Definition of a critical region on chromosome 18 for congenital aural atresia by arrayCGH

Biomedical application of materials for external auditory canal: History, challenges, and clinical prospects

Biomaterials play an integral role in treatment of external auditory canal (EAC) diseases. Regarding the special anatomic structure and physiological characteristics of EAC, careful selection of applicable biomaterials was essential step towards effective management of EAC conditions. The bioactive materials can provide reasonable biocompatibility, reduce risk of host pro-inflammatory response and immune rejection, and promote the healing process. In therapeutic procedure, biomaterials were employed for covering or packing the wound, protection of the damaged tissue, and maintaining of normal structures and functions of the EAC. Therefore, understanding and application of biomaterials was key to obtaining great rehabilitation in therapy of EAC diseases. In clinical practice, biomaterials were recognized as an important part in the treatment of different EAC diseases. The choice of biomaterials was distinct according to the requirements of various diseases. As a result, awareness of property regarding different biomaterials was fundamental for appropriate selection of therapeutic substances in different EAC diseases. In this review, we firstly introduced the characteristics of EAC structures and physiology, and EAC pathologies were summarized secondarily. From the viewpoint of biomaterials, the different materials applied to individual diseases were outlined in categories. Besides, the underlying future of therapeutic EAC biomaterials was discussed.

Severe Unilateral Microtia with Aural Atresia, Hair White Patch, Stereotypes in a Young Boy with De novo 16p13.11 Deletion: Reasons for a New Genotype-Phenotype Correlation

Background  Microtia is an uncommon congenital malformation ranging from mild anatomic structural abnormalities to partial or complete absence of the ear leading to hearing impairment. Congenital microtia may present as a single malformation (isolated microtia) or sometimes associated with other congenital anomalies involving various organs. Microtia has been classified in three degrees according to the complexity of the auricular malformation and to anotia referred to the total absence of the ear. Genetic role in causing auricular malformation has been widely demonstrated, and genotype-phenotype correlation has been reported in cases of syndromic microtia. Case Presentation  We report here a young patient with a third degree of scale classification and aural atresia. The patient showed unspecific facial dysmorphism, speech delay, precocious teething, hair white patch, and stereotypic anomalous movements. Genetic analysis displayed a de novo 16p13.11 deletion. Conclusion  Microtia with aural atresia is an uncommon and severe birth defect, which affects functional and esthetic aspects, often associated with other malformations. As traumatic this disorder may be for the parents, the microtia and aural atresia are treatable, thanks to the improving and evolving surgical techniques. Based on the genetic analysis and the clinical features observed in the present case, a genotype-phenotype correlation has been proposed.

Search for a genetic cause in children with unilateral isolated microtia and congenital aural atresia

PURPOSE

Microtia describes a spectrum of auricular malformations ranging from mild dysplasia to anotia. A vast majority of microtia patients demonstrate congenital aural atresia (CAA). Isolated microtia has a right ear predominance (58-61%) and is more common in the male sex. Isolated microtia is a multifactorial condition involving genetic and environmental causes. The aim of this study is to describe the phenotype of children with unilateral isolated microtia and CAA, and to search for a common genetic cause trough DNA analysis.

METHODS

Phenotyping included a complete clinical examination. Description on the degree of auricular malformation (Weerda classification-Weerda 1988), assessment for hemifacial microsomia and age-appropriate audiometric testing were documented. Computerized tomography of the temporal bone with 3-D rendering provided a histopathological classification (HEAR classification-Declau et al. 1999). Genetic testing was carried out by single nucleotide polymorphism (SNP) microarray.

RESULTS

Complete data are available for 44 children (50% was younger than 33 days at presentation; 59.1% boys; 72.7% right ear). Type III microtia was present in 28 patients. Type 2b CAA existed in 32 patients. All patients had a normal hearing at the non-affected side. Genome wide deletion duplication analysis using microarray did not reveal any pathological copy number variant (CNV) that could explain the phenotype.

CONCLUSIONS

Type III microtia (peanut-shell type) in combination with a type 2b CAA was the most common phenotype, present in 23 of 44 (52.3%) patients with isolated unilateral microtia. No abnormalities could be found by copy number variant (CNV) analysis. Whole exome sequencing in a larger sample with a similar phenotype may represent a future diagnostic approach.

Inconsistency of Karyotyping and Array Comparative Genomic Hybridization (aCGH) in a Mosaic Turner Syndrome Case

Purpose  Turner syndrome is a sex chromosomal aberration where majority of the patients have 45,X karyotype, while several patients are mosaic involving 45,X/46,XX; 46,X,i(Xq); and other variants. Cytogenetic analysis, karyotyping, is considered to be the “gold standard” to detect numerical and structural chromosomal abnormalities. In the recent years, alternative approaches, such as array comparative genomic hybridization (aCGH), have been widely used in genetic analysis to detect numerical abnormalities as well as unbalanced structural rearrangements. In this study, we report the use of karyotyping as well as aCGH in detecting a possible Turner syndrome variant.

Methods  An apparent 16-year-old female was clinically diagnosed as Turner syndrome with premature ovarian failure and short stature. The genetic diagnosis was performed for the patient and the parents by karyotyping analysis. aCGH was also performed for the patient.

Main Findings  Cytogenetic analysis of the patient was performed showing variant Turner syndrome (46,X,i(X)(q10)[26]/46,X,del(X)(q11.2)[11]/45,X[8]/46,XX[5]). The patient's aCGH result revealed that she has a deletion of 57,252kb of Xp22.33-p11.21 region; arr[GRCh37] Xp22.33-p11.21 (310,932–57,563–078)X1. Both aCGH and fluorescence in situ hybridization (FISH) results suggested that short stature Homeobox-containing ( SHOX ) gene, which is located on Xp22.33, was deleted, though FISH result indicated that this was in a mosaic pattern.

