2.5. Classification of GIPSeq results as suggestive of an occult malignancy

For classification of a GIPSeq result as suggestive of an underlying maternal malignancy, we applied the same QS, z- and zz-parameters as being used for routine NIPT analysis, in combination with a visual inspection of the GIPSeq profile. In particular, two types of GIPSeq profiles were flagged as being reminiscent of cancer-related CNAs (Fig. 1). First, since chromosomal instability, including whole chromosome (arm) gains and losses, is a hallmark of tumorigenesis [19], a non-interpretable NIPT result was classified as being suggestive of an underlying maternal malignancy when QS≥2·0 and genome-wide (sub)chromosomal gains and/or losses were present. For cases for whom a technical problem could not be ruled out as a potential cause of the aberrant GIPSeq profile, a second NIPT on an independent blood sample was performed. When GIPseq profiling of the second blood sample reproduced the CNAs found in the first sample, classification of the GIPSeq profile as suggestive of an occult malignancy was reinforced. Second, given that trisomy 8 as a sole change is one of the most frequent numerical aberrations in myeloid malignancies [20], an interpretable NIPT (i.e. a GIPSeq profile with an interpretable call for chromosomes 13, 18 and 21) in combination with a single gain of chromosome 8 (i.e. z- and zz-score≥3·0) was also flagged for follow-up. Where possible, amniocentesis and Fluorescent In Situ Hybridization (FISH) on maternal peripheral blood was done to assess whether the observed trisomy 8 was either from fetal or from maternal origin, respectively. Upon confirmation of a maternal origin of the observed trisomy 8, these GIPSeq profiles were also classified as being suggestive of a maternal cancer. In particular, for these cases a maternal hematological malignancy was suspected. When neither a foetal nor maternal origin of the observed trisomy 8 was found, postpartum analysis of placental tissue was done to examine whether the aberrant GIPSeq result reflected a confined placental mosaicism of trisomy 8.

Diagram representing the clinical specialties and cross-talk between the different units necessary to ensure efficient management of aberrant NIPT outcomes that are suggestive for an occult maternal malignancy. *interpretable NIPT result refers to a GIPSeq profile where quality standards are met in combination with an interpretable chromosome 21, 18 and 13 call, which is being communicated to the patient. **A non-interpretable NIPT result refers to a GIPSeq profile that does not allow a reliable estimation of the risk of fetal trisomy 13, 18, and 21 due to low fetal fraction or deviating quality parameters (QS-, z- or zz-scores). aCGH, array comparative genomic hybridization; FISH, fluorescent in situ hybridization; WB-DWI/MRI Whole-body Diffusion Weighted MRI.