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. 2022 May 18;12:8284. doi: 10.1038/s41598-022-12130-7

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Nanopore sequencing of PRNP and octapeptide repeat genotyping. (a) The human PRNP gene. Important pathogenic variants, such as deletions/insertions in the octapeptide repeat region (OPR), codon 129 (M129V) or codon 200 (E200K) SNVs are indicated in the protein-coding region in orange. Genetic diagnosis at the MRC Prion Unit at UCL is performed by Sanger sequencing of the protein-coding sequence (1015-bp amplicon) or specifically of the OPR (348-bp amplicon). Exon 1 and the beginning of the intron are particularly GC-rich (see GC % plot). This likely explains why producing a single amplicon spanning the entire genomic region was technically challenging. Instead, we amplified PRNP in two overlapping fragments for Nanopore sequencing (see Nanopore amplicons). (b) Sequence of PRNP’s OPR. The OPR is composed of five similar repeats for a total of 123 bp. The first repeat (R1) is 27 bp and encodes a sequence of 9 amino acids (nonapeptide), the subsequent ones (R2, R2, R3, R4) are 24 bp and all encode the same sequence of 8 amino acids (octapeptide). The two R2 repeats are identical. R2 vary with R3 and R4 by two nucleotides at wobble positions.