Establishment of patient-derived xenotransplant and cell line models for canine B-cell lymphoma
Data files
Sep 16, 2026 version files 6.04 KB
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94SNPs.bed
285 B
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94SNPs.bim
2.99 KB
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94SNPs.fam
271 B
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README.md
2.50 KB
Abstract
High grade canine B-cell lymphoma (cBCL) is a spontaneous cancer in dogs with a very similar pathology to human diffuse large B-cell lymphoma (DLBCL). The value of comparative oncology to both dogs and humans has long been recognized, but the progress in cBCL research has been hampered by a scarcity of preclinical models. This study aimed to establish and characterize novel patient-derived xenograft (PDX) and cell line models from primary cBCL tumors to address this critical gap. To this end, primary cBCL tumors from three canine patients were surgically excised and serially transplanted into immunodeficient NOD scid gamma (NSG) mice. The resulting PDX models were characterized across passages using histology, flow cytometry, SNP genotyping, and RNA sequencing, the results of which show that they retain much of their original characteristics, even after multiple NSG passages. Cancer cells from two of the PDX lines were successfully adapted to in vitro culture, creating two new established cell lines, one of which was then used in drug sensitivity assays. The successful generation and characterization of these cBCL PDX and cell lines provides a valuable resource in canine cancer research.
Dataset DOI: 10.5061/dryad.dncjsxmbg
Description of the data and file structure
These data were generated to identify that the PDX and cell line samples are genetically related to their original canine tumor samples. DNA was extracted from the samples and genotyped on the CanineHD 220k beadchip (Illumina Inc). Identifying information has not been included in this dataset.
One binary PLINK file dataset is included. PLINK is an open-source, free program commonly used for genotype data. The binary format includes three files: fam (sample information file), bim (variant information file), bed (biallelic genotype table). These are called using the command --bfile.
Pre-filtering of these genotype files includes removing SNPs with a genotyping rate < 95 %, SNPs with a minor allele frequency of < 5 % and SNPs that had previously been identified as discordant between duplicate samples run on the same array.
Files and variables
File: 94SNPs.fam
Description: text file containing information for each sample\
- family ID
- within-family ID
- paternal ID ("0" if not in dataset)
- maternal ID ("0" if not in dataset)
- sex (1 = male, 2 = female, 0 = unknown)
- phenotype value (1 = control, 2 = case, -9 = unknown)
File: 94SNPs.bim
Description: text file containing information for each variant
No header, 6 fields:
- chromosome code (1-38, 39 = X, 40 = Y, 41 = non-PAR X, 42 = mitochondrial, 0 = unknown)
- variant name
- genetic position, in morgans (or centimorgans) ("0" if unknown)
- position in base-pair
- allele 1
- allele 2
File: 94SNPs.bed
Description: binary file containing genotypes for each sample [in the same order as the fam file] at each variant [in the same order as the bim file]
Code/software
Raw data files were converted to PLINK format and quality control was performed in PLINK v 1.9 (https://www.cog-genomics.org/plink2/).
PLINK is an open-source, free program commonly used for genotype data. The binary format includes three files: fam (sample information file), bim (variant information file), bed (biallelic genotype table). These are called using the command --bfile in PLINK.
Access information
Data was derived from the following sources:
- Genotypes were generated by Illumina Inc (San Diego, CA) through Embark Veterinary Inc.