Leiden University Scholarly Publications

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Oever, J.M.E. van den; Balkassmi, S.; Johansson, L.F.; Scheltema, P.N.A. van; Suijkerbuijk, R.F.; Hoffer, M.J.V.; ... ; Boon, E.M.J. (2013)

Successful Noninvasive Trisomy 18 Detection Using Single Molecule Sequencing

Article / Letter to editor
BACKGROUND: Noninvasive trisomy 21 detection performed by use of massively parallel sequencing is achievable with high diagnostic sensitivity and low false-positive rates. Detection of fetal trisomy 18 and 13 has been reported as well but seems to be less accurate with the use of this approach. The reduced accuracy can be explained by PCR-introduced guanine-cytosine (GC) bias influencing sequencing data. Previously, we demonstrated that sequence data generated by single molecule sequencing show virtually no GC bias and result in a more pronounced noninvasive detection of fetal trisomy 21. In this study, single molecule sequencing was used for noninvasive detection of trisomy 18 and 13.METHODS: Single molecule sequencing was performed on the Helicos platform with free DNA isolated from maternal plasma from 11 weeks of gestation onward (n = 17). Relative sequence tag density ratios were calculated against male control plasma samples and results were compared to those of previous...Show moreBACKGROUND: Noninvasive trisomy 21 detection performed by use of massively parallel sequencing is achievable with high diagnostic sensitivity and low false-positive rates. Detection of fetal trisomy 18 and 13 has been reported as well but seems to be less accurate with the use of this approach. The reduced accuracy can be explained by PCR-introduced guanine-cytosine (GC) bias influencing sequencing data. Previously, we demonstrated that sequence data generated by single molecule sequencing show virtually no GC bias and result in a more pronounced noninvasive detection of fetal trisomy 21. In this study, single molecule sequencing was used for noninvasive detection of trisomy 18 and 13.METHODS: Single molecule sequencing was performed on the Helicos platform with free DNA isolated from maternal plasma from 11 weeks of gestation onward (n = 17). Relative sequence tag density ratios were calculated against male control plasma samples and results were compared to those of previous karyotyping.RESULTS: All trisomy 18 fetuses were identified correctly with a diagnostic sensitivity and specificity of 100%. However, low diagnostic sensitivity and specificity were observed for fetal trisomy 13 detection.CONCLUSIONS: We successfully applied single molecule sequencing in combination with relative sequence tag density calculations for noninvasive trisomy 18 detection using free DNA from maternal plasma. However, noninvasive trisomy 13 detection was not accurate and seemed to be influenced by more than just GC content.Show less
All authors
Oever, J.M.E. van den; Balkassmi, S.; Johansson, L.F.; Scheltema, P.N.A. van; Suijkerbuijk, R.F.; Hoffer, M.J.V.; Sinke, R.J.; Bakker, E.; Sikkema-Raddatz, B.; Boon, E.M.J.
Date
2013-01-11
Journal
Clinical Chemistry
DOI
doi:10.1373/clinchem.2012.196212