title: Investigation of selected genomic deletions and duplications in a cohort of 338 patients presenting with syndromic obesity by multiplex ligation-dependent probe amplification using synthetic probes.
abstract: BACKGROUND
  Certain rare syndromes with developmental delay or intellectual disability caused by genomic copy number variants (CNVs), either deletions or duplications, are associated with higher rates of obesity. Current strategies to diagnose these syndromes typically rely on phenotype-driven investigation. However, the strong phenotypic overlap between syndromic forms of obesity poses challenges to accurate diagnosis, and many different individual cytogenetic and molecular approaches may be required. Multiplex ligation-dependent probe amplification (MLPA) enables the simultaneous analysis of multiple targeted loci in a single test, and serves as an important screening tool for large cohorts of patients in whom deletions and duplications involving specific loci are suspected. Our aim was to design a synthetic probe set for MLPA analysis to investigate in a cohort of 338 patients with syndromic obesity deletions and duplications in genomic regions that can cause this phenotype.
  
  
  RESULTS
  We identified 18 patients harboring copy number imbalances; 18 deletions and 5 duplications. The alterations in ten patients were delineated by chromosomal microarrays, and in the remaining cases by additional MLPA probes incorporated into commercial kits. Nine patients showed deletions in regions of known microdeletion syndromes with obesity as a clinical feature: in 2q37 (4 cases), 9q34 (1 case) and 17p11.2 (4 cases). Four patients harbored CNVs in the DiGeorge syndrome locus at 22q11.2. Two other patients had deletions within the 22q11.2 'distal' locus associated with a variable clinical phenotype and obesity in some individuals. The other three patients had a recurrent CNV of one of three susceptibility loci: at 1q21.1 'distal', 16p11.2 'distal', and 16p11.2 'proximal'.
  
  
  CONCLUSIONS
  Our study demonstrates the utility of an MLPA-based first line screening test to the evaluation of obese patients presenting with syndromic features. The overall detection rate with the synthetic MLPA probe set was about 5.3% (18 out of 338). Our experience leads us to suggest that MLPA could serve as an effective alternative first line screening test to chromosomal microarrays for diagnosis of syndromic obesity, allowing for a number of loci (e.g., 1p36, 2p25, 2q37, 6q16, 9q34, 11p14, 16p11.2, 17p11.2), known to be clinically relevant for this patient population, to be interrogated simultaneously.
authors.affiliation: Human Genome and Stem Cell Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil.
authors.forename: Carla S
authors.initials: CS
authors.lastname: D'Angelo
authors.affiliation: Human Genome and Stem Cell Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil.
authors.forename: Monica C
authors.initials: MC
authors.lastname: Varela
authors.affiliation: Human Genome and Stem Cell Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil.
authors.forename: Cláudia Ie
authors.initials: CIe
authors.lastname: de Castro
authors.affiliation: Genetics Unit, Department of Pediatrics, Children Institute, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil.
authors.forename: Chong A
authors.initials: CA
authors.lastname: Kim
authors.affiliation: Genetics Unit, Department of Pediatrics, Children Institute, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil.
authors.forename: Débora R
authors.initials: DR
authors.lastname: Bertola
authors.affiliation: Neurogenetics Unit, Department of Medical Genetics, School of Medicine, University of Sao Paulo, Ribeirao Preto, Brazil.
authors.forename: Charles M
authors.initials: CM
authors.lastname: Lourenço
authors.affiliation: Department of Morphology, Medical Genetics Center, Federal University of Sao Paulo, Sao Paulo, Brazil.
authors.forename: Ana Beatriz A
authors.initials: AB
authors.lastname: Perez
authors.affiliation: Human Genome and Stem Cell Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil.
authors.forename: Celia P
authors.initials: CP
authors.lastname: Koiffmann
keywords: Chromosomal microarray analysis (CMA); Copy number variants (CNVs); Developmental delay; Multiplex ligation-dependent probe amplification (MLPA); Obesity