Copy number variation analysis reveals additional variants contributing to endometriosis development

Abstract

Purpose

Endometriosis is a gynecological disease influenced by multiple genetic and environmental factors. The aim of the current study was to use SNP-array technology to identify genomic aberrations that may possibly contribute to the development of endometriosis.

Methods

We performed an SNP-array genotyping of pooled DNA samples from both patients (n = 100) and controls (n = 50). Copy number variation (CNV) calling and association analyses were performed using PennCNV software. MLPA and TaqMan Copy-Number assays were used for validation of CNVs discovered.

Results

We detected 49 CNV loci that were present in patients with endometriosis and absent in the control group. After validation procedures, we confirmed six CNV loci in the subtelomeric regions, including 1p36.33, 16p13.3, 19p13.3, and 20p13, representing gains, while 17q25.3 and 20q13.33 showed losses. Among the intrachromosomal regions, our results revealed duplication at 19q13.1 within the FCGBP gene (p = 0.007).

Conclusions

We identified CNVs previously associated with endometriosis, together with six suggestive novel loci possibly involved in this disease. The intergenic locus on chromosome 19q13.1 shows strong association with endometriosis and is under further functional investigation.

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Authors

Corresponding author

Correspondence to Fernanda Mafra.

Ethics declarations

Clinical data and peripheral blood samples were collected following signed informed consent, as approved by the local Research Ethics Committee (CEP FMABC n. 310.094).

Conflict of interest

The authors declare that they have no conflict of interest.

Funding

The work was supported by a grant from Fundação de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) no. 2011/01363-7. F.M. was supported by FAPESP with two different scholarships, a PhD scholarship no. 2012/22394-8 and a scholarship for internship abroad No. 2014/07136-8, which were realized in collaboration with the Center for Applied Genomics at The Children’s Hospital of Philadelphia.

Additional information

Capsule SNP array genotyping of pooled DNA samples revealed CNVs previously associated with endometriosis and also novel chromosome regions that may contribute to the pathogenesis of this disease.

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Mafra, F., Mazzotti, D., Pellegrino, R. et al. Copy number variation analysis reveals additional variants contributing to endometriosis development. J Assist Reprod Genet 34, 117–124 (2017). https://doi.org/10.1007/s10815-016-0822-1

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Keywords

  • Endometriosis
  • Infertility
  • Copy number variation
  • DNA pooling
  • SNP array