Long‐Read Sequencing Identifying the Genetic Complexity of Congenital Adrenal Hyperplasia in the Pedigree

ABSTRACT Background High sequence homology between CYP21A2 and CYP21A1P poses challenges to genetic diagnosis of congenital adrenal hyperplasia (CAH) due to 21‐hydroxylase deficiency (21‐OHD). Traditional genetic testing is unable to provide an accurate diagnosis due to the genetic complexity of CAH. Methods Deletions, duplications, and recombination breakpoints were precisely identified by long‐read sequencing (LRS). Results This study presented a pregnant woman, a 21‐OHD carrier detected by MLPA, and her husband, a normal subject also detected by MLPA. The fetus was suspected of having 21‐OHD based on clinical presentations such as enlarged adrenal glands, atypical external genitalia and karyotyping of 46, XX. LRS further identified the fetus as having the most severe salt‐wasting (SW) form of 21‐OHD with a compound heterozygote genotype. One allele was TNXA/TNXB CH‐2, while the other allele was CYP21A1P/CYP21A2 CH‐8. LRS precisely determined the genotypes of the fetus's father and grandmother with duplications, which misdiagnosed by MLPA. The multidisciplinary team recommended immediate glucocorticoid and mineralocorticoid treatment for the child after birth to prevent life‐threatening adrenal crisis. Conclusions LRS provides precise diagnosis for family members with CYP21A2 deletion or duplication, improving disease management and preventing potential adrenal crises. When used in pre‐pregnancy genetic testing, LRS can indicate high genetic risk and guide the appropriate therapy during pregnancy and immediately after birth. Long‐read sequencing (LRS) based on the long‐rang PCR identified the genetic complexities such as the deletion chimeras and duplicated CYP21A2 in congenital adrenal hyperplasia, enabling the precise diagnosis for the family pedigree.