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- Publisher Website: 10.1016/j.mex.2019.10.028
- Scopus: eid_2-s2.0-85074425899
- PMID: 31908979
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Article: High-resolution mapping of reciprocal translocation breakpoints using long-read sequencing
Title | High-resolution mapping of reciprocal translocation breakpoints using long-read sequencing |
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Authors | |
Keywords | Nanopore sequencing Breakpoint PGT-SR |
Issue Date | 2019 |
Publisher | Elsevier: Creative Commons Licenses. The Journal's web site is located at https://www.journals.elsevier.com/methodsx/ |
Citation | MethodsX, 2019, v. 6, p. 2499-2503 How to Cite? |
Abstract | Long-read nanopore sequencing enables direct high-resolution breakpoint mapping on balanced carriers of reciprocal translocation. The mean sequencing depth on the translocated chromosomes to achieve accurate mapping of breakpoints ranged from 2.5-fold to 6.2-fold. To speed up determination of the breakpoints from long-read sequencing data, alignment reads on the translocated chromosomes were extracted before piped into NanoSV. Checking the position of breakpoints on Interactive Genomics Viewer (IGV) was crucial to successful design of breakpoint PCR primers, especially when large deletion was involved at the breakpoints.
•Long-read sequencing enables accurate breakpoint mapping with base-pair resolution
•Splitting bam files by translocated chromosomes drastically speeded up the breakpoint determination
•IGV helps to identify the breakpoint positions and facilitate the design of breakpoint PCR primers |
Persistent Identifier | http://hdl.handle.net/10722/294187 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Chow, JFC | - |
dc.contributor.author | Cheng, HYH | - |
dc.contributor.author | Lau, EYL | - |
dc.contributor.author | Yeung, WSB | - |
dc.contributor.author | Ng, EHY | - |
dc.date.accessioned | 2020-11-23T08:27:37Z | - |
dc.date.available | 2020-11-23T08:27:37Z | - |
dc.date.issued | 2019 | - |
dc.identifier.citation | MethodsX, 2019, v. 6, p. 2499-2503 | - |
dc.identifier.uri | http://hdl.handle.net/10722/294187 | - |
dc.description.abstract | Long-read nanopore sequencing enables direct high-resolution breakpoint mapping on balanced carriers of reciprocal translocation. The mean sequencing depth on the translocated chromosomes to achieve accurate mapping of breakpoints ranged from 2.5-fold to 6.2-fold. To speed up determination of the breakpoints from long-read sequencing data, alignment reads on the translocated chromosomes were extracted before piped into NanoSV. Checking the position of breakpoints on Interactive Genomics Viewer (IGV) was crucial to successful design of breakpoint PCR primers, especially when large deletion was involved at the breakpoints. •Long-read sequencing enables accurate breakpoint mapping with base-pair resolution •Splitting bam files by translocated chromosomes drastically speeded up the breakpoint determination •IGV helps to identify the breakpoint positions and facilitate the design of breakpoint PCR primers | - |
dc.language | eng | - |
dc.publisher | Elsevier: Creative Commons Licenses. The Journal's web site is located at https://www.journals.elsevier.com/methodsx/ | - |
dc.relation.ispartof | MethodsX | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | Nanopore sequencing | - |
dc.subject | Breakpoint | - |
dc.subject | PGT-SR | - |
dc.title | High-resolution mapping of reciprocal translocation breakpoints using long-read sequencing | - |
dc.type | Article | - |
dc.identifier.email | Chow, JFC: jfcchow@hku.hk | - |
dc.identifier.email | Cheng, HYH: chy610a@hku.hk | - |
dc.identifier.email | Lau, EYL: eyllau@hku.hk | - |
dc.identifier.email | Yeung, WSB: wsbyeung@hku.hk | - |
dc.identifier.email | Ng, EHY: nghye@hku.hk | - |
dc.identifier.authority | Yeung, WSB=rp00331 | - |
dc.identifier.authority | Ng, EHY=rp00426 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1016/j.mex.2019.10.028 | - |
dc.identifier.pmid | 31908979 | - |
dc.identifier.pmcid | PMC6939040 | - |
dc.identifier.scopus | eid_2-s2.0-85074425899 | - |
dc.identifier.hkuros | 319319 | - |
dc.identifier.volume | 6 | - |
dc.identifier.spage | 2499 | - |
dc.identifier.epage | 2503 | - |
dc.identifier.eissn | 2215-0161 | - |
dc.identifier.isi | WOS:000498594100002 | - |
dc.publisher.place | Netherlands | - |
dc.identifier.issnl | 2215-0161 | - |