Original Article
Volume: 1 | Issue: 1 | Published: Jan 01, 1970 | Pages: 31 - 36 | DOI: 10.24911/JBCGenetics/183-1529928114
Clinical reassessment of post-laboratory variant call format (VCF) files
Authors: Lamia Alsubaie , Saeed Alturki , Ali Alothaim , Ahmed Alfares
Article Info
Authors
Lamia Alsubaie
King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Department of Pediatrics, Genetic Division, King Abdullah Specialized Children's Hospital, NGHA, Riyadh, Saudi Arabia
Saeed Alturki
King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Department of Pediatrics, Genetic Division, King Abdullah Specialized Children's Hospital, NGHA, Riyadh, Saudi Arabia
Ali Alothaim
King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Department of Pediatrics, Genetic Division, King Abdullah Specialized Children's Hospital, NGHA, Riyadh, Saudi Arabia
Ahmed Alfares
Department of Pediatrics, College of Medicine, Qassim University, Alqassim, Saudi Arabia
Publication History
Received: October 14, 2017
Revised: November 28, 2017
Accepted: December 02, 2017
Published: January 01, 1970
Abstract
Background: Next-generation sequencing has been leading the genetic study of human disease for the past 10 years, generating a huge amount of sequence variant data, which are stored in variant call format (VCF) files. The aim of the study was to reassess the utility of VCF files for reanalysis. Methodology: This is a descriptive observational study of Saudi patients with undiagnosed genetic conditions. VCF files from 20 samples were referred to the molecular laboratory by physicians for reanalysis using variant interpretation software. Results: Seven cases (n = 20) have been reported differently from the outside laboratory. This accounts for almost 35% of all cases and is mainly due to the ability to gather more information about the patient's phenotype. One whole-genome sequence (WGS) case changed from inconclusive to negative. In addition, we identified variants related to the patient's phenotype in six cases; two of them were WGS and four were whole-exome sequence, all reported as negative before the reanalysis. Conclusion: Comprehensive phenotyping of individuals is a crucial step in identifying candidate phenotype-related variants. We outline the benefit obtained from access to the patient's medical records and communication with referring physicians.
Keywords: report, variants, vcf, reassessment, genomic, genetic, NGS
