Toward a genetic etiology of CHARGE syndrome: I. A systematic scan for submicroscopic deletions

Clinical impact of copy number variation analysis using high-resolution microarray technologies: advantages, limitations and concerns

Copy number variation (CNV) analysis has had a major impact on the field of medical genetics, providing a mechanism to identify disease-causing genomic alterations in an unprecedented number of diseases and phenotypes. CNV analysis is now routinely used in the clinical diagnostic laboratory, and has led to a significant increase in the detection of chromosomal abnormalities. These findings are used for prenatal decision making, clinical management and genetic counseling. Although a powerful tool to identify genomic alterations, CNV analysis may also result in the detection of genomic alterations that have unknown clinical significance or reveal unintended information. This highlights the importance of informed consent and genetic counseling for clinical CNV analysis. This review examines the advantages and limitations of CNV discovery in the clinical diagnostic laboratory, as well as the impact on the clinician and family.

Clinical utility of contemporary molecular cytogenetics

The development of microarray-based comparative genomic hybridization (array CGH) methods represents a critical new advance in molecular cytogenetics. This new technology has driven a technical convergence between molecular diagnostics and clinical cytogenetics, questioned our naïve understanding of the complexity of the human genome, revolutionized the practice of medical genetics, challenged conventional wisdom related to the genetic bases of multifactorial and sporadic conditions, and is poised to impact all areas of medicine. The use of contemporary molecular cytogenetic techniques in research and diagnostics has resulted in the identification of many new syndromes, expanded our knowledge about the phenotypic spectrum of recognizable syndromes, elucidated the genomic bases of well-established clinical conditions, and refined our view about the molecular mechanisms of some chromosomal aberrations. Newer methodologies are being developed, which will likely lead to a new understanding of the genome and its relationship to health and disease.

Risk factors for poor bone health in adolescents and adults with CHARGE syndrome

CHARGE syndrome, is associated with genital hypoplasia, feeding difficulties and delayed puberty. In this study we examined the prevalence of risk factors for poor bone health in adolescents and adults with CHARGE. Questionnaires assessing fracture history, dietary intake of calcium and vitamin D, pubertal status and activity level using the Habitual Activity Estimation Scale (HAES) were completed by caregivers. Control data were collected for the HAES. When available, reports from dual-energy X-ray absorptiometry (DEXA) were obtained. Thirty individuals with CHARGE syndrome (n = 15 males; n = 15 females; age range 13 to 34 years; mean age 19.6 years) were recruited. Traumatic bony fractures were identified in 30% of the population. The recommended nutritional intake (RNI) for calcium and vitamin D were not met by 41% and 87% of the population, respectively, and 53% required past tube feeding. Delayed puberty was experienced by 87% with only 4 individuals (2 female, 2 males) having experienced normal puberty. Hormone replacement therapy (HRT) was taken by 33% of females and 60% of males. According to the HAES, adolescents with CHARGE syndrome (13-18 years) were significantly less active than controls. Individuals with CHARGE syndrome age 19 and older were also less active than controls, although this difference was not significant. DEXA scan data was obtained, however, due to small sample size (n = 10) and confounding variables (i.e., short stature, pubertal stage, height, weight), it was difficult to draw meaningful conclusions. Feeding difficulties, inactivity and hypogonadism are predisposing factors for the development of poor bone health among individuals with CHARGE syndrome. Education is necessary to raise awareness regarding the importance of HRT, proper nutrition and weight-bearing activity for healthy bone development and maintenance in individuals with CHARGE syndrome.

Identification of disease genes by whole genome CGH arrays

Small, submicroscopic, genomic deletions and duplications (1 kb to 10 Mb) constitute up to 15% of all mutations underlying human monogenic diseases. Novel genomic technologies such as microarray-based comparative genomic hybridization (array CGH) allow the mapping of genomic copy number alterations at this submicroscopic level, thereby directly linking disease phenotypes to gene dosage alterations. At present, the entire human genome can be scanned for deletions and duplications at over 30,000 loci simultaneously by array CGH ( approximately 100 kb resolution), thus entailing an attractive gene discovery approach for monogenic conditions, in particular those that are associated with reproductive lethality. Here, we review the present and future potential of microarray-based mapping of genes underlying monogenic diseases and discuss our own experience with the identification of the gene for CHARGE syndrome. We expect that, ultimately, genomic copy number scanning of all 250,000 exons in the human genome will enable immediate disease gene discovery in cases exhibiting single exon duplications and/or deletions.

