Comprehensive genome-wide analysis of routine non-invasive test data allows cancer prediction: A single-center retrospective analysis of over 85,000 pregnancies

Abstract

Background: Implausible false positive results in non-invasive prenatal testing (NIPT) have been occasionally associated with the detection of occult maternal malignancies. Hence, there is a need for approaches allowing accurate prediction of whether the NIPT result is pointing to an underlying malignancy, as well as for organized programs ensuring efficient downstream clinical management of these cases.

Methods: Using a data set of 88,294 NIPT performed at University Hospital Leuven (Belgium) between November 2013 and March 2020, we retrospectively evaluated the positive predictive value (PPV) of our NIPT approach for cancer detection. In this approach, whole-genome cell-free DNA (cfDNA) data from NIPT were scrutinized for the presence of (sub)chromosomal copy number alterations (CNAs) predictive for a malignancy, using an unbiased NIPT analysis pipeline coined GIPSeq. For suspected cases, the presence of a maternal cancer was evaluated via subsequent multidisciplinary clinical follow-up examinations. The cancer-specificity of the identified CNAs in cfDNA was assessed through genetic analyses of a tumor biopsy.

Findings: Fifteen women without a cancer history were identified with a GIPSeq result suggestive of a malignant process. Their cfDNA profiles showed either genome-wide aberrations or a single trisomy 8. Upon clinical examinations, a solid or hematological cancer was identified in 4 and 7 cases, respectively. Three women were identified as having a clonal mosaicism. For one case no underlying condition was found. These numbers add to a PPV of 73%. Based on this experience, we presented a multidisciplinary care path for efficient clinical management of these cases.

Interpretation: The presented approach for analysing NIPT results has a high PPV, yet unknown sensitivity, for detecting asymptomatic malignancies upon routine NIPT. Given the complexity of diagnosing a pregnant woman with cancer, clinical follow-up should occur in a well-designed multidisciplinary setting, such as via the care model that we presented here.

Funding: This work was supported by Research Foundation Flanders and KU Leuven funding.

Keywords: Cancer detection; Clinical follow-up; Non-invasive prenatal testing.

Fig. 1

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.

Fig. 2

Results from routine NIPT testing performed in University Hospitals Leuven between November 2013 and March 2020.

Fig. 3

A. Chromosomal aberrations observed in plasma cfDNA of asymptomatic pregnant cases with GIPSeq profiles suggestive of cancer. Cases are those listed in Table 1. Where possible, plotting was based on the GIPseq results of the first plasma sample of each case, showing chromosomal anomalies with a z-score≥3.0 (suggesting gain; in green) or ≤3.0 (suggesting loss; in red). Chromosomal regions with clear reproducible gains and losses, resulting in a neutral z-score are displayed as well. For n = 13 cases with no a priori known cancer diagnosis, genome-wide chromosomal aberrations were observed in cfDNA, resulting in QS≥2.0. For some of these cases, high z-scores for almost every chromosome were observed. This indicates that either all chromosomes are indeed affected, or the z-scores of particular individual chromosomes or chromosomal fragments might be skewed due to excessive presentation of other, highly amplified chromosomes or chromosome arms. Two cases presented with a single chromosomal gain of chromosome 8 (z- and zz-scores ≥3•0). Finally, for one case (case ID-2) the GIPSeq profile showed (segmental) gains on multiple chromosomes, but this profile was not classified as suggestive of an occult malignancy because of a QS<2.0. For every case, the genomic representation profile of the autosomal chromosomes is shown in clockwise order, aligned with chromosomal ideograms (outer circle). Cases are shown from the periphery to the center in ascending order from ID-1 to ID-16. B. Pie chart displaying the numbers and types of cancers and premalignant conditions identified in pregnant women undergoing routine NIPT testing in our University Hospital and with a GIPSeq profile suggestive of cancer. Eight hematological malignancies were identified, namely 3 classical Hodgkin lymphomas (type nodular sclerosis Hodgkin lymphoma; stages II, II and IV), 3 non-Hodgkin lymphomas (type primary mediastinal B-cell lymphoma, stage I; follicular lymphoma, stage III; diffuse large B-cell lymphoma, stage II), 1 acute myeloid leukemia (stage M5), 1 multiple myeloma (type light chain lambda). Four pregnant women were diagnosed with a solid cancer type, namely 2 breast cancers (invasive breast carcinoma of no special type, hormone receptor positive, stage II and stage IV), 1 osteosarcoma (conventional high-grade osteosarcoma, stage III) and 1 ovarian cancer (high grade serous ovarian carcinoma, stage IV). Three cases were diagnosed with a clonal mosaicism. Finally, for one case, no disease was identified.

Fig. 4

Molecular analyses in tumor biopsies of two pregnant women for whom a cancer diagnosis was made upon aberrant routine NIPT testing. A, Circos plots of matched cfDNA:tumor DNA samples of pregnant case ID-16 who was diagnosed with a stage IV breast cancer. Plotting was done similarly as for Fig. 2. The outer circle shows the copy number profile of genomic tumor DNA extracted from tumor biopsy (whole-genome low-pass sequencing, 0.1x coverage). The inner circle depicts the matched genome-wide GIPSeq profile in plasma cfDNA (NIPT sample), showing high congruency with aberrancies observed in most of the chromosomes in tumor DNA. Inconsistencies, noticed on some chromosomes, might be explained by the metastatic status of the tumor with potential presence of additional circulating subclones. B, Pregnant woman ID-13 was diagnosed with a diffuse large B-cell non-Hodgkin lymphoma upon aberrant GIPSeq profiling. FISH, performed on a lymph node biopsy, confirmed the tumor origin of specific copy number gains and losses observed in cfDNA, namely tri-/tetrasomy of the region 8q24/MYC and of the centromeric region of chromosome 8 in 20% of nuclei {LSI MYC (spectrum orange/green)  [8q24,Vysis]/ CEP 8 (spectrum aqua)  [8p11.1-q11.1,Vysis]}, trisomy 12 in 60% of nuclei {XCE11 (spectrum orange)  [Metasystems] + LSI CEP 12 (spectrum green)  [12p11.1-q11, Vysis]} and monoallelic loss of the region 17p13/TP53 with disomy of the centromeric region of chromosome 17 in 80% of nuclei {XL TP53 (spectrum orange) /17cen (spectrum green) [17p13/17cen, Metasystems]}.