Sayyab Shumaila, Viluma Agnese, Bergvall Kerstin, Brunberg Emma, Jagannathan Vidhya, Leeb Tosso, Andersson Göran, Bergström Tomas F
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden Research Center for Modeling and Simulation, National University of Sciences and Technology, Sector H-12, Islamabad, Pakistan.
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden.
G3 (Bethesda). 2016 Jan 8;6(3):521-7. doi: 10.1534/g3.115.025643.
Over 250 Mendelian traits and disorders, caused by rare alleles have been mapped in the canine genome. Although each disease is rare in the dog as a species, they are collectively common and have major impact on canine health. With SNP-based genotyping arrays, genome-wide association studies (GWAS) have proven to be a powerful method to map the genomic region of interest when 10-20 cases and 10-20 controls are available. However, to identify the genetic variant in associated regions, fine-mapping and targeted resequencing is required. Here we present a new approach using whole-genome sequencing (WGS) of a family trio without prior GWAS. As a proof-of-concept, we chose an autosomal recessive disease known as hereditary footpad hyperkeratosis (HFH) in Kromfohrländer dogs. To our knowledge, this is the first time this family trio WGS-approach has been used successfully to identify a genetic variant that perfectly segregates with a canine disorder. The sequencing of three Kromfohrländer dogs from a family trio (an affected offspring and both its healthy parents) resulted in an average genome coverage of 9.2X per individual. After applying stringent filtering criteria for candidate causative coding variants, 527 single nucleotide variants (SNVs) and 15 indels were found to be homozygous in the affected offspring and heterozygous in the parents. Using the computer software packages ANNOVAR and SIFT to functionally annotate coding sequence differences, and to predict their functional effect, resulted in seven candidate variants located in six different genes. Of these, only FAM83G:c155G > C (p.R52P) was found to be concordant in eight additional cases, and 16 healthy Kromfohrländer dogs.
超过250种由罕见等位基因引起的孟德尔性状和疾病已在犬类基因组中定位。虽然每种疾病在犬类物种中都很罕见，但它们总体上很常见，并且对犬类健康有重大影响。利用基于单核苷酸多态性（SNP）的基因分型芯片，当有10至20个病例和10至20个对照时，全基因组关联研究（GWAS）已被证明是一种绘制感兴趣基因组区域的强大方法。然而，要识别相关区域中的遗传变异，需要进行精细定位和靶向重测序。在此，我们提出一种新方法，即对一个家系三联体进行全基因组测序（WGS），而无需事先进行GWAS。作为概念验证，我们选择了一种常染色体隐性疾病，即克罗姆弗勒犬的遗传性脚垫角化过度（HFH）。据我们所知，这是首次成功使用这种家系三联体WGS方法来识别与犬类疾病完美分离的遗传变异。对一个家系三联体中的三只克罗姆弗勒犬（一只患病后代及其两只健康父母）进行测序，结果显示个体平均基因组覆盖率为9.2倍。在对候选致病编码变异应用严格的筛选标准后，发现527个单核苷酸变异（SNV）和15个插入缺失在患病后代中是纯合的，而在父母中是杂合的。使用计算机软件包ANNOVAR和SIFT对编码序列差异进行功能注释，并预测其功能效应，结果在六个不同基因中发现了七个候选变异。其中，只有FAM83G:c155G > C（p.R52P）在另外八只病例和16只健康的克罗姆弗勒犬中被发现是一致的。
