Original Article
JBCGenetics. 2018; 1(1): 31-36

Clinical reassessment of post-laboratory variant call format (VCF) files

Authors: Lamia Alsubaie, Saeed Alturki, Ali Alothaim, Ahmed Alfares.

View PDF HTML Fulltext DOI: 10.24911/JBCGenetics/183-1529928114

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


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Clinical reassessment of post-laboratory variant call format (VCF) files


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
PubMed articlesGoogle scholar articles

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
PubMed articlesGoogle scholar articles

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
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Ahmed Alfares
Department of Pediatrics, College of Medicine, Qassim University, Alqassim, Saudi Arabia
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Correspondence to:
. Ahmed Alfares, Department of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia; alfaresah@ngha.med.sa

Publication history
Received 14 Oct 2017
Revised 28 Nov 2017
Accepted 02 Dec 2017
Published in print 01 Jan 2018

How to cite this article

Pubmed Style

Alsubaie L, Alturki S, Alothaim A, Alfares A. Clinical reassessment of post-laboratory variant call format (VCF) files. JBCGenetics. 2018; 1(1): 31-36. doi:10.24911/JBCGenetics/183-1529928114


Web Style

Alsubaie L, Alturki S, Alothaim A, Alfares A. Clinical reassessment of post-laboratory variant call format (VCF) files. https://www.jbcgenetics.com//?mno=302716 [Access: December 13, 2018]. doi:10.24911/JBCGenetics/183-1529928114


AMA (American Medical Association) Style

Alsubaie L, Alturki S, Alothaim A, Alfares A. Clinical reassessment of post-laboratory variant call format (VCF) files. JBCGenetics. 2018; 1(1): 31-36. doi:10.24911/JBCGenetics/183-1529928114


Vancouver/ICMJE Style

Alsubaie L, Alturki S, Alothaim A, Alfares A. Clinical reassessment of post-laboratory variant call format (VCF) files. JBCGenetics. (2018), [cited December 13, 2018]; 1(1): 31-36. doi:10.24911/JBCGenetics/183-1529928114


Harvard Style

Alsubaie, L., Alturki, . S., Alothaim, . A. & Alfares, . A. (2018) Clinical reassessment of post-laboratory variant call format (VCF) files. JBCGenetics, 1 (1), 31-36. doi:10.24911/JBCGenetics/183-1529928114


Turabian Style

Alsubaie, Lamia, Saeed Alturki, Ali Alothaim, and Ahmed Alfares. 2018. Clinical reassessment of post-laboratory variant call format (VCF) files. Journal of Biochemical and Clinical Genetics, 1 (1), 31-36. doi:10.24911/JBCGenetics/183-1529928114


Chicago Style

Alsubaie, Lamia, Saeed Alturki, Ali Alothaim, and Ahmed Alfares. "Clinical reassessment of post-laboratory variant call format (VCF) files." Journal of Biochemical and Clinical Genetics 1 (2018), 31-36. doi:10.24911/JBCGenetics/183-1529928114


MLA (The Modern Language Association) Style

Alsubaie, Lamia, Saeed Alturki, Ali Alothaim, and Ahmed Alfares. "Clinical reassessment of post-laboratory variant call format (VCF) files." Journal of Biochemical and Clinical Genetics 1.1 (2018), 31-36. Print. doi:10.24911/JBCGenetics/183-1529928114


APA (American Psychological Association) Style

Alsubaie, L., Alturki, . S., Alothaim, . A. & Alfares, . A. (2018) Clinical reassessment of post-laboratory variant call format (VCF) files. Journal of Biochemical and Clinical Genetics, 1 (1), 31-36. doi:10.24911/JBCGenetics/183-1529928114


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