title: Multicolour FISH and quantitative PCR can detect submicroscopic deletions in holoprosencephaly patients with a normal karyotype.
abstract: Holoprosencephaly (HPE) is the most common structural malformation of the developing forebrain. At birth, nearly 50% of children with HPE have cytogenetic anomalies. Approximately 20% of infants with normal chromosomes have sequence mutations in one of the four main HPE genes (SHH, ZIC2, SIX3, and TGIF). The other non-syndromic forms of HPE may be due to environmental factors or mutations in other genes, or potentially due to submicroscopic deletions of HPE genes. We used two complementary assays to test for HPE associated submicroscopic deletions. Firstly, we developed a multicolour fluorescent in situ hybridisation (FISH) assay using probes for the four major HPE genes and for two candidate genes (DISP1 and FOXA2). We analysed lymphoblastoid cell lines (LCL) from 103 patients who had CNS findings of HPE, normal karyotypes, and no point mutations, and found seven microdeletions. We subsequently applied quantitative PCR to 424 HPE DNA samples, including the 103 samples studied by FISH: 339 with CNS findings of HPE, and 85 with normal CNS and characteristic HPE facial findings. Microdeletions for either SHH, ZIC2, SIX3, or TGIF were found in 16 of the 339 severe HPE cases (that is, with CNS findings; 4.7%). In contrast, no microdeletion was found in the 85 patients at the mildest end of the HPE spectrum. Based on our data, microdeletion testing should be considered as part of an evaluation of holoprosencephaly, especially in severe HPE cases.
authors.affiliation: Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, 35 Convent Drive, MSC 3717, Building 35, Room 1B-203, Bethesda, MD 20892-3717, USA.
authors.forename: C
authors.initials: C
authors.lastname: Bendavid
authors.forename: B R
authors.initials: BR
authors.lastname: Haddad
authors.forename: A
authors.initials: A
authors.lastname: Griffin
authors.forename: M
authors.initials: M
authors.lastname: Huizing
authors.forename: C
authors.initials: C
authors.lastname: Dubourg
authors.forename: I
authors.initials: I
authors.lastname: Gicquel
authors.forename: L R
authors.initials: LR
authors.lastname: Cavalli
authors.forename: L
authors.initials: L
authors.lastname: Pasquier
authors.forename: A L
authors.initials: AL
authors.lastname: Shanske
authors.forename: R
authors.initials: R
authors.lastname: Long
authors.forename: M
authors.initials: M
authors.lastname: Ouspenskaia
authors.forename: S
authors.initials: S
authors.lastname: Odent
authors.forename: F
authors.initials: F
authors.lastname: Lacbawan
authors.forename: V
authors.initials: V
authors.lastname: David
authors.forename: M
authors.initials: M
authors.lastname: Muenke
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D005136:Eye Proteins / Q000235:genetics; D005820:Genetic Testing; D053823:Hedgehog Proteins; D051542:Hepatocyte Nuclear Factor 3-beta / Q000235:genetics; D016142:Holoprosencephaly / Q000175:diagnosis / Q000235:genetics*; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D007621:Karyotyping; D009419:Nerve Tissue Proteins / Q000235:genetics; D009687:Nuclear Proteins; D016133:Polymerase Chain Reaction; D012097:Repressor Proteins / Q000235:genetics; D017384:Sequence Deletion; D015534:Trans-Activators / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D000097607:Homeobox Protein SIX3
chemical_list: D005136:Eye Proteins; D053823:Hedgehog Proteins; D051542:Hepatocyte Nuclear Factor 3-beta; D018398:Homeodomain Proteins; D009419:Nerve Tissue Proteins; D009687:Nuclear Proteins; D012097:Repressor Proteins; D015534:Trans-Activators; D014157:Transcription Factors; D000097607:Homeobox Protein SIX3; C496502:FOXA2 protein, human; C509239:SHH protein, human; C097504:TGIF1 protein, human; C491812:ZIC2 protein, human