Jonatan Blais1, Sylvie Giroux2, André Caron2, Valérie Clément2, Alexandre Dionne-Laporte3, Loubna Jouan4, Julie Gauthier4, Tina MacLeod5, Richard Moore5, Jeremy Parker5, Lucas Swanson5, Yongjun Zhao5, Guy Rouleau3, Aly Karsan6, Sylvie Langlois7, François Rousseau8. 1. Service of Medical Biochemistry, Department of Medical Biology, CHU de Québec - Université Laval, Quebec, Canada; Department of Molecular Biology, Medical Biochemistry, and Pathology, Faculty of Medicine, Université Laval, Quebec, Canada; Human and Molecular Genetics Research Unit, Research Center, CHU de Québec, Quebec, Canada. Electronic address: Jonatan_blais@ssss.gouv.qc.ca. 2. Human and Molecular Genetics Research Unit, Research Center, CHU de Québec, Quebec, Canada. 3. Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada. 4. Molecular Diagnostic Laboratory and Division of Medical Genetics, CHU Sainte-Justine, Montreal, Quebec, Canada. 5. Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada. 6. Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, BC Cancer Agency, Vancouver, BC, Canada. 7. Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. 8. Service of Medical Biochemistry, Department of Medical Biology, CHU de Québec - Université Laval, Quebec, Canada; Department of Molecular Biology, Medical Biochemistry, and Pathology, Faculty of Medicine, Université Laval, Quebec, Canada; Human and Molecular Genetics Research Unit, Research Center, CHU de Québec, Quebec, Canada; PEGASUS, Quebec, Canada.
Abstract
OBJECTIVES: Non-invasive prenatal aneuploidy testing (NIPT) by next-generation sequencing of circulating cell-free DNA in maternal plasma relies on chromosomal ratio (chrratio) measurements to detect aneuploid values that depart from euploid ratios. Diagnostic performances are known to depend on the fraction of fetal DNA (FF) present in maternal plasma, although how this translates into specific quantitative changes in specificity/positive predictive values and which other variables might also be important is not well understood. DESIGN & METHODS: To explore this issue, theoretical relationships between FF and various measures of diagnostic performances were assessed for a range of parameter values. Empirical data from three NIPT assays were then used to validate theoretical calculations. RESULTS: For a given positivity threshold, dramatic changes in specificity and positive predictive values (PPV) as a function of both FF and the coefficient of variation (CV) of the chrratio measurement were observed. Theoretically predicted and observed chrratio z-scores agreed closely, confirming the determinant impact of small changes in both FF and chrratio CV. CONCLUSIONS: Evaluation of NIPT assay performances therefore requires knowledge of the FF distribution in the population in which the test is intended to be used and, in particular, of the precise value of the assay chrratio CV for each chromosome or genomic region of interest. Laboratories offering NIPT testing should carefully measure these parameters to ensure test reliability and clinical usefulness in interpreting individual patients' results.
OBJECTIVES: Non-invasive prenatal aneuploidy testing (NIPT) by next-generation sequencing of circulating cell-free DNA in maternal plasma relies on chromosomal ratio (chrratio) measurements to detect aneuploid values that depart from euploid ratios. Diagnostic performances are known to depend on the fraction of fetal DNA (FF) present in maternal plasma, although how this translates into specific quantitative changes in specificity/positive predictive values and which other variables might also be important is not well understood. DESIGN & METHODS: To explore this issue, theoretical relationships between FF and various measures of diagnostic performances were assessed for a range of parameter values. Empirical data from three NIPT assays were then used to validate theoretical calculations. RESULTS: For a given positivity threshold, dramatic changes in specificity and positive predictive values (PPV) as a function of both FF and the coefficient of variation (CV) of the chrratio measurement were observed. Theoretically predicted and observed chrratio z-scores agreed closely, confirming the determinant impact of small changes in both FF and chrratio CV. CONCLUSIONS: Evaluation of NIPT assay performances therefore requires knowledge of the FF distribution in the population in which the test is intended to be used and, in particular, of the precise value of the assay chrratio CV for each chromosome or genomic region of interest. Laboratories offering NIPT testing should carefully measure these parameters to ensure test reliability and clinical usefulness in interpreting individual patients' results.