Journal Article

Phenotype-specific effect of chromosome 1q21.1 rearrangements and <i>GJA5</i> duplications in 2436 congenital heart disease patients and 6760 controls

Rachel Soemedi, Ana Topf, Ian J. Wilson, Rebecca Darlay, Thahira Rahman, Elise Glen, Darroch Hall, Ni Huang, Jamie Bentham, Shoumo Bhattacharya, Catherine Cosgrove, J. David Brook, Javier Granados-Riveron, Kerry Setchfield, Frances Bu'Lock, Chris Thornborough, Koenraad Devriendt, Jeroen Breckpot, Michael Hofbeck, Mark Lathrop, Anita Rauch, Gillian M. Blue, David S. Winlaw, Matthew Hurles, Mauro Santibanez-Koref, Heather J. Cordell, Judith A. Goodship and Bernard D. Keavney

in Human Molecular Genetics

Volume 21, issue 7, pages 1513-1520
Published in print April 2012 | ISSN: 0964-6906
Published online December 2011 | e-ISSN: 1460-2083 | DOI: http://dx.doi.org/10.1093/hmg/ddr589

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Recurrent rearrangements of chromosome 1q21.1 that occur via non-allelic homologous recombination have been associated with variable phenotypes exhibiting incomplete penetrance, including congenital heart disease (CHD). However, the gene or genes within the ∼1 Mb critical region responsible for each of the associated phenotypes remains unknown. We examined the 1q21.1 locus in 948 patients with tetralogy of Fallot (TOF), 1488 patients with other forms of CHD and 6760 ethnically matched controls using single nucleotide polymorphism genotyping arrays (Illumina 660W and Affymetrix 6.0) and multiplex ligation-dependent probe amplification. We found that duplication of 1q21.1 was more common in cases of TOF than in controls [odds ratio (OR) 30.9, 95% confidence interval (CI) 8.9–107.6); P = 2.2 × 10−7], but deletion was not. In contrast, deletion of 1q21.1 was more common in cases of non-TOF CHD than in controls [OR 5.5 (95% CI 1.4–22.0); P = 0.04] while duplication was not. We also detected rare (n = 3) 100–200 kb duplications within the critical region of 1q21.1 in cases of TOF. These small duplications encompassed a single gene in common, GJA5, and were enriched in cases of TOF in comparison to controls [OR = 10.7 (95% CI 1.8–64.3), P = 0.01]. These findings show that duplication and deletion at chromosome 1q21.1 exhibit a degree of phenotypic specificity in CHD, and implicate GJA5 as the gene responsible for the CHD phenotypes observed with copy number imbalances at this locus.

Journal Article.  5311 words.  Illustrated.

Subjects: Genetics and Genomics

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