The quality and detection limits of mitochondrial heteroplasmy by long read nanopore sequencing
Abstract This study evaluates long-read and short-read sequencing for mitochondrial DNA (mtDNA) heteroplasmy detection. 592,315 bootstrapped datasets generated from two single-nucleotide mismatched ultra-deep sequenced mtDNA samples were used to assess basecalling error and accuracy, limit of hetero...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-11-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-024-78270-0 |
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| author | Barbara Slapnik Robert Šket Klementina Črepinšek Tine Tesovnik Barbara Jenko Bizjan Jernej Kovač |
| author_facet | Barbara Slapnik Robert Šket Klementina Črepinšek Tine Tesovnik Barbara Jenko Bizjan Jernej Kovač |
| author_sort | Barbara Slapnik |
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| description | Abstract This study evaluates long-read and short-read sequencing for mitochondrial DNA (mtDNA) heteroplasmy detection. 592,315 bootstrapped datasets generated from two single-nucleotide mismatched ultra-deep sequenced mtDNA samples were used to assess basecalling error and accuracy, limit of heteroplasmy detection, and heteroplasmy detection across various coverage depths. Results showed high Phred scores of data with GC-rich sequence bias for long reads. Limit of detection of 12% heteroplasmy was identified, showing strong correlation (R2 ≥ 0.955) with expected heteroplasmy but underreporting tendency of high-level variants. Nanopore sequencing shows potential for direct applicability in mitochondrial diseases diagnostics, but stringent validation processes to ensure diagnostic result quality are required. |
| format | Article |
| id | doaj-art-82b7807f8a204fae9861eef7fd4647dd |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-82b7807f8a204fae9861eef7fd4647dd2024-11-10T12:21:23ZengNature PortfolioScientific Reports2045-23222024-11-0114111210.1038/s41598-024-78270-0The quality and detection limits of mitochondrial heteroplasmy by long read nanopore sequencingBarbara Slapnik0Robert Šket1Klementina Črepinšek2Tine Tesovnik3Barbara Jenko Bizjan4Jernej Kovač5Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre LjubljanaClinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre LjubljanaClinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre LjubljanaClinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre LjubljanaClinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre LjubljanaClinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre LjubljanaAbstract This study evaluates long-read and short-read sequencing for mitochondrial DNA (mtDNA) heteroplasmy detection. 592,315 bootstrapped datasets generated from two single-nucleotide mismatched ultra-deep sequenced mtDNA samples were used to assess basecalling error and accuracy, limit of heteroplasmy detection, and heteroplasmy detection across various coverage depths. Results showed high Phred scores of data with GC-rich sequence bias for long reads. Limit of detection of 12% heteroplasmy was identified, showing strong correlation (R2 ≥ 0.955) with expected heteroplasmy but underreporting tendency of high-level variants. Nanopore sequencing shows potential for direct applicability in mitochondrial diseases diagnostics, but stringent validation processes to ensure diagnostic result quality are required.https://doi.org/10.1038/s41598-024-78270-0mtDNAHeteroplasmyMitochondrial diseaseLong-read sequencing |
| spellingShingle | Barbara Slapnik Robert Šket Klementina Črepinšek Tine Tesovnik Barbara Jenko Bizjan Jernej Kovač The quality and detection limits of mitochondrial heteroplasmy by long read nanopore sequencing Scientific Reports mtDNA Heteroplasmy Mitochondrial disease Long-read sequencing |
| title | The quality and detection limits of mitochondrial heteroplasmy by long read nanopore sequencing |
| title_full | The quality and detection limits of mitochondrial heteroplasmy by long read nanopore sequencing |
| title_fullStr | The quality and detection limits of mitochondrial heteroplasmy by long read nanopore sequencing |
| title_full_unstemmed | The quality and detection limits of mitochondrial heteroplasmy by long read nanopore sequencing |
| title_short | The quality and detection limits of mitochondrial heteroplasmy by long read nanopore sequencing |
| title_sort | quality and detection limits of mitochondrial heteroplasmy by long read nanopore sequencing |
| topic | mtDNA Heteroplasmy Mitochondrial disease Long-read sequencing |
| url | https://doi.org/10.1038/s41598-024-78270-0 |
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