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. 2018 Jun 7:2018:9498140.
doi: 10.1155/2018/9498140. eCollection 2018.

Noninvasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield

Irene Gómez-Manjón  1 , Ana Moreno-Izquierdo  1   2 , Sonia Mayo  1 , Marta Moreno-García  1   2 , Aitor Delmiro  3   4 , David Escribano  5 , F Javier Fernández-Martínez  1   2
Affiliations

Noninvasive Prenatal Testing: Comparison of Two Mappers and Influence in the Diagnostic Yield

Irene Gómez-Manjón et al. Biomed Res Int. .

Abstract

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.

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Figures

Figure 1
Figure 1
Results of NIPT for common aneuploidies using maternal plasma DNA by massively parallel Bioconductor sequencing.
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