title: Large-scale targeted sequencing comparison highlights extreme genetic heterogeneity in nephronophthisis-related ciliopathies.
abstract: BACKGROUND
  The term nephronophthisis-related ciliopathies (NPHP-RC) describes a group of rare autosomal-recessive cystic kidney diseases, characterised by broad genetic and clinical heterogeneity. NPHP-RC is frequently associated with extrarenal manifestations and accounts for the majority of genetically caused chronic kidney disease (CKD) during childhood and adolescence. Generation of a molecular diagnosis has been impaired by this broad genetic heterogeneity. However, recently developed high-throughput exon sequencing techniques represent powerful and efficient tools to screen large cohorts for dozens of causative genes.
  
  
  METHODS
  Therefore, we performed massively multiplexed targeted sequencing using the modified molecular inversion probe strategy (MIPs) in an international cohort of 384 patients diagnosed with NPHP-RC.
  
  
  RESULTS
  As a result, we established the molecular diagnoses in 81/384 unrelated individuals (21.1%). We detected 127 likely disease-causing mutations in 18 of 34 evaluated NPHP-RC genes, 22 of which were novel. We further compared a subgroup of current findings to the results of a previous study in which we used an array-based microfluidic PCR technology in the same cohort. While 78 likely disease-causing mutations were previously detected by the array-based microfluidic PCR, the MIPs approach identified 94 likely pathogenic mutations. Compared with the previous approach, MIPs redetected 66 out of 78 variants and 28 previously unidentified variants, for a total of 94 variants.
  
  
  CONCLUSIONS
  In summary, we demonstrate that the modified MIPs technology is a useful approach to screen large cohorts for a multitude of established NPHP genes in order to identify the underlying molecular cause. Combined application of two independent library preparation and sequencing techniques, however, may still be indicated for Mendelian diseases with extensive genetic heterogeneity in order to further increase diagnostic sensitivity.
authors.affiliation: Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Markus
authors.initials: M
authors.lastname: Schueler
authors.affiliation: Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Divison of Nephrology, Department of Internal Medicine, University Clinic Leipzig, Leipzig, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Halbritter
authors.affiliation: Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.
authors.forename: Ian G
authors.initials: IG
authors.lastname: Phelps
authors.affiliation: Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Daniela A
authors.initials: DA
authors.lastname: Braun
authors.affiliation: Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: Edgar A
authors.initials: EA
authors.lastname: Otto
authors.affiliation: Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Porath
authors.affiliation: Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Heon Yung
authors.initials: HY
authors.lastname: Gee
authors.affiliation: University of Washington, Genome Sciences, Seattle, Washington, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
authors.affiliation: Oregon Health and Science University, Molecular and Medical Genetics, Portland, Oregon, USA.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: O'Roak
authors.affiliation: Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Lawson
authors.affiliation: Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt.
authors.forename: Marwa M
authors.initials: MM
authors.lastname: Nabhan
authors.affiliation: Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt.
authors.forename: Neveen A
authors.initials: NA
authors.lastname: Soliman
authors.affiliation: Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.
authors.forename: Dan
authors.initials: D
authors.lastname: Doherty
authors.affiliation: Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
authors.forename: Friedhelm
authors.initials: F
authors.lastname: Hildebrandt
mesh_terms: D018740:Genetic Heterogeneity; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D052177:Kidney Diseases, Cystic / Q000235:genetics*; D025202:Molecular Diagnostic Techniques; D012680:Sensitivity and Specificity
keywords: Diagnostics; Genetics; Molecular genetics; Renal Medicine