A domestic cat whole exome sequencing resource for trait discovery

Abstract

Over 94 million domestic cats are considered pets, who, as our companions, are also susceptible to cancers, common and rare diseases. Whole exome sequencing (WES) is a cost-effective strategy to study their putative disease-causing variants. Presented is ~35.8 Mb exome capture design based on the annotated Felis_catus_9.0 genome assembly, covering 201,683 regions of the cat genome. WES was conducted on 41 cats from various breeds with known and unknown diseases and traits, including 10 cats with prior whole genome sequence (WGS) data available, to test WES capture probe performance. A WES and WGS comparison was completed to understand variant discovery capability of each platform. At ~80x exome coverage, the percent of on-target base coverage >20x was 96.4% with an average of 10.4% off-target. For variant discovery, greater than 98% of WGS SNPs were also discovered by WES. Platform specific variants were mainly restricted to a small number of sex chromosome and olfactory receptor genes. Within the 41 cats with ~31 diseases and normal traits, 45 previously known disease or trait causal variants were observed, such as Persian progressive retinal degeneration and hydrocephalus. Novel candidate variants for polycystic kidney disease and atrichia in the Peterbald breed were also identified as well as a new cat patient with a known variant for cystinuria. These results show the discovery potential of deep exome sequencing to validate existing disease gene models and identify novel gene candidate alleles for many common and rare diseases in cats.

Neuronal Ceroid Lipofuscinosis in a Domestic Cat Associated with a DNA Sequence Variant That Creates a Premature Stop Codon in CLN6

“…The WES dataset used for analysis includes unaffected domestic cats (Buckley et al 2020b;Rodney et al 2020). The depth of exon coverage for the proband cat averaged 94.2x.…”

“…Whole genome sequencing (WGS) and whole exome sequencing (WES) are now feasible approaches for the interrogation of genomes for causal variants of diseases in domestic cats (Mauler et al 2017;Guevar et al 2019;Rodney et al 2020). The associated costs of WGS and in particular, WES, are competitive with the time and resources costs associated with direct targeted Sanger sequencing of candidate genes.…”

“…The V9.0 cat genome assembly has notable improvements due to the use of long-read sequences and an optical map for its construction (Buckley et al 2020a). This strong cat assembly supported the development of an exome capture resource for use in domestic cat disease investigations (Rodney et al 2020). Via the 99 Lives Cat Genome Project (http://felinegenetics.missouri.edu/ 99lives) a variant database of 200 cat genomes has been compiled (Buckley et al 2020b).…”

CTSK variant implicated in suspected pyknodysostosis in a domestic cat

“…DNA was isolated from the whole blood sample by organic extraction, and approximately 2.9 µg was submitted to whole-exome sequencing (WES), which was performed as previously described. 5 Felis catus 9.0 reference alignment 6 and Ensembl 94 gene annotation were used, as previously reported. 5 The variant call file was combined with variants determined from 39 additional cats with WES data.…”

“… 5 Felis catus 9.0 reference alignment 6 and Ensembl 94 gene annotation were used, as previously reported. 5 The variant call file was combined with variants determined from 39 additional cats with WES data. Variant data were analysed using VarSeq software (GoldenHelix) by assuming the affected cat was homozygous for a causal variant and no other cat in the data set had the variant present.…”