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RESEARCH ARTICLE
Genetic epidemiology of blood type, disease
and trait variants, and genome-wide genetic
diversity in over 11,000 domestic cats
Heidi AndersonID
1
*, Stephen DavisonID
1
, Katherine M. LytleID
1
, Leena HonkanenID
1
,
Jamie FreyerID
1
, Julia Mathlin
1
, Kaisa Kyo
¨stila
¨
2,3,4
, Laura InmanID
1
, Annette LouviereID
1
,
Rebecca Chodroff ForanID
1
, Oliver P. FormanID
1
, Hannes LohiID
2,3,4
, Jonas DonnerID
1
1Wisdom Panel Research Team, Wisdom Panel, Kinship, Portland, Oregon, United States of America,
2Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland, 3Department of
Veterinary Biosciences, University of Helsinki, Helsinki, Finland, 4Folkha
¨lsan Research Center, Helsinki,
Finland
*heidi.anderson@kinship.co
Abstract
In the largest DNA-based study of domestic cats to date, 11,036 individuals (10,419 pedi-
greed cats and 617 non-pedigreed cats) were genotyped via commercial panel testing eluci-
dating the distribution and frequency of known disease, blood type, and physical trait
associated genetic variants across cat breeds. This study provides allele frequencies for
many disease-associated variants for the first time and provides updates on previously
reported information with evidence suggesting that DNA testing has been effectively used to
reduce disease associated variants within certain pedigreed cat populations over time. We
identified 13 disease-associated variants in 47 breeds or breed types in which the variant
had not previously been documented, highlighting the relevance of comprehensive genetic
screening across breeds. Three disease-associated variants were discovered in non-pedi-
greed cats only. To investigate the causality of nine disease-associated variants in cats of
different breed backgrounds our veterinarians conducted owner interviews, reviewed clinical
records, and invited cats to have follow-up clinical examinations. Additionally, genetic vari-
ants determining blood types A, B and AB, which are relevant clinically and in cat breeding,
were genotyped. Appearance-associated genetic variation in all cats is also discussed.
Lastly, genome-wide SNP heterozygosity levels were calculated to obtain a comparable
measure of the genetic diversity in different cat breeds. This study represents the first com-
prehensive exploration of informative Mendelian variants in felines by screening over
10,000 pedigreed cats. The results qualitatively contribute to the understanding of feline var-
iant heritage and genetic diversity and demonstrate the clinical utility and importance of
such information in supporting breeding programs and the research community. The work
also highlights the crucial commitment of pedigreed cat breeders and registries in support-
ing the establishment of large genomic databases, that when combined with phenotype
information can advance scientific understanding and provide insights that can be applied to
improve the health and welfare of cats.
PLOS GENETICS
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OPEN ACCESS
Citation: Anderson H, Davison S, Lytle KM,
Honkanen L, Freyer J, Mathlin J, et al. (2022)
Genetic epidemiology of blood type, disease and
trait variants, and genome-wide genetic diversity in
over 11,000 domestic cats. PLoS Genet 18(6):
e1009804. https://doi.org/10.1371/journal.
pgen.1009804
Editor: Sally Louise Ricketts, University of
Cambridge, UNITED KINGDOM
Received: September 7, 2021
Accepted: May 6, 2022
Published: June 16, 2022
Copyright: ©2022 Anderson et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited.
Data Availability Statement: All 11k dataset used
for assessment of genetic diversity among breeds
required to replicate the study findings without
disclosing sensitive information related to study
participants is available from the Dryad Digital
Repository https://doi.org/10.5061/dryad.
gb5mkkwrg. All other relevant data are within the
manuscript and its Supporting Information files.
Funding: Finnish Cat Association (https://www.
kissaliitto.fi), Jane and Aatos Erkko Foundation
Author summary
Domestic cats are one of the world’s most popular companion animals, of which pedi-
greed cats represent small unique subpopulations. Genetic research on pedigreed cats has
facilitated discoveries of heritable conditions resulting in the availability of DNA testing
for studying and managing inherited disorders and traits in specific cat breeds. We have
explored an extensive study cohort of 11,036 domestic cat samples representing pedigreed
cats of 90 breeds and breed types. This work provided insight into the heritage of feline
disease and trait alleles. We gained knowledge on the most common and relevant genetic
markers for inherited disorders and physical traits, and the genetic determinants of the
clinically relevant AB blood group system. We also used a measure of genetic diversity to
compare inbreeding levels within and between breeds. This information can help support
sustainable breeding goals within the cat fancy. Direct-to-consumer genetic tests help to
raise awareness of various inherited single gene conditions in cats and provide informa-
tion that owners can share with their veterinarians. In due course, ventures of this type
will enable the genetics of common complex feline disease to be deciphered, paving the
way for precision healthcare with the potential to ultimately improve welfare for all cats.
Introduction
Domestic cats are valued companions to humans, with owners seeking high quality veterinary
care to support long-term wellness and positive outcomes for disease treatment. Cat genomes
are structured in a similar way to humans, with 90% of their genes having a human homo-
logue, and cats and humans also suffer from many similar diseases [1]. Domestic cats, like
dogs, can serve as naturally occurring models for many human diseases, in which the develop-
ment of therapeutic treatments may be helpful for both veterinary and human patients [1–6].
Genomic medicine, encompassing the understanding of individual genetic variability in dis-
ease risk and the customization of healthcare by patient subgroups, is now feasible and likely
to become a future standard-of-care in veterinary medicine and the care of companion ani-
mals, including cats [1]. Fueling this development for felines specifically are improved geno-
mic resources and technologies, combined with a steady increase in the discovery of
Mendelian disease and trait variants [7,8]. Genetic testing is a form of genomic medicine when
used for diagnosing diseases or traits of clinical relevance, as the results are patient-specific
and can potentially be used to tailor treatment to the disease and the patient [9]. Direct-to-con-
sumer genetic testing is now readily available, and further empowers owners to proactively
invest in potentially changing the medical care for their pet.
Domestication of cats occurred approximately 10,000 years ago [10], with pedigreed cats
emerging over the last 150 years representing genetically unique domestic cat subpopulations.
The majority of the approximately 100 cat breeds, breed types (or varieties of the breed)
known today, including several new breeds being developed, represent breeds that are less
than 75 years old. The genetic research of isolated populations in humans, dogs, and more
recently cats has vastly improved identification of genetic disease and trait variants for use in
genetic diagnostics and medicine. As an example, through studies of pedigreed cats, research-
ers have identified disease-associated variants for both diseases that are affecting cats world-
wide such as Polycystic Kidney Disease and rare disorders within a specific breed such as
Hypotrichosis in Birman cats [11–19]. Moreover, studies of cat breeds have enabled discovery
of the genetic variants determining blood types of the AB blood group system that associate
PLOS GENETICS
Genetic epidemiology of over 11,000 cats
PLOS Genetics | https://doi.org/10.1371/journal.pgen.1009804 June 16, 2022 2 / 30
(https://jaes.fi) and Wisdom Panel (https://www.
wisdompanel.com) partially covered biobanking
costs (HL). The funders had no role in study
design, data collection and analysis, decision to
publish, or preparation of the manuscript.
Competing interests: I have read the journal’s
policy and the authors of this manuscript have the
following competing interests: HA, SD, LH, KML,
JF, JM, LI, AL, RCF, OPF and JD are present or
former employees of Wisdom Panel Kinship that
offers canine and feline DNA testing as a
commercial service. HL consults Wisdom Panel,
Kinship.
with neonatal isoerythrolysis and hemolytic transfusion reactions; and many of the physical
traits, which are an integral part of breed development [8,20–25]. Research on genetically iso-
lated populations has further highlighted that reduced genetic diversity, because of isolation
and generations of selective breeding to consistently produce animals with uniform appear-
ance, can manifest as an increase in the number of health conditions that are identified [26–
29]. For more than a decade, it has been common practice to eradicate disease-associated vari-
ants from pedigreed cat breeding populations using DNA testing. However, the focus on eradi-
cating single DNA variants from a breed could contribute to severe loss of genetic diversity,
especially if implemented strictly instead of thoughtfully [30]. Improved genomic perspective
on domestic cats, and the breeds’ level of genetic diversity, have propelled a growing number
of breeders to incorporate breeding strategies for sustaining genetic diversity and increasing it
through crossbreeding. Crossbreeding in cat breeding is also used to introduce a trait that is
new to the breed. In addition, the cat breeds that are becoming increasingly more common
have a hybrid origin such as the world’s most popular cat breed, the Bengal, that is a result of
breeding an Asian Leopard Cat with the domestic cat.
Our previous work has elucidated that the comprehensive screening of genetic variants in
dogs is convenient and justified as it provides information to support breeding programs, vet-
erinary care and health research [31]. Further large-scale multiplex screening approaches were
taken to characterize canine disease heritage and the relative frequency and distribution of dis-
ease-associated variants across breeds and to explore the frequency of known canine appear-
ance-associated variants among dog breeds [32,33]. As we will demonstrate, such efforts are
now equally feasible in cats and hold comparable promise for gaining insight into the genetic
epidemiology of feline diseases and traits to better inform feline breeding decisions and estab-
lish the foundation for precision medicine of individuals, populations, and breeds.
This study represents the first comprehensive genetic evaluation of known feline disease
and trait variants through the examination of 87 variants in 10,419 pedigreed cats and 617
non-pedigreed cats. These results provide a first glance into feline variant heritage across cat
breeds and underscore the importance of large-scale population screening studies in improv-
ing veterinary diagnostics, breeding programs, and health recommendations for all cats.
Materials and methods
Ethics statement
Feline DNA was obtained by Wisdom Panel as owner submitted, non-invasive cheek swab
samples or was collected by certified veterinary clinics as cheek swab and blood samples in
accordance with international standards for animal care and research. All cat owners provided
consent for the use of their cat’s DNA sample in scientific research. University biobank sam-
ples were collected under the permit ESAVI/6054/04.10.03/2012 by the Animal Ethics Com-
mittee of the State Provincial Office of Southern Finland, Ha¨meenlinna, Finland.
Study sample population
The cat study population consisted of 10,419 pedigreed cats and 617 non-pedigreed cats whose
samples were obtained during the development and provision of the commercially available
MyCatDNA and Optimal Selection Feline tests (Wisdom Panel, Helsinki, Finland and Wis-
dom Panel, Vancouver, WA, USA, respectively) between 2016 and 2021. The 10,419 pedigreed
cat samples represented 90 breeds and breed types (or variants of the breed) with 60 (66.6%)
breeds and breed types represented by 15 or more individuals (S1 Table).
