Molecular evaluation of foetuses with holoprosencephaly shows high incidence of microdeletions in the HPE genes

Hum Genet. 2006 Mar;119(1-2):1-8. doi: 10.1007/s00439-005-0097-6. Epub 2005 Dec 2.


Holoprosencephaly (HPE), the most common structural malformation of the forebrain in humans, can be detected early during pregnancy using prenatal ultrasonography . Among foetuses with a normal karyotype, 14% have mutations in the four main HPE genes (SHH, ZIC2, SIX3 and TGIF). Genomic rearrangements have now been implicated in many genetic diseases, so we hypothesized that microdeletions in the major HPE genes may also be common in HPE foetuses with severe phenotype or other associated malformations. We screened the DNA obtained from 94 HPE foetuses with a normal karyotype for the presence of microdeletions involving the four major HPE genes (SHH, ZIC2, SIX3 and TGIF). Thirteen of the foetuses had a point mutation in one of the 4 genes and 81 had no known mutations. Quantitative multiplex PCR of short fluorescent fragments (QMPSF) analysis was used for rapid determination of HPE genes copy numbers and the identified microdeletions were confirmed by real time quantitative PCR, or fluorescent in situ hybridization (FISH) (if a cell line was available). Microdeletions were detected in 8 of 94 foetuses (8.5%) (2 in SHH, 2 in SIX3, 3 in ZIC2 and 1 in TGIF genes), and only among the 81 foetuses with a normal karyotype and no point mutations. These data suggest that microdeletions in the four main HPE genes are a common cause of prenatal HPE, as well as point mutations, and increase the total diagnosis rate close to approximately 22.3% of foetuses with normal karyotype. Detection can be achieved by the QMPSF testing method that proved to be efficient for testing several genes in a single assay.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Deletion*
  • DNA / analysis
  • DNA / genetics
  • DNA / isolation & purification
  • DNA Mutational Analysis / methods
  • Eye Proteins / genetics
  • Female
  • Fetal Diseases / genetics*
  • Fetal Diseases / pathology
  • Hedgehog Proteins / genetics
  • Holoprosencephaly / genetics*
  • Holoprosencephaly / pathology
  • Homeodomain Proteins / genetics
  • Humans
  • In Situ Hybridization, Fluorescence
  • Mutation
  • Nerve Tissue Proteins / genetics
  • Nuclear Proteins
  • Polymerase Chain Reaction
  • Pregnancy
  • Prenatal Diagnosis
  • Repressor Proteins / genetics
  • Transcription Factors / genetics


  • Eye Proteins
  • Hedgehog Proteins
  • Homeodomain Proteins
  • Nerve Tissue Proteins
  • Nuclear Proteins
  • Repressor Proteins
  • SHH protein, human
  • Sine oculis homeobox homolog 3 protein
  • TGIF1 protein, human
  • Transcription Factors
  • ZIC2 protein, human
  • DNA

Associated data

  • RefSeq/NM_000193
  • RefSeq/NM_003244
  • RefSeq/NM_005413