Cecal Volvulus in a Child with CHARGE Syndrome

Cecal volvulus occurring in a child with CHARGE syndrome is presented. This boy was known to have CHARGE syndrome with multiple congenital anomalies, including coloboma, ventricular septal defect, choanal atresia, growth and mental retardation, bilateral cryptorchidism, dysplasia of the right ear, cleft lip, and hydrocephalus. Nissen's fundoplication had been previously performed for severe hiatal hernia and gastroesophageal regurgitation at the age of 1 year. Cecal volvulus occurred with a 540-degree clockwise rotation of terminal ileum to the right transverse colon and a displacement of the rotated loop to the right upper quadrant of the abdomen when he was 10 years old. Right hemicolectomy with divided ileo- and colostomy was performed. A second staged ileocolostomy was performed uneventfully 3 months later. The midline structural defects with nonfixation of the cecum and ascending colon, chronic constipation, and previous abdominal surgery might have been the predisposing factors.

Coarctation of the aorta and mild to moderate developmental delay in a child with a de novo deletion of chromosome 15(q21.1q22.2)

Background

Deletion of 15q21q22 is a rare chromosomal anomaly. To date, there have been nine reports describing ten individuals with different segmental losses involving 15q21 and 15q22. Many of these individuals have common features of growth retardation, hypotonia and moderate to severe mental retardation. Congenital heart disease has been described in three individuals with interstitial deletion involving this region of chromosome 15.

Case presentation

We report a child with coarctation of the aorta, partial agenesis of corpus callosum and mild to moderate developmental delay, with a de novo deletion of 15q21.1q22.2, detected by the array Comparative Genomic Hybridization (CGH). We utilized chromosome 15-specific microarray-based CGH to define the chromosomal breakpoints in this patient.

Conclusion

This is the first description of mapping of an interstitial deletion involving the chromosome 15q21q22 segment using the chromosome 15-specific array-CGH. The report also expands the spectrum of clinical phenotype associated with 15q21q22 deletion.

Spectrum of CHD7 mutations in 110 individuals with CHARGE syndrome and genotype-phenotype correlation

CHARGE syndrome is a well-established multiple-malformation syndrome with distinctive consensus diagnostic criteria. Characteristic associated anomalies include ocular coloboma, choanal atresia, cranial nerve defects, distinctive external and inner ear abnormalities, hearing loss, cardiovascular malformations, urogenital anomalies, and growth retardation. Recently, mutations of the chromodomain helicase DNA-binding protein gene CHD7 were reported to be a major cause of CHARGE syndrome. We sequenced the CHD7 gene in 110 individuals who had received the clinical diagnosis of CHARGE syndrome, and we detected mutations in 64 (58%). Mutations were distributed throughout the coding exons and conserved splice sites of CHD7. Of the 64 mutations, 47 (73%) predicted premature truncation of the protein. These included nonsense and frameshift mutations, which most likely lead to haploinsufficiency. Phenotypically, the mutation-positive group was more likely to exhibit cardiovascular malformations (54 of 59 in the mutation-positive group vs. 30 of 42 in the mutation-negative group; P=.014), coloboma of the eye (55 of 62 in the mutation-positive group vs. 30 of 43 in the mutation-negative group; P=.022), and facial asymmetry, often caused by seventh cranial nerve abnormalities (36 of 56 in the mutation-positive group vs. 13 of 39 in the mutation-negative group; P=.004). Mouse embryo whole-mount and section in situ hybridization showed the expression of Chd7 in the outflow tract of the heart, optic vesicle, facio-acoustic preganglion complex, brain, olfactory pit, and mandibular component of the first branchial arch. Microarray gene-expression analysis showed a signature pattern of gene-expression differences that distinguished the individuals with CHARGE syndrome with CHD7 mutation from the controls. We conclude that cardiovascular malformations, coloboma, and facial asymmetry are common findings in CHARGE syndrome caused by CHD7 mutation.

