Nanopore sequencing to decipher the cause of repeat-associated disorders

More than 50 human diseases associated with abnormal repeat expansion or contraction have been genetically “solved.” Long-read sequencing technologies are anticipated to help determine the genetic causes of more repeat-associated disorders. Repeat expansion regions are refractory to regular sequencing technologies and are only estimated by incomplete information from conventional genomic technologies like Sanger sequencing, repeat-primed PCR, and Southern blot. However, even long-read whole-genome sequencing provides imprecise sequence information of repeat-expanded regions.

To obtain complete sequencing information, Naomichi Matsumoto and colleagues have been using Cas9-based enrichment technologies to obtain consensus sequences. They compared Oxford Nanopore and PacBio long-read sequencing technologies and obtained comparable accuracy in both.

In this webinar, Dr. Matsumoto discussed his work applying Oxford Nanopore technology to determine the complete sequences of abnormally expanded (TTTCA)_n insertion/expansion regions of SAMD12 in 25 benign adult familial myoclonus epilepsy (BAFME) patients. His team found a novel repeat configuration that was interfering with repeat-primed PCR, and an abnormally short (TTTCA)₁₄ expansion, which was far below the pathological consensus repeat expansion (TTTCA)₄₀₀. His findings show that complete sequences of abnormal repeats are invaluable to obtain new insights into human repeat disorders.