Risks and Recommendations in Prenatally Detected De Novo Balanced Chromosomal Rearrangements from Assessment of Long-Term Outcomes

Christina Halgren, Nete M Nielsen, Lusine Nazaryan-Petersen, Asli Silahtaroglu, Ryan L Collins, Chelsea Lowther, Susanne Kjaergaard, Morten Frisch, Maria Kirchhoff, Karen Brøndum-Nielsen, Allan Lind-Thomsen, Yuan Mang, Zahra El-Schich, Claire A Boring, Mana M Mehrjouy, Peter K A Jensen, Christina Fagerberg, Lotte N Krogh, Jan Hansen, Thue BryndorfClaus Hansen, Michael E Talkowski, Mads Bak, Niels Tommerup, Iben Bache

25 Citations (Scopus)


The 6%-9% risk of an untoward outcome previously established by Warburton for prenatally detected de novo balanced chromosomal rearrangements (BCRs) does not account for long-term morbidity. We performed long-term follow-up (mean 17 years) of a registry-based nationwide cohort of 41 individuals carrying a prenatally detected de novo BCR with normal first trimester screening/ultrasound scan. We observed a significantly higher frequency of neurodevelopmental and/or neuropsychiatric disorders than in a matched control group (19.5% versus 8.3%, p = 0.04), which was increased to 26.8% upon clinical follow-up. Chromosomal microarray of 32 carriers revealed no pathogenic imbalances, illustrating a low prognostic value when fetal ultrasound scan is normal. In contrast, mate-pair sequencing revealed disrupted genes (ARID1B, NPAS3, CELF4), regulatory domains of known developmental genes (ZEB2, HOXC), and complex BCRs associated with adverse outcomes. Seven unmappable autosomal-autosomal BCRs with breakpoints involving pericentromeric/heterochromatic regions may represent a low-risk group. We performed independent phenotype-aware and blinded interpretation, which accurately predicted benign outcomes (specificity = 100%) but demonstrated relatively low sensitivity for prediction of the clinical outcome in affected carriers (sensitivity = 45%-55%). This sensitivity emphasizes the challenges associated with prenatal risk prediction for long-term morbidity in the absence of phenotypic data given the still immature annotation of the morbidity genome and poorly understood long-range regulatory mechanisms. In conclusion, we upwardly revise the previous estimates of Warburton to a morbidity risk of 27% and recommend sequencing of the chromosomal breakpoints as the first-tier diagnostic test in pregnancies with a de novo BCR.

Original languageEnglish
JournalAmerican Journal of Human Genetics
Issue number6
Pages (from-to)1090-1103
Number of pages14
Publication statusPublished - 7 Jun 2018


  • Chromosome Aberrations
  • Chromosome Breakpoints
  • Cohort Studies
  • Conserved Sequence/genetics
  • Evolution, Molecular
  • Female
  • Genome, Human
  • Humans
  • Karyotyping
  • Pregnancy
  • Prenatal Diagnosis/methods
  • RNA, Long Noncoding/genetics
  • Risk Factors
  • Sequence Analysis, DNA
  • Time Factors


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