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High-resolution mapping of reciprocal translocation breakpoints using long-read sequencing

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 br...

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Detalles Bibliográficos
Autores principales: Chow, Judy F.C., Cheng, Heidi H.Y., Lau, Estella Y.L., Yeung, William S.B., Ng, Ernest H.Y.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6939040/
https://www.ncbi.nlm.nih.gov/pubmed/31908979
http://dx.doi.org/10.1016/j.mex.2019.10.028
Descripción
Sumario: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.