The breed of a cat was reported by its owner with accompanying registration information
confirming the cat was registered with The International Cat Association (TICA), Fe
´de
´ration
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Internationale Fe
´line (FiFe), The Cat Fanciers’ Association (CFA), or World Cat Federation
(WCF) standards. Additional breeds not yet recognized by any major breed registry but with
an established community of breed hobbyists were also considered breeds for the purposes of
this study. The non-pedigreed cat sample set consisted of mixed breeds, breed crosses, or ran-
dom-bred cats. The tested cats were most often from the United States of America (54.9%),
while cats from Finland (17.4%), Canada (5.3%), United Kingdom (3.5%), Norway (3.5%) and
Sweden (3.3%), Russia (2.5%) and France (1%) represented other notable subgroups (>1% of
the sample).
Microarray development and validation
A custom genotyping microarray for selected feline disease and trait associated variants (S2
Table) was developed based on the Illumina Infinium XT platform (Illumina, Inc., San Diego,
CA, USA), commercially available as the Wisdom Panel Complete for Cats / MyCatDNA /
Optimal Selection Feline tests. The microarray was designed and validated for use following
the same protocol and principles as previously described for canines [21]. Firstly, public data-
bases [8] and searches of the scientific literature were used to identify likely causal variants for
feline Mendelian disorders and traits. Secondly, genotyping assays for the identified variants
were designed according to the manufacturer’s guidelines (Illumina, Inc.). At least three tech-
nical replicates of each target sequence were included in the array design. Thirdly, the valida-
tion of each specific disease and trait assay was completed with the use of control samples of
known genotype or synthetic oligonucleotides in the case of rare conditions for which no con-
trol samples were available. In addition, owner-provided photographs contributed to pheno-
typic validation of trait variant tests.
Genotyping
Microarray genotyping analyses were carried out following manufacturer-recommended stan-
dard protocols for the Illumina XT platform (Illumina, Inc.). All genotype data from samples
with call rates below 98% of the analyzed markers were discarded to ensure high quality data
and all disease-associated variant calls were confirmed by manual review. Only disease and
trait variants reaching 100% sensitivity and specificity upon testing with natural control sam-
ples that are homozygous/heterozygous for the disease or trait associated variant (70/87 vari-
ants), or validated using synthetic control oligonucleotides (17/87 variants), were considered
for reporting. Genome-wide genetic diversity was measured as a percentage of heterozygous
SNPs across a set of 7,815 informative SNPs. Data available at Dryad Digital Repository [34].
Selected disease-associated variant findings were genotyped using standard capillary sequenc-
ing on an ABI3730xl DNA Analyzer platform (Thermo Fisher Scientific, Waltham, MA, USA)
as a secondary technology to provide further validation of results that were unexpected for the
breed. Sequencing was performed at the Sanger Sequencing Unit of the Finnish Institute of
Molecular Medicine (FIMM). The DNA extractions and PCR-product preparation and purifi-
cation were carried out as previously described in detail [31] using ~20 ng of genomic template
DNA and an Amplitaq Gold Master Mix-based protocol according to the manufacturer’s
instructions (Applied Biosystems, Waltham, MA, USA).
Clinical validations
Medical history information for genetically affected cats was collected through interviews with
cat owners and veterinary clinicians. Clinical examinations were performed for confirmation
of a Factor XII deficiency diagnosis by collecting a blood sample for an activated partial throm-
boplastin time screening test through IDEXX Laboratories (IDEXX Europe B.V., Hoofddorp,
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Genetic epidemiology of over 11,000 cats
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The Netherlands). Progressive Retinal Atrophy diagnosis was confirmed via ophthalmic exam-
ination performed by an ECVO (European College of Veterinary Ophthalmologists) board-
certified veterinary specialist. A set of blood type determination data was available through the
records of the former Genlab Niini (Helsinki, Finland). All additional phenotype information
(clinical or trait) and documentation was obtained through voluntary owner submissions.
Results
Overview of genotyping results
A total of 11,036 domestic cats, mainly pedigreed cats (N = 10,419) representing 90 breeds and
breed types (or variants of the breed) and an additional 617 non-pedigreed cats, were success-
fully genotyped on the custom array (the sample failure rate for DNA extracted from buccal
swabs was <1%). Genetic screening included genotyping of 7,815 informative SNP markers
across the genome and 87 variants associated with blood type, diseases, and/or physical
appearance; 83 of which were evaluated in the entire 11,036 cat study sample and four more
recently included variants to the genotyping platform that were screened for in a subset of
2,186 samples (Tables 1and S1–S4). We observed 57 (65.5%) of the 87 tested variants at least
once in this study cohort, including 22 (38.6%) disease-associated variants and 35 (61.4%) vari-
ants associated with an appearance-associated trait or blood type (Tables 1and S2–S4). The
maximum number of disease-associated variants observed in any one individual was four. We
observed that 2,480 (22.5%) of the tested cats had at least one disease-associated variant present
and 452 (4.1%) of the tested cats were potentially at risk for at least one health condition, in
accordance with the disorders’ modes of inheritance. The maximum number of different dis-
ease-associated variants present in a single breed was 9; this was observed in the Maine Coon,
which was the breed that was represented by the most individuals (N = 1971) tested in this
dataset. Three genetic variants for the diseases Hyperoxaluria Type II [35], Lipoprotein Lipase
Deficiency [36] and Myotonia Congenita [37], were solely observed in non-pedigreed cat
samples.
While we observed several disease-associated variants in the breeds with documented
occurrence, we also detected 13 disease-associated variants in additional breeds or breed types
in which the variants had not previously been reported. For each additional breed finding,
extensive review of the breed information was performed, including use of the proprietary
Wisdom Panel cat breed determination algorithm where necessary. Details of the variants
found in additional breeds are listed in Table 2. Within these additional breeds, individuals
that were genetically affected (having one copy of a dominant variant or two copies of a reces-
sive variant) were identified and flagged for clinical follow-up. Individuals that were genetically
affected for candidate disease-associated variants previously presented by a case study, were
also shortlisted for follow-up.
Genetic epidemiology of the common AB blood group system across breeds
and breed types
The major feline AB blood groups including blood type A, blood type B and the rare blood
type AB are caused by functional differences in the cytidine monophospho-N-acetylneurami-
nic acid hydroxylase enzyme, encoded by the CMAH gene, that impact the ability of the
enzyme to convert sialic acid N-acetylneuraminic acid (Neu5Ac) to N-glycolylneuraminic acid
(Neu5Gc) on erythrocytes [20–25]. For purpose-bred cats, the current convention (2019 typ-
ing panel recommendation) [23,24], proposes that genetic testing for blood types A, B and AB
should be based on panel testing of the four following variants c.179G>T, c.268T>A,
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Table 1. Prevalence and frequency of the tested disease, blood type and trait -associated variants in all cats.
Disease OMIA ID Gene OMIA
variant ID
MOI Derived Allele
Frequency (%) in
all cats
Cats genotyped
with 0 copies
Cats genotyped
with 1 copy
Cats genotyped
with 2 copies
Acute Intermittent Porphyria—5
variants
001493–
9685
HMBS 596, 530,
135, 402,
501
AD not present 11036
Autoimmune Lymphoproliferative
Syndrome
002064–
9685
FASLG 613 AR not present 11036
Burmese Head Defect 001551–
9685
ALX1 550 AR 0.02% 11034 2
Congenital Adrenal Hyperplasia 001661–
9685
CYP11B1 117 AR not present 10990
Congenital Erythropoietic Porphyria 001175–
9685
UROS 137 AR not present 11036
Congenital Myasthenic Syndrome 001621–
9685
COLQ 944 AR 0.1% 11025 11
Cystinuria Type 1A 000256–
9685
SCL3A1 141 AR not present 11036
Cystinuria Type B 002023–
9685
SLC7A9 143 AR 0.1% 11025 10
Cystinuria Type B—2 variants 002023–
9685
SCL7A9 142, 144 AR not present 11036
Dihydropyrimidinase Deficiency 001776–
9685
DPYS 125 AR not present 11036
Factor XII Deficiency 000364–
9685
F12 533 AR 1.3% 10640 264 12
Factor XII Deficiency�000364–
9685
F12 147 AR 7.0% 1894 261 22
Familial Episodic Hypokalemic
Polymyopathy
001759–
9685
