Early-Onset Progressive Retinal Atrophy Associated with an IQCB1 Variant in African Black-Footed Cats (Felis nigripes)

Oh, Annie; Pearce, Jacqueline W.; Gandolfi, Barbara; Creighton, Erica K.; Suedmeyer, William Kirk; Selig, Michael; Bosiack, Ann P.; Castaner, Leilani J.; Whiting, Rebecca E.H.; Belknap, Ellen B.; Lyons, Leslie A.; Aderdein, Danielle; Alves, Paulo C.; Barsh, Gregory S.; Beale, Holly C.; Boyko, Adam R.; Castelhano, Marta G.; Chan, Patricia P.; Ellinwood, N. Matthew; Garrick, Dorian J.; Helps, Christopher R; Kaelin, Christopher B.; Leeb, Tosso; Lohi, Hannes; Longeri, M.; Malík, Richard; Montague, Michæl J.; Munday, John S.; Murphy, William J.; Pedersen, Niels C; Rothschild, Max F.; Swanson, William F.; Terio, Karen A.; Todhunter, Rory J.; Warren, Wesley C.

doi:10.1038/srep43918

Cited by 24 publications

(17 citation statements)

References 55 publications

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“…Three unrelated dwarf cats were submitted for whole genome sequencing as part of the 99 Lives Cat Genome Sequencing Consortium as previously described [23][24][25][26] (BioProject PRJNA308208, PRJNA288177; BioSamples: SAMN05980349, SAMN05980348, SAMN05980352). Reads were mapped to Felis_catus_9.0 (GCF_000181335.3/) and assigned to read groups using BWA-MEM from Burrows-Wheeler Aligner version 0.7.17 27 .…”

Section: Whole Genome Sequencingmentioning

confidence: 99%

Localization of a feline autosomal dominant dwarfism locus: a novel model of chondrodysplasia

Lyons

Fox

Chesney

et al. 2019

Preprint

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Despite the contribution of a few major genes for disproportionate dwarfism in humans, many dwarf patients are yet genetically undiagnosed. In domestic cats, disproportionate dwarfism has led to the development of a defined breed, the Munchkin or Minuet. This study examined the genetic aspects of feline dwarfism to consider cats as a new biomedical model. DNA from dwarf cats was genetically analyzed using parentage, linkage, and genome-wide association studies as well as whole genome sequencing.Each genetic approach localized the dwarfism phenotype to a region on cat chromosome B1. No coding variants suspected as causal for the feline dwarfism were identified but a critical region of ~5.7 Mb from B1:170,278,183-175,975,857 was defined, which implicates a novel gene controlling disproportionate dwarfism. A yet unidentified but novel gene variant, likely structural or regulatory, produces disproportionate dwarfism in cats, which may define undiagnosed human patients.

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Section: Whole Genome Sequencingmentioning

confidence: 99%

Localization of a feline autosomal dominant dwarfism locus: a novel model of chondrodysplasia

Lyons

Fox

Chesney

et al. 2019

Preprint

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“…However, an analysis of large structural variants as CNV in the domestic cat across breeds and individuals has not been attempted. New cat genomes are now available from the 99 Lives cat genome sequencing project, which has produced high quality NGS data of 30× coverage, using similar techniques and technologies [ 21 – 24 ]. In such a context, the present study is the first genome-wide CNV detection in the domestic cat and is based on the sequence data from the cat 99 Lives Project.…”

Section: Introductionmentioning

confidence: 99%

First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data

et al. 2018

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BackgroundCopy Number Variations (CNVs) have becoming very significant variants, representing a major source of genomic variation. CNVs involvement in phenotypic expression and different diseases has been widely demonstrated in humans as well as in many domestic animals. However, genome wide investigation on these structural variations is still missing in Felis catus. The present work is the first CNV mapping from a large data set of Next Generation Sequencing (NGS) data in the domestic cat, performed within the 99 Lives Consortium.ResultsReads have been mapped on the reference assembly_6.2 by Maverix Biomics. CNV detection with cn.MOPS and CNVnator detected 592 CNVs. These CNVs were used to obtain 154 CNV Regions (CNVRs) with BedTools, including 62 singletons. CNVRs covered 0.26% of the total cat genome with 129 losses, 19 gains and 6 complexes. Cluster Analysis and Principal Component Analysis of the detected CNVRs showed that breeds tend to cluster together as well as cats sharing the same geographical origins. The 46 genes identified within the CNVRs were annotated.ConclusionThis study has improved the genomic characterization of 14 cat breeds and has provided CNVs information that can be used for studies of traits in cats. It can be considered a sound starting point for genomic CNVs identification in this species.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5297-2) contains supplementary material, which is available to authorized users.

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“…A single lykoi cat was whole genome sequenced as previously described [32]. The selected cat was an F1 from the mating of two independently discovered foundation lineages from Virginia and Tennessee.…”

Section: Methodsmentioning

confidence: 99%

“…These variants were validated in the WGS cat by Sanger sequencing ( Supplementary Table 1 ). An assay was designed as previously described [32] to genotype the identified variants in pedigree A ( Supplementary Figure 1 ) and the additional cats, using the Agena Bioscience iPLEX Gold Genotyping reagent set (Agena Bioscience Inc., San Diego, CA) ( Supplementary Table 2 ). Products were genotyped with the MassARRAY System with Nanodispenser RS1000 (Agena Bioscience Inc., San Diego, CA).…”

Section: Methodsmentioning

confidence: 99%

Werewolf, there wolf: variants in Hairless associated with hypotrichia and roaning in the lykoi cat breed

Buckley

Gandolfi

Creighton

et al. 2020

Preprint

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A variety of cat breeds have been developed via novelty selection on aesthetic, dermatological traits, such as coat colors and fur types. A recently developed breed, the lykoi, was bred from cats with a sparse hair coat with roaning, implying full color and all white hairs. The lykoi phenotype is a form of hypotrichia, presenting as significant reduction in the average numbers of follicles per hair follicle group as compared to domestic shorthair cats, a mild to severe perifollicular to mural lymphocytic infiltration in 77% of observed hair follicle groups, and the follicles are often miniaturized, dilated, and dysplastic. Whole genome sequencing was conducted on a single lykoi cat that was a cross between two independently ascertained lineages. Comparison to the 99 Lives dataset of 194 non-lykoi cats suggested two variants in the cat homolog for Hairless (HR: lysine demethylase and nuclear receptor corepressor) as candidate causal variants. The lykoi cat was a compound heterozygote for two loss of function variants in HR, an exon 3 c.1255_1256dupGT (chrB1:36040783), which should produce a stop codon at amino acid 420 (p.Gln420Serfs*100) and, an exon 18 c.3389insGACA (chrB1:36051555), which should produce a stop codon at amino acid position 1130 (p.Ser1130Argfs*29). Ascertainment of 14 additional cats from founder lineages from Canada, France and different areas of the USA identified four additional loss of function HR variants likely causing the highly similar phenotypic hair coat across the diverse cats. The novel variants in HR for cat hypotrichia can now be established between minor differences in the phenotypic presentations.

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Early-Onset Progressive Retinal Atrophy Associated with an IQCB1 Variant in African Black-Footed Cats (Felis nigripes)

Cited by 24 publications

References 55 publications

Localization of a feline autosomal dominant dwarfism locus: a novel model of chondrodysplasia

Localization of a feline autosomal dominant dwarfism locus: a novel model of chondrodysplasia

First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data

Werewolf, there wolf: variants in Hairless associated with hypotrichia and roaning in the lykoi cat breed

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