Genetics of Charge

The CHARGE association (OMIM 214800) refers to a nonrandom pattern of congenital anomalies, most notably coloboma, heart defects, choanal atresia, retarded growth and development and/or CNS abnormalities, genital anomalies and ear anomalies or deafness. It has a birth incidence of about 1:12,000. Most cases occur sporadically, although there is some evidence of a genetic component, ie, rare reports of familial cases and cytogenetic abnormalities. Attempts to identify the genetic component have been unsuccessful to date including sequencing suspected candidate genes PAX2 and PITX2 and conventional comparative genomic hybridization (CGH).

CGH involves hybridizing genomic DNA from a test patient and from a reference (normal) individual to fragments of DNA arrayed so that they correspond to ordered segments of chromosomes. CGH reveals DNA sequence that is present in greater or lesser amounts than normal and maps its chromosomal location, thereby allowing detection of submicroscopic deletions, insertions and gene amplifications. The use of smaller and smaller DNA fragments and chip technology to array the fragments and analyze hybridization has made high-throughput, high-resolution, genome-wide screening for submicroscopic copy number changes possible.^1,2 Vissers and co-workers have utilized this approach to identify mutations responsible for the CHARGE association.

The investigators co-hybridized genomic DNA from 2 patients with CHARGE and reference DNA onto a genome-wide BAC (bacterial artificial chromosome) array with 1 Mb resolution. The CGH profile of one of the patients revealed a deletion of ~5 Mb that mapped to chromosome 8q12. DNA from this patient was then hybridized to a more precise array of 918 overlapping BAC clones corresponding to a linear representation of chromosome 8. The results showed deletion of 31 overlapping BAC clones spanning 4.8 Mb of chromosome 8q12.

The authors next confirmed 2 microdeletions in a patient with CHARGE association previously reported with a balanced chromosome 8 translocation. Comparing DNA from the 2 patients with microdeletions, they narrowed the region of deletion overlap to 2.3 Mb and screened 17 patients with CHARGE association for similar deletions. None were detected. However, when they sequenced the coding regions and intron-exon boundaries of the 9 genes thought to reside in or adjacent to the critical 2.3 Mb region, they detected 10 heterozygous mutations in one of the resident genes – CHD7. Seven of the mutations were stop codon mutation predicted to cause loss of function leading the authors to conclude that CHARGE association results from haploinsufficiency of CHD7.

CHD7 encodes a member of the chromodomain helicase DNA-binding proteins. They are believed to have important roles in modulating chromatin structure and regulating gene expression during early development.

First Editor’s Comment: This paper is informative not only because it identifies the genetic basis of the CHARGE association, but it validates the use of high-throughput, high-resolution CGH to screen for submicroscopic changes in gene copy number in infants with sporadic malformation syndromes. As the technology becomes widely available it will likely become a valuable diagnostic tool for the clinical geneticist/dysmorphologist.

Second Editor’s Comment: Within the structure of the chromodomain helicase DNA-binding protein superfamily are 2 amino acid sequences or domains shared by its members - a "chromo (chromatin organization modifier) domain" and an SNF2-related helicase/ATPase domain (OMIM 602118). These proteins alter gene expression by modifying chromatin structure, thereby altering access of transcription factors to their gene targets. With the identification of a specific gene defect in patients with the cited association of structural anomalies (CHARGE), the disorder may now be referred to as the CHARGE syndrome. For their studies, the investigators employed an optimized, high resolution "array comparative genomic hybridization" assay that may be applicable to the study of other patients with sporadic multi-malformation syndromes.

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Table of Contents 21-1 Genetics of Charge
Volume 21, Issue 1, March 2005 © 2005 Prime Health Consultants, Inc.

