Estimation of cell-free fetal DNA fraction from maternal plasma based on linkage disequilibrium information
Abstract Cell-free fetal DNA fraction (FF) in maternal plasma is a key parameter affecting the performance of noninvasive prenatal testing (NIPT). Accurate quantitation of FF plays a pivotal role in these tests. However, there are few methods that could determine FF with high accuracy using shallow‐...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2021-10-01
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| Series: | npj Genomic Medicine |
| Online Access: | https://doi.org/10.1038/s41525-021-00247-z |
| _version_ | 1818892471195664384 |
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| author | Jia Ju Jia Li Siyang Liu Haiqiang Zhang Jinjin Xu Yu Lin Ya Gao Yulin Zhou Xin Jin |
| author_facet | Jia Ju Jia Li Siyang Liu Haiqiang Zhang Jinjin Xu Yu Lin Ya Gao Yulin Zhou Xin Jin |
| author_sort | Jia Ju |
| collection | DOAJ |
| description | Abstract Cell-free fetal DNA fraction (FF) in maternal plasma is a key parameter affecting the performance of noninvasive prenatal testing (NIPT). Accurate quantitation of FF plays a pivotal role in these tests. However, there are few methods that could determine FF with high accuracy using shallow‐depth whole‐genome sequencing data. In this study, we hypothesized that the actual FF in maternal plasma should be proportional to the discrepancy rate between the observed genotypes and inferred genotypes based on the linkage disequilibrium rule in certain polymorphism sites. Based on this hypothesis, we developed a method named Linkage Disequilibrium information-based cell-free Fetal DNA Fraction (LDFF) to accurately quantify FF in maternal plasma. This method achieves a high performance and outperforms existing methods in the fetal DNA fraction estimation. As LDFF is a gender-independent method and developed on shallow-depth samples, it can be easily incorporated into routine NIPT test and may enhance the current NIPT performance. |
| first_indexed | 2024-12-19T17:57:14Z |
| format | Article |
| id | doaj.art-f1e4c69988e4495daab29bd108f24ecb |
| institution | Directory Open Access Journal |
| issn | 2056-7944 |
| language | English |
| last_indexed | 2024-12-19T17:57:14Z |
| publishDate | 2021-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Genomic Medicine |
| spelling | doaj.art-f1e4c69988e4495daab29bd108f24ecb2022-12-21T20:11:47ZengNature Portfolionpj Genomic Medicine2056-79442021-10-01611810.1038/s41525-021-00247-zEstimation of cell-free fetal DNA fraction from maternal plasma based on linkage disequilibrium informationJia Ju0Jia Li1Siyang Liu2Haiqiang Zhang3Jinjin Xu4Yu Lin5Ya Gao6Yulin Zhou7Xin Jin8College of Life Sciences, University of Chinese Academy of SciencesBGI-genomics, BGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenBGI-ShenzhenUnited Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine & School of Public Health, Xiamen UniversityBGI-ShenzhenAbstract Cell-free fetal DNA fraction (FF) in maternal plasma is a key parameter affecting the performance of noninvasive prenatal testing (NIPT). Accurate quantitation of FF plays a pivotal role in these tests. However, there are few methods that could determine FF with high accuracy using shallow‐depth whole‐genome sequencing data. In this study, we hypothesized that the actual FF in maternal plasma should be proportional to the discrepancy rate between the observed genotypes and inferred genotypes based on the linkage disequilibrium rule in certain polymorphism sites. Based on this hypothesis, we developed a method named Linkage Disequilibrium information-based cell-free Fetal DNA Fraction (LDFF) to accurately quantify FF in maternal plasma. This method achieves a high performance and outperforms existing methods in the fetal DNA fraction estimation. As LDFF is a gender-independent method and developed on shallow-depth samples, it can be easily incorporated into routine NIPT test and may enhance the current NIPT performance.https://doi.org/10.1038/s41525-021-00247-z |
| spellingShingle | Jia Ju Jia Li Siyang Liu Haiqiang Zhang Jinjin Xu Yu Lin Ya Gao Yulin Zhou Xin Jin Estimation of cell-free fetal DNA fraction from maternal plasma based on linkage disequilibrium information npj Genomic Medicine |
| title | Estimation of cell-free fetal DNA fraction from maternal plasma based on linkage disequilibrium information |
| title_full | Estimation of cell-free fetal DNA fraction from maternal plasma based on linkage disequilibrium information |
| title_fullStr | Estimation of cell-free fetal DNA fraction from maternal plasma based on linkage disequilibrium information |
| title_full_unstemmed | Estimation of cell-free fetal DNA fraction from maternal plasma based on linkage disequilibrium information |
| title_short | Estimation of cell-free fetal DNA fraction from maternal plasma based on linkage disequilibrium information |
| title_sort | estimation of cell free fetal dna fraction from maternal plasma based on linkage disequilibrium information |
| url | https://doi.org/10.1038/s41525-021-00247-z |
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