Ontiveros Eric S, Ueda Yu, Harris Samantha P, Stern Joshua A
Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA.
Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA.
J Feline Med Surg. 2019 Dec;21(12):1086-1093. doi: 10.1177/1098612X18816460. Epub 2018 Dec 18.
The objective of this study was to perform a proof-of-concept experiment that validates a precision medicine approach to identify variants associated with hypertrophic cardiomyopathy (HCM). We hypothesized that whole-genome sequencing would identify variant(s) associated with HCM in two affected Maine Coon/Maine Coon cross cats when compared with 79 controls of various breeds.
Two affected and two control Maine Coon/Maine Coon cross cats had whole-genome sequencing performed at approximately × 30 coverage. Variants were called in these four cats and 77 cats of various breeds as part of the 99 Lives Cat Genome Sequencing Initiative ( http://felinegenetics.missouri.edu/99lives ) using Platypus v0.7.9.1, annotated with dbSNP ID, and variants' effect predicted by SnpEff. Strict filtering criteria (alternate allele frequency >49%) were applied to identify homozygous-alternate or heterozygous variants in the two HCM-affected samples when compared with 79 controls of various breeds.
A total of four variants were identified in the two Maine Coon/Maine Coon cross cats with HCM when compared with 79 controls after strict filtering. Three of the variants identified in genes 12, and 5 did not segregate with disease in a separate cohort of seven HCM-affected and five control Maine Coon/Maine Coon cross cats. The remaining variant 3 segregated with disease status. Furthermore, this gene was previously associated with heart disease and encodes for a protein with sarcomeric function.
This proof-of-concept experiment identified the previously reported 3 A31P Maine Coon variant in two HCM-affected cases. This result validates and highlights the power of whole-genome sequencing for feline precision medicine.
本研究的目的是进行一项概念验证实验，以验证一种精准医学方法来识别与肥厚型心肌病（HCM）相关的变异。我们假设，与79只不同品种的对照猫相比，全基因组测序将在两只患HCM的缅因库恩猫/缅因库恩杂交猫中识别出与HCM相关的变异。
两只患HCM的和两只对照缅因库恩猫/缅因库恩杂交猫进行了全基因组测序，测序深度约为30倍覆盖度。作为99 Lives猫基因组测序计划（http://felinegenetics.missouri.edu/99lives）的一部分，使用Platypus v0.7.9.1在这四只猫以及77只不同品种的猫中检测变异，用dbSNP ID注释，并通过SnpEff预测变异的效应。应用严格的筛选标准（替代等位基因频率>49%），以在两只患HCM的样本中识别纯合替代或杂合变异，并与79只不同品种的对照猫进行比较。
与79只对照猫经过严格筛选后，在两只患HCM的缅因库恩猫/缅因库恩杂交猫中总共鉴定出四个变异。在另外一组七只患HCM的和五只对照缅因库恩猫/缅因库恩杂交猫中，在基因12、 和5中鉴定出的三个变异与疾病不共分离。其余变异3与疾病状态共分离。此外，该基因先前与心脏病相关，并编码一种具有肌节功能的蛋白质。
这项概念验证实验在两例患HCM的病例中鉴定出先前报道的3 A³¹P缅因库恩变异。这一结果验证并突出了全基因组测序在猫科动物精准医学中的作用。