WNK4 312 AR 0.02% 11031 5
Glutaric Aciduria Type II 001457–
9685
ETFDH 1439 AR not present 11036
Glycogen Storage Disease 000420–
9685
GBE1 742 AR 0.01% 11035 1
GM1 Gangliosidosis 000402–
9685
GLB1 126 AR not present 11036
GM2 Gangliosidosis 001427–
9685
GM2A 496 AR not present 11034
GM2 Gangliosidosis Type II
(Discovered in the Burmese)
001462–
9685
HEXB 381 AR 0.01% 11034 2
GM2 Gangliosidosis Type II—2
variants (Discovered in domestic
cats)
001462–
9685
HEXB 741, 309 AR not present 11036
Hemophilia B -2 variants 000438–
9685
F9 127, 310 X-linked not present 11036
Hyperoxaluria Type II 000821–
9685
GRHPR 383 AR 0.04% 11028 8
Hypertrophic Cardiomyopathy;
HCM (Discovered in the Ragdoll)
000515–
9685
MYBPC3 902 AD 0.2% 10991 42 1
Hypertrophic Cardiomyopathy;
HCM (Discovered in the Maine
Coon)
000515–
9685
MYBPC3 901 AD 0.9% 10858 169 9
Hypotrichosis 001949–
9685
FOXN1 1319 AR not present 11018
(Continued)
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Table 1. (Continued )
Disease OMIA ID Gene OMIA
variant ID
MOI Derived Allele
Frequency (%) in
all cats
Cats genotyped
with 0 copies
Cats genotyped
with 1 copy
Cats genotyped
with 2 copies
Lipoprotein Lipase Deficiency 001210–
9685
LPL 131 AR 0.02% 11032 4
MDR1 Medication Sensitivity 001402–
9685
ABCB1 322 AR 0.6% 10910 123 3
Mucopolysaccharidosis Type I 000664–
9685
IDUA 500 AR not present 10952
Mucopolysaccharidosis Type VI 000666–
9685
ARSB 132 AR not present 11036
Mucopolysaccharidosis Type VII—2
variants
000667–
9685
GUSB 133, 139 AR not present 11036
Myotonia Congenita 000698–
9685
CLCN1 408 AR 0.00% 11035 1
Osteochondrodysplasia and Earfold 000319–
9685
TRPV4 140 AD 0.4% 10945 90 1
Polycystic Kidney Disease; PKD 000807–
9685
PKD1 314 AD 0.1% 10965 11
Progressive Retinal Atrophy
(Discovered in the Bengal)
002267–
9685
KIF3B 1191 AR 1.1% 11765 241 2
Progressive Retinal Atrophy
(Discovered in the Persian)�
001222–
9685
AIPL1 1214 AR not present 2178
Progressive Retinal Atrophy; rdAc-
PRA
001244–
9685
CEP290 384 AR 1.1% 10792 227 17
Pyruvate Kinase Deficiency; PK-def 000844–
9685
PKLR 899 AR 2.9% 10286 588 18
Sphingomyelinosis; Niemann-Pick
C1
000725–
9685
NPC1 134 AR not present 11036
Sphingomyelinosis; Niemann-Pick
C2
002065–
9685
NPC2 420 AR not present 10969
Spinal Muscular Atrophy
(Discovered in the Maine Coon)
002389–
9685
LIX1 649 AR 0.1% 11016 13
Vitamin D-Dependent Rickets 001661–
9685
CYP27B1 315 AR not present 11025
Blood type, Allele Designation
Blood type B, b
1
(2019 Typing panel) 000119–
9685
CMAH 119 AR 12.9% 8626 1981 428
Blood type B, c (2019 Typing panel) 000119–
9685
CMAH 799 AR 1.5% 10707 318 11
Blood type B, b
2
(2019 Typing panel) 000119–
9685
CMAH 800 AR 1.6% 10707 301 28
Blood type B, b
3
(2019 Typing
panel)�
000119–
9685
CMAH 1062 AR 2.4% 2081 90 8
Trait, Allele Designation
Albinism, c
a
(Discovered in Oriental
breeds)
000202–
9685
TYR 494 AR not present 11022
Amber, e (Discovered in the
Norwegian Forrest Cat)
001199–
9685
MC1R 123 AR 0.03% 10982 4 1
Chocolate, b 001249–
9685
TYRP1 379 AR 13.2% 8762 1636 638
Cinnamon, b
l
001249–
9685
TYRP1 306 AR 4.0% 10308 4264 2402
(Continued)
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Table 1. (Continued )
Disease OMIA ID Gene OMIA
variant ID
MOI Derived Allele
Frequency (%) in
all cats
Cats genotyped
with 0 copies
Cats genotyped
with 1 copy
Cats genotyped
with 2 copies
Charcoal, A
Pb
(Discovered in the
Bengal) -2 variants
000201–
9685
ASIP 1451, 1450 intermediate 1.9% 10660 328 48
Colorpoint, c
b
(Discovered in the
Burmese)
000202–
9685
TYR 121 AR 6.8% 9860 859 317
Colorpoint, c
s
(Discovered in the
Siamese)
000202–
9685
TYR 122 AR 30.5% 6537 2247 2238
Dilution, d 000031–
9685
MLPH 495 AR 41.6% 4364 4370 2402
Gloving, w
g
001580–
9685
KIT 620 AR 12.7% 8661 1943 432
Hairlessness, re
hr
(Discovered in the
Sphynx)
001583–
9685
KRT71 382 AR 3.9% 10774 232 30
Long Hair, M1 (Discovered in the
Ragdoll)
000439–
9685
FGF5 595 AR 3.10% 10394 576 64
Long Hair, M2 (Discovered in the
Norwegian Forrest Cat)
000439–
9685
FGF5 311 AR 2.7% 10540 390 103
Long Hair, M3 (Discovered in the
Ragdoll and Maine Coon)
000439–
9685
FGF5 498 AR 12.0% 8253 1661 414
Long Hair, M4 (Discovered in many
breeds)
000439–
9685
FGF5 130 AR 38.10% 5188 3273 576
Partial and Full White, w
s
, W 001737–
9685
KIT 732 AD 20.8% 7478 2504 1046
Polydactyly, Hw 000810–
9685
LMBR1 432 AD
(incomplete)
1.30% 10774 232 30
Polydactyly, UK1 000810–
9685
LMBR1 433 AD
(incomplete)
0.02% 11033 2 1
Polydactyly, UK2 000810–
9685
LMBR1 434 AD
(incomplete)
not present 11036
Rexing, r (Discovered in the Cornish
Rex)
001684–
9685
LPAR6 522 AR 1.0% 10913 13 108
Rexing, re
dr
(Discovered in the
Devon Rex)�
001581–
9685
KRT71 380 AR 5.5% 1986 33 100
Russet, e
r
(Discovered in the
Burmese)
001199–
9685
MC1R 561 AR not present 10953
Short Kinked Tail, jb (Discovered in
the Japanese Bobtail)
001987–
9685
HES7 145 AD
(incomplete)
0.3% 10993 17 26
Short Tail, C1199del (Discovered in
the Manx)
000975–
9685
T525 AD 0.3% 10776 65
Short Tail, T988del (Discovered in
the Manx)
000975–
9685
T523 AD 1.8% 10900 99
Short Tail, C1169del (Discovered in
the Manx)
000975–
9685
T524 AD 0.06% 10883 14
Solid Color, a 000201–
9685
ASIP 493 AR 56.2% 3187 3280 4556
Other genotyped Variants
#
Congenital Erythropoietic Porphyria 001175–
9685
UROS 137 - 0.7% 10880 148 8
Mucopolysaccharidosis Type VI
Modifier
000666–
9685
ARSB 1320 - 2.5% 10537 443 56
Blood type B related 000119–
9685
CMAH 430 - 12.9% 7937 2589 509
(Continued)
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c.364C>T and c.1322delT of CMAH. In this study, we obtained genotypes for ten blood type-
associated CMAH variants; c.1-53delGTCGAAGCCAACGAGCAA (18bp indel), c.139C>T,
c.142G>A, c.179G>T, c.187A>G, c.268T>A, c.327A>C, c.364C>T, c. 1322delT and
c.1603G>A. All 11,036 cats were genotyped for nine of these CMAH variants, while
c.1322delT was more recently added to the genotyping platform providing genotype results for
a subset of 2,186 cats (19.7%). To evaluate the suitability of the proposed ‘2019 typing panel’ as
the blood type genotyping scheme, we compared the obtained genotype information to the
immunological blood type results available for 220 cats of this study cohort (S5 Table). We
found that blood types assigned according to the cat’s 2019 typing panel-based genotype
showed a 99.1% concordance with immunologically determined blood types. One Ragdoll
with the c/c genotype indicative of blood type AB [20,23,24], had been determined serologi-
cally to have blood type A according to the cat’s owner and one Donskoy with the A/b geno-
type indicative of blood type A had been determined serologically to have blood type AB.
Retesting or further clinical investigation were not performed for these cats due to lack of
availability.
After determining the suitability of 2019 typing panel, we based genetic blood typing on the
variants: c.268T>A, (b
1
); c.179G>T, (b
2
); c.364C>T, (c—resulting in blood type AB); and
c.1322delT (b
3
). The variants b
1
, b
2
and c were observed widely distributed across breeds with
frequencies of 12.6%, 1.6% and 1.5% in all cats, respectively (S4 Table). No more than two vari-
ants in total were found in any individual cat. Though generally uncommon in all cats, variant
b
2
was a major variant associated with blood type in the breeds Chartreux, Donskoy, Egyptian
Mau, Minuet Longhair, Pixiebob, Siberian, Tennessee Rex, Tonkinese, Toybob, Turkish
Angora and Turkish Van. Variant b
3
was exclusively found in Ragdolls (16.9% allele fre-
quency) and in a Ragdoll mix across the subset of 2,186 genotyped cats representing 69 breeds
and varieties (S4 Table). As the data suggested that variant b
3
is private to the Ragdoll popula-
tion, blood type frequencies for each breed were estimated considering variants b
1
, b
2
and c
genotype (available across the entire study sample) for non-Ragdoll breeds and including b
3
genotype results for the Ragdoll breed only.
Based on genetic blood type determination, blood type B was most common in the follow-
ing five breeds or breed groups with >15 individuals tested: American Curl (40.4%), British
Shorthair breed types (20.3%), Cornish Rex (33%), Devon Rex (30.3%) and Havana Brown
Table 1. (Continued )
Disease OMIA ID Gene OMIA
variant ID
MOI Derived Allele
Frequency (%) in
all cats
Cats genotyped
with 0 copies
Cats genotyped
with 1 copy
Cats genotyped
with 2 copies
Blood type B related 000119–
9685
CMAH 1431 - 6.5% 9844 953 238
Blood type B related 000119–
9685
CMAH 118 - 16.3% 8621 1985 430
Blood type B related 000119–
9685
CMAH 801 - 25.2% 6554 3398 1081
Blood type B related 000119–
9685
CMAH 1446 - 30.2% 5901 3613 1522
Blood type B related 000119–
9685
CMAH 120 - 12.8% 8614 2021 399
�The allele frequencies and genotypes are based on a subset of 2,186 samples (19.8% of the full study sample) screened for this variant.
# Genetic screening for these variants is available, but the predictive value is low. Abbreviations: MOI; mode of inheritance, AR; autosomal recessive, AD; autosomal
dominant.
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Table 2. Summary of disease-associated variant findings in additional breeds and breed types.
