Clinical heterogeneity and molecular genetic causes in a cohort of patients with disorders/differences of sex development

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Abstract

Background. Disorders of sex development (DSD) are a group of rare congenital conditions. Clinical management of patients with DSD is often difficult and requires multidisciplinary approach.

Aim. Analysis of the frequency of establishing genetic causes in various forms of DSD by using an original targeted sequencing panel with subsequent establishment of associations of the identified genetic variants with the nature of clinical manifestations.

Materials and methods. Conducted a clinical examination, karyotype analysis followed by the next generation sequencing (NGS) using MiSeq (Illumina) with the twenty-eight patients with different forms of 46, XY DSD were included. We designed HaloPlex (Agilent) gene panel that included coding regions of 80 candidate genes associated with DSD. All variants identified by NGS were confirmed by Sanger sequencing. We performed bioinformatics analysis using OMIM, “1000 genomes”, ESP6500, Genome Aggregation Database projects. To assess the clinical significance of the identified variants we used ClinVar database and American College of Medical Genetics and Genomics criteria.

Results. Out of 28 patients pathogenic, likely pathogenic, variants with unknown significance were identified in 11 patients (39%). In combination with clinical phenotype these variants were determined as causative for DSD. Nine patients (82%) had likely causative variants in one gene (of monogenic origin), while 18% had variants in two genes simultaneously (of oligogenic origin). 43% of the identified gene variants have not been previously reported. The variants in NR5A1 were associated with gonadal dysgenesis in two patients; the variants in MAP3K1 were also found in another two patients with gonadal dysgenesis, variants in AR – in three patients with CAIS, variant in MAMLD1 was associated with proximal form of hypospadias, variant in CYP17A1 was associated with testosterone biosynthetic defect. Among the two patients with variants of oligogenic origin, one had variants in MAP3K1 and MAMLD1 genes and was clinically characterized by hypospadias; the second had variants in AR and SEMA3A and was diagnosed with PAIS. There were also two patients with variants in NR5A1 of familial inheritance.

Conclusion. NGS-based targeted sequencing is a promising technique to improve the differential diagnosis, genetic counseling and management strategies for patients with DSD. Complex clinical examination followed by molecular genetic analysis improves the diagnosis, genetic counseling, and management strategies for patients with DSD including the assignment of sex of rearing.

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About the authors

Irina L. Nikitina

Almazov National Medical Research Centre

Author for correspondence.
Email: nikitina0901@gmail.com
ORCID iD: 0000-0002-3713-5350

D. Sci. (Med.), Almazov National Medical Research Centre

Russian Federation, Saint Petersburg

Leyla R. Sarakaeva

Almazov National Medical Research Centre

Email: sarale723@gmail.com
ORCID iD: 0000-0002-2752-861X

Res. Assist., Almazov National Medical Research Centre

Russian Federation, Saint Petersburg

Anna A. Kostareva

Almazov National Medical Research Centre

Email: nikitina0901@gmail.com
ORCID iD: 0000-0002-9349-6257

D. Sci. (Med.), Almazov National Medical Research Centre

Russian Federation, Saint Petersburg

Elena K. Kudryashova

Almazov National Medical Research Centre

Email: aksi-lena@rambler.ru

Cand. Sci. (Med.), Almazov National Medical Research Centre

Russian Federation, Saint Petersburg

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Supplementary files

Supplementary Files
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1. Fig. 1. Molecular genetic study of MAP3K1 gene (sequencing fragment of the gene with the identified variant).

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2. Fig. 2. Patient 2. Molecular genetic study of the MAMLD1 gene, MAP3K1 gene (sequencing fragment of the gene with the identified variant).

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3. Fig. 3. Patient 2. Molecular genetic study of the MAMLD1 gene, MAP3K1 gene (sequencing fragment of the gene with the identified variant).

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4. Fig. 4. Patient 3. Molecular genetic study of the MAMLD1 gene (sequencing fragment of the gene with the identified variant).

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5. Fig. 5. Patient 5. Molecular genetic study of the AR gene (sequencing fragment of the gene with the identified variant).

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6. Fig. 6. Patient 6. Molecular genetic study of the AR gene (sequencing fragment of the gene with the identified variant).

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7. Fig. 7. Patient 8. Molecular genetic study of the NR5A1 gene (sequencing fragment of the gene with the identified variant).

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8. Fig. 8. Patient 9. Molecular genetic study of SEMA3A gene, AR gene (sequencing fragment of the gene with identified variant).

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9. Fig. 9. Patient 9. Molecular genetic study of the SEMA3A gene, AR gene (sequencing fragment of the gene with the identified variant).

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10. Fig. 10. Patient 10. Molecular genetic study of NR5A1 gene (sequencing fragment of the gene with the identified variant).

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11. Fig. 11. Patient 11. Molecular genetic study of the MAP3K1 gene (sequencing fragment of the gene with the identified variant).

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12. Fig. 12. Differentiated testicular tissue, hyperplasia of Leydig and Sertoli cells, no spermatogenesis. Hematoxylin-eosin staining, ×100.

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