Next-generation sequencing for molecular diagnosis of autosomal recessive polycystic kidney disease

Burhan M Edrees; Mohammad Athar; Faisal A Al-Allaf; Mohiuddin M Taher; Wajahatullah Khan; Abdellatif Bouazzaoui; Naffaa Al-Harbi; Ramzia Safar; Howaida Al-Edressi; Khawala Alansary; Abulkareem Anazi; Naji Altayeb; Muawia A Ahmed; Zainularifeen Abduljaleel

doi:10.1016/j.gene.2016.07.021

Next-generation sequencing for molecular diagnosis of autosomal recessive polycystic kidney disease

Gene. 2016 Oct 10;591(1):214-226. doi: 10.1016/j.gene.2016.07.021. Epub 2016 Jul 9.

Authors

Affiliations

¹ Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; King Fahad Medical City, P.O. Box 59046, Riyadh 11525, Saudi Arabia.
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; Molecular Diagnostics Unit, Department of Laboratory and Blood Bank, King Abdullah Medical City, Makkah 21955, Saudi Arabia. Electronic address: faallaf@uqu.edu.sa.
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 3660, Riyadh 11426, Saudi Arabia.
⁶ Department of Pediatric, King Faisal Specialist Hospital and Research Centre, P.O. Box 40047, Jeddah 21499, Saudi Arabia.
⁷ Madinah Maternity and Children's Hospital, P.O. Box 5073, Madinah 42318, Saudi Arabia.
⁸ King Fahad Medical City, P.O. Box 59046, Riyadh 11525, Saudi Arabia.
⁹ King Salman Armed Forces Hospital, PO Box 100, Tabuk, Saudi Arabia.
¹⁰ 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.

PMID: 27401137
DOI: 10.1016/j.gene.2016.07.021

Abstract

Autosomal recessive polycystic kidney disease (ARPKD) a rare genetic disorder, described by formation of cysts in the kidney. A targeted customized sequencing of genes implicated in ARPKD phenotype was performed to identify candidate variants using the Ion torrent PGM next-generation sequencing. The results identified likely pathogenic disease causing variants during the validation process. Four potential pathogenic variants [c.4870C>T, p.(Arg1624Trp)], [c.5725C>T, p.(Arg1909Trp)], c.1736C>T, p.(Thr579Met)] and [(c.10628T>G), p.(Leu3543Trp)] were observed in PKHD1 gene among 12 out of 18 samples. The rest of the patient samples also showed few variants in ADPKD (Autosomal Dominant Polycystic Kidney Disease) disease causing genes PKD1 and PKD2 i.e. [c.12433G>A, p.(Val4145Ile)] and [c.1445T>G, p.(Phe482Cys)], respectively. All causative variants were validated by capillary sequencing, confirming the presence of a novel homozygous variants [c.10628T>G, p.(Leu3543Trp)] found in exon 61 of a male proband. All potentially deleterious variants identified in PKHD1, PKD1, and PKD2 gene, also exhibited pathologically or clinically significance based on the computational predictions involved in predicting the impact of non-synonymous SNPs (nsSNPs) on protein function such as Sorting Intolerant From Tolerant (SIFT) and Polymorphism Phenotyping (PolyPhen2). SIFT classified 50% of our nsSNPs as "deleterious", while PolyPhen2 identified 45% of our nsSNPs as "Probably damaged" and the results from both programs were largely complementary. Taken together, these results suggest that the NGS strategies provide a fast, accurate and cost-effective molecular diagnostic tool for identifying mutations in targeted genes sequence analysis.

Keywords: Autosomal recessive polycystic kidney disease (ARPKD); Genotypic and phenotypic; Next generation sequencing (NGS); Pathogenicity prediction; Polycystic kidney and hepatic disease 1 (PKHD1).

MeSH terms

Base Sequence
Female
Gene Ontology
Genetic Association Studies
High-Throughput Nucleotide Sequencing / methods*
Humans
Male
Molecular Dynamics Simulation
Molecular Sequence Annotation
Mutation / genetics
Polycystic Kidney, Autosomal Recessive / diagnosis
Polycystic Kidney, Autosomal Recessive / genetics*
Polymorphism, Single Nucleotide / genetics
Reproducibility of Results