A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism

Buckley, R.; Davis, Brian W.; Brashear, Wesley; Farias, Fabiana H.G.; Kuroki, Kei; Graves, Tina; Hillier, LaDeana W.; Kremitzki, Milinn; Li, Gang; Middleton, Rondo; Minx, Patrick; Tomlinson, Chad; Lyons, Leslie A.; Murphy, William J.; Warren, Wesley C.

doi:10.1101/2020.01.06.896258

Cited by 35 publications

(43 citation statements)

References 94 publications

(14 reference statements)

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“…The following tools/packages were applied to WGS and WES samples in accordance with variant processing as previously described 34 , BWA-MEM version 0.7.17 35 , Picard tools version 2.1.1 (http://broadinstitute.github.io/picard/), Samtools version 1.9, 36 and Genome Analysis toolkit version 3.8 37,38,39 . Code used for the variant calling workflow can be found at https://github.com/mu-feline-genome/batch_GATK_workflow.…”

Section: Methodsmentioning

confidence: 99%

A domestic cat whole exome sequencing resource for trait discovery

Rodney

Buckley

Fulton

et al. 2020

Preprint

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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.

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Section: Methodsmentioning

confidence: 99%

A domestic cat whole exome sequencing resource for trait discovery

Rodney

Buckley

Fulton

et al. 2020

Preprint

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“…The resulting probes were synthesized in a four-plex microarray format using Agilent SurePrint G3 technology, and used for DNA copy number profiling as described below. Upon the release of the felCat9 cat reference genome sequence assembly [8], each cat probe was remapped using BLAT [13] to assess their relative distribution and to interpret genomic profiling data in context with the architecture of the cat karyotype.…”

Section: Design and Construction Of The Feline Oligonucleotide Cgh Arraymentioning

confidence: 99%

“…With a more comprehensive feline reference genome assembly still in development, we embarked on an in-silico strategy that instead used a well-characterized dog microarray design to guide the construction of a second-generation feline CGH platform. Following the integration of our arrayed probe set into the most recent cat reference sequence assembly build [8], this platform now provides 350-fold higher overall resolution than our first generation array [7], bringing feline cytogenomic resources more closely in line with those of other model systems.…”

Section: Introductionmentioning

confidence: 99%

Development of a Genome-Wide Oligonucleotide Microarray Platform for Detection of DNA Copy Number Aberrations in Feline Cancers

Thomas

Pontius

Borst

et al. 2020

Veterinary Sciences

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The utility of the domestic cat as a model system for biomedical studies was constrained for many years by the absence of a comprehensive feline reference genome sequence assembly. While such a resource now exists, the cat continues to lag behind the domestic dog in terms of integration into the ‘One Health’ era of molecular medicine. Stimulated by the advances being made within the evolving field of comparative cancer genomics, we developed a microarray platform that allows rapid and sensitive detection of DNA copy number aberrations in feline tumors using comparative genomic hybridization analysis. The microarray comprises 110,456 unique oligonucleotide probes anchored at mean intervals of 22.6 kb throughout the feline reference genome sequence assembly, providing ~350-fold higher resolution than was previously possible using this technique. We demonstrate the utility of this resource through genomic profiling of a feline injection-site sarcoma case, revealing a highly disrupted profile of DNA copy number imbalance involving several key cancer-associated genes including KIT, TP53, PTEN, FAS and RB1. These findings were supported by targeted fluorescence in-situ hybridization analysis, which identified major alterations in chromosome structure, including complex intrachromosomal reorganization events typical of those seen in aggressive soft-tissue sarcomas of other species. We then characterized a second mass that was identified at a nearby site in the same patient almost 12 months later. This mass demonstrated a remarkably conserved genomic profile consistent with a recurrence of the original tumor; however the detection of subtle differences reflected evolution of the tumor over time. These findings exemplify the diverse potential of this microarray platform to incorporate domestic cat cancers into comparative and translational research efforts in molecular oncology.

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“…Fifty-two genomic DNA samples (~600 ng each) were submitted to GeneSeek (Neogene, Lincoln, NE, USA) for SNP genotyping on the Illumina Infinium Feline 63K iSelect DNA Array (Illumina, San Diego, CA, USA) [21]. Since SNP positions were based on an early assembly of the cat genome [25], the SNPs were relocalized to the 6 latest feline genome assembly, Felis_catus_9.0 [26]. Quality control of the SNP data was performed using PLINK (v1.07) [27].…”

Section: Dna Array Genotypingmentioning

confidence: 99%

“…Sequence reads were mapped to the latest feline genome assembly, Felis_catus_9.0, and processed as previously described [26]. Briefly, read mapping was conducted with Burrows-Wheeler Aligner (BWA) version 0.7.17 [31].…”

Section: Whole Genome Sequencingmentioning

confidence: 99%

A deletion inGDF7is associated with a heritable forebrain commissural malformation concurrent with ventriculomegaly and interhemispheric cysts in cats

Creighton

Buckley

et al. 2020

Preprint

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An inherited neurologic syndrome in a family of mixed-breed Oriental cats has been characterized as forebrain commissural malformation concurrent with ventriculomegaly and interhemispheric cysts. However, the genetic basis for this autosomal recessive syndrome in cats is unknown. Forty-three cats were genotyped on the Illumina Infinium Feline 63K iSelect DNA Array and used for analyses. Genome-wide association studies, including a sib-transmission disequilibrium test, a case-control association analysis, and homozygosity mapping, identified a critical region on cat chromosome A3. Short-read whole genome sequencing was completed for a cat trio segregating with the syndrome. A homozygous 7 bp deletion in growth differentiation factor 7 (GDF7) (c.221_227delGCCGCGC [p.Arg74Profs]) was identified in affected cats by comparison to the 99 Lives Cat variant dataset, validated using Sanger sequencing, and genotyped by fragment analyses. This variant was not identified in 192 unaffected cats in the 99Lives dataset. The variant segregated concordantly in an extended pedigree. Obligate carrier cats were heterozygous. In mice, GDF7 mRNA is expressed within the roof plate when commissural axons initiate ventrally-directed growth. This finding emphasizes the importance of GDF7 in the neurodevelopmental process in the mammalian brain. A genetic test can be developed for use by cat breeders to eradicate this variant.

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A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism

Cited by 35 publications

References 94 publications

A domestic cat whole exome sequencing resource for trait discovery

A domestic cat whole exome sequencing resource for trait discovery

Development of a Genome-Wide Oligonucleotide Microarray Platform for Detection of DNA Copy Number Aberrations in Feline Cancers

A deletion inGDF7is associated with a heritable forebrain commissural malformation concurrent with ventriculomegaly and interhemispheric cysts in cats

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