Highly Sensitive Blocker Displacement Amplification and Droplet Digital PCR Reveal Low-Level Parental FOXF1 Somatic Mosaicism in Families with Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins

J Mol Diagn. 2020 Apr;22(4):447-456. doi: 10.1016/j.jmoldx.2019.12.007. Epub 2020 Feb 7.


Detection of low-level somatic mosaicism [alternate allele fraction (AAF) ≤ 10%] in parents of affected individuals with the apparent de novo pathogenic variants enables more accurate estimate of recurrence risk. To date, only a few systematic analyses of low-level parental somatic mosaicism have been performed. Herein, highly sensitive blocker displacement amplification, droplet digital PCR, quantitative PCR, long-range PCR, and array comparative genomic hybridization were applied in families with alveolar capillary dysplasia with misalignment of pulmonary veins. We screened 18 unrelated families with the FOXF1 variant previously determined to be apparent de novo (n = 14), of unknown parental origin (n = 1), or inherited from a parent suspected to be somatic and/or germline mosaic (n = 3). We identified four (22%) families with FOXF1 parental somatic mosaic single-nucleotide variants (n = 3) and copy number variant deletion (n = 1) detected in parental blood samples and an AAF ranging between 0.03% and 19%. In one family, mosaic allele ratio in tissues originating from three germ layers ranged between <0.03% and 0.65%. Because the ratio of parental somatic mosaicism have significant implications for the recurrence risk, this study further implies the importance of a systematic screening of parental samples for low-level and very-low-level (AAF ≤ 1%) somatic mosaicism using methods that are more sensitive than those routinely applied in diagnostics.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alleles
  • Amino Acid Substitution
  • DNA Copy Number Variations
  • DNA Mutational Analysis
  • Female
  • Forkhead Transcription Factors / genetics*
  • Genotype
  • Humans
  • Male
  • Mosaicism*
  • Pedigree
  • Persistent Fetal Circulation Syndrome / diagnosis*
  • Persistent Fetal Circulation Syndrome / genetics*
  • Polymorphism, Single Nucleotide
  • Pulmonary Alveoli / abnormalities*
  • Pulmonary Veins / abnormalities*
  • Real-Time Polymerase Chain Reaction


  • FOXF1 protein, human
  • Forkhead Transcription Factors

Supplementary concepts

  • Alveolar capillary dysplasia