Targeted long-read sequencing facilitates effective carrier screening for complex monogenic diseases including spinal muscular atrophy, α-/β-thalassemia, 21-hydroxylase deficiency, and fragile-X syndrome.

Abstract

Background: Next-generation sequencing (NGS) has been applied for carrier screening, effectively reducing the incidence of severe diseases. However, some severe, high-prevalent and complex diseases, including spinal muscular atrophy (SMA), α-/β-thalassemia, 21-hydroxylase deficiency (21-OHD), and fragile-X syndrome (FXS), cannot be fully addressed by NGS, resulting in a high residual risk ratio. This study aims to evaluate the clinical utility of a long-read sequencing (LRS) panel for carrier screening of these five complex diseases.

Methods: A total of 2926 participants were retrospectively enrolled from International Peace Maternity and Child Health Hospital from Jan 2019 to Dec 2022. All the participants were previously screened for 149 genes correlated to 147 diseases by NGS. The samples were collected and analyzed with the LRS panel targeting the five complex diseases.

Results: LRS identified 236 carrier variants, including 54 for SMA, 113 for α-thalassemia, 19 for β-thalassemia, 47 for 21-OHD, and three for FXS. NGS identified only 56.4% (133/236) of the variants detected by LRS. NGS failed to detect three SMA carriers with SMN1 intragenic variants, while reported 10 false-positive carriers for α-thalassemia (HKαα miscalled as -α3.7). Both 21-OHD and FXS were beyond its detection scope. NGS identified only three of the seven at-risk couples determined by LRS. The total estimated at-risk couple rate for 151 genes in NGS and LRS panels was 1.0996%. SMA, α-/β-thalassemia, 21-OHD, and FXS were among the top 30 high-prevalent diseases and had a combined at-risk couple rate of 0.2433%, accounting for 22.1% of the total ratio. NGS could only identify 22.7% of the at-risk couples for the five diseases in the LRS panel.

Conclusions: Comprehensive carrier screening for high-prevalent diseases had higher clinical utility than expanding the list of low-prevalent diseases. Incorporating LRS into the NGS carrier screening strategy would facilitate more effective carrier screening.