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Radhakrishna U, Nath SK, McElreavey K, et al. Genome-wide linkage and copy number variation analysis reveals 710 kb duplication on chromosome 1p31.3 responsible for autosomal dominant omphalocele. J Med Genet. 2012;49(4):270-6doi: 10.1136/jmedgenet-2012-100826.
Radhakrishna, U., Nath, S. K., McElreavey, K., Ratnamala, U., Sun, C., Maiti, A. K., Gagnebin, M., Béna, F., Newkirk, H. L., Sharp, A. J., Everman, D. B., Murray, J. C., Schwartz, C. E., Antonarakis, S. E., & Butler, M. G. (2012). Genome-wide linkage and copy number variation analysis reveals 710 kb duplication on chromosome 1p31.3 responsible for autosomal dominant omphalocele. Journal of medical genetics, 49(4), 270-6. https://doi.org/10.1136/jmedgenet-2012-100826
Radhakrishna, Uppala, et al. "Genome-wide linkage and copy number variation analysis reveals 710 kb duplication on chromosome 1p31.3 responsible for autosomal dominant omphalocele." Journal of medical genetics vol. 49,4 (2012): 270-6. doi: https://doi.org/10.1136/jmedgenet-2012-100826
Radhakrishna U, Nath SK, McElreavey K, Ratnamala U, Sun C, Maiti AK, Gagnebin M, Béna F, Newkirk HL, Sharp AJ, Everman DB, Murray JC, Schwartz CE, Antonarakis SE, Butler MG. Genome-wide linkage and copy number variation analysis reveals 710 kb duplication on chromosome 1p31.3 responsible for autosomal dominant omphalocele. J Med Genet. 2012 Apr;49(4):270-6. doi: 10.1136/jmedgenet-2012-100826. PMID: 22499347; PMCID: PMC5312754.
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J Med Genet. 2012 Apr;49(4):270-6. doi: 10.1136/jmedgenet-2012-100826.

Genome-wide linkage and copy number variation analysis reveals 710 kb duplication on chromosome 1p31.3 responsible for autosomal dominant omphalocele.

Journal of medical genetics

Uppala Radhakrishna, Swapan K Nath, Ken McElreavey, Uppala Ratnamala, Celi Sun, Amit K Maiti, Maryline Gagnebin, Frédérique Béna, Heather L Newkirk, Andrew J Sharp, David B Everman, Jeffrey C Murray, Charles E Schwartz, Stylianos E Antonarakis, Merlin G Butler

Affiliations

  1. Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland. [email protected]

PMID: 22499347 PMCID: PMC5312754 DOI: 10.1136/jmedgenet-2012-100826

Abstract

BACKGROUND: Omphalocele is a congenital birth defect characterised by the presence of internal organs located outside of the ventral abdominal wall. The purpose of this study was to identify the underlying genetic mechanisms of a large autosomal dominant Caucasian family with omphalocele.

METHODS AND FINDINGS: A genetic linkage study was conducted in a large family with an autosomal dominant transmission of an omphalocele using a genome-wide single nucleotide polymorphism (SNP) array. The analysis revealed significant evidence of linkage (non-parametric NPL = 6.93, p=0.0001; parametric logarithm of odds (LOD) = 2.70 under a fully penetrant dominant model) at chromosome band 1p31.3. Haplotype analysis narrowed the locus to a 2.74 Mb region between markers rs2886770 (63014807 bp) and rs1343981 (65757349 bp). Molecular characterisation of this interval using array comparative genomic hybridisation followed by quantitative microsphere hybridisation analysis revealed a 710 kb duplication located at 63.5-64.2 Mb. All affected individuals who had an omphalocele and shared the haplotype were positive for this duplicated region, while the duplication was absent from all normal individuals of this family. Multipoint linkage analysis using the duplication as a marker yielded a maximum LOD score of 3.2 at 1p31.3 under a dominant model. The 710 kb duplication at 1p31.3 band contains seven known genes including FOXD3, ALG6, ITGB3BP, KIAA1799, DLEU2L, PGM1, and the proximal portion of ROR1. Importantly, this duplication is absent from the database of genomic variants.

CONCLUSIONS: The present study suggests that development of an omphalocele in this family is controlled by overexpression of one or more genes in the duplicated region. To the authors' knowledge, this is the first reported association of an inherited omphalocele condition with a chromosomal rearrangement.

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