Next generation sequencing to identify novel genetic variants causative of autosomal dominant familial hypercholesterolemia associated with increased risk of coronary heart disease

Faisal A Al-Allaf; Mohammad Athar; Zainularifeen Abduljaleel; Mohiuddin M Taher; Wajahatullah Khan; Faisal A Ba-Hammam; Hala Abalkhail; Abdullah Alashwal

doi:10.1016/j.gene.2015.03.064

Next generation sequencing to identify novel genetic variants causative of autosomal dominant familial hypercholesterolemia associated with increased risk of coronary heart disease

Gene. 2015 Jul 1;565(1):76-84. doi: 10.1016/j.gene.2015.03.064. Epub 2015 Apr 1.

Authors

Faisal A Al-Allaf¹, Mohammad Athar², Zainularifeen Abduljaleel³, Mohiuddin M Taher⁴, Wajahatullah Khan⁵, Faisal A Ba-Hammam⁶, Hala Abalkhail⁷, Abdullah Alashwal⁷

Affiliations

¹ Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Molecular Diagnostics Unit, Department of Laboratory and Blood Bank, King Abdullah Medical City, Makkah 21955, Saudi Arabia. Electronic address: fallaf@uqu.edu.sa.
² Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia. Electronic address: athar80@gmail.com.
³ Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia. Electronic address: zainulbio@gmail.com.
⁴ Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia.
⁵ Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, PO Box 3124, Riyadh 11426, Saudi Arabia.
⁶ Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia.
⁷ Department of Pediatrics, MBC 58, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia.

PMID: 25839937
DOI: 10.1016/j.gene.2015.03.064

Abstract

Familial hypercholesterolemia (FH) is an autosomal dominant inherited disease characterized by elevated plasma low-density lipoprotein cholesterol (LDL-C). It is an autosomal dominant disease, caused by variants in Ldlr, ApoB or Pcsk9, which results in high levels of LDL-cholesterol (LDL-C) leading to early coronary heart disease. Sequencing whole genome for screening variants for FH are not suitable due to high cost. Hence, in this study we performed targeted customized sequencing of FH 12 genes (Ldlr, ApoB, Pcsk9, Abca1, Apoa2, Apoc3, Apon2, Arh, Ldlrap1, Apoc2, ApoE, and Lpl) that have been implicated in the homozygous phenotype of a proband pedigree to identify candidate variants by NGS Ion torrent PGM. Only three genes (Ldlr, ApoB, and Pcsk9) were found to be highly associated with FH based on the variant rate. The results showed that seven deleterious variants in Ldlr, ApoB, and Pcsk9 genes were pathological and were clinically significant based on predictions identified by SIFT and PolyPhen. Targeted customized sequencing is an efficient technique for screening variants among targeted FH genes. Final validation of seven deleterious variants conducted by capillary resulted to only one novel variant in Ldlr gene that was found in exon 14 (c.2026delG, p. Gly676fs). The variant found in Ldlr gene was a novel heterozygous variant derived from a male in the proband.

Keywords: Coronary heart disease (CHD); Familial hypercholesterolemia (FH); Functional changes; LDLR; Low-density lipoprotein cholesterol (LDLc).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Apolipoprotein B-100 / genetics*
Coronary Disease / etiology
Coronary Disease / genetics*
Female
Genetic Variation
High-Throughput Nucleotide Sequencing
Humans
Hyperlipoproteinemia Type II / complications
Hyperlipoproteinemia Type II / genetics*
Male
Pedigree
Proprotein Convertase 9
Proprotein Convertases / genetics*
Receptors, LDL / genetics*
Sequence Analysis, DNA
Serine Endopeptidases / genetics*

Substances

APOB protein, human
Apolipoprotein B-100
LDLR protein, human
Receptors, LDL
PCSK9 protein, human
Proprotein Convertase 9
Proprotein Convertases
Serine Endopeptidases