Direct-to-consumer DNA testing of 6,000 dogs reveals 98.6-kb duplication associated with blue eyes and heterochromia in Siberian Huskies

Consumer genomics enables genetic discovery on an unprecedented scale by linking very large databases of personal genomic data with phenotype information voluntarily submitted via web-based surveys. These databases are having a transformative effect on human genomics research, yielding insights on increasingly complex traits, behaviors, and disease by including many thousands of individuals in genome-wide association studies (GWAS). The promise of consumer genomic data is not limited to human research, however. Genomic tools for dogs are readily available, with hundreds of causal Mendelian variants already characterized, because selection and breeding have led to dramatic phenotypic diversity underlain by a simple genetic structure. Here, we report the results of the first consumer genomics study ever conducted in a non-human model: a GWAS of blue eyes based on more than 3,000 customer dogs with validation panels including nearly 3,000 more, the largest canine GWAS to date. We discovered a novel association with blue eyes on chromosome 18 (P = 1.3x10-68) and used both sequence coverage and microarray probe intensity data to identify the putative causal variant: a 98.6-kb duplication directly upstream of the Homeobox gene ALX4, which plays an important role in mammalian eye development. This duplication is largely restricted to Siberian Huskies, is strongly associated with the blue-eyed phenotype (chi-square P = 5.2x10-290), and is highly, but not completely, penetrant. These results underscore the power of consumer-data-driven discovery in non-human species, especially dogs, where there is intense owner interest in the personal genomic information of their pets, a high level of engagement with web-based surveys, and an underlying genetic architecture ideal for mapping studies.

消费级基因组学（consumer genomics）通过将超大规模个人基因组数据库与受试者通过网络调研自愿提交的表型信息进行关联分析，实现了规模空前的遗传发现。此类数据库正对人类基因组学研究产生变革性影响：通过在全基因组关联研究（GWAS）中纳入数千名人类受试者，相关研究得以解析愈发复杂的性状、行为与疾病关联。不过消费级基因组数据的应用前景并不局限于人类研究领域。由于犬类的选择育种造就了以简单遗传结构为基础的显著表型多样性，目前已有数百种致病孟德尔变异被成功表征，因此面向犬类的基因组学工具已较为成熟。本研究首次开展了非人类模式生物的消费级基因组学研究：基于超过3000只宠物犬的样本开展蓝眼性状全基因组关联研究，并使用近3000个额外样本作为验证队列，这也是目前规模最大的犬类全基因组关联研究。我们在18号染色体上发现了一个与蓝眼性状相关的全新位点（P = 1.3×10^-68），并结合测序覆盖度与微阵列探针强度数据，鉴定出推定致病变异：一段位于同源盒基因ALX4（Homeobox gene ALX4）上游直接区域的98.6kb重复序列，该基因在哺乳动物眼部发育中发挥关键作用。该重复序列主要存在于西伯利亚哈士奇群体中，与蓝眼表型呈强相关性（卡方检验P值 = 5.2×10^-290），且具有极高但并非完全的外显率。本研究结果凸显了消费级数据驱动的非人类物种（尤其是犬类）研究的优势：犬主对宠物个人基因组信息具有极高关注度，且乐于参与网络调研，同时犬类的遗传结构也非常适合开展定位研究。