Targeted high-throughput sequencing for diagnosis of genetically heterogeneous diseases: efficient mutation detection in Bardet-Biedl and Alström Syndromes
- Claire Redin1,
- Stéphanie Le Gras2,
- Oussema Mhamdi3,
- Véronique Geoffroy4,
- Corinne Stoetzel5,
- Marie-Claire Vincent6,
- Pietro Chiurazzi7,
- Didier Lacombe8,
- Ines Ouertani3,
- Florence Petit9,
- Marianne Till10,
- Alain Verloes11,
- Bernard Jost2,
- Habiba Bouhamed Chaabouni3,
- Helene Dollfus5,12,
- Jean-Louis Mandel1,6,13,
- Jean Muller1,6
- 1Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch, France
- 2Microarrays and Sequencing Platform, IGBMC, Illkirch, France
- 3Laboratory of Human genetics, University of Medicine of Tunis, Tunis, Tunisia
- 4Bioinformatics Platform, IGBMC, Illkirch, France
- 5Laboratoire de Génétique Médicale EA3949 Inserm Avenir, Université de Strasbourg, Strasbourg, France
- 6Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- 7Istituto di Genetica Medica, Universita' Cattolica, Roma, Italy
- 8CHU Bordeaux, University of Bordeaux, Department of Medical Genetics, Bordeaux, France
- 9Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHRU de Lille, Lille, France
- 10Service de Cytogénétique Constitutionnelle, Hospices Civils de Lyon, CBPE, Bron Cedex, France
- 11Department of Genetics, INSERM U676, Assistance Publique Hôpitaux de Paris (AP-HP), Robert Debré University Hospital, Paris, France
- 12Service de Génétique Médicale, Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- 13Chaire de Génétique Humaine, Collége de France, Illkirch, France
- Correspondence to Professor Jean-Louis Mandel, Department of Neurogenetics & Translational medicine, IGBMC, 1 rue Laurent Fries, Illkirch cedex 67404, France;
Contributors CR, JLM and JM designed the study; CR, OM, CS, BJ performed experiments; CR, SLG, VG, JM performed the bioinformatics studies; CR, SLG, OM, VG, CS, JLM and JM collected and analysed data; OM, CS, MCV, PC, DL, IO, FP, MT, AV, HBC and HD provided DNA samples and clinical information; CR, JLM and JM wrote the manuscript; MCV, BJ, HBC, HD, JLM and JM provided technical support, conceptual advice and project coordination.
- Received 7 March 2012
- Revised 15 May 2012
- Accepted 28 May 2012
- Published Online First 7 July 2012
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.
Method 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.
Conclusion 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.
Funding This work was partially supported by a grant from Agence de Biomédecine to JLM and JM, by funds from APLM and by the Association Française contre les Myopathies (AFM) thanks to its support to the IGBMC sequencing platform.
Competing interests None.
Patient consent For children, consent was signed by the parents.
Provenance and peer review Not commissioned; externally peer reviewed.
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