Precision Medicine in Dogs and Cats

MVMA Lyons Proceeding 2023

Disclosure: Dr. Lyons studies are periodically supported by donations to the 99 Lives project, the NIH, pet food companies, the EveryCat Foundation and Royal Canin provides food for her cat research colony. Dr. Lyons has strong interactions with the UC Davis Veterinary Genetics Laboratory and will assist any commercial laboratory seeking counseling and information for their improved commercial services. These activities have no influence on Dr. Lyons’ research or scientific presentations. One form of Precision Medicine is the use of genetic testing. The first genetic tests for the domestic cat were developed over 25 years ago. Presently, 167 different mutations affecting 101 genes have been identified, producing interesting phenotypes and traits but also diseases and other health concerns. Current genetic and genomic technologies can be employed to test nearly all the known mutations in one assay (parallel genotyping) using DNA arrays, mass spectroscopy or genotyping-by-sequencing. Unlike in human medicine, where traditionally a physician had to request a genetic test, the owner of a pet can directly purchase genetic tests from a company, i.e., direct – to – consumer testing (DTC). DTC of large panels of DNA variants developed for humans and are now easily available for cats and dogs as DTC tests. Thus, no longer are genetic tests only available from the researcher who identified the mutations or a laboratory associated with a veterinary / research facility. Private companies now offer genetic tests at lower costs by using the massively parallel genotyping, however, provide little genetic counseling and education to the owner, breeder or veterinarian. These large panel tests generally do not have documented sensitivities and specificities for the mutation being tested. How to use Direct to Consumer Testing (DTC) Veterinarians should consider using genetic testing, either submitted by the veterinarian or by the client, to support clinical diagnoses. Note that genetic tests are only one aspect of a diagnosis and only a part of the overall healthcare of the patient. Hopefully, the genetic test may lead to a more appropriate treatment plan and prognosis. Genetic testing should be considered once other environmental factors, including nutrition, toxic and viral exposures have been considered. A genetic test will not be useful if the condition is not genetic. Most genetic testing is limited to Mendelian traits, i.e., traits with simple autosomal or X-linked dominant or recessive modes of inheritance. Environment can influence the presentation, including age-at-onset and severity of genetic conditions. If a condition is genetic, likely a veterinary specialist may need to be consulted. Once a tentative diagnosis has been established and a genetic test may be supportive, use the Online Mendelian Inheritance in Animals (//OMIA.org) to see if this condition has been previously documented and if a genetic test is available. Provided below is a table of the genetic tests for disease variants in domestic cat breeds in which many companies provide genetic testing, including research universities. But also, several genetic service laboratories provide genetic tests for DNA variants that were originally identified in a random bred cat. The rediscovery of these variants is extremely rare but can occur. The OMIA website lists all the DNA variants that are associated with diseases in companion animals. This site also collates the scientific information and publications associated with the disease and will list the year of the variant discovery as well as the researchers involved. Researchers are often keen to be of assistance and realize the genetic implications may not be familiar to the veterinarian. Thus, don’t hesitate to ask the researcher first for advice on genetic testing as they may perform the testing within their own laboratory! The published manuscripts often have the email address for the

corresponding author of the publications. Otherwise, preferably use a DTC laboratory associated with a research university, which will be invested in the science, provide the best education, genetic counseling and customer service. Pros & Cons / Dos & Don’ts of DTC Large panel DTC tests allow an effective screening method for many diseases and traits. No one technology can accurately genotype all the various different types of mutations that cause diseases, thus, look for services that can use a second method, or use a secondary service, which are generally associated with research universities. Many tests are not valid in different breeds, which is not generally divulged by some services. Thus, conversations with the researcher who made the discovery will help clarify the risks. While some services work towards scientific standardizations, others are more profit oriented. The World Small Animal Veterinary Association (WSAVA) and other groups are working towards standards that will help clarify genetic testing results. The WSAVA Hereditary Disease Committee can be contacted for assistance.

Don’t make health & neutering decisions based on results from large panel DCT testing. Request a single gene test for a second opinion. Use the overall health indications of an animal. Where to find genetic testing? • Use OMIA to find the researcher who found the variant – ask the researcher first! (google them!) See instructions below. • Preferably use a laboratory associated with a research university – invested in the science! These labs will have the best customer services and most thorough counseling! • Various canine registries sites have lists of genetic tests • The Orthopedic Foundation of America (OFA) has phenotypic and genetic test information

• The World Small Animal Veterinary Association (WSAVA) has genetic information Precision / Genomic (P4) Medicine

If a genetic test has a negative result – consider whole genome sequencing (WGS)

