Carrier screening for multiple complex monogenic diseases using long-read sequencing: a population-based study of...

Carrier screening for severe recessive genetic diseases in couples undergoing premarital examinations is a crucial strategy for reducing the incidence of birth defects and promoting reproductive health. However, many high-prevalence but genetically complex diseases cannot be reliably detected using conventional PCR-based methods or short-read next-generation sequencing (NGS).

In this study, 1,203 couples who received free premarital medical examinations at seven units in Shanghai were recruited. PacBio long-read sequencing (LRS) was applied for simultaneous carrier screening of five genetically complex monogenic diseases, including spinal muscular atrophy (SMA), α-/β-thalassemia, congenital adrenal hyperplasia (CAH) (refers to 21-hydroxylase deficiency, 21-OHD), and fragile X syndrome (FXS). A total of 161 individuals were identified as carriers of a single disease, while four individuals carried pathogenic variants associated with two distinct diseases. Four couples were determined to be at high reproductive risk, including one classic CAH family, one SMA family, one hemoglobin H (Hb H) disease family, and one family in which the female was an FXS premutation carrier. In addition, one couple at risk of having a child with non-classic CAH (NCCAH), as well as one male individual with a confirmed diagnosis of NCCAH, were identified.

LRS provides substantial clinical value for comprehensive carrier screening in the premarital population. It enables accurate detection of structural variants and repeat expansions that are often missed by conventional methods. These findings support the integration of LRS into routine premarital genetic screening protocols to enhance early identification of at-risk couples and improve reproductive decision-making.