title: Next-generation sequencing for molecular diagnosis of autosomal recessive polycystic kidney disease.
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.
authors.affiliation: 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.
authors.forename: Burhan M
authors.initials: BM
authors.lastname: Edrees
authors.affiliation: 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.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Athar
authors.affiliation: 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.
authors.forename: Faisal A
authors.initials: FA
authors.lastname: Al-Allaf
authors.affiliation: 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.
authors.forename: Mohiuddin M
authors.initials: MM
authors.lastname: Taher
authors.affiliation: 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.
authors.forename: Wajahatullah
authors.initials: W
authors.lastname: Khan
authors.affiliation: 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.
authors.forename: Abdellatif
authors.initials: A
authors.lastname: Bouazzaoui
authors.affiliation: Department of Pediatric, King Faisal Specialist Hospital and Research Centre, P.O. Box 40047, Jeddah 21499, Saudi Arabia.
authors.forename: Naffaa
authors.initials: N
authors.lastname: Al-Harbi
authors.affiliation: Madinah Maternity and Children's Hospital, P.O. Box 5073, Madinah 42318, Saudi Arabia.
authors.forename: Ramzia
authors.initials: R
authors.lastname: Safar
authors.affiliation: Madinah Maternity and Children's Hospital, P.O. Box 5073, Madinah 42318, Saudi Arabia.
authors.forename: Howaida
authors.initials: H
authors.lastname: Al-Edressi
authors.affiliation: King Fahad Medical City, P.O. Box 59046, Riyadh 11525, Saudi Arabia.
authors.forename: Khawala
authors.initials: K
authors.lastname: Alansary
authors.affiliation: King Fahad Medical City, P.O. Box 59046, Riyadh 11525, Saudi Arabia.
authors.forename: Abulkareem
authors.initials: A
authors.lastname: Anazi
authors.affiliation: King Fahad Medical City, P.O. Box 59046, Riyadh 11525, Saudi Arabia.
authors.forename: Naji
authors.initials: N
authors.lastname: Altayeb
authors.affiliation: King Salman Armed Forces Hospital, PO Box 100, Tabuk, Saudi Arabia.
authors.forename: Muawia A
authors.initials: MA
authors.lastname: Ahmed
authors.affiliation: 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.
authors.forename: Zainularifeen
authors.initials: Z
authors.lastname: Abduljaleel
mesh_terms: D001483:Base Sequence; D005260:Female; D063990:Gene Ontology; D056726:Genetic Association Studies; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D056004:Molecular Dynamics Simulation; D058977:Molecular Sequence Annotation; D009154:Mutation / Q000235:genetics; D017044:Polycystic Kidney, Autosomal Recessive / Q000175:diagnosis / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D015203:Reproducibility of Results
keywords: Autosomal recessive polycystic kidney disease (ARPKD); Genotypic and phenotypic; Next generation sequencing (NGS); Pathogenicity prediction; Polycystic kidney and hepatic disease 1 (PKHD1)