| Literature DB >> 30028859 |
Atiyeh Peiravan1, Francesca Bertolini2, Max F Rothschild2, Kenneth W Simpson3, Albert E Jergens4, Karin Allenspach4, Dirk Werling1.
Abstract
Canine Inflammatory Bowel Disease (IBD) is considered a multifactorial disease caused by complex interactions between the intestinal immune system, intestinal microbiota and environmental factors in genetically susceptible individuals. Although IBD can affect any breed, German shepherd dogs (GSD) in the UK are at increased risk of developing the disease. Based on previous evidence, the aim of the present study was to identify single nucleotide polymorphisms (SNPs), which may confer genetic susceptibility or resistance to IBD using a genome-wide association study (GWAS). Genomic DNA was extracted from EDTA blood or saliva samples of 96 cases and 98 controls. Genotyping of cases and controls was performed on the Canine Illumina HD SNP array and data generated was analyzed using PLINK. Several SNPs and regions on chromosomes 7,9,11 and 13 were detected to be associated with IBD using different SNP-by-SNP association methods and FST windows approach. Searching one Mb up-and down-stream of the most significant SNPs, as identified by single SNP analysis as well as 200Kb before and after the start and the end position of the associated regions identified by FST windows approach, we identified 63 genes. Using a combination of pathways analysis and a list of genes that have been reported to be involved in human IBD, we identified 16 candidate genes potentially associated with IBD in GSD.Entities:
Mesh:
Year: 2018 PMID: 30028859 PMCID: PMC6054420 DOI: 10.1371/journal.pone.0200685
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Fig 1Scatter plot for the first 2 dimensions.
The x-axis is principal component 1 and y-axis is principal component 2. Green: case, Blue: control.
Fig 2Admixture plot of the case-control dataset (showed on the right) using the K with the lowest cross-validation error (showed on the left).
Fig 3Manhattan plots of basic case-control association test (a), logistic regression without covariate (b) and logistic regression with covariate (c). Suggestive association threshold is indicated with the blue line. SNPs of the logistic analyses with the lowest p-value that overlapped the basic association study are within red circles.
The most significant SNPs found by basic case/control association analysis.
| CHR | SNP | BP | A1 | F_A | F_U | A2 | CHISQ | P | OR |
|---|---|---|---|---|---|---|---|---|---|
| 9 | BICF2P753594 | 51531181 | C | 0,07609 | 0,2447 | G | 19,54 | 9,86E-06 | 0,2542 |
| 9 | BICF2P436494 | 51541093 | G | 0,07609 | 0,25 | A | 20,52 | 5,91E-06 | 0,2471 |
| 9 | BICF2P812982 | 51544743 | G | 0,07609 | 0,2553 | A | 21,51 | 3,52E-06 | 0,2402 |
| 11 | BICF2S23033111 | 20056580 | C | 0,212 | 0,04787 | A | 22,28 | 2,36E-06 | 5,349 |
CHR: Chromosome
SNP: SNP ID
BP: Physical position on CanFam3.1
A1: Minor allele name (based on whole sample)
F A: Frequency of this allele in cases
F U: Frequency of this allele in controls
A2: Major allele name
CHISQ: Basic allelic test chi-square
P: Asymptotic p-value for this test
OR:Estimated odds ratio (for A1, i.e. A2 is reference)
Fig 4Single FST approach result.
SNPs with the highest FST value that overlap the basic case/control association test and logistic association are within red circles.
Regions on chromosome 7 and 13, found by FST windows approach.
| chromosome | Start | End | N.Snps | mFST |
|---|---|---|---|---|
| 7 | 4000000 | 5000000 | 31 | 0.0362679 |
| 7 | 3500000 | 4500000 | 44 | 0.0384714 |
| 13 | 2500000 | 3500000 | 33 | 0.038702 |
| 7 | 2500000 | 3500000 | 17 | 0.0403834 |
| 7 | 3000000 | 4000000 | 39 | 0.0408544 |
Start: start position of the window. End: End position of the window. N.Snps: number of SNPs included in each window. mFST: mean FST value calculated for SNPs included in each window.
Enricher results.
Genes found to be enriched in biological processes and/or molecular components that are associated or directly/indirectly involved with human IBD.
| Chromosme region | gene symbol | gene name | gene start | gene end | database |
|---|---|---|---|---|---|
| 7 | PTPRC* | Protein tyrosine phosphatase, receptor type C | 4156687 | 4282147 | KEEG |
| 9 | TSC1 | Tuberous sclerosis 1 | 51419149 | 51454668 | KEEG |
| RALGDS | Ral guanine nucleotide dissociation stimulator | 51308323 | 51330270 | KEEG | |
| COL5A1 | Collagen type V alpha 1 chain | 50741552 | 50856744 | Wikipathways20016 | |
| RAPGEF1 | Rap guanine nucleotide exchange factor 1 | 52450597 | 52562778 | Wikipathways20016 | |
| 11 | IL4* | Interleukin-4 | 20972693 | 20981541 | KEEG; Wikipathways20016; Panther 2016; NCI-Nature 2016 |
| IL5* | Interleukin-5 | 20825469 | 20827269 | KEEG; Wikipathways20016; Panther 2016; NCI-Nature 2016 | |
| CSF2* | Granulocyte-macrophage colony-stimulating factor | 20344009 | 20346959 | KEEG; Wikipathways20016 | |
| IL13* | Interleukin-13 precursor | 20958464 | 20961391 | KEEG; Wikipathways20016; Panther 2016; NCI-Nature 2016 | |
| SLC22A4* | Solute carrier family 22 member 4 | 20598888 | 20644639 | KEEG | |
| SLC22A5* | Solute carrier family 22 member 5 | 20659221 | 20683073 | KEEG | |
| IRF1* | Interferon regulatory factor 1 | 20772643 | 20781207 | NCI-Nature 2016 | |
| ACSL6* | acyl-CoA synthetase long-chain family member 6 | 20223930 | 20285138 | - | |
| IL3* | Interleukin-3 | 20330480 | 20332668 | - | |
| PDLIM4* | PDZ and LIM domain 4 | 20570752 | 20587263 | - | |
| 13 | YWHAZ | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta | 2729503 | 2763613 | Wikipathways20016 |
*Genes found already to be associated with human IBD.