Genomic Imbalances in the Placenta Contribute to Poor Fetal Growth

Background: Fetal growth restriction (FGR) is associated with increased risks for complications before, during, and after birth, in addition to risk of disease through to adulthood. Although placental insufficiency, failure to supply the fetus with adequate nutrients, underlies most cases of FGR, its causes are diverse and not fully understood. One of the few diagnosable causes of placental insufficiency in ongoing pregnancies is the presence of large chromosomal imbalances such as trisomy confined to the placenta; however, the impact of smaller copy number variants (CNVs) has not yet been adequately addressed. In this study, we comprehensively evaluate the contribution of both placental aneuploidy and CNVs to fetal growth. Methods: We used molecular-cytogenetic approaches to identify aneuploidy in placentas from N=101 infants born small-for-gestational age (SGA), typically used as a surrogate for FGR, and from N=173 non-SGA controls from uncomplicated pregnancies. We confirmed aneuploidies and assessed mosaicism by microsatellite genotyping. We then profiled CNVs using high-resolution microarrays in a subset of N=53 SGA and N=61 control euploid placentas, and compared the load, impact, gene enrichment and clinical relevance of CNVs between groups. Candidate CNVs were confirmed using quantitative PCR.Results: Aneuploidy was over 10-fold more frequent in SGA-associated placentas compared to controls (11.9% vs. 1.1%; p=0.0002, OR=11.4), was confined to the placenta, and typically involved autosomes, whereas only sex chromosome abnormalities were observed in controls. We found no significant difference in CNV load or number of placental-expressed or imprinted genes in CNVs between SGA and controls, however, a rare and likely clinically-relevant germline CNV was identified in 5.7% of SGA cases. These CNVs involved candidate genes INHBB, HSD11B2, CTCF, and CSMD3. Conclusions: We conclude that placental genomic imbalances at the cytogenetic and submicroscopic level may underlie up to ~18% of SGA cases in our population. This work contributes to the understanding of the underlying causes of placental insufficiency and FGR, which is important for counselling and prediction of long term outcomes for affected cases.