Whole-exome and whole-transcriptome sequencing of canine mammary gland tumors

Abstract

Studies of naturally occurring cancers in dogs, which share many genetic and environmental factors with humans, provide valuable information as a comparative model for studying the mechanisms of human cancer pathogenesis. While individual and small-scale studies of canine cancers are underway, more generalized multi-omics studies have not been attempted due to the lack of large-scale and well-controlled genomic data. Here, we produced reliable whole-exome and whole-transcriptome sequencing data of 197 canine mammary cancers and their matched controls, annotated with rich clinical and biological features. Our dataset provides useful reference points for comparative analysis with human cancers and for developing novel diagnostic and therapeutic technologies for cancers in pet dogs.

Quantitative analysis of HER2 mRNA expression by RNA in situ hybridization in canine mammary gland tumors: Comparison with immunohistochemistry analysis

“…Forty-eight CMT samples and 14 non-neoplastic canine mammary tissue samples that were suspected tumors but diagnosed as mammary gland hyperplasia were selected from the archived FFPE database from 2017 to 2019 at the Department of Veterinary Pathology, Konkuk University. Simple random sampling was performed for CMT samples yielding HER2 IHC data (available from our previous data descriptor [21] and validation studies) with complete clinical data. During RNA-ISH, tissue samples not suitable for analysis were excluded Quantitative analysis of mRNA levels by RNA in situ hybridization in formalin-fixed paraffin-embedded samples PLOS ONE | https://doi.org/10.Quantitative analysis of mRNA levels by RNA in situ hybridization in formalin-fixed paraffin-embedded samples PLOS ONE | https://doi.…”

“…To prevent unequal distribution of the HER2 IHC score in malignant CMTs, additional selections were performed until each HER2 IHC score (1+, 2+, and 3+) was obtained from at least 10 samples. Ultimately, 38 FFPE CMT specimens were included in our previous data descriptor article [21].…”

A Kmer-based paired-end read (KPR) de novo assembler and genotyper to genotype major histocompatibility complex class I (MHC-I) alleles for the dog

“…Six paired tumor and normal RNA-seq samples from 3 dogs from a published study 21 were used for the simulation. They are: 1) SRR7779554 and SRR7779476 from dog CMT-162; 2) SRR7779670 and SRR7779671 from dog CMT-785; 3) SRR7779469 and SRR7779468 from dog CMT-149 (Table S3B).…”

“…RNA-seq data of 158 tumors and 64 normal samples (222 total) of 158 dogs (Table S4A) published 21 were downloaded from the SRA database (PRJNA489087), and quality controlled as follows. First, MultiQC 23 (version 1.5) was used to examine GC content and duplicate level ( Figure S4B-C, S4F).…”

A domestic cat whole exome sequencing resource for trait discovery

“…Since the development of the dog WES capabilities, several studies have been successful in identification of causal variants for various diseases including a two base pair deletion in SGCD for muscular dystrophy, and a splice site variant in INPP5E in dogs with cystic renal dysplasia 19,20 . The domestic dog with a large number of isolated breeds are an important genetic resource for cancer studies, and WES has shown similar oncogene variant patterns that enable comparative analysis in humans 21,22 . On the other hand, an analysis of human and canine bladder cancer using WES data identified novel mutations in FAM133B , RAB3GAP2 , and ANKRD52 that are unique to canine bladder cancer suggesting biological differences in origin 23 .…”