Vuthy Ea1, Anne Bergougnoux1, Pascal Philibert2, Nadège Servant-Fauconnet3, Alice Faure4, Jean Breaud5, Laura Gaspari6, Charles Sultan2, Françoise Paris7, Nicolas Kalfa8. 1. Centre de Référence Maladies Rares DEVGEN Constitutif Sud, CHU de Montpellier, France; Laboratoire de Génétique de Maladies Rares, EA7402, Université de Montpellier, Montpellier, France; Laboratoire de Génétique Moléculaire, IURC, CHU de Montpellier, Montpellier, France. 2. Centre de Référence Maladies Rares DEVGEN Constitutif Sud, CHU de Montpellier, France. 3. Centre de Référence Maladies Rares DEVGEN Constitutif Sud, CHU de Montpellier, France; Laboratoire de Génétique Moléculaire, IURC, CHU de Montpellier, Montpellier, France. 4. Service de Chirurgie et Urologie Pédiatrique, Hôpital la Timone, AP-HM, Marseille, France. 5. Service de Chirurgie et Urologie Pédiatrique, Hôpital Lenval, CHU de Nice, France. 6. Centre de Référence Maladies Rares DEVGEN Constitutif Sud, CHU de Montpellier, France; Unité d'Endocrinologie Pédiatrique, Service de Pédiatrie, Hopital Arnaud de Villeneuve, Montpellier, France. 7. Centre de Référence Maladies Rares DEVGEN Constitutif Sud, CHU de Montpellier, France; Laboratoire de Génétique Moléculaire, IURC, CHU de Montpellier, Montpellier, France; Unité d'Endocrinologie Pédiatrique, Service de Pédiatrie, Hopital Arnaud de Villeneuve, Montpellier, France. 8. Centre de Référence Maladies Rares DEVGEN Constitutif Sud, CHU de Montpellier, France; Laboratoire de Génétique de Maladies Rares, EA7402, Université de Montpellier, Montpellier, France; Chirurgie et Urologie Pédiatrique, Hôpital Lapeyronie, CHU de Montpellier, et Université de Montpellier, Montpellier, France. Electronic address: n-kalfa@chu-montpellier.fr.
Abstract
BACKGROUND: Next-generation sequencing (NGS) is generally used for patients with severe disorders of sex development (DSD). However, NGS has not been applied extensively for patients with hypospadias only, and most affected children do not benefit from an etiological diagnosis. OBJECTIVE: To evaluate the clinical usefulness of NGS for patients with hypospadias, regardless of severity. DESIGN, SETTING, AND PARTICIPANTS: Prospective multicenter research included 293 children with glandular to penoscrotal hypospadias (no undescended testis and no micropenis). After excluding likely pathogenic androgen receptor (AR) variants by Sanger sequencing, an NGS panel tested 336 genes including unexplored candidates in 284 patients. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: The rate of pathogenic and likely pathogenic variants was assessed using REVEL, ClinVar, and in-house tools (Captain-ACHAB, MobiCNV, and MobiDetails). RESULTS AND LIMITATIONS: Likely pathogenic variants were identified in 16 (5.5%) patients with both Sanger sequencing and NGS taken into account. Some genes were related to DSD (AR, NR5A1, HSD17B3, and MAMLD1), but reverse phenotyping revealed two syndromic disorders with midline defects (MID1) and alteration in the retinoic acid signaling pathway (RARA). Coverage analysis revealed an 18q deletion. Identification of likely pathogenic variants increased with hypospadias severity. Other variants of unknown significance (VUSs) in genes implicated in hypogonadotropic hypogonadism, Noonan syndrome, and genital tubercle development were also identified. Genetic study mainly focused on exonic variants, and most cases remain unexplained. CONCLUSIONS: NGS reveals minor forms of DSD, undiagnosed syndromes, or candidate rare variants in new genes, indicating that even patients with mild hypospadias benefit from advanced sequencing techniques. Early molecular diagnosis would help improve follow-up at puberty and medical counseling for initially undiagnosed syndromes. Future studies will improve the diagnosis by investigating the contribution of VUSs. PATIENT SUMMARY: Next-generation sequencing enables simultaneous testing of numerous genes and should not be limited to disorders of sex development cases. Even patients with mild hypospadias would benefit from early diagnosis of a genetic defect implicated in sex development or other syndromes.
BACKGROUND: Next-generation sequencing (NGS) is generally used for patients with severe disorders of sex development (DSD). However, NGS has not been applied extensively for patients with hypospadias only, and most affected children do not benefit from an etiological diagnosis. OBJECTIVE: To evaluate the clinical usefulness of NGS for patients with hypospadias, regardless of severity. DESIGN, SETTING, AND PARTICIPANTS: Prospective multicenter research included 293 children with glandular to penoscrotal hypospadias (no undescended testis and no micropenis). After excluding likely pathogenic androgen receptor (AR) variants by Sanger sequencing, an NGS panel tested 336 genes including unexplored candidates in 284 patients. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: The rate of pathogenic and likely pathogenic variants was assessed using REVEL, ClinVar, and in-house tools (Captain-ACHAB, MobiCNV, and MobiDetails). RESULTS AND LIMITATIONS: Likely pathogenic variants were identified in 16 (5.5%) patients with both Sanger sequencing and NGS taken into account. Some genes were related to DSD (AR, NR5A1, HSD17B3, and MAMLD1), but reverse phenotyping revealed two syndromic disorders with midline defects (MID1) and alteration in the retinoic acid signaling pathway (RARA). Coverage analysis revealed an 18q deletion. Identification of likely pathogenic variants increased with hypospadias severity. Other variants of unknown significance (VUSs) in genes implicated in hypogonadotropic hypogonadism, Noonan syndrome, and genital tubercle development were also identified. Genetic study mainly focused on exonic variants, and most cases remain unexplained. CONCLUSIONS: NGS reveals minor forms of DSD, undiagnosed syndromes, or candidate rare variants in new genes, indicating that even patients with mild hypospadias benefit from advanced sequencing techniques. Early molecular diagnosis would help improve follow-up at puberty and medical counseling for initially undiagnosed syndromes. Future studies will improve the diagnosis by investigating the contribution of VUSs. PATIENT SUMMARY: Next-generation sequencing enables simultaneous testing of numerous genes and should not be limited to disorders of sex development cases. Even patients with mild hypospadias would benefit from early diagnosis of a genetic defect implicated in sex development or other syndromes.
Authors: Melissa A Richard; Jenil Patel; Renata H Benjamin; Emine Bircan; Stephen J Canon; Lisa K Marengo; Mark A Canfield; A J Agopian; Philip J Lupo; Wendy N Nembhard Journal: JAMA Netw Open Date: 2022-07-01