An epidemiological analysis of CHARGE syndrome: preliminary results from a Canadian study

CHARGE syndrome is a well-characterized clinical diagnosis with recent data supporting a genetic etiology. A 3-year national surveillance coordinated by the Canadian Pediatric Surveillance Program (CPSP) was started in September 2001. Physicians notified the CPSP if they had cared for individuals with CHARGE syndrome within their practice, and then completed a detailed reporting form. To date, there are 77 confirmed cases of CHARGE syndrome. The highest provincial prevalence of CHARGE syndrome in Canada was estimated at 1 in 8,500 live births. Subgroups of cases with particular clusters of anomalies were identified. In older individuals, bilateral posterior choanal atresia (BPCA) was predictive of the presence of the three other major criteria and of aortic arch anomalies. Individuals with CHARGE syndrome who demonstrated a less extensive phenotype (<or=3 major criteria) were more likely to present with minor cardiovascular malformations, including small atrial or ventricular septal defects (VSD) or patent ductus arteriosus (PDA). A significant cause of morbidity was severe feeding difficulty, including problems with chewing, swallowing, and gastroesophageal reflux, which were prevalent throughout childhood. Infant mortality is high in individuals with CHARGE syndrome. However, life expectancy has improved for those surviving their first year. Increased mortality was associated with distinct cardiovascular malformations or ventriculomegaly combined with brainstem or cerebellar anomalies. From this study, revised diagnostic criteria are proposed for infants, children, and adolescents to help identify a group of individuals who represent CHARGE syndrome with more of the classical features as apposed to the boarder association.

Interstitial deletion 8q11.2-q13 with congenital anomalies of CHARGE association

Specific genetic loci responsible for CHARGE association are currently unknown. Herein, we describe a neonate with clinical manifestations consistent with CHARGE association who has a de novo interstitial deletion involving bands 8q11.2 to 8q13. Genetic mapping and genomic microarray technology have been used to more accurately define the breakpoints of this deletion. Within the deleted region, there are approximately 150 expressed genes, one or more of which may contribute to the manifestations of CHARGE association.

SNP genotyping to screen for a common deletion in CHARGE syndrome

Background

CHARGE syndrome is a complex of birth defects including coloboma, choanal atresia, ear malformations and deafness, cardiac defects, and growth delay. We have previously hypothesized that CHARGE syndrome could be caused by unidentified genomic microdeletion, but no such deletion was detected using short tandem repeat (STR) markers spaced an average of 5 cM apart. Recently, microdeletion at 8q12 locus was reported in two patients with CHARGE, although point mutation in CHD7 on chromosome 8 was the underlying etiology in most of the affected patients.

Methods

We have extended our previous study by employing a much higher density of SNP markers (3258) with an average spacing of approximately 800 kb. These SNP markers are diallelic and, therefore, have much different properties for detection of deletions than STRs.

Results

A global error rate estimate was produced based on Mendelian inconsistency. One marker, rs431722 exceeded the expected frequency of inconsistencies, but no deletion could be demonstrated after retesting the 4 inconsistent pedigrees with local flanking markers or by FISH with the corresponding BAC clone. Expected deletion detection (EDD) was used to assess the coverage of specific intervals over the genome by deriving the probability of detecting a common loss of heterozygosity event over each genomic interval. This analysis estimated the fraction of unobserved deletions, taking into account the allele frequencies at the SNPs, the known marker spacing and sample size.

Conclusions

The results of our genotyping indicate that more than 35% of the genome is included in regions with very low probability of a deletion of at least 2 Mb.

CHARGE association in Sweden: Malformations and functional deficits

CHARGE association (CA) consists of a non-random association of ocular coloboma (C), heart anomaly (H), atresia of choanae (A), retarded growth and/or development (R), genital hypoplasia (G), and ear anomalies and/or hearing impairment (E). A prospective multidisciplinary study of 31 Swedish patients with CA was undertaken in order to describe the associated malformations and functional deficits, find possible etiological factors and identify critical time periods for the maldevelopment. The clinical files were analyzed, the mothers answered a questionnaire on history of prenatal events, and a clinical evaluation of systemic findings, vision, hearing, balance, speech, oral and swallowing function, and neuro-psychiatric function, especially autism, was performed. The most frequent physical abnormalities affected ears (90%), eyes (90%), brain (61%), heart (52%), retarded growth (48%), genitals (38%), choanae (35%), and facial nerve (32%). Sixty-one percent of the patients were visually impaired or blind, and 74% had hearing loss or deafness. Problems in balance, speech, and eating were common. Forty percent of the patients had autism/atypical autism, and 82% had developmental delay. Three children were born following assisted fertilization and two mothers had diabetes. The mothers reported infections, bleedings, and drug use during pregnancy. Analysis of possible critical time periods suggested that most malformations were produced early in pregnancy, mainly during post conceptual weeks 4, 5, and 6. A multidisciplinary approach is essential in the assessment and management of CA.

