Noninvasive prenatal testing for β-thalassemia by targeted nanopore sequencing combined with relative haplotype dosage (RHDO): a feasibility study
Abstract Noninvasive prenatal testing (NIPT) for single gene disorders remains challenging. One approach that allows for accurate detection of the slight increase of the maternally inherited allele is the relative haplotype dosage (RHDO) analysis, which requires the construction of parental haplotyp...
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2021
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oai:doaj.org-article:a9e696309ee54b9796c8e78e93f38f862021-12-02T13:20:21ZNoninvasive prenatal testing for β-thalassemia by targeted nanopore sequencing combined with relative haplotype dosage (RHDO): a feasibility study10.1038/s41598-021-85128-22045-2322https://doaj.org/article/a9e696309ee54b9796c8e78e93f38f862021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85128-2https://doaj.org/toc/2045-2322Abstract Noninvasive prenatal testing (NIPT) for single gene disorders remains challenging. One approach that allows for accurate detection of the slight increase of the maternally inherited allele is the relative haplotype dosage (RHDO) analysis, which requires the construction of parental haplotypes. Recently, the nanopore sequencing technologies have become available and may be an ideal tool for direct construction of haplotypes. Here, we explored the feasibility of combining nanopore sequencing with the RHDO analysis in NIPT of β-thalassemia. Thirteen families at risk for β-thalassemia were recruited. Targeted region of parental genomic DNA was amplified by long-range PCR of 10 kb and 20 kb amplicons. Parental haplotypes were constructed using nanopore sequencing and next generation sequencing data. Fetal inheritance of parental haplotypes was classified by the RHDO analysis using data from maternal plasma DNA sequencing. Haplotype phasing was achieved in 12 families using data from 10 kb library. While data from the 20 kb library gave a better performance that haplotype phasing was achieved in all 13 families. Fetal status was correctly classified in 12 out of 13 families. Thus, targeted nanopore sequencing combined with the RHDO analysis is feasible to NIPT for β-thalassemia.Fuman JiangWeiqiang LiuLongmei ZhangYulai GuoMin ChenXiaojing ZengYang WangYufan LiJiaJia XianBoLe DuYuhuan XieShuming OuyangSheng LiYinghong YangChunsheng ZhangFei LuoXiaofang SunNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021) |
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Medicine R Science Q Fuman Jiang Weiqiang Liu Longmei Zhang Yulai Guo Min Chen Xiaojing Zeng Yang Wang Yufan Li JiaJia Xian BoLe Du Yuhuan Xie Shuming Ouyang Sheng Li Yinghong Yang Chunsheng Zhang Fei Luo Xiaofang Sun Noninvasive prenatal testing for β-thalassemia by targeted nanopore sequencing combined with relative haplotype dosage (RHDO): a feasibility study |
| description |
Abstract Noninvasive prenatal testing (NIPT) for single gene disorders remains challenging. One approach that allows for accurate detection of the slight increase of the maternally inherited allele is the relative haplotype dosage (RHDO) analysis, which requires the construction of parental haplotypes. Recently, the nanopore sequencing technologies have become available and may be an ideal tool for direct construction of haplotypes. Here, we explored the feasibility of combining nanopore sequencing with the RHDO analysis in NIPT of β-thalassemia. Thirteen families at risk for β-thalassemia were recruited. Targeted region of parental genomic DNA was amplified by long-range PCR of 10 kb and 20 kb amplicons. Parental haplotypes were constructed using nanopore sequencing and next generation sequencing data. Fetal inheritance of parental haplotypes was classified by the RHDO analysis using data from maternal plasma DNA sequencing. Haplotype phasing was achieved in 12 families using data from 10 kb library. While data from the 20 kb library gave a better performance that haplotype phasing was achieved in all 13 families. Fetal status was correctly classified in 12 out of 13 families. Thus, targeted nanopore sequencing combined with the RHDO analysis is feasible to NIPT for β-thalassemia. |
| format |
article |
| author |
Fuman Jiang Weiqiang Liu Longmei Zhang Yulai Guo Min Chen Xiaojing Zeng Yang Wang Yufan Li JiaJia Xian BoLe Du Yuhuan Xie Shuming Ouyang Sheng Li Yinghong Yang Chunsheng Zhang Fei Luo Xiaofang Sun |
| author_facet |
Fuman Jiang Weiqiang Liu Longmei Zhang Yulai Guo Min Chen Xiaojing Zeng Yang Wang Yufan Li JiaJia Xian BoLe Du Yuhuan Xie Shuming Ouyang Sheng Li Yinghong Yang Chunsheng Zhang Fei Luo Xiaofang Sun |
| author_sort |
Fuman Jiang |
| title |
Noninvasive prenatal testing for β-thalassemia by targeted nanopore sequencing combined with relative haplotype dosage (RHDO): a feasibility study |
| title_short |
Noninvasive prenatal testing for β-thalassemia by targeted nanopore sequencing combined with relative haplotype dosage (RHDO): a feasibility study |
| title_full |
Noninvasive prenatal testing for β-thalassemia by targeted nanopore sequencing combined with relative haplotype dosage (RHDO): a feasibility study |
| title_fullStr |
Noninvasive prenatal testing for β-thalassemia by targeted nanopore sequencing combined with relative haplotype dosage (RHDO): a feasibility study |
| title_full_unstemmed |
Noninvasive prenatal testing for β-thalassemia by targeted nanopore sequencing combined with relative haplotype dosage (RHDO): a feasibility study |
| title_sort |
noninvasive prenatal testing for β-thalassemia by targeted nanopore sequencing combined with relative haplotype dosage (rhdo): a feasibility study |
| publisher |
Nature Portfolio |
| publishDate |
2021 |
| url |
https://doaj.org/article/a9e696309ee54b9796c8e78e93f38f86 |
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