Disease OMIA ID Gene; OMIA
variant ID
Derived allele prevalence in previously
known breeds (with % for breeds with
>15 genotyped cats)
Cats in additional breed(s) with Derived allele
prevalence in additional breed(s) (with % for breeds
with >15 individuals genotyped)
Cystinuria Type B 002023–
9685
SLC7A9; 143 non-pedigree cat (0/617) 0.0%
Maine Coon (3/1971) 0.2%
Sphynx (0/547) 0.0%
Maine Coon Polydactyl (3/150) 0.02%
Siberian (4/559) 0.7%
Factor XII Deficiency�000364–
9685
F12; 147 non-pedigreed cat (21/90) 23.3%
Bengal (63/311) 20.3%
Maine Coon (53/497) 10.6%
Siamese (2/21) 9.5%
Balinese (2/9)
Bombay (1/1)
British Shorthair (4/96) 4.1%
Cashmere (2/3)
Devon Rex (17/97) 17.5%
Donskoy (2/4)
Elf (1/8)
Exotic Shorthair (4/9)
Highlander (1/94) 1.0%
Himalayan (1/2)
Lykoi (3/19) 15.8%
Maine Coon Polydactyl (1/43) 2.3%
Minuet (1/4)
Minuet Longhair (3/11)
Munchkin (1/15) 6.7%
Munchkin Longhair (2/5)
Neva Masquerade (1/12)
Oriental Longhair (1/2)
Oriental Shorthair (2/12)
Persian (1/5)
Peterbald (3/6)
Ragdoll (36/298) 12.0%
Savannah (5/12)
Scottish Fold Shorthair (3/31) 9.7%
Scottish Straight (1/21) 4.8%
Scottish Straight Longhair (1/5)
Selkirk Rex (8/17) 47.0%
Selkirk Rex Longhair (6/16) 37.5%
Siberian (5/97) 5.1%
Sphynx (9/110) 8.1%
Tennessee Rex (10/13)
Turkish Angora (5/13)
Factor XII Deficiency 000364–
9685
F12; 533 non-pedigree cat (29/606) 4.8%
Bengal (1/1668) 0.06%
Maine Coon (195/1964) 9.9%
Siamese (2/144) 1.4%
American Shorthair (1/48) 2.0%
Balinese (1/76) 1.3%
Cymric (2/16) 12.5%
Highlander (1/201) 0.5%
Himalayan (1/16) 6.3%
Maine Coon Polydactyl 3.02% (9/149) 6.0%
Manx (2/29) 6.9%
Minuet (1/11)
Munchkin (2/38) 5.2%
Munchkin Longhair (1/10)
Ragdoll (1/1110) 0.01%
Savannah (5/78) 6.4%
Tennessee Rex (22/32) 68.7%
GM2 Gangliosidosis Type II 001462–
9685
HEXB; 381 Burmese (1/113) 0.9% non-pedigreed cat (Burmese mix) (1/617) 0.7%
Hypertrophic Cardiomyopathy; HCM
(Discovered in the Maine Coon)
000515–
9685
MYBPC3; 901 Maine Coon (163/1971) 0.8% Maine Coon Polydactyl (10/150) 6.7%
non-pedigree cat (2/617) 0.3%
Pixiebob Longhair (1/12)
Siberian (1/559) 0.2%
(Continued)
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Table 2. (Continued )
Disease OMIA ID Gene; OMIA
variant ID
Derived allele prevalence in previously
known breeds (with % for breeds with
>15 genotyped cats)
Cats in additional breed(s) with Derived allele
prevalence in additional breed(s) (with % for breeds
with >15 individuals genotyped)
Hypertrophic Cardiomyopathy; HCM
(Discovered in the Ragdoll)
000515–
9685
MYBPC3; 902 Ragdoll (33/1115) 3.0% American Bobtail Longhair (4/35) 11.4%
American Bobtail Shorthair (1/9)
Highlander (1/201) 0.5%
Munchkin 1.25% (1/40) 2.5%
RagaMuffin (2/118) 1.7%
non-pedigree cat (1/617) 0.2%
MDR1 Medication Sensitivity 001402–
9685
ABCB1; 322 non-pedigree cat (5/617) 0.8%
Ragdoll (0/1115) 0.0%
Russian Blue (0/64) 0.0%
Siamese (1/146) 0.7%
Balinese (2/76) 2.6%
Maine Coon (107/1971) 5.4%
Maine Coon Polydactyl (10/150) 6.7%
Turkish Angora (1/110) 0.9%
Osteochondrodysplasia and Earfold 000319–
9685
TRPV4; 140 Scottish Fold Longhair (13/14)
Scottish Fold Shorthair (72/76) 94.7%
non-pedigree cat (Scottish Fold mix) (6/617) 1.0%
Polycystic Kidney Disease; PKD 000807–
9685
PKD1; 314 Persian (0/118) 0.0%
Exotic Shorthair (1/68) 1.5%
Scottish Fold Shorthair (2/76) 2.6%
Siberian (1/559) 0.2%
Ragdoll (1/1114) 0.09%
Maine Coon (5/1966) 0.3%
Scottish Straight (1/61) 1.6%
Progressive Retinal Atrophy
(Discovered in the Bengal)
002267–
9685
KIF3B; 1191 Bengal (322/1703) 18.9% Highlander (7/201) 3.5%
Highlander Shorthair (2/30) 6.7%
Savannah (1/80) 1.3%
non-pedigree cat (Bengal Mix) (1/607) 0.2%
Progressive Retinal Atrophy; rdAc-
PRA (Discovered in the Abyssinian)
001244–
9685
CEP290; 384 Abyssinian (18/167) 10.7%
Balinese (15/76) 19.7%
Cornish Rex (31/106) 29.2%
Oriental Shorthair (41/178) 23.0%
Pederbald (8/17) 47.0%
Siamese (44/146) 30.1%
Somali (6/47) 12.7%
American Shorthair (1/49) 2.0%
Devon Rex (14/447) 3.1%
Donskoy (1/17) 5.9%
European Shorthair (1/91) 1.1%
Havana Brown (1/30) 3.3%
Highlander (1/201) 0.5%
Maine Coon (2/1971) 0.1%
Manx (3/30) 10.0%
non-pedigree cat (14/617) 0.2%
Oriental Longhair (17/51) 33.3%
Pixiebob Longhair (1/12)
Ragdoll (11/1115) 1.0%
Savannah (10/80) 12.5%
Scottish Fold Shorthair (2/76) 2.6%
Sphynx (1/547) 0.2%
Tennessee Rex (1/35) 2.9%
Pyruvate Kinase Deficiency; PK-def 000844–
9685
PKLR; 899 Abyssinian (9/163) 5.5%
Somali (11/78) 14.1%
Bengal (190/1692) 11.2%
Egyptian Mau (12/51) 23.5%
Laperm (1/35) 2.9%
non-pedigree cat (15/607) 2.9%
Norwegian Forest Cat (4/121) 3.3%
Maine Coon (280/1955) 14.3%
Savannah (11/78) 14.1%
Singapura (2/45) 4.4%
Caracat (1/1)
Chausie (1/6)
European Shorthair (1/91) 1.1%
Highlander (4/201) 2.0%
Highlander Shorthair (2/30) 6.7%
Lykoi (7/104) 6.7%
Maine Coon Polydactyl (30/150) 20.2%
Minuet Longhair (2/24) 8.3%
Munchkin (2/39) 5.1%
Neva Masquerade (1/23) 4.3%
Pixiebob (5/19) 26.3%
Pixiebob Longhair (4/11)
Toyger (1/13)
Spinal Muscular Atrophy 002389–
9685
LIX1; 649 Maine Coon (11/1971) 0.6% Highlander (1/201) 0.5%
Maine Coon Polydactyl (1/150) 0.7%
�There was a subset of 2,186 samples (19.8% of the full study sample) screened for this variant.
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(20%). In addition, the breeds in which the rare blood type AB was present with a frequency of
>1% were European Shorthair (2.2%), Lykoi (1%), Scottish Fold (3.3%), RagaMuffin (3.4%),
Ragdoll (2.2%) and Russian Blue breed types (1.5%). The proportions of type A, type B and
type AB blood for each breed or breed group with >15 individuals tested are shown in Table 3
(breed groups listed in S6 Table).
Factor XII Deficiency and Pyruvate Kinase Deficiency are widespread
blood disorders in the cat population
Factor XII Deficiency is a widely distributed heritable trait in the domestic cat population [38].
Factor XII Deficiency is a clinical hemostatic defect that manifests as a prolonged activated
partial thromboplastin time (aPTT) which would be observed in a presurgical coagulation
assay, but does not require transfusions [39]. Two variants of the F12 gene: c.1321delC and
c.1631G>C, have been identified in a colony of inbred cats from the United States and in a lit-
ter of cats from Japan, respectively [40,41]. These variants are both considered common in the
domestic cat [39]. The most severe aPTT prolongation is observed in cats homozygous for
both variants [39]. In accordance with previous observations [39], we noted that the
c.1321delC variant always co-segregates with c.1631G>C, while one or two copies of the latter
can be inherited in the absence of the c.1321delC variant. The observed variant frequencies for
the c.1321delC and c.1631G>C variants were 1.3% and 7% in all cats (Table 1). The frequency
of the c.1631G>C variant was based on a subset of 2,186 genotyped cats, as the variant repre-
sented a more recent discovery added to the genotyping platform. The presence of the tested
F12 variants was found in the following breeds in which cases of clinical Factor XII Deficiency
have been documented: Himalayan, Maine Coon, Manx, Munchkin, Oriental Shorthair, Per-
sian, Ragdoll, Siberian, and Siamese. This supports the tested variants’ causal role in Factor XII
Deficiency. Moreover, we discovered the presence of the c.1631G>C variant in the Turkish
Angora, which is related to the Turkish Van breed, in which clinical cases of Factor XII Defi-
ciency have been documented [39], but no representatives of this breed were in the subset of
2,186 cats screened for the presence of the c.1631G>C variant. Additionally, the tested F12
gene variants were absent in Norwegian Forest Cats, in which the recently identified candidate
variant c.1549C>T of F12 gene could potentially be a more common cause of observed cases
of Factor XII Deficiency [39]. In all, we identified the two variants of the F12 gene present in
13 more breeds and breed types, and the c.1631G>C variant present alone in 19 additional
breeds and breed types. The Tennessee Rex represents a breed with high frequency (>40%) for
both variants observed together (Table 2). Finally, we obtained laboratory results from a
10-month-old intact female Maine Coon homozygous for the c.1321delC and c.1631G>C var-
iants of F12 gene. This individual showed a prolonged aPTT of >180 seconds (laboratory ref-
erence <13.4 seconds), confirming Factor XII Deficiency in a Maine Coon and further
evidence of association between the tested variants and clinical signs.
Pyruvate Kinase Deficiency (PK-def) is an inherited anemia characterized by low levels of
the pyruvate kinase enzyme. The insufficient presence of the pyruvate kinase enzyme causes
red blood cells to break easily, resulting in hemolytic anemia. PK-def shows a marked clinical
variability, including variation in the age of disease onset and severity [42,43]. A single nucleo-
tide substitution (c.693+304G>A) in intron 5 of the PKLR gene, with a hypothesized impact
on splicing, has been associated with the manifestation of PK-def in the Abyssinian and Somali
breeds [43], but has also been previously reported in at least 15 additional cat breeds. Across
the entire dataset the PK-def associated variant was found at 3.1% and 2.2% in the Abyssinian
and Somali breeds respectively, and was also present in 21 additional breeds (Tables 2and S4).
Several cats from the Bengal, Maine Coon, and Maine Coon Polydactyl breeds were identified
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Table 3. Genetically determined proportions of type A, type B and type AB blood for each breed or breed type
with >15 individuals tested.
