Comparative analysis of canine and human melanomas

This paper presents epidemiological and clinical data from 2350 cases of melanocytic tumours from dogs sampled in France. In addition, we present the histological and genetic characterization of subsets of melanoma cases (n=153 and n=100, respectively), with a comparative aspect to human melanomas. Dog melanomas occur at the same anatomical sites than human melanomas, but with different frequency and severity. We demonstrate that the specificities of dog melanomas make them good models to understand the non-UV pathways of human melanomas. Interestingly, somatic mutations in oral canine melanomas were detected in the NRAS and PTEN genes, precisely at the same hotspots as human mutations. In contrast, mutations in the BRAF gene were not detected. This paper highlights the similarities and differences of dog and human melanoma types and the strong potential of dog melanomas to decipher the non-UV light pathways in different melanoma types, especially mucosal and acral types.Cet article présente les données épidémiologiques et cliniques de 2350 cas de tumeurs mélanocytaires canines collectées en France. Nous avons réalisé la caractérisation histologique (n = 153) et génétique (n = 100) d'un sous-groupe de mélanomes dont les résultats ont été comparés aux données des mélanomes humains. Les mélanomes apparaissent aux mêmes sites anatomiques chez le chien et l'Homme, mais avec des fréquences et des sévérités différentes. Nous montrons les prédispositions raciales des mélanomes canins et l'intérêt de ce modèle pour rechercher les gènes prédisposant difficiles à identifier chez l'Homme. Des mutations somatiques dans les gènes NRAS et PTEN ont été détectées dans les mélanomes buccaux canins, précisément aux mêmes points chauds (hotspots) que les mutations de ces gènes chez l'homme. Au contraire, aucune mutation dans le gène BRAF n'a été retrouvée dans les échantillons canins analysés. Ce travail met en lumière les homologies et différences entre les types de mélanomes humains et canins et démontre la force du modèle canin pour analyser les voies de signalisation non UV-dépendantes des mélanomes humains, particulièrement dans les types muqueux et acraux

Restriction site-associated DNA sequencing technologies as an alternative to low-density SNP chips for genomic selection: a simulation study in layer chickens

Abstract Background To reduce the cost of genomic selection, a low-density (LD) single nucleotide polymorphism (SNP) chip can be used in combination with imputation for genotyping selection candidates instead of using a high-density (HD) SNP chip. Next-generation sequencing (NGS) techniques have been increasingly used in livestock species but remain expensive for routine use for genomic selection. An alternative and cost-efficient solution is to use restriction site-associated DNA sequencing (RADseq) techniques to sequence only a fraction of the genome using restriction enzymes. From this perspective, use of RADseq techniques followed by an imputation step on HD chip as alternatives to LD chips for genomic selection was studied in a pure layer line. Results Genome reduction and sequencing fragments were identified on reference genome using four restriction enzymes (EcoRI, TaqI, AvaII and PstI) and a double-digest RADseq (ddRADseq) method (TaqI-PstI). The SNPs contained in these fragments were detected from the 20X sequence data of the individuals in our population. Imputation accuracy on HD chip with these genotypes was assessed as the mean correlation between true and imputed genotypes. Several production traits were evaluated using single-step GBLUP methodology. The impact of imputation errors on the ranking of the selection candidates was assessed by comparing a genomic evaluation based on ancestry using true HD or imputed HD genotyping. The relative accuracy of genomic estimated breeding values (GEBVs) was investigated by considering the GEBVs estimated on offspring as a reference. With AvaII or PstI and ddRADseq with TaqI and PstI, more than 10 K SNPs were detected in common with the HD SNP chip, resulting in an imputation accuracy greater than 0.97. The impact of imputation errors on genomic evaluation of the breeders was reduced, with a Spearman correlation greater than 0.99. Finally, the relative accuracy of GEBVs was equivalent. Conclusions RADseq approaches can be interesting alternatives to low-density SNP chips for genomic selection. With more than 10 K SNPs in common with the SNPs of the HD SNP chip, good imputation and genomic evaluation results can be obtained. However, with real data, heterogeneity between individuals with missing data must be considered

PNPLA1 mutations cause autosomal recessive congenital ichthyosis in golden retriever dogs and humans.

International audienceIchthyoses comprise a heterogeneous group of genodermatoses characterized by abnormal desquamation over the whole body, for which the genetic causes of several human forms remain unknown. We used a spontaneous dog model in the golden retriever breed, which is affected by a lamellar ichthyosis resembling human autosomal recessive congenital ichthyoses (ARCI), to carry out a genome-wide association study. We identified a homozygous insertion-deletion (indel) mutation in PNPLA1 that leads to a premature stop codon in all affected golden retriever dogs. We subsequently found one missense and one nonsense mutation in the catalytic domain of human PNPLA1 in six individuals with ARCI from two families. Further experiments highlighted the importance of PNPLA1 in the formation of the epidermal lipid barrier. This study identifies a new gene involved in human ichthyoses and provides insights into the localization and function of this yet uncharacterized member of the PNPLA protein family