Mutation analysis of 18 nephronophthisis associated ciliopathy disease genes using a DNA pooling and next generation sequencing strategy. Issue 2 (10th November 2010)

• Record Type: Journal Article
• Authors: Otto, Edgar A; Ramaswami, Gokul; Janssen, Sabine; Chaki, Moumita; Allen, Susan J; Zhou, Weibin; Airik, Rannar; Hurd, Toby W; Ghosh, Amiya K; Wolf, Matthias T; Hoppe, Bernd; Neuhaus, Thomas J; Bockenhauer, Detlef; Milford, David V; Soliman, Neveen A; Antignac, Corinne; Saunier, Sophie; Johnson, Colin A; Hildebrandt, Friedhelm
• Is Part Of: Journal of medical genetics. Volume 48:Issue 2(2011)
• Page Start: 105
• Page End: 116
• Publication Date: 2010-11-10
• Subjects: Next-generation sequencing -- ciliopathy -- nephronophthisis -- genetics -- renal medicine; Medical genetics -- Periodicals; 616.042
• DOI: 10.1136/jmg.2010.082552
• Languages: English
• ISSNs: 1468-6244

Abstract

Abstract : Background: Nephronophthisis associated ciliopathies (NPHP-AC) comprise a group of autosomal recessive cystic kidney diseases that includes nephronophthisis (NPHP), Senior-Loken syndrome (SLS), Joubert syndrome (JBTS), and Meckel-Gruber syndrome (MKS). To date, causative mutations in NPHP-AC have been described for 18 different genes, rendering mutation analysis tedious and expensive. To overcome the broad genetic locus heterogeneity, a strategy of DNA pooling with consecutive massively parallel resequencing (MPR) was devised. Methods: In 120 patients with severe NPHP-AC phenotypes, five pools of genomic DNA with 24 patients each were prepared which were used as templates in order to PCR amplify all 376 exons of 18 NPHP-AC genes ( NPHP1, INVS, NPHP3, NPHP4, IQCB1, CEP290, GLIS2, RPGRIP1L, NEK8, TMEM67, INPP5E, TMEM216, AHI1, ARL13B, CC2D2A, TTC21B, MKS1, and XPNPEP3 ). PCR products were then subjected to MPR on an Illumina Genome-Analyser and mutations were subsequently assigned to their respective mutation carrier via CEL I endonuclease based heteroduplex screening and confirmed by Sanger sequencing. Results: For proof of principle, DNA from patients with known mutations was used and detection of 22 out of 24 different alleles (92% sensitivity) was demonstrated. MPR led to the molecular diagnosis in 30/120 patients (25%) and 54 pathogenic mutations (27 novel) were identified in seven different NPHP-AC genes. Additionally, in 24 patients only single heterozygous variants of unknown significance were found. Conclusions: The combined approach of DNA pooling followed by MPR strongly facilitates mutation analysis in broadly heterogeneous single gene disorders. The lack of mutations in 75% of patients in this cohort indicates further extensive heterogeneity in NPHP-AC.