Noninvasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield
Objective. The aim of this study was to determine if the use of different mappers for NIPT may vary the results considerably. Methods. Peripheral blood was collected from 217 pregnant women, 58 pathological (34 pregnancies with trisomy 21, 18 with trisomy 18, and 6 with trisomy 13) and 159 euploid....
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doaj-fdd68f1c043a4e13b6dafae32c038c752020-11-24T21:04:44ZengHindawi LimitedBioMed Research International2314-61332314-61412018-01-01201810.1155/2018/94981409498140Noninvasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic YieldIrene Gómez-Manjón0Ana Moreno-Izquierdo1Sonia Mayo2Marta Moreno-García3Aitor Delmiro4David Escribano5F. Javier Fernández-Martínez6Genetics and Inheritance Research Group, Instituto de Investigación Hospital Universitario 12 de Octubre (i+12), Avda. de Córdoba s/n, Madrid 28041, SpainGenetics and Inheritance Research Group, Instituto de Investigación Hospital Universitario 12 de Octubre (i+12), Avda. de Córdoba s/n, Madrid 28041, SpainGenetics and Inheritance Research Group, Instituto de Investigación Hospital Universitario 12 de Octubre (i+12), Avda. de Córdoba s/n, Madrid 28041, SpainGenetics and Inheritance Research Group, Instituto de Investigación Hospital Universitario 12 de Octubre (i+12), Avda. de Córdoba s/n, Madrid 28041, SpainDepartment of Biochemistry, Hospital Universitario 12 de Octubre, Avda. de Córdoba s/n, Madrid 28041, SpainFetal Medicine Unit, Department of Obstetrics and Gynaecology, Hospital Universitario 12 de Octubre, Avda. de Córdoba s/n, Madrid 28041, SpainGenetics and Inheritance Research Group, Instituto de Investigación Hospital Universitario 12 de Octubre (i+12), Avda. de Córdoba s/n, Madrid 28041, SpainObjective. The aim of this study was to determine if the use of different mappers for NIPT may vary the results considerably. Methods. Peripheral blood was collected from 217 pregnant women, 58 pathological (34 pregnancies with trisomy 21, 18 with trisomy 18, and 6 with trisomy 13) and 159 euploid. MPS was performed following a manufacturer’s modified protocol of semiconductor sequencing. Obtained reads were mapped with two different software programs: TMAP and HPG-Aligner, comparing the results. Results. Using TMAP, 57 pathological samples were correctly detected (sensitivity 98.28%, specificity 93.08%): 33 samples as trisomy 21 (sensitivity 97.06%, specificity 99.45%), 16 as trisomy 18 (sensibility 88.89%, specificity 93.97%), and 6 as trisomy 13 (sensibility 100%, specificity 100%). 11 false positives, 1 false negative, and 2 samples incorrectly identified were obtained. Using HPG-Aligner, all the 58 pathological samples were correctly identified (sensibility 100%, specificity 96.86%): 34 as trisomy 21 (sensibility 100%, specificity 98.91%), 18 as trisomy 18 (sensibility 100%, specificity 98.99%), and 6 as trisomy 13 (sensibility 100%, specificity 99.53%). 5 false positives were obtained. Conclusion. Different mappers use slightly different algorithms, so the use of one mapper or another with the same batch file can provide different results.http://dx.doi.org/10.1155/2018/9498140 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Irene Gómez-Manjón Ana Moreno-Izquierdo Sonia Mayo Marta Moreno-García Aitor Delmiro David Escribano F. Javier Fernández-Martínez |
spellingShingle |
Irene Gómez-Manjón Ana Moreno-Izquierdo Sonia Mayo Marta Moreno-García Aitor Delmiro David Escribano F. Javier Fernández-Martínez Noninvasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield BioMed Research International |
author_facet |
Irene Gómez-Manjón Ana Moreno-Izquierdo Sonia Mayo Marta Moreno-García Aitor Delmiro David Escribano F. Javier Fernández-Martínez |
author_sort |
Irene Gómez-Manjón |
title |
Noninvasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield |
title_short |
Noninvasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield |
title_full |
Noninvasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield |
title_fullStr |
Noninvasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield |
title_full_unstemmed |
Noninvasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield |
title_sort |
noninvasive prenatal testing: comparison of two mappers and influence in the diagnostic yield |
publisher |
Hindawi Limited |
series |
BioMed Research International |
issn |
2314-6133 2314-6141 |
publishDate |
2018-01-01 |
description |
Objective. The aim of this study was to determine if the use of different mappers for NIPT may vary the results considerably. Methods. Peripheral blood was collected from 217 pregnant women, 58 pathological (34 pregnancies with trisomy 21, 18 with trisomy 18, and 6 with trisomy 13) and 159 euploid. MPS was performed following a manufacturer’s modified protocol of semiconductor sequencing. Obtained reads were mapped with two different software programs: TMAP and HPG-Aligner, comparing the results. Results. Using TMAP, 57 pathological samples were correctly detected (sensitivity 98.28%, specificity 93.08%): 33 samples as trisomy 21 (sensitivity 97.06%, specificity 99.45%), 16 as trisomy 18 (sensibility 88.89%, specificity 93.97%), and 6 as trisomy 13 (sensibility 100%, specificity 100%). 11 false positives, 1 false negative, and 2 samples incorrectly identified were obtained. Using HPG-Aligner, all the 58 pathological samples were correctly identified (sensibility 100%, specificity 96.86%): 34 as trisomy 21 (sensibility 100%, specificity 98.91%), 18 as trisomy 18 (sensibility 100%, specificity 98.99%), and 6 as trisomy 13 (sensibility 100%, specificity 99.53%). 5 false positives were obtained. Conclusion. Different mappers use slightly different algorithms, so the use of one mapper or another with the same batch file can provide different results. |
url |
http://dx.doi.org/10.1155/2018/9498140 |
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