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Series GSE241367 Query DataSets for GSE241367
Status Public on Aug 28, 2023
Title Association analysis of invasive urinary carcinoma in the Shetland sheepdogs and related breeds.
Organism Canis lupus familiaris
Experiment type SNP genotyping by SNP array
Summary Naturally occurring canine invasive urinary carcinoma (iUC) closely resembles human muscle invasive bladder cancer in terms of histopathology, metastases, response to therapy and, low survival rate. The heterogeneous nature of the disease has led to the association of large numbers of risk loci in humans, however most are of small effect. There exists a need for new and accurate animal models of invasive bladder cancer. In dogs, distinct breeds show markedly different rates of iUC, thus presenting an opportunity to identify additional risk factors and overcome the locus heterogeneity encountered in human mapping studies. In the association study presented here, inclusive of 100 Shetland sheepdogs and 58 dogs of other breeds, we identify a homozygous protein altering point mutation within the NIPAL1 gene which increases risk by eight-fold (OR=8.42, CI=3.12-22.71), accounting for nearly 30% of iUC risk in the Shetland sheepdog. Inclusion of six additional loci accounts for the majority of disease risk in the breed and explains nearly 75% of the phenotypes in this study. When combined with sequence data from tumors, we show that variation in the MAPK signaling pathway is an overarching cause of iUC susceptibility in dogs.
 
Overall design DNA was collected from Shetland sheepdogs, Collies, Border collies, and Australian shepherds with and without diagnosis of invasive urothelial carcinoma (iUC) also known as transitional cell carcinoma of the bladder. SNPs were genotyed using the Illumina CanineHD SNP chip. These data were used in associated studies to find regions of the genome associated with risk or development of iUC.
 
Contributor(s) Parker HG, Ostrander EA, Harris A
Citation(s) 38778091
Submission date Aug 21, 2023
Last update date Oct 02, 2024
Contact name Heidi G Parker
E-mail(s) hgparker@mail.nih.gov
Organization name NHGRI
Department CGB
Lab CGS
Street address 50 South Dr. Rm 5347
City Bethesda
State/province MD
ZIP/Postal code 20874
Country USA
 
Platforms (1)
GPL17481 Illumina CanineHD BeadChip
Samples (160)
GSM7727728 20365
GSM7727729 16124
GSM7727730 11617
Relations
Reanalyzed by GSE278600
BioProject PRJNA1007761

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE241367_RAW.tar 423.8 Mb (http)(custom) TAR (of IDAT)
GSE241367_processed_data.txt.gz 467.0 Mb (ftp)(http) TXT
GSE241367_signal.txt.gz 354.0 Mb (ftp)(http) TXT
Processed data are available on Series record

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