X-chromosome tiling path array detection of copy number variants in patients with chromosome X-linked mental retardation

doi:10.1186/1471-2164-8-443

BMC Genomics
Volume 8

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Madrigal I
Rodríguez-Revenga L
Armengol L
González E
Rodriguez B
Badenas C
Sánchez A
Martínez F
Guitart M
Fernández-Carvajal I
Arranz JA
Tejada MI
Pérez-Jurado LA
Estivill X
Milà M

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Madrigal I
Rodríguez-Revenga L
Armengol L
González E
Rodriguez B
Badenas C
Sánchez A
Martínez F
Guitart M
Fernández-Carvajal I
Arranz JA
Tejada MI
Pérez-Jurado LA
Estivill X
Milà M
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Research article

X-chromosome tiling path array detection of copy number variants in patients with chromosome X-linked mental retardation

I Madrigal¹^,10^,11 , L Rodríguez-Revenga¹^,10^,11 , L Armengol² , E González³ , B Rodriguez⁴^,11 , C Badenas¹^,10^,11 , A Sánchez¹^,10^,11 , F Martínez⁵^,10 , M Guitart⁶^,10 , I Fernández-Carvajal⁷^,10 , JA Arranz⁸ , MI Tejada⁹^,10 , LA Pérez-Jurado⁴^,11 , X Estivill² and M Milà¹^,10^,11

¹Biochemistry and Molecular Genetics Department, Hospital Clínic and IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain

²Genes and Disease Program. Center for Genomic Regulation (CRG-UPF), Barcelona, Spain

³Microarray Laboratory, Bioinformatics and Genomics Program, (CRG-UPF), Barcelona, Spain

⁴Genetics Unit, Universitat Pompeu Fabra, Program in Molecular Medicine and Genetics, Hospital Vall d'Hebron, Barcelona, Spain

⁵Unidad de Genética. Hospital Universitario La Fe. Valencia, Spain

⁶Laboratori Genètica, UDIAT-Centre Diagnòstic, Corporació Sanitaria Parc Taulí, Institut Universitari Parc Taulí-UAB, Sabadell, Spain

⁷Instituto de Biología y Genética Molecular (IBGM-CSIC). Universidad de Valladolid, Spain

⁸Unitat de Metabolopaties, Hospital Universitari Materno-Infantil Vall d'Hebron, Spain

⁹Molecular Genetics Laboratory, Cruces Hospital, Barakaldo-Bizkaia, Spain

¹⁰GIRMOGEN (Spanish Network for Mental Retardation), Spain

¹¹Centre for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Barcelona, Spain

author email corresponding author email

BMC Genomics 2007, 8:443doi:10.1186/1471-2164-8-443


Published:	29 November 2007

Abstract

Background

Aproximately 5–10% of cases of mental retardation in males are due to copy number variations (CNV) on the X chromosome. Novel technologies, such as array comparative genomic hybridization (aCGH), may help to uncover cryptic rearrangements in X-linked mental retardation (XLMR) patients. We have constructed an X-chromosome tiling path array using bacterial artificial chromosomes (BACs) and validated it using samples with cytogenetically defined copy number changes. We have studied 54 patients with idiopathic mental retardation and 20 controls subjects.

Results

Known genomic aberrations were reliably detected on the array and eight novel submicroscopic imbalances, likely causative for the mental retardation (MR) phenotype, were detected. Putatively pathogenic rearrangements included three deletions and five duplications (ranging between 82 kb to one Mb), all but two affecting genes previously known to be responsible for XLMR. Additionally, we describe different CNV regions with significant different frequencies in XLMR and control subjects (44% vs. 20%).

Conclusion

This tiling path array of the human X chromosome has proven successful for the detection and characterization of known rearrangements and novel CNVs in XLMR patients.