Design and implementation of a custom next generation sequencing panel for selected vitamin D associated genes.
BMC Res Notes
; 10(1): 348, 2017 Jul 28.
Article
em En
| MEDLINE
| ID: mdl-28754147
ABSTRACT
BACKGROUND:
Biologically active vitamin D has an important regulatory role within the genome. It binds the vitamin D receptor (VDR) in order to control the expression of a wide range of genes as well as interacting with the epigenome to modify chromatin and methylation status. Vitamin D deficiency is associated with several human diseases including end-stage renal disease.METHODS:
This article describes the design and testing of a custom, targeted next generation sequencing (NGS) panel for selected vitamin D associated genes. Sequencing runs were used to determine the effectiveness of the panel for variant calling, to compare efficiency and data across different sequencers, and to perform representative, proof of principle association analyses. These analyses were underpowered for significance testing. Amplicons were designed in two pools (163 and 166 fragments respectively) and used to sequence two cohorts of renal transplant recipients on the Ion Personal Genome Machine (PGM)™ and Ion S5™ XL desktop sequencers.RESULTS:
Coverage was provided for 43.8 kilobases across seven vitamin D associated genes (CYP24A1, CUBN, VDR, GC, NADSYN1, CYP27B1, CYP2R1) as well as 38 prioritised SNPs. Sequencing runs provided sufficient sequencing quality, data output and validated the effective library preparation and panel design.CONCLUSIONS:
This novel, custom-designed, validated panel provides a fast, cost effective, and specific approach for the analysis of vitamin D associated genes in a wide range of patient cohorts. This article does not report results from a controlled health-care intervention.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Vitamina D
/
Deficiência de Vitamina D
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Sequenciamento de Nucleotídeos em Larga Escala
Tipo de estudo:
Risk_factors_studies
Limite:
Adolescent
/
Adult
/
Aged
/
Female
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Humans
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Male
/
Middle aged
Idioma:
En
Ano de publicação:
2017
Tipo de documento:
Article