Location of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore Platform
Genomic structural variants, including translocations, inversions, insertions, deletions, and duplications, are challenging to be reliably detected by traditional genomic technologies. In particular, balanced translocations and inversions can neither be identified by microarrays since they do not al...
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Frontiers Media S.A.
2020-01-01
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Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.01313/full |
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doaj-08bc34d8e93a4c478f8346b981f2fed8 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Liang Hu Liang Hu Liang Hu Liang Hu Fan Liang Dehua Cheng Dehua Cheng Zhiyuan Zhang Guoliang Yu Jianjun Zha Yang Wang Qi Xia Daoli Yuan Yueqiu Tan Yueqiu Tan Yueqiu Tan Yueqiu Tan Depeng Wang Yu Liang Ge Lin Ge Lin Ge Lin Ge Lin |
spellingShingle |
Liang Hu Liang Hu Liang Hu Liang Hu Fan Liang Dehua Cheng Dehua Cheng Zhiyuan Zhang Guoliang Yu Jianjun Zha Yang Wang Qi Xia Daoli Yuan Yueqiu Tan Yueqiu Tan Yueqiu Tan Yueqiu Tan Depeng Wang Yu Liang Ge Lin Ge Lin Ge Lin Ge Lin Location of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore Platform Frontiers in Genetics Oxford Nanopore Technologies structural variants balanced translocation long-read sequencing preimplantation genetic testing |
author_facet |
Liang Hu Liang Hu Liang Hu Liang Hu Fan Liang Dehua Cheng Dehua Cheng Zhiyuan Zhang Guoliang Yu Jianjun Zha Yang Wang Qi Xia Daoli Yuan Yueqiu Tan Yueqiu Tan Yueqiu Tan Yueqiu Tan Depeng Wang Yu Liang Ge Lin Ge Lin Ge Lin Ge Lin |
author_sort |
Liang Hu |
title |
Location of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore Platform |
title_short |
Location of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore Platform |
title_full |
Location of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore Platform |
title_fullStr |
Location of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore Platform |
title_full_unstemmed |
Location of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore Platform |
title_sort |
location of balanced chromosome-translocation breakpoints by long-read sequencing on the oxford nanopore platform |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2020-01-01 |
description |
Genomic structural variants, including translocations, inversions, insertions, deletions, and duplications, are challenging to be reliably detected by traditional genomic technologies. In particular, balanced translocations and inversions can neither be identified by microarrays since they do not alter chromosome copy numbers, nor by short-read sequencing because of the unmappability of short reads against repetitive genomic regions. The precise localization of breakpoints is vital for exploring genetic causes in patients with balanced translocations or inversions. Long-read sequencing techniques may detect these structural variants in a more direct, efficient, and accurate manner. Here, we performed whole-genome, long-read sequencing using the Oxford Nanopore GridION sequencer to detect breakpoints in six balanced chromosome translocation carriers and one inversion carrier. The results showed that all the breakpoints were consistent with the karyotype results with only ~10× coverage. Polymerase chain reaction (PCR) and Sanger sequencing confirmed 8 out of 14 breakpoints; however, other breakpoint loci were slightly missed since they were either in highly repetitive regions or pericentromeric regions. Some of the breakpoints interrupted normal gene structure, and in other cases, micro-deletions/insertions were found just next to the breakpoints. We also detected haplotypes around the breakpoint regions. Our results suggest that long-read, whole-genome sequencing is an ideal strategy for precisely localizing translocation breakpoints and providing haplotype information, which is essential for medical genetics and preimplantation genetic testing. |
topic |
Oxford Nanopore Technologies structural variants balanced translocation long-read sequencing preimplantation genetic testing |
url |
https://www.frontiersin.org/article/10.3389/fgene.2019.01313/full |
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doaj-08bc34d8e93a4c478f8346b981f2fed82020-11-25T01:46:43ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-01-011010.3389/fgene.2019.01313488902Location of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore PlatformLiang Hu0Liang Hu1Liang Hu2Liang Hu3Fan Liang4Dehua Cheng5Dehua Cheng6Zhiyuan Zhang7Guoliang Yu8Jianjun Zha9Yang Wang10Qi Xia11Daoli Yuan12Yueqiu Tan13Yueqiu Tan14Yueqiu Tan15Yueqiu Tan16Depeng Wang17Yu Liang18Ge Lin19Ge Lin20Ge Lin21Ge Lin22Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, ChinaDepartment of Genetics, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, ChinaKey Laboratory of Reproductive and Stem Cell Engineering, National Health and Family Planning Commission, Changsha, ChinaDepartment of Research, National Engineering Research Center of Human Stem Cells, Changsha, ChinaGrandOmics Biosciences, Beijing, ChinaInstitute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, ChinaDepartment of Research, National Engineering Research Center of Human Stem Cells, Changsha, ChinaGrandOmics Biosciences, Beijing, ChinaGrandOmics Biosciences, Beijing, ChinaGrandOmics Biosciences, Beijing, ChinaGrandOmics Biosciences, Beijing, ChinaGrandOmics Biosciences, Beijing, ChinaGrandOmics Biosciences, Beijing, ChinaInstitute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, ChinaDepartment of Genetics, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, ChinaKey Laboratory of Reproductive and Stem Cell Engineering, National Health and Family Planning Commission, Changsha, ChinaDepartment of Research, National Engineering Research Center of Human Stem Cells, Changsha, ChinaGrandOmics Biosciences, Beijing, ChinaGrandOmics Biosciences, Beijing, ChinaInstitute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, ChinaDepartment of Genetics, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, ChinaKey Laboratory of Reproductive and Stem Cell Engineering, National Health and Family Planning Commission, Changsha, ChinaDepartment of Research, National Engineering Research Center of Human Stem Cells, Changsha, ChinaGenomic structural variants, including translocations, inversions, insertions, deletions, and duplications, are challenging to be reliably detected by traditional genomic technologies. In particular, balanced translocations and inversions can neither be identified by microarrays since they do not alter chromosome copy numbers, nor by short-read sequencing because of the unmappability of short reads against repetitive genomic regions. The precise localization of breakpoints is vital for exploring genetic causes in patients with balanced translocations or inversions. Long-read sequencing techniques may detect these structural variants in a more direct, efficient, and accurate manner. Here, we performed whole-genome, long-read sequencing using the Oxford Nanopore GridION sequencer to detect breakpoints in six balanced chromosome translocation carriers and one inversion carrier. The results showed that all the breakpoints were consistent with the karyotype results with only ~10× coverage. Polymerase chain reaction (PCR) and Sanger sequencing confirmed 8 out of 14 breakpoints; however, other breakpoint loci were slightly missed since they were either in highly repetitive regions or pericentromeric regions. Some of the breakpoints interrupted normal gene structure, and in other cases, micro-deletions/insertions were found just next to the breakpoints. We also detected haplotypes around the breakpoint regions. Our results suggest that long-read, whole-genome sequencing is an ideal strategy for precisely localizing translocation breakpoints and providing haplotype information, which is essential for medical genetics and preimplantation genetic testing.https://www.frontiersin.org/article/10.3389/fgene.2019.01313/fullOxford Nanopore Technologiesstructural variantsbalanced translocationlong-read sequencingpreimplantation genetic testing |