Precision Medicine is an emerging approach for disease treatment & prevention that takes into account individual variability in genes, environment, and lifestyle. Precision medicine is used to understand the complex mechanisms underlying a patient’s health, disease, or condition, and to better predict which treatments will be most effective – not the average or average for an ethnic group! DNA testing is a form of Precision Medicine. Large panel genetic testing is an improvement and further facilitates the use of genetics for diagnoses and potentially treatment of health concerns. Whole exome and whole genome sequencing of a patient is a larger scale effort to even further advance precision medicine. Genome and exome sequencing projects are available for cats and dogs and these techniques are becoming common place for the identification of mutations that

cause heritable diseases and traits. Generally, if a result is negative for genetic test, the patient may have a novel genetic cause for their presentation. WGS and WES help to find novel causes. Genetic testing only confirms the presence or absence of an already known DNA mutation for a disease or trait. Precision Medicine hence incorporates discovery, which hopefully will lead to diagnosis and more precise treatment. Only a few research laboratories are equipped to conduct WGS and WES sequencing for companion animals on a Precision Medicine basis. The University of Missouri, laboratories of Dr. Gary Johnson and Dr. Leslie Lyons (99 Lives Cat Genome Sequencing Consortium), are discovering new disease-causing DNA variants for dogs and cats, respectively. Many of the researchers involved with DNA discoveries should also be able to suggest contacts for WGS / WES. As costs lower and data processing becomes cheaper and more streamline, genome sequencing can become a commercial service for veterinary diagnostics and be used by the everyday practitioner.

Different laboratories and different species use different methods for DNA collection. Talk to the laboratory to find the most efficient means for DNA submission for genetic testing or for whole genome sequencing.

How to use the OMIA website

1) Go to the OMIA website: https://omia.org 2) Select the “likely causal variants” for your species a. Example: Dog = 477 and Cats = 167 3) Scroll through the list of diseases for your species and select the “OMIA Phene Species - ID” that you think might be your disease 4) Read through the provided information. A list of published articles regarding the disease and DNA variant are present. Select the publication for the discovery of the variant. 5) Contact the investigator from the provided contacts in the publication OR Google them!

Disease / Trait (alleles) OMIA Entry (-9685) MO‡

Phenotype (Breeds affected)* Gene

Acrodermatitis Enteropathica 000593 AR Turkish Van SLC39A4 ALPS - Autoimmune lymphoproliferative Disease 002064 AR non-neoplastic lymphoproliferative disease (British Shorthair) FASL Centronuclear myopathy 001508 X Neurological (Maine coon) MTM1 Chediak-Higashi Syndrome 000185 AR Storage disorder (Persian) LYST Craniofacial Defect 001551 AR Craniofacial Defect (Burmese) ALX1 Cystinuria 002023 AR (MCC, Sphynx, Siamese) SLC7A9 Ehlers-Danlos 002165 AR Stretchy skin (Bengal, Bombay) COL5A1 Factor XI Deficiency 000363 AR Bleeding disorder (Maine Coon) F11 Gangliosidosis 1 000402 AR Lipid storage disorder (GM1) (Korat, Siamese, S.E. Asia) GLB1 Gangliosidosis 2 01462 AR Lipid storage disorder (GM2) (Burmese) HEXB Gangliosidosis 2 01462 AR Lipid storage disorder (GM2) (Korat) HEXB Glycogen Storage Disease Type IV 000420 AR Glycogen storage disorder (GSD) (Norwegian Forest Cat) GBE1 Hermansky-Pudlak syndrome-5 002161 AR Ocular albinism (Donskoy) HPS5 Holoprosencephaly 002366 AR Forebrain malformation (Toyger) GDF7 HCM 002316 AD Cardiac disease (Sphynx)) ALMS1 HCM 000515 AD Cardiac disease (Maine Coon, Ragdoll) MYBPC

Hypokalemia 001759 AR Potassium deficiency (HK) (Burmese)

Hypotrichosis 001949 WNK4

AR Hairless, early death (Birman) FOXN1

Hypothyroidism 000536

AR Small size, low T4 (British) TPO Progressive Retinal Atrophy 001244 AR Late onset blindness (rdAC) (Abyssinian) CEP290 Progressive Retinal Atrophy 000881 AR Rod-cone dysplasia (Abyssinian) CRX Progressive Retinal Atrophy 001613 AR Mid onset blindness (Bengal) KIF3B Progressive Retinal Atrophy 001222 AR Early onset blindness (Persian) AIPL1 Polycystic Kidney Disease 1 000807 AD Kidney cysts (PKD) (Persian) PKD1 Polycystic Kidney Disease 2 002525 AR Polycystic kidney disease (Siberian) PKD2 Pyruvate Kinase Deficiency 000844 AR Hemopathy (PK Deficiency) (Abyssinian, Siberian, MCC) PKLR

Skeletal dysplasia 002485 AR Skeletal dysplasia (British) LTBP3

Spasticity 001621 AR Congenital myasthenic syndrome (CMS) (Devon Rex) COLQ

Spinal Muscular Atrophy 000939 AR Muscular atrophy (SMA) (Maine Coon) LIX1- LNPEP

‡ Mode of inheritance of the variant allele (disease-causing allele). *The breed affected represents the breed in which the DNA variant was identified. Other breeds may be affected if they have common ancestry, especially other breeds in a breed family. In reference to the variant allele, AD implies autosomal dominant, AR implies autosomal recessive, co-D implies co-dominant, X implies X-linked. OMIA: Online Mendelian Inheritance in Animals (http://omia.org) entries provides links to citations and clinical descriptions of the phenotypes and the diseases.

MU-CVM Lectures

Owen Skinner, BVSc DECVS DACVS-SA MRCVS

Assistant Professor of Small Animal Surgical Oncology University of Missouri College of Veterinary Medicine Columbia, Mo.

134