Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory
- Author
- Annelies Dheedene (UGent) , Tom Sante (UGent) , Matthias De Smet (UGent) , Jean-François Vanbellinghen, Bernard Grisart, Sarah Vergult (UGent) , Sandra Janssens (UGent) and Björn Menten (UGent)
- Organization
- Abstract
- Objectives: To implement non-invasive prenatal testing (NIPT) for fetal aneuploidies with semiconductor sequencing in an academic cytogenomic laboratory and to evaluate the first 15-month experience on clinical samples. Methods: We validated a NIPT protocol for cell-free fetal DNA sequencing from maternal plasma for the detection of trisomy 13, 18 and 21 on a semiconductor sequencing instrument. Fetal DNA fraction calculation for all samples and several quality parameters were implemented in the workflow. One thousand eighty-one clinical NIPT samples were analysed, following the described protocol. Results: Non-invasive prenatal testing was successfully implemented and validated on 201 normal and 74 aneuploid samples. From 1081 clinical samples, 17 samples showed an abnormal result: 14 trisomy 21 samples, one trisomy 18 and one trisomy 16 were detected. Also a maternal copy number variation on chromosome 13 was observed, which could potentially lead to a false positive trisomy 13 result. One sex discordant result was reported, possibly attributable to a vanishing twin. Moreover, our combined fetal fraction calculation enabled a more reliable risk estimate for trisomy 13, 18 and 21. Conclusions: Non-invasive prenatal testing for trisomy 21, 18 and 13 has a very high specificity and sensitivity. Because of several biological phenomena, diagnostic invasive confirmation of abnormal results remains required.
- Keywords
- CELL-FREE DNA, COPY-NUMBER VARIATION, MATERNAL PLASMA, FETAL ANEUPLOIDY, TRISOMY 16, SUBCHROMOSOMAL ABNORMALITIES, SIZE DISTRIBUTIONS, DIAGNOSIS, PERFORMANCE, ABERRATIONS
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-8515850
- MLA
- Dheedene, Annelies, et al. “Implementation of Non-Invasive Prenatal Testing by Semiconductor Sequencing in a Genetic Laboratory.” PRENATAL DIAGNOSIS, vol. 36, no. 8, 2016, pp. 699–707, doi:10.1002/pd.4841.
- APA
- Dheedene, A., Sante, T., De Smet, M., Vanbellinghen, J.-F., Grisart, B., Vergult, S., … Menten, B. (2016). Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory. PRENATAL DIAGNOSIS, 36(8), 699–707. https://doi.org/10.1002/pd.4841
- Chicago author-date
- Dheedene, Annelies, Tom Sante, Matthias De Smet, Jean-François Vanbellinghen, Bernard Grisart, Sarah Vergult, Sandra Janssens, and Björn Menten. 2016. “Implementation of Non-Invasive Prenatal Testing by Semiconductor Sequencing in a Genetic Laboratory.” PRENATAL DIAGNOSIS 36 (8): 699–707. https://doi.org/10.1002/pd.4841.
- Chicago author-date (all authors)
- Dheedene, Annelies, Tom Sante, Matthias De Smet, Jean-François Vanbellinghen, Bernard Grisart, Sarah Vergult, Sandra Janssens, and Björn Menten. 2016. “Implementation of Non-Invasive Prenatal Testing by Semiconductor Sequencing in a Genetic Laboratory.” PRENATAL DIAGNOSIS 36 (8): 699–707. doi:10.1002/pd.4841.
- Vancouver
- 1.Dheedene A, Sante T, De Smet M, Vanbellinghen J-F, Grisart B, Vergult S, et al. Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory. PRENATAL DIAGNOSIS. 2016;36(8):699–707.
- IEEE
- [1]A. Dheedene et al., “Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory,” PRENATAL DIAGNOSIS, vol. 36, no. 8, pp. 699–707, 2016.
@article{8515850,
abstract = {{Objectives: To implement non-invasive prenatal testing (NIPT) for fetal aneuploidies with semiconductor sequencing in an academic cytogenomic laboratory and to evaluate the first 15-month experience on clinical samples.
Methods: We validated a NIPT protocol for cell-free fetal DNA sequencing from maternal plasma for the detection of trisomy 13, 18 and 21 on a semiconductor sequencing instrument. Fetal DNA fraction calculation for all samples and several quality parameters were implemented in the workflow. One thousand eighty-one clinical NIPT samples were analysed, following the described protocol.
Results: Non-invasive prenatal testing was successfully implemented and validated on 201 normal and 74 aneuploid samples. From 1081 clinical samples, 17 samples showed an abnormal result: 14 trisomy 21 samples, one trisomy 18 and one trisomy 16 were detected. Also a maternal copy number variation on chromosome 13 was observed, which could potentially lead to a false positive trisomy 13 result. One sex discordant result was reported, possibly attributable to a vanishing twin. Moreover, our combined fetal fraction calculation enabled a more reliable risk estimate for trisomy 13, 18 and 21.
Conclusions: Non-invasive prenatal testing for trisomy 21, 18 and 13 has a very high specificity and sensitivity. Because of several biological phenomena, diagnostic invasive confirmation of abnormal results remains required.}},
author = {{Dheedene, Annelies and Sante, Tom and De Smet, Matthias and Vanbellinghen, Jean-François and Grisart, Bernard and Vergult, Sarah and Janssens, Sandra and Menten, Björn}},
issn = {{0197-3851}},
journal = {{PRENATAL DIAGNOSIS}},
keywords = {{CELL-FREE DNA,COPY-NUMBER VARIATION,MATERNAL PLASMA,FETAL ANEUPLOIDY,TRISOMY 16,SUBCHROMOSOMAL ABNORMALITIES,SIZE DISTRIBUTIONS,DIAGNOSIS,PERFORMANCE,ABERRATIONS}},
language = {{eng}},
number = {{8}},
pages = {{699--707}},
title = {{Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory}},
url = {{http://doi.org/10.1002/pd.4841}},
volume = {{36}},
year = {{2016}},
}
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