title: QMPSF is sensitive and specific in the detection of NPHP1 heterozygous deletions.
abstract: BACKGROUND
  Nephronophthisis, an autosomal recessive nephropathy, is responsible for 10% of childhood chronic renal failure. The deletion of its major gene, NPHP1, with a minor allele frequency of 0.24% in the general population, is the most common mutation leading to a monogenic form of childhood chronic renal failure. It is challenging to detect it in the heterozygous state. We aimed to evaluate the sensitivity and the specificity of the quantitative multiplex PCR of short fluorescent fragments (QMPSF) in its detection.
  
  
  METHODS
  After setting up the protocol of QMPSF, we validated it on 39 individuals diagnosed by multiplex ligation-dependent probe amplification (MLPA) with normal NPHP1 copy number (n=17), with heterozygous deletion (n=13, seven parents and six patients), or with homozygous deletion (n=9). To assess the rate of the deletions that arise from independent events, deleted alleles were haplotyped.
  
  
  RESULTS
  The results of QMPSF and MLPA correlated perfectly in the identification of 76 heterozygously deleted and 56 homozygously deleted exons. The inter-experimental variability of the dosage quotient obtained by QMPSF was low: control, 1.05 (median; range, 0.86-1.33, n = 102 exons); heterozygous deletion, 0.51 (0.42-0.67, n = 76 exons); homozygous deletion, 0 (0-0, n = 56 exons). All patients harboring a heterozygous deletion were found to carry a hemizygous mutation. At least 15 out of 18 deletions appeared on different haplotypes and one deletion appeared de novo.
  
  
  CONCLUSIONS
  The cost- and time-effective QMPSF has a 100% sensitivity and specificity in the detection of NPHP1 deletion. The potential de novo appearance of NPHP1 deletions makes its segregation analysis highly recommended in clinical practice.
authors.affiliation: MTA-SE Lendulet Nephrogenetic Laboratory, Budapest.
authors.forename: Eszter
authors.initials: E
authors.lastname: Jávorszky
authors.affiliation: Assistance Publique-Hôpitaux de Paris, Department of Genetics, Necker Hospital, Paris.
authors.forename: Vincent
authors.initials: V
authors.lastname: Morinière
authors.affiliation: 1st Department of Pediatrics, Semmelweis University, Budapest.
authors.forename: Andrea
authors.initials: A
authors.lastname: Kerti
authors.affiliation: MTA-SE Lendulet Nephrogenetic Laboratory, Budapest.
authors.forename: Eszter
authors.initials: E
authors.lastname: Balogh
authors.affiliation: National Institute of Environmental Health, Department of Molecular Genetics and Diagnostics, Budapest.
authors.forename: Henriett
authors.initials: H
authors.lastname: Pikó
authors.affiliation: Inserm UMR 1163, Laboratory of Hereditary Kidney Diseases, Paris.
authors.forename: Sophie
authors.initials: S
authors.lastname: Saunier
authors.affiliation: National Institute of Environmental Health, Department of Molecular Genetics and Diagnostics, Budapest.
authors.forename: Veronika
authors.initials: V
authors.lastname: Karcagi
authors.affiliation: Assistance Publique-Hôpitaux de Paris, Department of Genetics, Necker Hospital, Paris.
authors.forename: Corinne
authors.initials: C
authors.lastname: Antignac
authors.affiliation: MTA-SE Lendulet Nephrogenetic Laboratory, Budapest.
authors.forename: Kálmán
authors.initials: K
authors.lastname: Tory
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics*; D001483:Base Sequence; D003598:Cytoskeletal Proteins; D005091:Exons / Q000235:genetics; D017353:Gene Deletion; D006579:Heterozygote; D006801:Humans; D052177:Kidney Diseases, Cystic / Q000151:congenital / Q000235:genetics; D057230:Limit of Detection; D008565:Membrane Proteins / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods*
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D003598:Cytoskeletal Proteins; D008565:Membrane Proteins; C108725:NPHP1 protein, human
keywords: NPHP1; copy number variation; deletion; nephronophthisis; quantitative multiplex PCR of short fluorescent fragments (QMPSF)