Long-read sequencing solves complex structure of CYP21A2 in a large 21-hydroxylase deficiency cohort.

Context: Genetic testing for 21-hydroxylase deficiency (21-OHD) is always challenging. Current approaches, short-read sequencing and multiplex ligation-dependent probe amplification (MLPA), are insufficient for the detection of chimeric genes or complicated variants from multiple copies. Recently developed long-read sequencing (LRS) can solve this problem.

Objective: To investigate the clinical utility of LRS in precision diagnosis of 21-hydroxylase deficiency.

Methods: In the cohort of 832 patients with 21-OHD, the current approaches provided the precise molecular diagnosis for 81.7% (680/832) of cases. LRS was performed to solve the remaining 144 cases with complex chimeric variants and eight cases with variants from multiple copies. Clinical manifestations in patients with continuous deletions of CYP21A2 extending to TNXB (namely CAH-X) were further evaluated.

Results: Using LRS in combination with previous genetic test results, a total of 16.9% (281/1664) CYP21A1P/CYP21A2 or TNXA/TNXB chimeric alleles were identified in 832 patients, with CYP21A1P/CYP21A2 accounting for 10.4% and TNXA/TNXB for 6.5%. The top three common chimeras were CYP21 CH-1, TNX CH-1 and TNX CH-2, accounting for 77.2% (217/281) of all chimeric alleles. The eight patients with variants on multiple copies of CYP21A2 were accurately identified with LRS. The prevalence of CAH-X in our cohort was 12.1%, and a high frequency of connective tissue-related symptoms was observed in CAH-X patients.

Conclusion: LRS can detect all types of CYP21A2 variants, including complex chimeras and pathogenic variants on multiple copies in patients with 21-OHD, which could be utilized as a first-tier routine test for the precision diagnosis and categorization of congenital adrenal hyperplasia.