University of Santiago de Compostela (USC), Spain. Genomes and Disease Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Santiago de Compostela, Spain; Unit of Diagnosis and Treatment of Congenital Metabolic Diseases (UDyTEMC) from Pediatric Department, Hospital Clínico Universitario de Santiago de Compostela, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Spain.
Galician Research and Development Center in Advanced Telecomunications, GRADIANT, Vigo, Spain.
Genomics. 2020 Mar;112(2):1245-1256. doi: 10.1016/j.ygeno.2019.07.011. Epub 2019 Jul 23.
Genetic laboratories use custom-commercial targeted next-generation sequencing (tg-NGS) assays to identify disease-causing variants. Although the high coverage achieved with these tests allows for the detection of copy number variants (CNVs), which account for an important proportion of the genetic burden in human diseases, an easy-to-use tool for automatic CNV detection is still lacking. This article presents a new CNV detection tool optimized for tg-NGS data: PattRec. PattRec was evaluated using a wide range of data, and its performance compared with those of other CNV detection tools. The software includes features for selecting optimal controls, discarding polymorphic CNVs prior to analysis, and filtering out deletions based on SNV zygosity, and automatically creates an in-house CNV database. There is no need for high level bioinformatic expertise and users can choose color-coded xlsx output that helps to prioritize potentially pathogenic CNVs. PattRec is presented as a Java based GUI, freely available online: https://github.com/irotero/PattRec.
遗传实验室使用定制的商业靶向下一代测序（tg-NGS）检测来识别致病变体。尽管这些测试实现的高覆盖率允许检测拷贝数变异（CNVs），这些 CNVs 在人类疾病的遗传负担中占重要比例，但仍然缺乏易于使用的自动 CNV 检测工具。本文提出了一种针对 tg-NGS 数据优化的新型 CNV 检测工具：PattRec。使用广泛的数据评估了 PattRec，并将其性能与其他 CNV 检测工具进行了比较。该软件具有选择最佳对照、在分析前丢弃多态性 CNVs、根据 SNV 杂合性过滤缺失以及自动创建内部 CNV 数据库的功能。无需高级生物信息学专业知识，用户可以选择彩色编码的 xlsx 输出，有助于优先考虑潜在的致病性 CNVs。PattRec 以基于 Java 的图形用户界面的形式呈现，可在线免费获取：https://github.com/irotero/PattRec。
