Sanger sequencing confirmation of the disease segregating variant identified in the linked region.

<p>Candidate region identified using linkage analysis in PACG pedigree animals (left). Sequence chromatograms from a carrier (C), confirms heterozygous genotype whereas affected animals (A) display a homozygous state of variant identified in <i>NEB</i> (g.5588214 A->G) (Right).</p

Basset Hound Pedigree used in this study.

<p>The affected Basset 5a in the second generation was duplicated twice (5b and 5c) in order to break two otherwise computationally confounding breeding loops. Genotypes of typed markers within region uncovered following two-point linkage analysis are shown. Shading indicates the transmission pattern of heterozygous parental haplotypes to affected, homozygous offspring. Additional patterns of shading including diagonal lines indicate variation to the same haplotype identified in the other pedigree members. Complete concordance of homozygous haplotype inheritance with the disease phenotype is observed in all affected animals.</p

Whole genome homozygosity mapping results.

<p>A red peak reaching a 1.0 max score of statistical significance depicts a homozygous region on chromosome 19. The region coincides with the 0.49 Mbp locus identified using two-point linkage analysis and is bracketed by recombination spots (indicated in red). The identified haploblock fulfills the zygosity criterion by displaying homozygosity in affected animals (indicated in red) and heterozygosity in unaffected carriers (indicated in green).</p

Genome-wide linkage analysis of SNP genotype data.

<p>Using two-point linkage analysis, a maximum LOD_two-point score of 3.07 was achieved for a 0.49 Mb locus on chromosome 19. The red line of statistical significance indicates LOD scores values > 3 (A). Using multipoint linkage analysis, an increased maximum LOD_multipoint score of 3.24 was achieved for a locus mapped to the same location (B). A schematic view of the maximum LOD scores achieved across chromosome 19. The statistically significant locus is located at the distal end of chromosome 19 (Chr19: 54,949,124–56,765,346) and spans 1.82 Mbp (C).</p

A Fisher exact contingency table of genotypes observed in a confirmatory animal cohort for the <i>RIF1</i> variant (g.55723957 C->T).

<p>Forty-four additional unaffected and affected Basset Hounds were selected for confirmatory sequencing of the <i>RIF1</i> variant (g.55723957 C->T). The observed total of individuals and percentage of individuals displaying a specific genotype is shown for each cell respectively. The two-tailed P value is 0.57 (Fisher Exact Probability Test)</p><p>A Fisher exact contingency table of genotypes observed in a confirmatory animal cohort for the <i>RIF1</i> variant (g.55723957 C->T).</p

A Fisher exact contingency table of genotypes observed in a confirmatory animal cohort for the <i>NEB</i> variant (g.55885214 A->G).

<p>Forty-four additional unaffected and affected Basset Hounds were selected for confirmatory sequencing of the <i>NEB</i> variant (g.55885214 A->G). The observed total of individuals and percentage of individuals displaying a specific genotype is shown for each cell respectively.</p><p>The two-tailed P value is 0.00034 (Fisher Exact Probability Test)</p><p>A Fisher exact contingency table of genotypes observed in a confirmatory animal cohort for the <i>NEB</i> variant (g.55885214 A->G).</p

Alignment of the amino acid sequence of exon 48 in Nebulin in several vertebrate species.

<p>The Lysine (K) residue (highlighted in blue) at position p.2051 is conserved among 23 vertebrate species.</p

Analysis of the <i>CEP290</i> cryptic exons.

<p>(A) Expected transcripts for each model. (B) Exon Y is expressed in all tissues in either <i>Cep290</i>^{<i>hum/hum</i>} and <i>Cep290</i>^{<i>lca/lca</i>} mice. (C) Only in the <i>Cep290</i>^{<i>lca/lca</i>} model, exon X is expressed, either with exon Y or without, at very low levels. The arrow indicates the band that contains both cryptic exons (exon X and exon Y) in the same transcript. <i>Cep290</i>^lca/lca PCR products were run longer to clearly separate the two different bands. (D) Schematic representation of the different transcripts containing cryptic exons found in the three mouse models. Mouse exons and introns are depicted in black, while human exons and introns are represented in blue. Cryptic exons X and Y are shown in grey and red, respectively. Arrows and letters indicate the position of the oligonucleotides in the cryptic exons. Semi-quantification was performed using ImageJ software [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079369#B21" target="_blank">21</a>]. MQ: H₂O (negative control); F: human LCA fibroblasts; B: Brain; K: Kidney; R: Retina; Lu: Lung; S: Spleen; T: Testis and Li: Liver.</p

Transcriptional characterisation of <i>Cep290</i> in humanized mouse models.

<p>(A-B) <i>Cep290</i> expression levels in various mouse tissues were assessed by RT-PCR. Regions containing murine exons 10 to 13 (A) and 24 to 27 (B) were analyzed. No differences were observed. (C) Amplification using human primers was also assessed in the three models. Only humanized models showed amplification. (D) Actin was used for normalization and comparison among tissues and models. MQ: H₂O (negative control); B: Brain; K: Kidney; R: Retina; Lu: Lung; S: Spleen; T: Testis and Li: Liver.</p

Generation of the <i>Cep290</i> humanized mouse models.

<p>(A) Structure of the <i>CEP290</i> gene in human and mouse (drawn to scale). (B) Two mouse models were generated by introducing human exons 26 and 27 and intron 26, either with or without the LCA-causing mutation (depicted with *), to the mouse <i>Cep290</i> gene. Human and mouse loci, targeting vector and recombinant locus are depicted. Arrows and letters indicate the position of the oligonucleotides (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079369#pone.0079369.s001" target="_blank">Table S1</a>). </p