The CHARGE association (OMIM 214800) refers to a nonrandom pattern of congenital anomalies, most notably coloboma, heart defects, choanal atresia, retarded growth and development and/or CNS abnormalities, genital anomalies and ear anomalies or deafness. It has a birth incidence of about 1:12,000. Most cases occur sporadically, although there is some evidence of a genetic component, ie, rare reports of familial cases and cytogenetic abnormalities. Attempts to identify the genetic component have been unsuccessful to date including sequencing suspected candidate genes PAX2 and PITX2 and conventional comparative genomic hybridization (CGH). CGH involves hybridizing genomic DNA from a test patient and from a reference (normal) individual to fragments of DNA arrayed so that they correspond to ordered segments of chromosomes. CGH reveals DNA sequence that is present in greater or lesser amounts than normal and maps its chromosomal location, thereby allowing detection of submicroscopic deletions, insertions and gene amplifications. The use of smaller and smaller DNA fragments and chip technology to array the fragments and analyze hybridization has made high-throughput, high-resolution, genome-wide screening for submicroscopic copy number changes possible.^1,2 Vissers and co-workers have utilized this approach to identify mutations responsible for the CHARGE association. The investigators co-hybridized genomic DNA from 2 patients with CHARGE and reference DNA onto a genome-wide BAC (bacterial artificial chromosome) array with 1 Mb resolution. The CGH profile of one of the patients revealed a deletion of ~5 Mb that mapped to chromosome 8q12. DNA from this patient was then hybridized to a more precise array of 918 overlapping BAC clones corresponding to a linear representation of chromosome 8. The results showed deletion of 31 overlapping BAC clones spanning 4.8 Mb of chromosome 8q12. The authors next confirmed 2 microdeletions in a patient with CHARGE association previously reported with a balanced chromosome 8 translocation. Comparing DNA from the 2 patients with microdeletions, they narrowed the region of deletion overlap to 2.3 Mb and screened 17 patients with CHARGE association for similar deletions. None were detected. However, when they sequenced the coding regions and intron-exon boundaries of the 9 genes thought to reside in or adjacent to the critical 2.3 Mb region, they detected 10 heterozygous mutations in one of the resident genes – CHD7. Seven of the mutations were stop codon mutation predicted to cause loss of function leading the authors to conclude that CHARGE association results from haploinsufficiency of CHD7. CHD7 encodes a member of the chromodomain helicase DNA-binding proteins. They are believed to have important roles in modulating chromatin structure and regulating gene expression during early development. Vissers LE, van Ravenswaaij CM, Admiraal R, et al. Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nat Genet 2004;36:955-7. Reprinted with permission from Albertson DG, Pinkel D. Hum Mol Genet 2003;12:R145-2. Copyright © 2003 Oxford University Press. All rights reserved. First Editor’s Comment: This paper is informative not only because it identifies the genetic basis of the CHARGE association, but it validates the use of high-throughput, high-resolution CGH to screen for submicroscopic changes in gene copy number in infants with sporadic malformation syndromes. As the technology becomes widely available it will likely become a valuable diagnostic tool for the clinical geneticist/dysmorphologist. William A. Horton, MD Second Editor’s Comment: Within the structure of the chromodomain helicase DNA-binding protein superfamily are 2 amino acid sequences or domains shared by its members - a "chromo (chromatin organization modifier) domain" and an SNF2-related helicase/ATPase domain (OMIM 602118). These proteins alter gene expression by modifying chromatin structure, thereby altering access of transcription factors to their gene targets. With the identification of a specific gene defect in patients with the cited association of structural anomalies (CHARGE), the disorder may now be referred to as the CHARGE syndrome. For their studies, the investigators employed an optimized, high resolution "array comparative genomic hybridization" assay that may be applicable to the study of other patients with sporadic multi-malformation syndromes. Allen W. Root, MD References - (linked to ) Albertson DG, Pinkel D. Hum Mol Genet 2003;12:R145-2. Vissers LE, de Vries BB, Osoegawa K,et al. Am J Hum Genet 2003;73:1261-70.