Long read sequencing enhances pathogenic and novel variation discovery in patients with rare diseases
Shruti Sinha, Fatma Rabea, Sathishkumar Ramaswamy, Ikram Chekroun, Maha El Naofal, Ruchi Jain, Roudha Alfalasi, Nour Halabi, Sawsan Yaslam, Massomeh Sheikh Hassani, Shruti Shenbagam, Alan Taylor, Mohammed Uddin, Mohamed A. Almarri, Stefan S. du Plessis, Alawi Alsheikh‐Ali, Ahmad Abou Tayoun
Abstract
With ongoing improvements in the detection of complex genomic and epigenomic variations, long-read sequencing (LRS) technologies could serve as a unified platform for clinical genetic testing, particularly in rare disease settings, where nearly half of patients remain undiagnosed using existing technologies. Here, we report a simplified funnel-down filtration strategy aimed at enhancing the identification of small and large deleterious variants as well as abnormal episignature disease profiles from whole-genome LRS data. This approach detected all pathogenic single nucleotide, structural, and methylation variants in a positive control set (N = 76) including an independent sample set with known methylation profiles (N = 57). When applied to patients who previously had negative short-read testing (N = 51), additional diagnoses were uncovered in 10% of cases, including a methylation profile at the spinal muscular atrophy locus utilized for diagnosing this life-threatening, yet treatable, condition. Our study illustrates the utility of LRS in clinical genetic testing and the discovery of novel disease variation. Here the authors illustrate how long read whole genome sequencing can enhance the diagnosis of patients with rare diseases relative to standard methods, through identification of comprehensive small and large genomic variation on both alleles as well as methylation profiling.