Genomic analysis using high-resolution single-nucleotide polymorphism arrays reveals novel microdeletions associated with premature ovarian failure

Abstract

Objective: To analyze DNA from women with premature ovarian failure (POF) for genome-wide copy-number variations (CNVs), focusing on novel autosomal microdeletions.

Design: Case-control genetic association study.

Setting: Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas.

Patient(s): Of 89 POF patients, eight experienced primary amenorrhea and 81 exhibited secondary amenorrhea before age 40 years.

Intervention(s): Genomic DNA from peripheral blood samples was analyzed for CNVs using high-resolution single-nucleotide polymorphism (SNP) arrays.

Main outcome measure(s): Identification of novel CNVs in 89 POF cases, using the Database of Genomic Variants as a control population.

Result(s): A total of 198 autosomal CNVs were detected by SNP arrays, ranging in size from 0.1 Mb to 3.4 Mb. These CNVs (>0.1 Mb) included 17 novel microduplications and seven novel microdeletions, six of which contained the coding regions 8q24.13, 10p15-p14, 10q23.31, 10q26.3, 15q25.2, and 18q21.32. Most of the novel CNVs were derived from autosomes rather than the X chromosome.

Conclusion(s): The present pilot study revealed novel microdeletions/microduplications in women with POF. Two novel microdeletions caused haploinsufficiency for SYCE1 and CPEB1, genes known to cause ovarian failure in knockout mouse models. Chromosomal microarrays may be a useful adjunct to conventional karyotyping when evaluating genomic imbalances in women with POF.

Figure 1. Data from SNP arrays and qPCR plotted as Δ log R ratio and 2^{−Δ Δ Ct}, respectively, for five autosomal microdeletions in women with POF

Regions of interest were initially determined based on log R ratio shifts, where reported copy number reductions in gDNA from peripheral blood samples are indicated above by a negative Δ log R ratio. 2^{−Δ Δ Ct} values (fold changes) were then calculated from qPCR output for the target regions. Fold change values lying within the shaded region are indicative of a normal diploid copy number of 2, whereas those below the shaded region are indicative of a copy number reduction of 1, a fold change of approximately 0.5 (1/2). Hemizygous deletions were corroborated on 8q24.13 in POF-65, 10p15-p14 in POF-105, 10q26.3 in POF-108, 15q25.2 in POF-87 and 18q21.32 in POF-119.