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Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory

(2016) PRENATAL DIAGNOSIS. 36(8). p.699-707
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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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Chicago
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.
APA
Dheedene, A., Sante, T., De Smet, M., Vanbellinghen, J.-F., Grisart, B., Vergult, S., Janssens, S., et al. (2016). Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory. PRENATAL DIAGNOSIS, 36(8), 699–707.
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.
MLA
Dheedene, Annelies, Tom Sante, Matthias De Smet, et al. “Implementation of Non-invasive Prenatal Testing by Semiconductor Sequencing in a Genetic Laboratory.” PRENATAL DIAGNOSIS 36.8 (2016): 699–707. Print.
@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-Fran\c{c}ois and Grisart, Bernard and Vergult, Sarah and Janssens, Sandra and Menten, Bj{\"o}rn},
  isbn         = {0197-3851},
  journal      = {PRENATAL DIAGNOSIS},
  language     = {eng},
  number       = {8},
  pages        = {699--707},
  title        = {Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory},
  url          = {http://dx.doi.org/10.1002/pd.4841},
  volume       = {36},
  year         = {2016},
}

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