Breeds and breed types No. of tested cats Type A (A/A, A/b, A/c) Type AB (c/b, c/c) Type B (b/b)
Abyssinian breed types 214 100.0% 0.0% 0.0%
American Bobtail 44 84.1% 0.0% 15.9%
American Curl 47 59.6% 0.0% 40.4%
American Shorthair 49 98.0% 0.0% 2.0%
Bengal 1706 99.9% 0.1% 0.0%
Birman 174 89.1% 0.0% 10.9%
British Shorthair types 395 79.7% 0.0% 20.3%
Burmese breed types 161 98.8% 0.0% 1.2%
Chartreux 84 91.7% 0.0% 8.3%
Cornish Rex 106 66.0% 0.9% 33.0%
Devon Rex 446 69.7% 0.0% 30.3%
Donskoy 17 100.0% 0.0% 0.0%
Egyptian Mau 55 100.0% 0.0% 0.0%
European Shorthair 91 94.5% 2.2% 3.3%
Exotic Shorthair 68 95.6% 0.0% 4.4%
Havana Brown 30 80.0% 0.0% 20.0%
Highlander 231 99.6% 0.0% 0.4%
Khaomanee 21 100.0% 0.0% 0.0%
Korat 51 100.0% 0.0% 0.0%
LaPerm 35 100.0% 0.0% 0.0%
Lykoi 104 93.3% 1.0% 5.8%
Maine Coon 2121 99.2% 0.0% 0.8%
Manx breed types 46 97.8% 0.0% 2.2%
Munchkin breed types 109 97.2% 0.0% 2.8%
Norwegian Forest Cat 121 100.0% 0.0% 0.0%
Ocicat 76 100.0% 0.0% 0.0%
Oriental breed types 230 100.0% 0.0% 0.0%
Persian breed types 136 98.5% 0.0% 1.5%
Peterbald 17 100.0% 0.0% 0.0%
Pixiebob 33 93.9% 0.0% 6.1%
RagaMuffin 118 95.8% 3.4% 0.8%
Ragdoll 1115 96.1% 2.2% 1.7%
Russian Blue breed types 65 98.5% 1.5% 0.0%
Savannah 80 100.0% 0.0% 0.0%
Scottish Fold 90 87.8% 3.3% 8.9%
Scottish Straight 75 88.0% 0.0% 12.0%
Selkirk Rex 121 95.0% 0.0% 5.0%
Siamese breed types 233 99.6% 0.0% 0.4%
Siberian breed types 582 98.1% 0.0% 1.9%
Singapura 39 100.0% 0.0% 0.0%
Sphynx 547 92.1% 0.0% 7.9%
Tennessee Rex 35 100.0% 0.0% 0.0%
Tonkinese 41 100.0% 0.0% 0.0%
Toybob 56 87.5% 0.0% 12.5%
Turkish Angora 110 88.2% 0.0% 11.8%
Turkish Van 40 87.5% 0.0% 12.5%
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genetically at risk with two copies of the PK-def associated variant. Our veterinarians inter-
viewed owners of ten Maine Coons (including two Maine Coon Polydactyls) and three Bengal
cats. All the Maine Coons were 3 years old or younger at the time of interview. In three out of
ten cases owners reported occurrence of at least one mild potential episode with clinical signs
such as lethargy, anorexia, weight loss, and/or jaundice (S7 Table). One male Maine Coon, at
the age of 1 year and 5 months, become severely ill with anorexia, lethargy, and significant
weight loss (down to approximately 8 lbs from 17 lbs), another male had had episodes of mild
lethargy and hyporexia, and the one female cat may have potentially manifested mild symp-
toms directly after giving birth. The three Bengal cats were between 2-years-9-months-old and
6-years-7-months-old at the time of interview. The owner of one female cat reported that the
cat had stopped eating and seemed sick after an attempt to rehome, but fully recovered after
returning to the breeder (S7 Table). We also interviewed the owner of a genetically affected
Abyssinian cat. The 2-year-5-month-old male cat had four major episodes of illness each time
starting with hyporexia and lethargy followed by anorexia, anemia, fever and jaundice, and
each time had received significant veterinary care (S7 Table). Compared to the Abyssinian, all
owner-reported episodes in the Maine Coon and Maine Coon Polydactyl are milder and
should be considered preliminary results as they lack a complete blood count taken during the
episode and PK-def diagnoses by a veterinarian.
Autosomal dominant disease-associated variants are observed in additional
breeds
We screened for four feline disease-associated variants that most closely follow an autosomal
dominant mode of inheritance in clinical settings: Polycystic Kidney Disease (PKD) [14], two
Hypertrophic Cardiomyopathy (HCM) variants [44,45], and Osteochondrodysplasia and Ear-
fold [46].
Polycystic Kidney Disease (PKD) is a severe autosomal dominant (homozygous lethal) con-
dition in which clusters of cysts present at birth develop in the kidney and other organs, caus-
ing chronic kidney disease which can lead to kidney failure [47,48]. PKD is caused by a stop
codon in exon 29 of PKD1;c.9882C>A (published as c.10063C>A, coordinates updated to ref-
erence genome FelCat9), resulting in a truncated form of the gene, which was discovered in
Persian cats with ~40% frequency in the Persian cat population worldwide [16–19]. Genetic
testing was introduced into the breeding programs of Persians and some Persian-related cats.
Our findings indicate that the overall frequency of the PKD1 variant has decreased notably
from what was previously reported in these breeds (Tables 2and S4). However, the PKD1 vari-
ant was identified in the Maine Coon, a breed in which it had not been previously documented
in the peer-reviewed literature. Clinical manifestation of PKD in a genetically affected female
Maine Coon, diagnosed at the age of 3 months, was confirmed after interviewing the cat’s
owner and assessing associated diagnostic documentation including an ultrasound of the kid-
neys in which numerous, round, well-defined cysts were observed bilaterally throughout the
renal cortex and medulla (S7 Table). This finding provides evidence that genetic screening for
the PKD1 variant in the Maine Coon is clinically relevant.
Hypertrophic cardiomyopathy (HCM) is the most common heart disease in domestic cats.
Two independent variants of the MYBPC3 gene c.91G>C p.(A31P) and c.2453C>T p.
(R818W) (published as 2060C>T p.(R820W); coordinates updated to reference genome Fel-
Cat9) have been associated with HCM in the Maine Coon and Ragdoll breeds, respectively
[44,45,49]. In the heterozygous state, the likelihood of developing clinical HCM early in life is
very low. However, supporting the autosomal dominant mode of inheritance, regional dia-
stolic and systolic dysfunction has been observed in heterozygous asymptomatic cats [50,51].
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In the homozygous state, the development of HCM is highly likely in the Maine Coon with
risk increasing with age [52]. Similarly, in the Ragdoll, heterozygous cats have a normal life
expectancy, while homozygous cats are likely to have a shortened life span [53]. In the present
study, we found the A31P and the R818W variants present in the heterozygous state in addi-
tional breeds (Table 2). Our veterinarians interviewed owners of four American Bobtail cats
heterozygous for the R818Wvariant. One male had died suddenly at 5 to 6 years of age. Death
was preceded by labored breathing over a few days, which the owner suspects was caused by a
cardiac condition. However, no echocardiography had been applied to confirm a diagnosis of
HCM (S7 Table). All three female American Bobtails at ages 4-years-and-4-months, 6-years-
and-5-months and 10-years-and-5-months were still alive.
Osteochondrodysplasia and Earfold is a highly penetrant autosomal dominant condition caused
by a missense variant (c.1024G>T) in the TRPV4 gene resulting in congenital degenerative osteo-
chondrodysplasia or “Scottish Fold Syndrome”, manifesting as skeletal deformities such as a short,
thick, inflexible tail and malformation of the distal fore- and hindlimbs, which can lead to a stilted
gait [46]. We observed one copy of the TRPV4 variant in all 85 phenotype-confirmed Scottish Fold
cats, and the TRPV4 variant was absent in all 75 Scottish Straight cats tested. We also discovered
one copy of the TRPV4 variant in a crossbred cat resulting from the mating of a Scottish Fold and
a Highlander. As the ear phenotype of the kitten was curled-back as seen in the Highlander breed,
rather than folded forward as seen in the Scottish Fold, observation of the TRPV4 variant was not
entirely expected. However, the kitten did present a stiff and inflexible shortened tail, characteristic
of TRPV4 variant carriers. It therefore would appear that the yet unknown variant that causes the
Highlander ear type masks the Scottish Fold ear phenotype caused by the TRPV4 variant when the
two variants are inherited together. In another recent study, a cat registered as an American Curl
with curled ears was diagnosed with osteochondrodysplasia and genotypically showed one copy of
TRPV4 variant [54]. Thus, we report a second case of Osteochondrodysplasia in which the cat’s ear
phenotype belied the presence of the causal variant.
Molecular heterogeneity of feline hereditary retinal dystrophies
The disease-associated variants for retinal dystrophies screened in this study include CEP290,
KIF3B and AIPL1. The CEP290 variant is associated with late-onset Progressive Retinal Atro-
phy (PRA; discovered in the Abyssinian) and is present in many pedigreed breeds [55,56].
Here we document a frequency of 1.1% in all cats and have identified the presence of the
CEP290 variant in 20 additional breeds. The highest CEP290 variant frequencies were observed
in the Peterbald (26.5%) and in one of the additionally identified breeds, the Oriental Longhair
(19.6%). The variant of the KIF3B gene, recently associated with an early-onset PRA; discov-
ered in the Bengal) [57], was present in 6.9% of the Bengal breed (resulting in a frequency of
1.1% in all cats) (Tables 1and 2and S4). This variant was additionally discovered in the High-
lander breed types and the Savannah. The AIPL1 variant associated with PRA (discovered in
the Persian) was the rarest variant associated with retinal dystrophies [58]; this variant was
screened in a subset of 2,186 samples (including 5 Persian cats) and not observed at all (Tables
1and S4). To pursue clinical validation of our findings, we recruited a 10-year-3-month-old
female Oriental Longhair, homozygous for CEP290. Clinical validation was initiated with an
owner interview, in which the owner reported no apparent changes in the cat’s behavior that
were suggestive of vision loss (S7 Table). However, during an ophthalmic examination, a
marked discoloration of pigmentation of the tapetal fundus with a slight vascular attenuation
was noted, confirming the presence of retinal degeneration. This evidence suggests that rdAc-
PRA may manifest clinically in the Oriental Longhair, and suggests vision may be retained lon-
ger than the previously reported 3–7 years [2], at least for this particular breed example.
