title: Targeted next generation sequencing of the entire vitamin D receptor gene reveals polymorphisms correlated with vitamin D deficiency among older Filipino women with and without fragility fracture.
abstract: This study aimed to discover genetic variants in the entire 101 kB vitamin D receptor (VDR) gene for vitamin D deficiency in a group of postmenopausal Filipino women using targeted next generation sequencing (TNGS) approach in a case-control study design. A total of 50 women with and without osteoporotic fracture seen at the Philippine Orthopedic Center were included. Blood samples were collected for determination of serum vitamin D, calcium, phosphorus, glucose, blood urea nitrogen, creatinine, aspartate aminotransferase, alanine aminotransferase and as primary source for targeted VDR gene sequencing using the Ion Torrent Personal Genome Machine. The variant calling was based on the GATK best practice workflow and annotated using Annovar tool. A total of 1496 unique variants in the whole 101-kb VDR gene were identified. Novel sequence variations not registered in the dbSNP database were found among cases and controls at a rate of 23.1% and 16.6% of total discovered variants, respectively. One disease-associated enhancer showed statistically significant association to low serum 25-hydroxy vitamin D levels (Pearson chi-square P-value=0.009). The transcription factor binding site prediction program PROMO predicted the disruption of three transcription factor binding sites in this enhancer region. These findings show the power of TNGS in identifying sequence variations in a very large gene and the surprising results obtained in this study greatly expand the catalog of known VDR sequence variants that may represent an important clue in the emergence of vitamin D deficiency. Such information will also provide the additional guidance necessary toward a personalized nutritional advice to reach sufficient vitamin D status.
authors.affiliation: National Institute of Molecular Biology and Biotechnology, University of the Philippines, Diliman, Quezon City, Philippines; Philippine Genome Center, Quezon City, Philippines; Food and Nutrition Research Institute, Department of Science and Technology, Taguig City, Philippines.
authors.forename: Mark Pretzel
authors.initials: MP
authors.lastname: Zumaraga
authors.affiliation: Philippine Orthopedic Center, Banawe, Quezon City, Philippines; Mindanao State University - College of Medicine, Iligan City, Philippines.
authors.forename: Paul Julius
authors.initials: PJ
authors.lastname: Medina
authors.affiliation: National Institute of Molecular Biology and Biotechnology, University of the Philippines, Diliman, Quezon City, Philippines.
authors.forename: Juan Miguel
authors.initials: JM
authors.lastname: Recto
authors.affiliation: Philippine Orthopedic Center, Banawe, Quezon City, Philippines.
authors.forename: Lauro
authors.initials: L
authors.lastname: Abrahan
authors.affiliation: Philippine Orthopedic Center, Banawe, Quezon City, Philippines.
authors.forename: Edelyn
authors.initials: E
authors.lastname: Azurin
authors.affiliation: Food and Nutrition Research Institute, Department of Science and Technology, Taguig City, Philippines.
authors.forename: Celeste C
authors.initials: CC
authors.lastname: Tanchoco
authors.affiliation: Philippine Society of Endocrinology, Diabetes and Metabolism, Pasig City, Philippines.
authors.forename: Cecilia A
authors.initials: CA
authors.lastname: Jimeno
authors.affiliation: National Institute of Molecular Biology and Biotechnology, University of the Philippines, Diliman, Quezon City, Philippines; Philippine Genome Center, Quezon City, Philippines. Electronic address: cpsaloma@up.edu.ph.
authors.forename: Cynthia
authors.initials: C
authors.lastname: Palmes-Saloma
mesh_terms: D015652:25-Hydroxyvitamin D 2 / Q000097:blood; D000368:Aged; D000375:Aging / Q000208:ethnology; D002112:Calcifediol / Q000097:blood; D016022:Case-Control Studies; D019295:Computational Biology; D005260:Female; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease / Q000208:ethnology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D015994:Incidence; D008875:Middle Aged; D015663:Osteoporosis, Postmenopausal / Q000208:ethnology / Q000235:genetics* / Q000378:metabolism / Q000503:physiopathology; D058866:Osteoporotic Fractures / Q000453:epidemiology / Q000208:ethnology / Q000209:etiology*; D010679:Philippines / Q000453:epidemiology; D010865:Pilot Projects; D020641:Polymorphism, Single Nucleotide; D018167:Receptors, Calcitriol / Q000235:genetics* / Q000378:metabolism; D012307:Risk Factors; D014808:Vitamin D Deficiency / Q000208:ethnology / Q000235:genetics* / Q000378:metabolism / Q000503:physiopathology; D030181:Vitamin D Response Element
chemical_list: D018167:Receptors, Calcitriol; C579457:VDR protein, human; D015652:25-Hydroxyvitamin D 2; D002112:Calcifediol
keywords: Filipino women; Fragility fracture; Next generation sequencing; Vitamin D; Vitamin D receptor gene