title: Targeted high-throughput sequencing for diagnosis of genetically heterogeneous diseases: efficient mutation detection in Bardet-Biedl and Alström syndromes.
abstract: BACKGROUND
  Bardet-Biedl syndrome (BBS) is a pleiotropic recessive disorder that belongs to the rapidly growing family of ciliopathies. It shares phenotypic traits with other ciliopathies, such as Alström syndrome (ALMS), nephronophthisis (NPHP) or Joubert syndrome. BBS mutations have been detected in 16 different genes (BBS1-BBS16) without clear genotype-to-phenotype correlation. This extensive genetic heterogeneity is a major concern for molecular diagnosis and genetic counselling. While various strategies have been recently proposed to optimise mutation detection, they either fail to detect mutations in a majority of patients or are time consuming and costly.
  
  
  METHODS
  We tested a targeted exon-capture strategy coupled with multiplexing and high-throughput sequencing on 52 patients: 14 with known mutations as proof-of-principle and 38 with no previously detected mutation. Thirty genes were targeted in total including the 16 BBS genes, the 12 known NPHP genes, the single ALMS gene ALMS1 and the proposed modifier CCDC28B.
  
  
  RESULTS
  This strategy allowed the reliable detection of causative mutations (including homozygous/heterozygous exon deletions) in 68% of BBS patients without previous molecular diagnosis and in all proof-of-principle samples. Three probands carried homozygous truncating mutations in ALMS1 confirming the major phenotypic overlap between both disorders. The efficiency of detecting mutations in patients was positively correlated with their compliance with the classical BBS phenotype (mutations were identified in 81% of 'classical' BBS patients) suggesting that only a few true BBS genes remain to be identified. We illustrate some interpretation problems encountered due to the multiplicity of identified variants.
  
  
  CONCLUSIONS
  This strategy is highly efficient and cost effective for diseases with high genetic heterogeneity, and guarantees a quality of coverage in coding sequences of target genes suited for diagnosis purposes.
authors: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch, France.
authors: Claire
authors: C
authors: Redin
authors: Stéphanie
authors: S
authors: Le Gras
authors: Oussema
authors: O
authors: Mhamdi
authors: Véronique
authors: V
authors: Geoffroy
authors: Corinne
authors: C
authors: Stoetzel
authors: Marie-Claire
authors: MC
authors: Vincent
authors: Pietro
authors: P
authors: Chiurazzi
authors: Didier
authors: D
authors: Lacombe
authors: Ines
authors: I
authors: Ouertani
authors: Florence
authors: F
authors: Petit
authors: Marianne
authors: M
authors: Till
authors: Alain
authors: A
authors: Verloes
authors: Bernard
authors: B
authors: Jost
authors: Habiba Bouhamed
authors: HB
authors: Chaabouni
authors: Helene
authors: H
authors: Dollfus
authors: Jean-Louis
authors: JL
authors: Mandel
authors: Jean
authors: J
authors: Muller
mesh_terms: D056769:Alstrom Syndrome / Q000175:diagnosis* / Q000235:genetics; D020788:Bardet-Biedl Syndrome / Q000175:diagnosis* / Q000235:genetics; D018797:Cell Cycle Proteins / Q000235:genetics; D015331:Cohort Studies; D003598:Cytoskeletal Proteins; D004252:DNA Mutational Analysis / Q000379:methods*; D005091:Exons; D056726:Genetic Association Studies; D030342:Genetic Diseases, Inborn / Q000175:diagnosis / Q000235:genetics; D018740:Genetic Heterogeneity; D005820:Genetic Testing / Q000379:methods; D015894:Genome, Human; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006720:Homozygote; D006801:Humans; D011506:Proteins / Q000235:genetics; D015203:Reproducibility of Results; D017384:Sequence Deletion
chemical_list: C490729:ALMS1 protein, human; C507668:CCDC28B protein, human; D018797:Cell Cycle Proteins; D003598:Cytoskeletal Proteins; D011506:Proteins