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Feline MDR1 Medication Sensitivity associated with adverse medication
reactions in the Maine Coon
Feline MDR1 Medication Sensitivity is a disorder associated with severe adverse reactions
after exposure to medications that use the p-glycoprotein drug transporter. This genetic condi-
tion is caused by a two base pair deletion within exon 15 of the ABCB1 gene resulting in abnor-
mal p-glycoprotein [59]. While functional p-glycoprotein plays a significant part in the blood-
brain barrier that prevents various drugs and chemicals in the bloodstream from entering the
brain, a defective p-glycoprotein allows more drugs to cross this barrier, thus increasing the
neurological effects of some medications. Severe macrocyclic lactone-induced neurologic toxi-
cosis has previously been reported in cats homozygous for the MDR1 variant receiving either a
subcutaneously administered dose of ivermectin or a topically administered eprinomectin-
containing antiparasitic product labeled for cats [59,60]. We report the frequency of the
ABCB1 variant as 0.6% of all genotyped cats, in addition to the discovery of the variant in the
Balinese, Maine Coon, Maine Coon Polydactyl, Ragdoll, Siamese and Turkish Angora breeds
(Tables 1and 2and S4). Our veterinarians interviewed three owners of cats identified as
homozygous for the MDR1 variant to assess their cat’s medical history (S7 Table). The cats
consisted of a 1-year-4-month-old intact female Maine Coon, a 2-year-3-month-old intact
female Ragdoll, and a 3-year-2-month-old intact male Maine Coon. All three cats had been
administered topical flea medications (of varying brands) with no discernable side effects,
however, none of the medications applied contained eprinomectin. One of the cats had under-
gone anesthesia and fully recovered, but reportedly was a bit more lethargic than expected.
Genetic diagnosis plays a crucial role in the diagnosis of uncommon
inherited disease
We identified a cat genetically affected with Myotonia Congenita, an uncommon recessively
inherited disorder manifesting as an inability of the muscles to relax after contraction, which is
caused by a variant in the CLCN1 gene [37]. This is a sporadic condition that was discovered
in a rescue domestic cat population in Winnipeg, Canada. While the variant was not identified
in any pedigreed cats (which make up a large proportion of the study sample), we discovered
two copies of the variant in a single non-pedigreed domestic cat in Oregon, United States. In
the owner interview, we learned that the genetic diagnosis was crucial in assisting with clinical
diagnosis (S7 Table). While this is an incurable condition, having the correct diagnosis helps
ensure that the cat is getting appropriate supportive care. The owner confirmed that this cat,
initially misdiagnosed with flea bite anemia at the age of 13 weeks, has a disease manifestation
that includes fainting spells when startled, prolonged prolapse of the nictitating membrane,
hypertrophic musculature, flattened ears, motor dysfunction, shortened gait, and limited
range of motion in the jaw. The cat also shows a characteristic “smile” after a yawn or a meow
due to delayed relaxation of the muscle in the upper lip as well as commonly has the paws pro-
tracted (Fig 1A). However, the owner mentioned that this cat, currently 4 years and 2 months
old, is not drooling or showing any dental defects, which differs from the original disease
description [37].
Panel screening enables dissociation of variants with clinical disease
In this study we determined the c.140C>T p.(S47F) variant of the UROS gene to be present in
0.7% of cats across the entire study sample (Tables 1and S4). This variant was previously dis-
covered along with c.331G>A p.(G111S) in a cat manifesting Congenital Erythropoietic Por-
phyria (CEP) [61]. The manifestation of CEP includes distinctively stained brownish-yellow
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teeth that turn fluorescent pink under UV light. However, we did not observe the c.331G>A
variant in any of the tested cats. While the original research revealed no cats carrying solely the
c.140C>T variant, functional studies have shown that c.140C>T alone does not significantly
alter the protein function [61]. Due to the high frequency of c.140C>T in some cat breeds and
because some DNA testing laboratories offer tests for the two variants separately, our veteri-
narians reached out to the owners of cats homozygous for only the c.140C>T variant resulting
in five cases: a 1-year-4-month-old intact female RagaMuffin, a 1-year-5-month-old intact
male RagaMuffin, a 1-year-7-month-old intact female Siberian, a 2-year-10-month-old intact
female Singapura and a 3-year-7-month-old intact male Toybob. None of these cats had clini-
cal signs suggestive of CEP. Thus, the existing evidence strongly suggests that c.140C>T is a
benign variant when it is not inherited along with c.331G>A.
Mucopolysaccharidosis Type VI (MPS VI), a lysosomal storage disease caused by a defi-
ciency of N-acetylgalactosamine-4-sulfatase (4S), is another disease in which the roles of two
variants, independently inherited in this case, have been under discussion [62]. While the MPS
VI variant c.1427T>C p.(L476P) of the ARSB gene is associated with severe disease [63], the
c.1558G>A p.(D520N) variant of the ARSB gene is sometimes referred to as the “mild” type
[64]. However, it is necessary for the D520N variant to be inherited as a compound heterozy-
gote with one copy of the L476P variant for the disease to manifest in its mild form. We have
elected to call the D520N variant MPS VI Modifier. The D520N variant is present in large num-
bers of cats, with a frequency of 2.5% (Tables 1and S4). It is also the major allele in the Havana
Brown, with an allele frequency of 76.7%. Additionally, we confirm that L476P is a scarce vari-
ant, and this study cohort did not identify any cats with MPS VI variant in concordance with
previously described observations [62]. The high variant frequency of the benign MPS VI Modi-
fier and very low frequency of the MPS VI variant (absent in many breeds) further confirm that
breeding to avoid MPS VI should concentrate solely on managing the L476P variant.
Appearance-associated variants distributed across breeds and breed types
In this study sample of mostly pedigreed cats (94.4%), the ancestral form of the appearance-
associated (trait) variant was the major allele, except for the ASIP gene in which the derived
allele a (non-agouti/solid color) [65] showed a 56.2% variant frequency in all cats (S4 Table;
include all within breed variant frequencies). The rarest derived allele observed was the e allele
of the MC1R gene associated with the coat color Amber (discovered in the Norwegian Forest
Cat) [66], which was observed in the Norwegian Forest Cat and one random-bred cat from
Finland. The random-bred cat was homozygous for the derived allele with pictures confirming
the expression of the Amber coat color (Fig 1B).
Fig 1. A) The signature “smile” of a cat with Myotonia Congenita; B) The rare coat color phenotype Amber in a random-bred
cat from Finland; C) Polydactyly variant Hw also associated with extra toes in all four feet. Photo credit (from A toC): Kimberly
Sullivan, Ari Kankainen, Samantha Bradley.
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Expectedly, a high number of breeds and breed types shared the same trait-associated vari-
ants in common (S4 Table). For example, the c.904G>A variant of the TYR gene resulting in
Colorpoints (discovered in the Siamese) [67], is also the cause of the Colorpoint phenotype in
the Birman, Himalayan (a colorpoint type of Persian cats) Ragdoll, Neva Masquerade (a color-
point type of Siberian), Ragdoll and Toybob. The derived variant is also present in >30% of
the representatives of American Curl, Bengal, British Longhair, Cornish Rex, Donskoy, High-
lander, LaPerm, Minuet, Munchkin, Oriental Longhair, Oriental Shorthair, Peterbald, Sphynx
and Tonkinese. Genotyping results of trait-associated variants showed overall concordance
with observed phenotypes, strongly supporting the variants’ causality. For the two variants
White Spotting and Dominant White, which are a result of a full or partial feline endogenous
retrovirus (FERV1) insertion into KIT gene [68], we had a genotyping assay that detected if
either one of the variants was present requiring combination of genotype with the cat’s pheno-
type for result interpretation. The White Spotting variant, which we believe to be more ances-
tral of the two, was much more common in cats than the Dominant White phenotype. In the
Turkish Van breed (the name for the breed comes from the “Van pattern” where the colored
areas are restricted to the area around the ears with a few additional spots), all the cats had two
copies of the White Spotting based on the phenotypic observations. In other breeds with phe-
notypes, both one and two copies of the White Spotting manifested as a variable coverage of
white areas on the cat and based on the cat’s appearance, it was not possible to determine how
many copies of the White Spotting was present. However, we observed that in cats with white
paws (even when the rest of the legs had color), at least one copy of the White Spotting was
present in all breed backgrounds. The only exception were the Birman cats, in which the
breed-defining white paws (aka Gloves) are associated with the two adjacent missense changes
of the KIT gene [69]. This derived variant had a frequency of 95.6% in the Birman breed and
the cats manifested white paws in the absence of White Spotting. Interestingly, we also
observed the derived variant as a minor allele in many breeds, in which white paws are not
seen. We identified two copies of the Gloves variant present in individuals of the Chartreux,
Highlander, Maine Coon, Ragdoll and Siberian breeds, in which they were not associated with
Gloving based on photographic evidence and owner reports. Of the phenotyped individuals
some white areas of hair were seen on the belly or toes in (3/17) Maine Coons and (1/2) Sibe-
rian cats. Our findings are supportive of a potential additional candidate locus that may play a
role in the regulation of the Gloves phenotype [70].
Moreover, we observed the Hairlessness variant (discovered in the Sphynx) [71], the Short-
ened Kinked Tail variant (discovered in the Japanese Bobtail) [72] and the three tested Short
tail variants (discovered in the Manx cat) [73] result in their expected phenotypes, but also not
explain all observed bald and short tail phenotypes. The c.816+1G>A variant in the KRT71
gene which is known to result in the hairless phenotype of the Sphynx cat had a variant fre-
quency of 74.7% in the Sphynx breed [71] (S4 Table). Compound heterozygotes for the Sphynx
c.816+1G>A variant with the Devon Rex associated curly coat variant are also hairless [71].
We also identified 22 hairless Sphynx cats without any copies of the Hairlessness variant, sug-
gesting that an additional unknown variant in the same or another gene entirely causes the
hairless phenotype in some cats of this breed. We also confirmed that the Hairlessness variant
was not present in the Donskoy and Peterbald breeds, which also represent hairless pheno-
types. It was recently suggested that a novel 4 base pair variant of the LPAR6 gene identified in
a Peterbald cat potentially results in a hairless coat phenotype as a homozygote or as a com-
pound heterozygote with the c.250_253_delTTTG variant in the LPAR6 gene which causes the
curly coat of the Cornish Rex [74]. We show a variant frequency of 25% for the Cornish Rex
coat variant in the Donskoy, but did not identify any Cornish Rex coat variant carriers among
the 17 tested Peterbald cats of this study.
