Diagnosis of autosomal dominant polycystic kidney disease using efficient pkd1 and pkd2 targeted next-generation sequencing

Daniel Trujillano, Gemma Bullich, Stephan Ossowski, Josée Ballaréın, Roser Torra, Xavier P. Estivill, Elisabet Ars

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

Molecular diagnostics of autosomal dominant polycystic kidney disease (AD-PKD) relies on mutation screening of PKD1 and PKD2, which is complicated by extensive allelic heterogeneity and the presence of six highly homologous sequences of PKD1. To date, specific sequencing of PKD1 requires laborious long-range amplifications. The high cost and long turnaround time of PKD1 and PKD2 mutation analysis using conventional techniques limits its widespread application in clinical settings. We performed targeted next-generation sequencing (NGS) of PKD1 and PKD2. Pooled barcoded DNA patient libraries were enriched by in-solution hybridization with PKD1 and PKD2 capture probes. Bioinformatics analysis was performed using an in-house developed pipeline. We validated the assay in a cohort of 36 patients with previously known PKD1 and PKD2 mutations and five control individuals. Then, we used the same assay and bioinformatics analysis in a discovery cohort of 12 unchar-acterized patients. We detected 35 out of 36 known definitely, highly likely, and likely pathogenic mutations in the validation cohort, including two large deletions. In the discovery cohort, we detected 11 different pathogenic mutations in 10 out of 12 patients. This study demonstrates that laborious long-range PCRs of the repeated PKD1 region can be avoided by in-solution enrichment of PKD1 and PKD2 and NGS. This strategy significantly reduces the cost and time for simultaneous PKD1 and PKD2 sequence analysis, facilitating routine genetic diagnostics of ADPKD.

Original languageEnglish
Pages (from-to)412-421
Number of pages10
JournalMolecular Genetics and Genomic Medicine
Volume2
Issue number5
DOIs
Publication statusPublished - 1 Jan 2014

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Autosomal Dominant Polycystic Kidney
Mutation
Computational Biology
Costs and Cost Analysis
Molecular Pathology
Sequence Homology
Gene Library
Sequence Analysis
Polymerase Chain Reaction

Keywords

  • Autosomal dominant polycystic kidney disease
  • Genetic counseling
  • Molecular diagnostics
  • Targeted NGS

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

Diagnosis of autosomal dominant polycystic kidney disease using efficient pkd1 and pkd2 targeted next-generation sequencing. / Trujillano, Daniel; Bullich, Gemma; Ossowski, Stephan; Ballaréın, Josée; Torra, Roser; Estivill, Xavier P.; Ars, Elisabet.

In: Molecular Genetics and Genomic Medicine, Vol. 2, No. 5, 01.01.2014, p. 412-421.

Research output: Contribution to journalArticle

Trujillano, Daniel ; Bullich, Gemma ; Ossowski, Stephan ; Ballaréın, Josée ; Torra, Roser ; Estivill, Xavier P. ; Ars, Elisabet. / Diagnosis of autosomal dominant polycystic kidney disease using efficient pkd1 and pkd2 targeted next-generation sequencing. In: Molecular Genetics and Genomic Medicine. 2014 ; Vol. 2, No. 5. pp. 412-421.
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