PLINK breed data showing SLAMF1 is associated with canine atopic dermatitis
Data files
Apr 01, 2025 version files 1.23 GB
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atopy_beagle_349_cases_362_controls.bed
16.02 MB
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atopy_beagle_349_cases_362_controls.bim
2.61 MB
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atopy_beagle_349_cases_362_controls.fam
17.70 KB
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atopy_boston_478_cases_531_controls.bed
22.46 MB
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atopy_boston_478_cases_531_controls.bim
2.58 MB
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atopy_boston_478_cases_531_controls.fam
25.62 KB
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atopy_boxer_447_cases_515_controls.bed
20.37 MB
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atopy_boxer_447_cases_515_controls.bim
2.45 MB
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atopy_boxer_447_cases_515_controls.fam
24.18 KB
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atopy_chihuahua_304_cases_363_controls.bed
15.24 MB
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atopy_chihuahua_304_cases_363_controls.bim
2.65 MB
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atopy_chihuahua_304_cases_363_controls.fam
16.72 KB
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atopy_dachshund_436_cases_507_controls.bed
21.36 MB
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atopy_dachshund_436_cases_507_controls.bim
2.63 MB
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atopy_dachshund_436_cases_507_controls.fam
24.24 KB
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atopy_frenchie_2138_cases_645_controls.bed
58.84 MB
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atopy_frenchie_2138_cases_645_controls.bim
2.45 MB
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atopy_frenchie_2138_cases_645_controls.fam
72.87 KB
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atopy_golden_1056_cases_1057_controls.bed
44.92 MB
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atopy_golden_1056_cases_1057_controls.bim
2.46 MB
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atopy_golden_1056_cases_1057_controls.fam
54.22 KB
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atopy_greatdane_215_cases_212_controls.bed
9.27 MB
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atopy_greatdane_215_cases_212_controls.bim
2.51 MB
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atopy_greatdane_215_cases_212_controls.fam
10.84 KB
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atopy_gsd_1494_cases_1599_controls.bed
68.18 MB
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atopy_gsd_1494_cases_1599_controls.bim
2.55 MB
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atopy_gsd_1494_cases_1599_controls.fam
77.83 KB
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atopy_husky_227_cases_315_controls.bed
12.10 MB
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atopy_husky_227_cases_315_controls.bim
2.58 MB
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atopy_husky_227_cases_315_controls.fam
13.69 KB
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atopy_lab_1668_cases_1064_controls.bed
61.21 MB
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atopy_lab_1668_cases_1064_controls.bim
2.59 MB
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atopy_lab_1668_cases_1064_controls.fam
69.45 KB
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atopy_min_schnauzer_559_cases_631_controls.bed
26.49 MB
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atopy_min_schnauzer_559_cases_631_controls.bim
2.58 MB
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atopy_min_schnauzer_559_cases_631_controls.fam
30.38 KB
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atopy_minpoodle_385_cases_464_controls.bed
19.39 MB
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atopy_minpoodle_385_cases_464_controls.bim
2.64 MB
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atopy_minpoodle_385_cases_464_controls.fam
21.70 KB
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atopy_poodle_461_cases_498_controls.bed
21.66 MB
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atopy_poodle_461_cases_498_controls.bim
2.62 MB
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atopy_poodle_461_cases_498_controls.fam
24.89 KB
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atopy_shiba_239_cases_284_controls.bed
10.57 MB
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atopy_shiba_239_cases_284_controls.bim
2.34 MB
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atopy_shiba_239_cases_284_controls.fam
13.21 KB
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atopy_shih_tzu_797_cases_929_controls.bed
38.54 MB
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atopy_shih_tzu_797_cases_929_controls.bim
2.58 MB
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atopy_shih_tzu_797_cases_929_controls.fam
44 KB
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atopy_singlebreed_14378_cases_14633_controls.bed
663.97 MB
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atopy_singlebreed_14378_cases_14633_controls.bim
2.66 MB
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atopy_singlebreed_14378_cases_14633_controls.fam
738.65 KB
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atopy_wpcorgi_398_cases_477_controls.bed
18.35 MB
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atopy_wpcorgi_398_cases_477_controls.bim
2.43 MB
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atopy_wpcorgi_398_cases_477_controls.fam
22.46 KB
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atopy_yorkie_663_cases_786_controls.bed
32.84 MB
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atopy_yorkie_663_cases_786_controls.bim
2.63 MB
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atopy_yorkie_663_cases_786_controls.fam
36.60 KB
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README.md
7.22 KB
Abstract
Canine atopic dermatitis (CAD) is a common inflammatory skin condition in dogs. It is a life-long problem which poses a significant welfare issue due to the chronic skin discomfort and pruritus (itch) experienced. Excessive scratching, licking and chewing cause self-trauma to the skin and increased risk of secondary infections. Several breeds are predisposed including the Labrador Retriever, Boxer and French Bulldog, suggesting a genetic component to the condition. Our access to a sizeable population of dogs genotyped on a medium density single-nucleotide polymorphism (SNP) array along with linked clinical record information allows for large-scale and highly powered genome-wide association study (GWAS) analysis. In this study, over 28 thousand dogs were used to look for genetic changes associated with CAD. We identified a statistically significant signal on canine chromosome 38, with a particularly strong association in the French Bulldog breed. Genome resequencing revealed a provocative splice donor variant in SLAMF1 (Signaling lymphocytic activation molecule 1), an immune system associated gene. Analysis of further genome sequences and RNA samples from the Mars Petcare Biobank confirmed the SLAMF1 variant as a strong candidate for causing an increased risk of atopic dermatitis.
