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Fig. 6 | Molecular Neurodegeneration

Fig. 6

From: Long-read sequencing across the C9orf72 ‘GGGGCC’ repeat expansion: implications for clinical use and genetic discovery efforts in human disease

Fig. 6

PacBio Sequel reads traverse the repeat region for pathogenic and non-pathogenic alleles. The PacBio Sequel sequenced through both pathogenic and non-pathogenic alleles, demonstrating the platform is capable of characterizing repeat expansions. All of these reads were first aligned by graphmap, and then hand curated to determine the repeat region. a The human genome reference sequence (hg38) contains three G4C2 repeats (18 nucleotides). We identified specific “landmarks” before and after the repeat region in the reference sequence to properly locate the repeat region in the reads, and to hand curate the alignments. Landmarks are identified by red bars adjacent to the repeat region. b We obtained four PacBio Sequel reads covering the eight-repeat sequence, spanning 48 nucleotides. There was a net gain of 29 nucleotides within the defined repeat region, which equates to approximately 5 additional repeats; this concurs with our fragment analysis (Fig. 5a). c We also obtained four reads that covered an expanded allele, one of which bridged the entire repeat expansion, with approximately 1324 repeats (7941 nucleotides). The other three reads ended before bridging the repeat region, where one captured approximately 30 repeats (178 nucleotides), another captured approximately 69 repeats (419 nucleotides), and the third captured approximately 912 repeats (5471 nucleotides)

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