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The c.5T>C variant in the gene HES7 associated with a shortened and kinked tail in the
Japanese Bobtail [72] was observed as homozygous in all Japanese Bobtail cats of this study,
with the derived variant also prevalent in the Kurilian Bobtail and Mekong Bobtail. In addi-
tional bobtail breeds, Cymric and Toybob, a few individuals were also observed with the
derived variant (S4 Table). All studied cats with one or more copies of HES7 variant and avail-
able phenotypic information presented with a shortened tail.
We genotyped three out of four known variants (c.995delT, c.1166delC, c.1196delC) (pub-
lished as 998delT, c.1169delC and c.1199delC; coordinates updated to reference genome Fel-
Cat9) of the Tgene (discovered in the Manx) causing shortened tail [73]; the fourth T variant
(c.995_1011dup;1011_1014del on FelCat9 reference genome, published as 998_1014dup17-
delGCC), which has only been previously observed in one cat, could not be genotyped. We
found one of the three tested variants in all the Pixiebobs (including longhair variant), 9/30
(30.0%) Manx and 7/14 (40.0%) Cymric (a Manx type with longhair). The derived variants of
the T-box were always observed in the heterozygous state, further suggesting that in the homo-
zygous state these variants are lethal in utero [73], and therefore in the mating of two short-
tailed cats 25% of cats conceived are born with longtail. Long-tailed Manx and Cymric cats are
part of the breeding programs and because there was no phenotype information available for
all tested Manx and Cymric cats, it could not be estimated if the tested three variants explained
all short tail phenotypes in these two breeds. In addition, in line with previous study [73], the
variant c.995delT of the Tgene was also observed in American Bobtails (combined group of
both Longhair and Shorthair variants). The tested Manx shorttail variants were also remark-
ably common in the Highlander breed, in which there is believed to be a different cause for the
short tail phenotype. In this study cohort, 40.6% (94/231) of the Highlanders had one of the
tested short tail variants (discovered in the Manx) (S4 Table). The photographic evidence in
the American Bobtail and Highlander breeds confirm several short-tailed cats that were not
carrying any known bobtail variant (S4 Table).
Lastly, we found that of the three tested polydactyly (extra toes) associated variants, the
Hw variant of the LMBR1 gene was predominantly observed in polydactylous cats, includ-
ing the Maine Coon, Pixiebob and Highlander breed types, and some non-pedigreed cats
from North America. Both heterozygous and homozygous cats observed, and based on the
photographic evidence presenting with four (normal number of digits) to seven toes per
paw. Higher variant penetrance was seen in homozygous cats, which is in line with previous
observations [75]. However, extra toes did not manifest solely in the front feet as previously
reported; photographic evidence and owner-provided details revealed the presence of extra
toes on all four feet (Fig 1C), which was formerly considered to be characteristic of the UK1
and UK2 variants only [75]. We also confirmed that a non-pedigreed cat with two copies of
the UK1 variant had two extra digits on each paw, per the owner’s description. Various
owner-reported cases of polydactyl cats testing negative for the screened variants were also
noted. Such cats are likely to be carrying additional variants of the LMBR1 gene or other not
yet identified locus.
Genome-wide analysis of genetic diversity demonstrates differences
between and within cat breeds
The entire data set of 11,036 samples was genotyped for 7,815 informative SNP markers dis-
tributed across the genome. In the pedigreed cat population, the median heterozygosity was
34.0% and the typical range (defined as the 10th and 90th percentile) was 27.2%-38.3%, in the
non-pedigreed population, the median heterozygosity was 38.8%; and the typical range was
29.8%-41.3% (Fig 2). The median heterozygosity was calculated for 60 breeds and breed types
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that were represented by at least 15 individuals in the dataset (S8 Table). The most diverse
breeds include three of the newer cat breeds: the short-legged Munchkin, produced from a sib-
ling mating followed by regular non-pedigreed cat outcrosses [7,67]; the Highlander, a cross-
breed of two recent experimental hybrid cat breeds the Desert Lynx and Jungle Curl; and the
Lykoi breed founded by unrelated cats expressing hypotrichosis, whose unique sparse and
roaned coat phenotype may be caused by any of six different variants of the HR gene from six
independent lineages found in four different states of the United States, Canada and France
[76]. The heterozygosity levels of the European Shorthair, Norwegian Forest Cat, Siberian, and
Manx, which were developed from the local domestic populations that likely had a larger
diversity in the founder population, were above average compared with the entire pedigreed
cat population. The lowest median heterozygosity measures in any pedigreed cat population
were observed in the Burmese, Birman, Havana Brown, Korat, Singapura and breeds of the
Siamese group (such as Balinese, Siamese and Oriental Shorthair), in line with previous obser-
vations [30]. A full breakdown of the diversity levels per breed can be found in S8 Table.
Discussion
In the largest DNA-based feline study cohort to date, a custom genetic panel screening test
was used to determine blood type, disease and phenotypic trait heritage, as well as the relative
genome-wide genetic diversity in 11,036 domestic cats.
Fig 2. The median genetic diversity in pedigree and non-pedigreed cat populations with typical range (the 10th
and 90th percentile).
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One specific area of focus was blood type determination, which is important in cat breeding
due to its link with neonatal isoerythrolysis, a significant cause of fading kitten syndrome and
neonatal death if the blood types of breeding pairs are not appropriately matched. Here we
show that cats with blood type B are present in a vast majority of the breeds. We identified 11
breed types in which at least one out of ten cats in the population were blood type B. We also
observed the rare blood type AB, previously described with notable prevalence only in the Rag-
doll, to be present in the European Shorthair, Scottish Fold breed types, and the RagaMuffin.
Based on the proposed DNA genotyping scheme for purpose-bred cats, and serological blood
type based on the 220 pedigreed cat results available for analysis in this study, we confirm a
high concordance between blood type determination. However, while there are several studies
confirming genotypes associated with blood type AB [20,23], the genetic blood type determi-
nation and immunological blood type determination for two cats were unconcordant. In a
recent study [77], type AB cats which carried one copy of a variant resulting in blood type B,
had a higher level of Neu5Ac present that could depending on the technologies used impact
results. This provides further justification for the supportive role of the DNA-based blood type
determination approaches in breeding and veterinary care, provided that the appropriate care-
fully validated genetic variants are assayed. However, additional genetic variants of the CMAH
gene have been identified that may play a role in blood type determination in domestic short-
hair and stray cats [23,77], and further investigations are warranted.
Panel screening of disease-associated variants provides potential clinically relevant informa-
tion in addition to blood type determination. We show that the genomic data available
through routine genetic screening of any cat today can assist in disease diagnosis, treatment,
and preventative care. Through the comprehensive investigation of variant allele frequencies
in this study cohort, we re-evaluate and provide updated variant frequency information com-
pared to estimates provided in conjunction with the original variant discoveries. We identify
several disease-associated variants as common and widely spread across breeds, suggesting
that they are ancient in their origin. The most common disease-associated genetic variants of
this study are Factor XII Deficiency, PK-def and rdAC-PRA. Factor XII deficiency is likely
non-pathological but nevertheless a major clinical differential of genetically affected cats that
despite the prolonged aPTT do not manifest extensive bleeding or require transfusion [39–41].
The c.707-53G>A variant of PKLR (published as c.693+304G>A; coordinates updated to ref-
erence genome FelCat9) associated with PK-def in the Abyssinian and Somali breeds is also
found across multiple breeds in which genetic testing for PK-def has been employed [43],
though the clinical manifestation of PK-def in these additional breeds has not been docu-
mented in the scientific literature. This may be partly explained by the episodic nature of this
disease and its remarkable variability in expressivity, making it diagnostically challenging
[42,43,78], and the fact that the advent of genetic testing made it rare. Clinical diagnosis using
appropriate clinical examination of cats that are genetically predisposed to PK-def with symp-
toms is still needed to confirm the variant’s penetrance in different breed backgrounds. The
variant rdAC-PRA (discovered in the Abyssinian) causes a late onset disease with documented
variant penetrance across several breeds [55]. Today, the highest allele frequencies are seen in
the cat breeds of the Siamese group, which also have decreased genetic diversities. The man-
agement of rdAC-PRA in these breeds requires a well-planned breeding program that includes
keeping carriers in breeding and using them responsibly.
Extensive DNA panel screening also allows investigation of putative or candidate variants
that have been previously described in a limited number of samples or in a single domestic cat.
We report Feline MDR1 Medication Sensitivity to be present in 126/11,036 (1.1%) cats of this
study in representatives of the breeds Balinese, Maine Coon, Maine Coon Polydactyl, Ragdoll,
Siamese, Turkish Angora, and non-pedigreed cats. This variant was also recently discovered in
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4% of domestic shorthairs, Ragdoll, Russian Blue and Siamese [59,60]. The existence of Feline
MDR1 Medication Sensitivity is not yet well known in the veterinary community, but a recent
study shows that affected cats develop severe neurologic symptoms even when treated with
eprinomectin-containing products labeled for use in cats and administered according to label
instructions [60]. When treating cats with this variant, precautions to those recommended for
dogs with MDR1 are advised. We report three rare genetic variants associated with disorders
present in the heterogeneous non-pedigreed cat study sample, of which a discovery of Myoto-
nia Congenita confirmed clinical diagnosis for a cat that ensures its appropriate treatment and
care.
Our data indicate that known disease-associated variant frequencies are now lower for
many conditions (GM2 and Hypokalemia in Burmese, Glycogen Storage Disease in Norwe-
gian Forest Cats, HCM and Spinal Muscular Atrophy in Maine Coon, HCM in Ragdoll and
PKD in Persian) compared to the frequencies at the time of their discovery, perhaps reflecting
change over time within the breed, presumably due to genetic testing combined with informed
breeding selection. For example, the PKD1 variant, which initially affected nearly 40% of Per-
sian cats [14], was found at higher frequency in breeds with Persian background or non-
related breeds than it was in the Persian breed. In fact, none of the Persian cat samples in this
study had the PKD1 variant. Additional recent studies indicate that the prevalence of PKD in
Persian cats of Iranian origin continues to be high [71], while PKD1 is common in pedigreed
and non-pedigreed cats in Iran, Japan and Turkey [11–13]. Moreover, we rarely observed the
known autosomal dominant disease-associated variants for HCM (discovered in the Maine
Coon) and HCM (discovered in the Ragdoll), in the homozygous state which confers signifi-
cantly higher risk for disease development compared to heterozygotes [52,53]. Similarly, in
this study sample the Scottish Fold cats were all heterozygous for the autosomal dominant
Osteochondrodysplasia and Earfold which may result in a milder phenotype [46]. Thus, this
data reveal that there is an active DNA testing culture in the feline fancy used to carefully man-
age disease predisposing variants that are known in the breed. Our study cohort was biased
towards breeding animals of the breeders with active DNA testing routines and interests,
which may account for some disease-associated variants being seen less commonly than would
be observed in randomly selected samples.