https://doi.org/10.5061/dryad.np5hqc053
Description of the data and file structure
Corresponding Author Contact Information
Name: Oliver P Forman
Institution: Wisdom Panel, Science and Diagnostics, Mars Petcare, US
Email: oliver.forman@effem.com
Dataset Overview
This dataset contains the Plink data required to replicate GWAS analysis in “A splice donor variant in SLAMF1 is associated with canine atopic dermatitis”, Oliver P. Forman, et al.
Description of the data and file structure
Each of the datasets contains a set of binary Plink files (.bed, .bim and .bam) annotated with breed abbreviations and case and control numbers.
Software
All available data was produced and can be manipulated with the free software Plink v1.9
Files with the extensions bim and fam are plain text and viewable with any text editor.
Files with the extension bed are binary PLINK files viewable with the free python software package, bed-reader, downloadable from pypi.
Files and variables
File: atopy_shiba_239_cases_284_controls.fam
File: atopy_shiba_239_cases_284_controls.bim
File: atopy_shiba_239_cases_284_controls.bed
Description: Shiba Inu samples in binary Plink format with 239 cases and 284 breed matched controls
File: atopy_husky_227_cases_315_controls.fam
File: atopy_husky_227_cases_315_controls.bim
File: atopy_husky_227_cases_315_controls.bed
Description: Husky samples in binary Plink format with 227 cases and 315 breed matched controls
File: atopy_greatdane_215_cases_212_controls.bed
File: atopy_greatdane_215_cases_212_controls.fam
File: atopy_greatdane_215_cases_212_controls.bim
Description: Great Dane samples in binary Plink format with 215 cases and 212 breed matched controls
File: atopy_chihuahua_304_cases_363_controls.fam
File: atopy_chihuahua_304_cases_363_controls.bim
File: atopy_chihuahua_304_cases_363_controls.bed
Description: Chihuahua samples in binary Plink format with 304 cases and 363 breed matched controls
File: atopy_shih_tzu_797_cases_929_controls.fam
File: atopy_shih_tzu_797_cases_929_controls.bim
File: atopy_shih_tzu_797_cases_929_controls.bed
Description: Shih Tzu samples in binary Plink format with 797 cases and 929 breed matched controls
File: atopy_yorkie_663_cases_786_controls.fam
File: atopy_yorkie_663_cases_786_controls.bim
File: atopy_yorkie_663_cases_786_controls.bed
Description: Yorkshire Terrier samples in binary Plink format with 663 cases and 786 breed matched controls
File: atopy_singlebreed_14378_cases_14633_controls.fam
File: atopy_singlebreed_14378_cases_14633_controls.bim
File: atopy_singlebreed_14378_cases_14633_controls.bed
Description: Single breed samples in binary Plink format with 14,378 cases and 14,633 breed matched controls
File: atopy_min_schnauzer_559_cases_631_controls.fam
File: atopy_min_schnauzer_559_cases_631_controls.bim
File: atopy_min_schnauzer_559_cases_631_controls.bed
Description: Miniature Schnauzer samples in binary Plink format with 559 cases and 631 breed matched controls
File: atopy_minpoodle_385_cases_464_controls.fam
File: atopy_minpoodle_385_cases_464_controls.bim
File: atopy_minpoodle_385_cases_464_controls.bed
Description: Miniature Poodle samples in binary Plink format with 385 cases and 464 breed matched controls
File: atopy_poodle_461_cases_498_controls.fam
File: atopy_poodle_461_cases_498_controls.bim
File: atopy_poodle_461_cases_498_controls.bed
Description: Poodle samples in binary Plink format with 461 cases and 498 breed matched controls
File: atopy_dachshund_436_cases_507_controls.fam
File: atopy_dachshund_436_cases_507_controls.bim
File: atopy_dachshund_436_cases_507_controls.bed
Description: Dachshund samples in binary Plink format with 436 cases and 507 breed matched controls
File: atopy_beagle_349_cases_362_controls.fam
File: atopy_beagle_349_cases_362_controls.bim
File: atopy_beagle_349_cases_362_controls.bed
Description: Beagle samples in binary Plink format with 349 cases and 362 breed matched controls
File: atopy_wpcorgi_398_cases_477_controls.fam
File: atopy_wpcorgi_398_cases_477_controls.bim
File: atopy_wpcorgi_398_cases_477_controls.bed
Description: Pembroke Welsh Corgi samples in binary Plink format with 398 cases and 477 breed matched controls
File: atopy_golden_1056_cases_1057_controls.fam
File: atopy_golden_1056_cases_1057_controls.bim
File: atopy_golden_1056_cases_1057_controls.bed
Description: Golden Retriever samples in binary Plink format with 1,056 cases and 1,057 breed matched controls
File: atopy_gsd_1494_cases_1599_controls.fam
File: atopy_gsd_1494_cases_1599_controls.bim
File: atopy_gsd_1494_cases_1599_controls.bed
Description: German Shepherd samples in binary Plink format with 1,494 cases and 1,599 breed matched controls
