Genomic analyses identify 15 susceptibility loci and reveal HDAC2, SOX2-OT, and IGF2BP2 in a naturally-occurring canine model of gastric cancer

Gastric cancer ranks as the fifth most common human cancer worldwide and has a poor survival rate and limited treatment options. Despite the high prevalence and mortality rate, the genetic etiology is largely unknown. In dogs, a clinically and histologically similar disease disproportionately affects two breeds, the Belgian Tervuren and Belgian Sheepdog, who develop the intestinal and diffuse tumor subtypes observed in humans. We performed a Bayesian genome-wide association study and selection analyses in this naturally-occurring canine model to elucidate underlying genetic risk factors for gastric cancer and identified 15 associated loci. Variant filtering revealed germline putative regulatory variants for the EPAS1 (HIF2A) and PTEN genes and a coding variant in CD101. Two loci are overrepresented among cases of intestinal tumor subtype. Although closely related to Tervuren and Sheepdogs, Belgian Malinois rarely develop gastric cancer. Across-breed analyses uncovered haplotypes enriche..., , , # Data from: Genomic analyses identify 15 susceptibility loci and reveal HDAC2, SOX2-OT, and IGF2BP2 in a naturally-occurring canine model of gastric cancer

[https://doi.org/10.5061/dryad.pg4f4qrzs](https://doi.org/10.5061/dryad.pg4f4qrzs)

## Description of the data and file structure

Manuscript entitled: \"Genomic analyses identify 15 susceptibility loci and reveal HDAC2, SOX2-OT, and IGF2BP2 in a naturally-occurring canine model of gastric cancer\"

Authors: Shawna R. Cook, Sanne Hugen, Jessica J. Hayward, Thomas R. Famula, Janelle M. Belanger, Elizabeth McNiel, Hille Fieten, Anita M. Oberbauer, Peter A.J. Leegwater, Elaine A. Ostrander, Paul J.J. Mandigers, Jacquelyn M. Evans

This fileset includes:

1\. Binary PLINK files containing genotype data of 363 Belgian shepherd dogs run on the 173k Illumina CanineHD BeadChip array with positions reported in CanFam3.1 reference.

173k_prephased_highcall.fam

173k_prephased_highcall.bim

173k_prephased_highcall.bed

2\. Binary PLINK files co...,

胃癌是全球范围内第五大常见的人类恶性肿瘤，其生存率低下且治疗选择有限。尽管发病率与死亡率均处于较高水平，但其遗传病因学仍未完全阐明。在犬类中，存在一种临床与组织学特征与人类胃癌高度相似的疾病，却不成比例地高发于两个品种：比利时特弗伦犬（Belgian Tervuren）和比利时牧羊犬（Belgian Sheepdog），这两个品种会罹患人类中所见的肠型与弥散型肿瘤亚型。我们针对这种自然发生的犬类胃癌模型开展了贝叶斯全基因组关联分析及选择分析，以阐明胃癌潜在的遗传风险因素，并鉴定出15个相关位点。变异过滤分析显示，EPAS1（HIF2A）与PTEN基因存在生殖系潜在调控变异，同时CD101基因存在一处编码区变异。其中两个位点在肠型肿瘤亚型病例中富集程度更高。尽管比利时马里努阿犬（Belgian Malinois）与特弗伦犬和牧羊犬亲缘关系密切，却极少罹患胃癌。跨品种分析揭示了富集的单倍型……
# 数据来源：《Genomic analyses identify 15 susceptibility loci and reveal HDAC2, SOX2-OT, and IGF2BP2 in a naturally-occurring canine model of gastric cancer》
[https://doi.org/10.5061/dryad.pg4f4qrzs]

## 数据与文件结构说明
论文标题：《基因组分析鉴定出15个易感位点并揭示自然发生的犬类胃癌模型中的HDAC2、SOX2-OT及IGF2BP2基因》
作者：Shawna R. Cook、Sanne Hugen、Jessica J. Hayward、Thomas R. Famula、Janelle M. Belanger、Elizabeth McNiel、Hille Fieten、Anita M. Oberbauer、Peter A.J. Leegwater、Elaine A. Ostrander、Paul J.J. Mandigers、Jacquelyn M. Evans
本数据集包含：
1. 基于173k密度的Illumina CanineHD BeadChip芯片进行基因分型的363只比利时牧羊犬的二进制PLINK格式基因型数据，基因组位置以CanFam3.1参考基因组注释。相关文件包括：173k_prephased_highcall.fam、173k_prephased_highcall.bim、173k_prephased_highcall.bed。
2. 二进制PLINK格式文件共……