Identification of genetic variants in patients with primary and secondary amenorrhea.

Objectives: To identify the cytogenetic and molecular pattern abnormalities and early diagnose the cause of primary and secondary amenorrhea.

Methods: A total of 320 patients in the age group of 14-35 years with clinically confirmed amenorrhea were screened using conventional cytogenetic methods. Patients with a normal karyotype, hypoplastic uterus, and no hormonal imbalance were extensively investigated using molecular cytogenetic platforms such as chromosomal microarrays and clinical exome sequencing (CES).

Results: Of the 266 patients with primary amenorrhea and 54 with secondary amenorrhea, 66.9% and 88.9%, independently, had a normal karyotype. The 20 patients with a normal karyotype, hypoplastic uterus, and no hormonal imbalance were further evaluated for microdeletions of <5 megabases using chromosomal microarray. In 20 cases, 5 samples with no microdeletions were investigated for 150 target genes using CES. A pathogenic variant at chromosome X BMP15, c.661T>C, p.W221R, HET-XL-VUS was observed in one patient (reclassification).

Conclusion: Cytogenetic evaluation of women with amenorrhea was performed in this study. One of the main etiological factors for primary amenorrhea is aberrant karyotypes. Identifying the underlying genetic cause may aid in devising effective treatment strategies. In addition, early diagnosis may enable treatment planning by the family before amenorrhea occurs.