PattRec: An easy-to-use CNV detection tool optimized for targeted NGS assays with diagnostic purposes

Iria Roca; Lorena González-Castro; Joan Maynou; Lourdes Palacios; Helena Fernández; Mª Luz Couce; Ana Fernández-Marmiesse

doi:10.1016/j.ygeno.2019.07.011

PattRec: An easy-to-use CNV detection tool optimized for targeted NGS assays with diagnostic purposes

Genomics. 2020 Mar;112(2):1245-1256. doi: 10.1016/j.ygeno.2019.07.011. Epub 2019 Jul 23.

Authors

Iria Roca¹, Lorena González-Castro², Joan Maynou³, Lourdes Palacios³, Helena Fernández², Mª Luz Couce⁴, Ana Fernández-Marmiesse⁵

Affiliations

¹ 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. Electronic address: iria.roca@rai.usc.es.
² Galician Research and Development Center in Advanced Telecomunications, GRADIANT, Vigo, Spain.
³ Progenika Biopharma, a Grifols company, Derio, Spain.
⁴ 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.
⁵ 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.

PMID: 31349009
DOI: 10.1016/j.ygeno.2019.07.011

Abstract

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.

Keywords: CNV detection; Deletion; Duplication; Gene panels.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA Copy Number Variations*
Genetic Testing / methods*
High-Throughput Nucleotide Sequencing / methods*
Humans
Sequence Analysis, DNA / methods*
Software*