File: atopy_lab_1668_cases_1064_controls.fam
File: atopy_lab_1668_cases_1064_controls.bim
File: atopy_lab_1668_cases_1064_controls.bed
Description: Labrador samples in binary Plink format with 1,668 cases and 1,064 breed matched controls
File: atopy_frenchie_2138_cases_645_controls.fam
File: atopy_frenchie_2138_cases_645_controls.bim
File: atopy_frenchie_2138_cases_645_controls.bed
Description: French Bulldog samples in binary Plink format with 2,138 cases and 645 breed matched controls
File: atopy_boxer_447_cases_515_controls.fam
File: atopy_boxer_447_cases_515_controls.bim
File: atopy_boxer_447_cases_515_controls.bed
Description: Boxer samples in binary Plink format with 447 cases and 515 breed matched controls
File: atopy_boston_478_cases_531_controls.fam
File: atopy_boston_478_cases_531_controls.bim
File: atopy_boston_478_cases_531_controls.bed
Description: Boston Terrier samples in binary Plink format with 478 cases and 531 controls
Access information
Data was derived from the following sources:
- DNA samples collected via commercial testing of Wisdom Panel™ Premium, Wisdom Panel™ Essential, Wisdom Panel™ Health and Optimal Selection™ retail products
- Banfield EMR (electronic medical records). For DNA samples collected and submitted by general retail consumers of Wisdom Panel products, data from genotyped dogs was linked with the Banfield EMR by anonymized cross matching of pet and owner information, in accordance with personally identifiable information (PII) regulations.
Samples
DNA samples were collected via commercial testing of Wisdom Panel™ Premium, Wisdom Panel™ Essential, Wisdom Panel™ Health and Optimal Selection™ retail products, and genetic testing performed as a part of Optimal Wellness Plans® for puppies, through Banfield Pet Hospital branches (Vancouver, WA, USA) and as part of the MARS PETCARE BIOBANK™. Samples were either collected through non-invasive cheek swabbing by dog owners or veterinary professionals or through blood sampling by a veterinary professional at a Banfield Pet Hospital in line with regulations governing diagnostic testing. Consent for use of DNA data in research was obtained through the client’s agreement with terms and conditions of DNA testing through Wisdom Panel. Analysis and sequencing of cDNA were performed using samples collected from dogs participating in the Mars Petcare Biobank. All samples originated from the United States or Mexico.
Analysis
An initial GWAS was performed using 14,378 single breed cases and 14,633 breed matched controls to tightly control against potential population stratification. Within breed GWAS was performed where at least 200 cases and controls were available for a given breed.
Inclusion criteria
CAD cases and controls were categorized based on labelling provided by general veterinary practitioners in the Banfield EMR and through criteria set by a board-certified veterinary dermatologist. Given the retrospective nature of the data, this is a diagnosis of atopic dermatitis in the broad sense which may include dogs with food allergic dermatitis.
CAD cases were in the age range of 0.3 to 20 years and must have received at least three months of ectoparasite control. CAD cases had also been diagnosed with recurrent (more than once) clinical signs of atopic dermatitis including: Dermatitis, Atopic Allergic; Otitis; Pododermatitis; Pruritus; Pyoderma or Malassezia. In addition, CAD cases could also have been prescribed recurrent systemic anti-inflammatories, antihistamines or medicated ear drops.
Controls were in the age range of 3 to 20 years and must not have been diagnosed with of any of the following recurrent symptoms: Acne; Alopecia Undetermined; Dermatitis (of any variety), Folliculitis; Lichenification; Malassezia; Otitis (of any variety); Paronychia; Pododermatitis; Pruritus; Pyoderma (of any variety). Controls also must not have been prescribed recurrent systemic or topical anti-inflammatories, antihistamines or medicated ear drops.
For breed assignment single breed dogs were defined as dogs with greater or equal to 80% single breed ancestry as defined by the Wisdom Panel breed classification algorithm (BCSYS).
Genotype Analysis
Genome-wide association study analysis was performed using a linear mixed-model approach in the software package GEMMA v0.98.5 including a centered relatedness matrix. PLINK v1.9 was used to apply the following quality control: Samples with an overall genotyping success rate of lower than 95% across all tested SNPs were also filtered out; then, variants below 1% minor allele frequency or lower than 95% genotyping success rate were filtered out.