CHARGE syndrome from birth to adulthood: An individual reported on from 0 to 33 years

CHARGE syndrome was independently reported by Hall [(1979): J Pediatr 95:395-398] and Hittner et al. [(1979): J Pediatr Ophthalmol Strabismus 16:122-128] and was initially considered to be a non-random association between distinct multiple congenital anomalies. It is now considered to be a recognizable syndrome with well-characterized diagnostic criteria and a genetic pathogenesis. We report on a 33-year-old adult male with CHARGE syndrome, with emphasis on the unique medical, behavioral, and psychological issues faced in adulthood. Characteristic facial and ear abnormalities were obvious in early childhood, and bilateral retinal colobomata, left choanal atresia, right congenital hip dislocation, and hypogonadism were diagnosed during the first year. Walking was delayed due to vestibular problems, speech was impaired due to moderately severe hearing loss, and use of sign communication was limited. Choanal atresia was surgically corrected in infancy, and atrial septal defect, ventricular septal defect, and patent ductus arteriosus were surgically corrected in childhood. Undescended testes were removed in adolescence, and gallstones were removed in early adulthood. Puberty was delayed until hormone replacement therapy began at 15 years. Behavioral disturbances and anxiety persisted throughout childhood, adolescence, and into adulthood, often resulting from communication challenges. At 33 years of age, he lives independently in a supervised group home, receives regular eye check-ups and is being monitored for severely reduced bone density.

Behavioral features of CHARGE syndrome (Hall-Hittner syndrome) comparison with Down syndrome, Prader-Willi syndrome, and Williams syndrome

CHARGE syndrome, or Hall-Hitner syndrome (HHS), has been delineated as a common syndrome that includes coloboma, choanal atresia, cranial nerve dysfunction (particularly asymmetric facial palsy and neurogenic swallowing problems), characteristic ear abnormalities, deafness with hypoplasia of the cochlea and semicircular canals, genital hypoplasia, and variable heart defects, orofacial clefting, tracheo-esophageal fistula, renal anomalies, thymic/parathyroid hypoplasia, spine anomalies, short broad neck with sloping shoulders, and characteristic facial features. We conducted behavioral and personality assessments in 14 boys with HHS syndrome aged 6-21 years, and compared their characteristics with similar data from 20 age-matched boys with Down syndrome (DS), 17 boys with Prader-Willi syndrome (PWS), and 16 boys with Williams syndrome (WS). We used the Reiss Profile of Fundamental Goals and Motivation Sensitivities, the Achenbach Child Behavior Checklist (CBCL), and the Aberrant Behavior Checklist (ABC). All 14 boys with HHS were legally deaf, and 10 of the 14 were also legally blind. In comparison these other syndromes, boys with HHS had behavior that resembled autistic spectrum disorder. They were socially withdrawn, lacked interest in social contact, and manifested reduced seeking of attention from others, with hyperactivity and a need to maintain order. Though the boys with HHS showed decreased social interaction, they were not as socially impaired as in classic autism. Their language was delayed due to dual sensory impairment, cranial nerve deficits, and chronic medical problems, but their language style was not abnormal (no echolalia or jargon, no scripted phrases, and no pronoun reversal). Boys with HSS appeared frustrated, but they were not aggressive, or at risk for delinquency, manifesting few stereotypic behaviors or unusual preoccupations. They did not have a restricted repertoire of activities and interests. Their behavioral features appeared to be due to dual sensory impairment affecting hearing and vision, rather than to primary autistic spectrum disorder, but successful remediation requires similar educational interventions, which are discussed herein.

