DOI: 10.5061/dryad.jdfn2z39b
title: Analysis of copy number variation in dogs implicates genomic structural variation in the development of anterior cruciate ligament rupture

description: Anterior cruciate ligament (ACL) rupture is an important condition of the
 human knee. Second ruptures are common and societal costs are substantial.
 Canine cranial cruciate ligament (CCL) rupture closely models the human
 disease. CCL rupture is common in the Labrador Retriever (5.79%
 prevalence), ~100-fold more prevalent than in humans. Labrador Retriever
 CCL rupture is a polygenic complex disease, based on genome-wide
 association study (GWAS) of single nucleotide polymorphism (SNP) markers.
 Dissection of genetic variation in complex traits can be enhanced by
 studying structural variation, including copy number variants (CNVs). Dogs
 are an ideal model for CNV research because of reduced genetic variability
 within breeds and extensive phenotypic diversity across breeds. We studied
 the genetic etiology of CCL rupture by association analysis of CNV regions
 (CNVRs) using 110 case and 164 control Labrador Retrievers. CNVs were
 called from SNPs using three different programs (PennCNV, CNVPartition,
 and QuantiSNP). After quality control, CNV calls were combined to create
 CNVRs using ParseCNV and an association analysis was performed. We found
 no strong effect CNVRs but found 46 small effect (max(T) permutation
 P&lt;0.05) CCL rupture associated CNVRs in 22 autosomes; 25 were
 deletions and 21 were duplications. Of the 46 CCL rupture associated
 CNVRs, we identified 39 unique regions. Thirty four were identified by a
 single calling algorithm, 3 were identified by two calling algorithms, and
 2 were identified by all three algorithms. For 42 of the associated CNVRs,
 frequency in the population was &lt;10% while 4 occurred at a
 frequency in the population ranging from 10-25%. Average CNVR length was
 198,872bp and CNVRs covered 0.11 to 0.15% of the genome. All CNVRs were
 associated with case status. CNVRs did not overlap previous canine CCL
 rupture risk loci identified by GWAS. Associated CNVRs contained 152
 annotated genes; 12 CNVRs did not have genes mapped to CanFam3.1. Using
 pathway analysis, a cluster of 19 homeobox domain transcript regulator
 genes was associated with CCL rupture (P=6.6E-13). This gene cluster
 influences cranial-caudal body pattern formation during embryonic limb
 development. Clustered genes were found in 3 CNVRs on chromosome 14
 (HoxA), 28 (NKX6-2), and 36 (HoxD). When analysis was limited to deletion
 CNVRs, the association was strengthened (P=8.7E-16). This study suggests a
 component of the polygenic risk of CCL rupture in Labrador Retrievers is
 associated with small effect CNVs and may include aspects of stifle
 morphology regulated by homeobox domain transcript regulator genes.
description: <strong>Lab_Ret_ACL_GenomeStudio_Sample_Sheet.csv</strong> Sample sheet (comma-delimited (.csv)) to load raw *.idat files into GenomeStudio for 274 Labrador Retrievers phenotyped for ACL rupture. File contains ACL phenotype, sex (gender), and age coding.  <strong>Instructions_to_Load_Raw_Intensity_Data_(*.idat)_Files_into_GenomeStudio.pdf</strong> Instructional sheet providing step-by-step instructions to load raw intensity data (*.idat) files in to GenomeStudio. GenomeStudio software and CanineHD BeadChip Manifest files are available for download through Illumina's website at the provided links listed under "Related Works". Links are also provided to Illumina's GenomeStudio User Guide and Illumina's technical information for Custom Cluster File creation.