TY - JOUR
T1 - Nanopore Long-Read Sequencing as a First-Tier Diagnostic Test to Detect Repeat Expansions in Neurological Disorders
AU - de Boer, Eddy N
AU - Scheper, Arjen J
AU - Hendriksen, Dennis
AU - Charbon, Bart
AU - van der Vries, Gerben
AU - ten Berge, Annelies M
AU - Grootscholten, Petra M
AU - Lemmink, Henny H
AU - Jongbloed, Jan D H
AU - Bosscher, Laura
AU - Knoers, Nine V A M
AU - Swertz, Morris A
AU - Sikkema-Raddatz, Birgit
AU - Dijkstra, Dorieke J
AU - Johansson, Lennart F
AU - van Diemen, Cleo C
PY - 2025/3/21
Y1 - 2025/3/21
N2 - Inherited neurological disorders, such as spinocerebellar ataxia (SCA) and fragile X (FraX), are frequently caused by short tandem repeat (STR) expansions. The detection and assessment of STRs is important for diagnostics and prognosis. We tested the abilities of nanopore long-read sequencing (LRS) using a custom panel including the nine most common SCA-related genes and FraX and created raw data to report workflow. Using known STR lengths for 23 loci in 12 patients, a pipeline was validated to detect and report STR lengths. In addition, we assessed the capability to detect SNVs, indels, and the methylation status in the same test. For the 23 loci, 22 were concordant with known STR lengths, while for the last, one of three replicates differed, indicating an artefact. All positive control STRs were detected as likely pathogenic, with no additional findings after a visual assessment of repeat motifs. Out of 226 SNV and Indel variants, two were false positive and one false negative (accuracy 98.7%). In all
FMR1 controls, a methylation status could be determined. In conclusion, LRS is suitable as a diagnostic workflow for STR analysis in neurological disorders and can be generalized to other diseases. The addition of SNV/Indel and methylation detection promises to allow for a one-test-fits-all workflow.
AB - Inherited neurological disorders, such as spinocerebellar ataxia (SCA) and fragile X (FraX), are frequently caused by short tandem repeat (STR) expansions. The detection and assessment of STRs is important for diagnostics and prognosis. We tested the abilities of nanopore long-read sequencing (LRS) using a custom panel including the nine most common SCA-related genes and FraX and created raw data to report workflow. Using known STR lengths for 23 loci in 12 patients, a pipeline was validated to detect and report STR lengths. In addition, we assessed the capability to detect SNVs, indels, and the methylation status in the same test. For the 23 loci, 22 were concordant with known STR lengths, while for the last, one of three replicates differed, indicating an artefact. All positive control STRs were detected as likely pathogenic, with no additional findings after a visual assessment of repeat motifs. Out of 226 SNV and Indel variants, two were false positive and one false negative (accuracy 98.7%). In all
FMR1 controls, a methylation status could be determined. In conclusion, LRS is suitable as a diagnostic workflow for STR analysis in neurological disorders and can be generalized to other diseases. The addition of SNV/Indel and methylation detection promises to allow for a one-test-fits-all workflow.
KW - Humans
KW - Nanopore Sequencing/methods
KW - Microsatellite Repeats/genetics
KW - Nervous System Diseases/genetics
KW - Fragile X Syndrome/genetics
KW - Fragile X Mental Retardation Protein/genetics
KW - DNA Repeat Expansion
KW - Spinocerebellar Ataxias/genetics
KW - Male
KW - DNA Methylation
KW - High-Throughput Nucleotide Sequencing
KW - Female
U2 - 10.3390/ijms26072850
DO - 10.3390/ijms26072850
M3 - Article
C2 - 40243408
SN - 1422-0067
VL - 26
JO - International Journal of Molecular Sciences
JF - International Journal of Molecular Sciences
IS - 7
M1 - 2850
ER -