Microsatellites versus single-nucleotide polymorphisms in confidence interval estimation of disease loci

With cost-effective high-throughput Single Nucleotide Polymorphism (SNP) arrays now becoming widely available, it is highly anticipated that SNPs will soon become the choice of markers in whole genome screens. This optimism raises a great deal of interest in assessing whether dense SNP maps offer at least as much information as their microsatellite (MS) counterparts. Factors considered to date include information content, strength of linkage signals, and effect of linkage disequilibrium. In the current report, we focus on investigating the relative merits of SNPs vs. MS markers for disease gene localization. For our comparisons, we consider three novel confidence interval estimation procedures based on confidence set inference (CSI) using affected sib-pair data. Two of these procedures are multipoint in nature, enabling them to capitalize on dense SNPs with limited heterozygosity. The other procedure makes use of markers one at a time (two-point), but is much more computationally efficient. In addition to marker type, we also assess the effects of a number of other factors, including map density and marker heterozygosity, on disease gene localization through an extensive simulation study. Our results clearly show that confidence intervals derived based on the CSI multipoint procedures can place the trait locus in much shorter chromosomal segments using densely saturated SNP maps as opposed to using sparse MS maps. Finally, it is interesting (although not surprising) to note that, should one wish to perform a quick preliminary genome screening, then the two-point CSI procedure would be a preferred, computationally cost-effective choice.

Behavior in CHARGE syndrome: Introduction to the special topic

Challenging behavior in children with CHARGE syndrome has been increasingly a concern of parents, educators, and health professionals. This article introduces the special topic in the American Journal of Medical Genetics on behavior in individuals with CHARGE syndrome. It provides background on CHARGE syndrome, diagnostic criteria, and the relationship of sensory and other physical deficits with both development and behavior. Four themes related to our developing understanding of behavior in CHARGE are described: children with CHARGE have behaviors different from those seen in other syndromes with or without deafblindness. The behavior they display is often very adaptive to their environment and to their own disabilities. These behaviors may be partially related to problems with arousal and self-regulation. And, finally, all papers point to behavior as communication, especially within relationships, where it is essential for maximizing intellectual and social outcomes.

Ribosomal protein L24 defect in belly spot and tail (Bst), a mouse Minute

Ribosomal protein mutations, termed Minutes, have been instrumental in studying the coordination of cell and tissue growth in Drosophila. Although abundant in flies, equivalent defects in mammals are relatively unknown. Belly spot and tail (Bst) is a semidominant mouse mutation that disrupts pigmentation, somitogenesis and retinal cell fate determination. Here, we identify Bst as a deletion within the Rpl24 riboprotein gene. Bst significantly impairs Rpl24 splicing and ribosome biogenesis. Bst/+ cells have decreased rates of protein synthesis and proliferation, and are outcompeted by wild-type cells in C57BLKS<-->ROSA26 chimeras. Bacterial artificial chromosome (BAC) and cDNA transgenes correct the mutant phenotypes. Our findings establish Bst as a mouse Minute and provide the first detailed characterization of a mammalian ribosomal protein mutation.

Mutations in a new member of the chromodomain gene family cause CHARGE syndrome

CHARGE syndrome is a common cause of congenital anomalies affecting several tissues in a nonrandom fashion. We report a 2.3-Mb de novo overlapping microdeletion on chromosome 8q12 identified by array comparative genomic hybridization in two individuals with CHARGE syndrome. Sequence analysis of genes located in this region detected mutations in the gene CHD7 in 10 of 17 individuals with CHARGE syndrome without microdeletions, accounting for the disease in most affected individuals.

Feingold syndrome: clinical review and genetic mapping

Feingold syndrome is characterized by autosomal dominant inheritance of microcephaly and limb malformations, notably hypoplastic thumbs, and clinodactyly of second and fifth fingers. Syndactyly frequently involves the second and third, as well as the fourth and fifth toes. Approximately one in three Feingold syndrome patients have esophageal or duodenal atresia or both. Anal atresia has been reported in a single case. At least 79 patients in 25 families have been reported. The syndrome has autosomal dominant inheritance with full penetrance, and variable expressivity. Vertebral anomalies, cardiac malformations, and deafness have been noted in a minority of patients. Here, we report a patient with hydronephrosis of one kidney and cystic dysplasia of the other, necessitating nephrectomy. The overall pattern of malformations in Feingold syndrome shows considerable overlap with the VATER/VACTERL association. The gene for Feingold syndrome maps to 2p23-p24, but remains to be identified. Comparison of the pattern of anomalies that occurs in the Feingold syndrome in humans and malformations that are present in mice with mutations of genes in the sonic hedgehog signaling pathway suggest, that the elusive Feingold syndrome gene may involve this signaling pathway as well.