Long-Read Sequencing to Improve Diagnosis Rate of Rare Diseases

By LabMedica International staff writers
Posted on 28 Jan 2025

Image: Researcher Shloka Negi analyzes long-read sequencing data in the UC Santa Cruz Computational Genomics lab (Photo courtesy of UC Santa Cruz)

Rare genetic diseases affect one in every 10 people globally, yet around 50% of cases remain undiagnosed despite advances in genetic technology and testing. The diagnosis process can take several years, especially for children, due to the limitations of current clinical testing methods, such as short-read sequencing, which often misses crucial genomic information. Researchers are now focusing on long-read sequencing as a promising alternative to speed up diagnoses and provide a more comprehensive dataset, potentially eliminating the need for multiple specialized tests.

A study led by researchers at the University of California - Santa Cruz (Santa Cruz, CA, USA) explored the potential of long-read sequencing for diagnosing rare monogenic diseases, which are caused by disruptions in a single gene. The study, published in The American Journal of Human Genetics, found that long-read sequencing could drastically reduce the time for diagnosis from years to days and at a significantly lower cost. The study utilized nanopore sequencing, a technique developed at UCSC, which provided end-to-end reads of the patients’ genomes at approximately USD 1,000 per sample, with data analysis costing around USD 100.

The research involved analyzing 42 patients with rare diseases, some of whom had been diagnosed through traditional short-read methods, while others remained undiagnosed. The long-read sequencing approach provided a more exhaustive dataset, identifying additional rare candidate variants, long-range phasing, and methylation information that short-read sequencing could not capture. This method enabled the researchers to provide conclusive diagnoses for 11 of the 42 patients, including cases of congenital adrenal hypoplasia, disorders of sex development, and neurodevelopmental disorders. On average, long-read sequencing covered 280 genes with significant protein-coding regions that had been missed by short reads, making the diagnosis process faster, more comprehensive, and more cost-effective.

One of the primary advantages of long-read sequencing is its ability to read long stretches of DNA at once, which helps overcome the limitations of short-read sequencing, particularly in complex genomic regions. Furthermore, it provides phasing data, which helps clinicians understand which variants were inherited from each parent, offering valuable insights for genetic diagnoses. The study suggests that long-read sequencing has the potential to transform the diagnosis of rare genetic diseases, offering a more efficient and effective approach to patient care and treatment.

“Long read sequencing is likely the next best test for unsolved cases with either compelling variants in a single gene or a clear phenotype,” said Shloka Negi, a UC Santa Cruz BME Ph.D. student who is the paper’s first author. “It can serve as a single diagnostic test, reducing the need for multiple clinical visits and transforming a years-long diagnostic journey into a matter of hours.”