Utilizing the DNA panel testing approach has many justifications, especially in felines in
which many breeds are the outcome of different cross-breedings and the molecular disease
heritage introduced in the resulting breed is unlikely to be fully known. Here we show identifi-
cation of 13 disease-associated variants in additional breeds and breed types that these variants
have not been previously reported in, including breed types that have been underrepresented
in many previous studies such as Balinese, Highlander, Munchkin, Minuet, Pixiebob, Savan-
nah, Tennessee Rex and Turkish Angora. Here we also provide variant allele frequencies for
breed types (varieties of the breed) separately, according to registry information reported by
the owner. While our findings in additional breeds include several that can be explained by the
history of known cross-breeding, we also report genetic diseases such as HCM (discovered in
the Ragdoll) in American Bobtail and PK-def in Maine Coon Polydactyl and Pixiebob are
observed more commonly in other breed backgrounds than in the original breeds in which
they were discovered, likely due to lack of awareness and inadvertent selection. Comprehen-
sive genetic testing has a very important role in a new breed’s development, in identifying
which disease variants have been introduced in conjunction with breed formation. For exam-
ple, in the Highlander, one of the most genetically diverse breeds, we found the presence of
disease-associated variants for HCM (discovered in the Ragdoll), PK-def, rdAC-PRA, PRA
(discovered in the Bengal) and Spinal Muscular Atrophy (discovered in the Maine Coon)
which represent targets for genetic screening and management in the breed. In this study we
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mainly focused on genotyping pedigreed cats and had a relatively small sample size of non-
pedigreed cats. We nevertheless discovered 13 disease-associated variants in non-pedigreed
cats, highlighting the relevance of genetic screening for diagnostic purposes in this population
as well.
This study cohort provides an extensive investigation of disease-associated variant heritage
across pedigreed cat populations. Large scale screening studies of isolated subpopulations of a
species such as pedigreed cats hold great value as a secondary independent tool for validating
original discoveries as often they are made by focusing on a limited number of individuals
from a single breed. Investigations that extend beyond the original discovery breed enable
researchers to conclusively understand the causal relationships between variants and diseases.
For each disease-associated variant discovered in additional breeds in this study, our follow up
investigations applied a similar validation protocol as previously recommended for dogs by
combining genotype information with clinical information collected and evaluated by veteri-
narians to assess variant manifestation in different breed backgrounds [32]. These clinical phe-
notype evaluation studies are crucial to ensure genetic counseling information that truly offers
solutions to improve the health of cats. Here we offer further supporting evidence for the
causal relationship between several disease-associated variants (F12,PKD1,TRPV4,CEP290,
ABCB1 and CLCN1) and their clinical manifestations. Our findings further highlight that the
PKD1 variant should be seen as a potential genetic cause of PKD in any breed, such as the pre-
viously documented Neva Masquerade [79], Chartreux [80], or the Maine Coon as reported in
this study. Moreover, we found that Scottish Fold crosses are of particular concern, as hetero-
zygous cats also manifest Osteochondrodysplasia and the presence of TRPV4 derived allele
cannot be reliably detected from the ear type if the cat has ear Curl, as also shown by others
previously [54]. Moreover, the heterozygosity for TRPV4 in chondrodysplastic (short-legged)
cats can be a cause of severe pain. Additionally, here we present a preliminary indication of a
phenotype for PK-def in Maine Coons (pending complete clinical examination and diagnosis)
and a potential case for MYBPC3 variant (R818W; discovered in the Ragdoll) contributing to a
suspected cardiac cause of death in an American Bobtail, which call for further investigations.
This study was fueled by the cat community and individual breeders’ willingness to provide
phenotype information, clinical documentation, and participate in veterinary examinations.
In the future, more systematic methods to collect phenotype information to associate with
genotype information could be obtained through surveys or by implementing genetic testing
as a part of the health care plan for the cat, allowing direct connection between genotype infor-
mation and medical records. Finally, after evaluation, we report two associated disease variants
that have little value as markers for genetic disease. Both the c.140C>T variant of the UROS
gene previously co-segregating with a second variant associated with CEP and the c.1558G>A
variant of ARSB gene were found to be the major variants in some breeds without any health
impact. We advise DNA testing laboratories to discontinue offering a test for CEP based solely
on the use of the c.140C>T variant, The MPS VI Modifier. Moreover, like previous investiga-
tions [62], we further emphasize that prevention of MPS VI should focus entirely on managing
the c.1427T>C variant in the cat population. The MPS VI Modifier is an asymptomatic variant
that contributes to a mild phenotypic expression of disease in compound heterozygotes [62–
64], suggesting that selecting against the c.1558G>A variant is not justified or recommended,
as it would also reduce the genetic variation in the breed.
The appearance of the cat is influenced by various genes which are often monitored by
genetic testing to inform breeding pair selection. In this study, all cats were tested for 26
appearance-associated variants. Information was provided on the frequency at which the trait
variants are encountered across breeds, to explain the observed phenotypes. The same trait
variants influencing coat color/type and morphology are highly frequent in cats of various
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breed backgrounds, providing evidence of likely causality. However, we note that the KIT gene
variant associated with breed-characteristic white feet in Birman cats [69], according to photo-
graphic evidence, is a low penetrance variant in various other breeds. Moreover, while most of
the trait phenotypes were explained by the known variants, the previously discovered variants
associated with shortened tail, extra digits, and hairlessness could only explain the presence of
some of these phenotypes.
Our analysis of genetic diversity in cat breed populations shows a wide range of diversity
levels within and between breeds. We found evidence that, as expected, more recently formed
breeds with a more significant number of founding individuals and breeds allowing continued
outcrossing tend to have the greatest diversity levels. Maintaining diversity in closed popula-
tions is challenging, and the use of outcrossing may help maintain and potentially increase
diversity levels if widely adopted. The importance of preserving diversity for health and vigor
has been widely documented [81–83].
In conclusion, we demonstrate that several feline disease-associated variants are more wide-
spread across cat breeds and breed types than previously reported, with both dominant and
recessive Mendelian disease-associated variants observed in additional breeds and often at
higher allele frequency than the breeds in which they were originally discovered. This, in part,
demonstrates the effectiveness of proactive genetic testing, which has reduced disease-associ-
ated variant frequencies in notably affected breeds over time. We have also shown that some
disease-associated variants are very rare and limited to specific breeds. We report the preva-
lence at which the three clinically relevant feline blood types occur within breeds and breed
types and provide trait variant frequencies across the feline population. We have combined
genotype information with phenotypic information to investigate and re-evaluate causality in
different breed backgrounds, confirming causal relationships for some variants and weak evi-
dence of penetrance for other variants. In summary, genetic testing can be used to inform
breeding decisions aiming to prevent genetic disease, while a concurrent goal should be to
maintain genetic diversity in a breed’s population, helping to sustain the breed. As more cats
are genotyped, we will learn more about feline variant heritage in the broader domestic cat
population, leading to improved health care advice for all cat owners. Direct-to-consumer
tests help to further raise awareness of various inherited conditions in cats, provide informa-
tion that owners can share with their veterinarians, and in time, as more genotypic and pheno-
typic data are collected, will enable the genetics of common complex feline disease to be
deciphered, paving the way for personalized precision healthcare with the potential to ulti-
mately improve welfare for all cats.
Supporting information
S1 Table. The summary of 11,036 tested pedigreed and non-pedigreed cats.
(XLSX)
S2 Table. Tested disease and trait associated variants.
(XLSX)
S3 Table. All tested disease and trait genotype data for 11,036 tested cats.
(XLSX)
S4 Table. All tested disease and trait variant frequencies for 11,036 tested cats.
(XLSX)
S5 Table. Immunological and genetic determination of the blood type for 220 cats.
(XLSX)
PLOS GENETICS
Genetic epidemiology of over 11,000 cats
PLOS Genetics | https://doi.org/10.1371/journal.pgen.1009804 June 16, 2022 24 / 30
S6 Table. Clustered breed information for representing the proportions of the different
blood types with >15 tested individuals.
(XLSX)
S7 Table. Phenotypic Information for Evaluation of Nine Disease-associated Variant’s
Penetrance in 31 cats.
(XLSX)
S8 Table. Genetic diversity for all breeds with >15 individuals tested.
(XLSX)
Acknowledgments
We extend our warmest thanks to all the cat owners and breeders who enabled the present
study by voluntarily submitting photos and clinical documentation through their interest in
advancing feline genetics research; we issue special thanks to the participants in the Wisdom
Panel-The International Cat Association (TICA) State of the Cat Study for their early support
and enthusiasm for this work. We thank Suvi Ruotanen, Sini Karjalainen, Dr. Susan Puckett,
Dr. Jason Huff and Dr. Casey A. Brookhart-Knox for expert technical assistance. We thank
Professor Leslie Lyons from the University of Missouri for providing validation samples and
critical review of the manuscript. Special thanks to Anne Marit Berge, Dr. Adriana E. Kajon
and Anthony Hutcherson.
Author Contributions
Conceptualization: Heidi Anderson, Hannes Lohi, Jonas Donner.
Data curation: Heidi Anderson, Stephen Davison, Katherine M. Lytle, Jamie Freyer.
Formal analysis: Heidi Anderson, Stephen Davison.
Investigation: Heidi Anderson, Stephen Davison, Katherine M. Lytle, Leena Honkanen, Jamie
Freyer, Julia Mathlin, Kaisa Kyo¨stila¨, Laura Inman, Annette Louviere, Jonas Donner.
Methodology: Heidi Anderson, Stephen Davison, Julia Mathlin, Jonas Donner.
Project administration: Heidi Anderson, Katherine M. Lytle, Leena Honkanen, Rebecca
Chodroff Foran, Oliver P. Forman, Hannes Lohi.
Resources: Heidi Anderson, Katherine M. Lytle, Kaisa Kyo¨stila¨, Rebecca Chodroff Foran,
Hannes Lohi.
Supervision: Heidi Anderson, Rebecca Chodroff Foran, Oliver P. Forman, Jonas Donner.
Validation: Heidi Anderson, Leena Honkanen.
Visualization: Heidi Anderson.
Writing – original draft: Heidi Anderson, Oliver P. Forman, Jonas Donner.
Writing – review & editing: Stephen Davison, Katherine M. Lytle, Leena Honkanen, Jamie
Freyer, Julia Mathlin, Kaisa Kyo¨stila¨, Laura Inman, Annette Louviere, Rebecca Chodroff
Foran, Hannes Lohi.
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