and white matter volume in the left and right temporoparietal as well as the left inferior frontal brain regions. In infants, this same variant was found to be associated with cingulate and prefrontal grey matter volumes. Our results suggest NCAN as a new candidate gene for DD and indicate that NCAN variants affect brain structure.Peer reviewe

Analysis of <i>ROBO1</i> in the Large Family Linked to <i>DYX5</i>

<div><p>(A) An abridged pedigree of the family linked to <i>DYX5</i> [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010050#pgen-0010050-b17" target="_blank">17</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010050#pgen-0010050-b19" target="_blank">19</a>]. Numbers refer to samples studied for <i>ROBO1</i> expression (C and D). A dot indicates carriers of the dyslexia-linked haplotype [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010050#pgen-0010050-b17" target="_blank">17</a>] and circled dots indicate individuals genotyped for all markers (B). Diamonds denote individuals genotyped for all markers, but not sharing the haplotype. Affected individuals are shaded black and unverified dyslectics are shaded gray.</p><p>(B) Markers (right) and alleles (left) that define the haplotype linked to dyslexia (A). The bar indicates the extent of the <i>ROBO1</i> haplotype carried by patients marked with a dot (A).</p><p>(C) Sequencing of cDNA reveals absent or attenuated expression (<i>p</i> < 0.017 for all measurements) of the <i>ROBO1</i> allele (SNP 6483A > T indicated by arrows) encoded by the dyslexia-linked haplotype as compared to genomic sequence. In the control, both alleles show equal allelic ratios in genomic and cDNA. Patient numbers refer to (A).</p><p>(D) Attenuation of <i>ROBO1</i> mRNA expression from the dyslexia-associated allele. Allelic expression of <i>ROBO1</i> was assessed by sequencing the SNP 6483 (A/T) as in (C). Allelic ratios were assessed by five to six replicated sequencing tracings in four controls (21 data points) and four dyslexic individuals (24 data points). The results are expressed as the mRNA level of the dyslexia-associated allele as compared to the corresponding allele mRNA level in controls. Data are shown as mean ± 1 standard error of the mean (bars). Significance was assessed by two-tailed <i>t</i> test.</p></div

Delineation of Translocation Breakpoint Region and <i>ROBO1</i> Structure

<div><p>(A) Fluorescence in situ hybridization with BAC clone RP11-143B12 as a probe, showing hybridization signals in Chromosome 3 (upward arrow), der(3), and der(8) (horizontal arrows).</p><p>(B) Southern hybridization with a probe derived from RP11-143B12 shows genomic rearrangements (arrowheads) with five restriction enzymes in translocation patient (P) compared to the control sample.</p><p>(C) A gene map of Chromosome 3p13-3q11.1 showing the cytogenetic localization of the translocation breakpoint (black bar). An arrow indicates the direction of <i>ROBO1</i> transcription. Localization of the translocation breakpoint (square bracket) to BACs AC117479 and AC117461.</p><p>(D) Splice variants and exon structure of <i>ROBO1</i> (exons numbered from 1–30). Novel exons a and 7b and additional sequence to exon 1 are indicated in solid black. Exons unique to <i>ROBO1</i> (hatched black) and <i>DUTT1</i> (hatched grey) and common to both <i>ROBO1</i> and <i>DUTT1</i> (solid grey) are indicated. Corresponding BACs to exons are shown below. The translocation disrupting <i>ROBO1</i> between exons 1 and 2 in AC117479 is shown by vertical grey bar. Dotted lines indicate <i>DUTT1</i> variants. Novel splice variants are shown by grey lines and numbered (1), exclusion of exon 2 (89–169 of AF040990) (2), exclusion of <i>DUTT1</i> exon 2 (1019–1345 of Z95705) (3), exclusion of exon 19 (2813–2829 of AF040990) (4), initial 165 bp of exon 22 (3037–3201 of AF040990) (5), 905 bp from exons 24–28 (3603–4508 of AF040990) (6), 878 bp from exons 25–28 (3641–4528 of AF040990) and (7), exclusion of exon 29 (4745–4939 of AF040990).</p></div

Coding Changes of <i>ROBO1</i> during Primate Evolution

<p>Phylogenetic tree of ROBO1 protein evolution in hominoids. Rat was used as the out-group in sequence comparisons. dN/dS ratios of the branches were calculated with the Codeml program, assuming a freely varying ratio. A model in which omega value was higher in lineages leading to humans, chimpanzees, and gorillas was significantly better than a free-ratio model (<i>p</i> < 0.001).</p

Polymorphisms in DCDC2 and S100B associate with developmental dyslexia

Genetic studies of complex traits have become increasingly successful as progress is made in next-generation sequencing. We aimed at discovering single nucleotide variation present in known and new candidate genes for developmental dyslexia: CYP19A1, DCDC2, DIP2A, DYX1C1, GCFC2 (also known as C2orf3), KIAA0319, MRPL19, PCNT, PRMT2, ROBO1 and S100B. We used next-generation sequencing to identify single-nucleotide polymorphisms in the exons of these 11 genes in pools of 100 DNA samples of Finnish individuals with developmental dyslexia. Subsequent individual genotyping of those 100 individuals, and additional cases and controls from the Finnish and German populations, validated 92 out of 111 different single-nucleotide variants. A nonsynonymous polymorphism in DCDC2 (corrected P=0.002) and a noncoding variant in S100B (corrected P=0.016) showed a significant association with spelling performance in families of German origin. No significant association was found for the variants neither in the Finnish case-control sample set nor in the Finnish family sample set. Our findings further strengthen the role of DCDC2 and implicate S100B, in the biology of reading and spelling.peerReviewe