JBCGenetics |

Original Article

Volume: 1 | Issue: 1 | Published: Feb 12, 2018 | 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

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&apos;s Hospital, NGHA, Riyadh, Saudi Arabia

Saeed Alturki

Ali Alothaim

Ahmed Alfares

Department of Pediatrics, College of Medicine, Qassim University, Alqassim, Saudi Arabia

Publication History

Received: October 14, 2017

Accepted: December 02, 2017

Published: February 12, 2018

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

Pubmed Style

Lamia Alsubaie, Saeed Alturki, Ali Alothaim, Ahmed Alfares. Clinical reassessment of post-laboratory variant call format (VCF) files. JBC Genetics. 2018; 12 (February 2018): 31-36. doi:10.24911/JBCGenetics/183-1529928114

Web Style

Lamia Alsubaie, Saeed Alturki, Ali Alothaim, Ahmed Alfares. Clinical reassessment of post-laboratory variant call format (VCF) files. https://jbcgenetics.com/articles/2016 [Access: June 27, 2025]. doi:10.24911/JBCGenetics/183-1529928114

AMA (American Medical Association) Style

Vancouver/ICMJE Style

Lamia Alsubaie, Saeed Alturki, Ali Alothaim, Ahmed Alfares. Clinical reassessment of post-laboratory variant call format (VCF) files. JBC Genetics. (2018), [cited June 27, 2025]; 12 (February 2018): 31-36. doi:10.24911/JBCGenetics/183-1529928114

Harvard Style

Lamia Alsubaie, Saeed Alturki, Ali Alothaim, Ahmed Alfares (2018) Clinical reassessment of post-laboratory variant call format (VCF) files. JBC Genetics, 12 (February 2018): 31-36. doi:10.24911/JBCGenetics/183-1529928114

Chicago Style

Lamia Alsubaie, Saeed Alturki, Ali Alothaim, Ahmed Alfares. "Clinical reassessment of post-laboratory variant call format (VCF) files." 12 (2018), 31-36. doi:10.24911/JBCGenetics/183-1529928114

MLA (The Modern Language Association) Style

Lamia Alsubaie, Saeed Alturki, Ali Alothaim, Ahmed Alfares. "Clinical reassessment of post-laboratory variant call format (VCF) files." 12.February 2018 (2018), 31-36. Print. doi:10.24911/JBCGenetics/183-1529928114

APA (American Psychological Association) Style

Lamia Alsubaie, Saeed Alturki, Ali Alothaim, Ahmed Alfares (2018) Clinical reassessment of post-laboratory variant call format (VCF) files. , 12 (February 2018), 31-36. doi:10.24911/JBCGenetics/183-1529928114