Conclusion  In the recent years, aCGH has become the preferred method in detecting numerical abnormalities and unbalanced chromosomal rearrangements. However, its use is hindered by its failure of detecting mosaicism, especially low-level partial mosaicism. Therefore, although the resolution of the aCGH is higher, the cytogenetic investigation is still the first in line to detect mosaicism.

NeuroArray, A Custom CGH Microarray to Decipher Copy Number Variants in Alzheimer's Disease

Background:

Copy Number Variants (CNVs) represent a prevailing type of structural variation (deletions or duplications) in the human genome. In the last few years, several studies have demonstrated that CNVs represent significant mutations in Alzheimer’s Disease (AD) hereditability. Currently, innovative high-throughput platforms and bioinformatics algorithms are spreading to screening CNVs involved in different neurological diseases. In particular, the use of custom arrays, based on libraries of probes that can detect significant genomic regions, have greatly improved the resolution of targeted regions and the identification of chromosomal aberrations.

Objective:

In this work, we report the use of NeuroArray, a custom CGH microarray useful to screening and further investigate the role of the recurring genomic aberrations in patients with confirmed or suspected AD.

Methods:

The custom oligonucleotide aCGH design includes 641 genes and 9118 exons, linked to AD. The genomic DNA was isolated from blood samples of AD affected patients. The entire protocol of custom NeuroArray included digestion, labelling and hybridization steps as a standard aCGH assay.

Results:

The NeuroArray analysis revealed the presence of amplifications in several genes associated with AD. In the coding regions of these genes, 14,586 probes were designed with a 348 bp median probe spacing. The majority of targeted AD genes map on chromosomes 1 and 10. A significant aspect of the NeuroArray design is that 95% of the total exon targets is covered by at least one probe, a resolution higher than CGH array platforms commercially available.

Conclusion:

By identifying with a high sensitivity the chromosomal abnormalities in a large panel of AD-related genes and other neurological diseases, the NeuroArray platform is a valid tool for clinical diagnosis.

Novel applications of array comparative genomic hybridization in molecular diagnostics

INTRODUCTION

In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus. Area covered: In this review, the authors summarize the evolution of array CGH technology from their diagnostic laboratory, highlighting exonic SNP arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity. The applications of array CGH to human diseases with different modes of inheritance with the emphasis on autosomal recessive disorders are discussed. Expert commentary: An exonic array is a powerful and most efficient clinical tool in detecting genome wide small copy number variants in both dominant and recessive disorders. However, whole-genome sequencing may become the single integrated platform for detection of copy number changes, single-nucleotide changes as well as balanced chromosomal rearrangements in the near future.

Low-Level Chromosomal Mosaicism in Neurodevelopmental Disorders

Chromosomal mosaicism, which represents a diagnostic challenge for detection and interpretation, has been described in several genetic conditions. It can contribute to a large phenotypic variation in diseases. At analysis of a well-characterized cohort of 714 patients with neurodevelopmental disorders (NDDs) of unknown etiology using a high-resolution chromosomal microarray platform, we found 2 cases (0.28%) of low-level mosaicism and defined a previously detected extra chromosome in a third patient. Two of the cases were mosaics for segmental imbalances (a partial trisomy 3q26.1q27.3 and a partial monosomy 18q21.2qter with 14.6 and 20% mosaic ratios in lymphocytes, respectively), and 1 was a mosaic for an entire chromosome (trisomy 14, mosaic ratio 20%). Our diagnostic yield is in line with the ratios previously published in patients with intellectual disability. Notably, the partial trisomy 3q26.1q27.3 case is an example of a rare and unusual class of a rearranged neocentric ring chromosome, which can neither be categorized in class I, nor in class II of such rearrangements. Our cases further elucidate the phenotypes related to the aberrations of the specific chromosome segments observed and underline the important role of low-level mosaics in the pathogenesis of NDDs of unknown etiology even in the absence of clinical signs of mosaicism.

Genetic Advances in the Understanding of Microtia

Microtia is a genetic condition affecting the external ears and presents clinically along a wide spectrum: minimally affected ears are small with minor shape abnormalities; extremely affected ears lack all identifiable structures, with the most extreme being absence of the entire external ear. Multiple genetic causes have been linked to microtia in both animal models and humans, which are improving our understanding of the condition and may lead to the identification of a unified cause for the condition. Microtia is also a prominent feature of several genetic syndromes, the study of which has provided further insight into the possible causes and genetic mechanisms of the condition. This article reviews our current understanding of microtia including epidemiological characteristics, classification systems, environmental and genetic causative factors leading to microtia. Despite our increased understanding of the genetics of microtia, we do not have a means of preventing the condition and still rely on complex staged, surgical correction.

Evolution of prenatal genetics: from point mutation testing to chromosomal microarray analysis

Molecular genetic testing involves DNA analysis using various methods for the purpose of diagnosing genetic disorders. In the prenatal DNA diagnostic setting, fetal DNA is usually tested for a specific single-gene disorder for which the fetal risk is 25% or more. In contrast, cytogenetic testing is often used to detect fetal chromosomal abnormalities in cases that involve a wider range of indications. Classic cytogenetic and DNA-based testing methods provide a range of aberrations detected with different levels of genomic resolution. More recently developed molecular cytogenetic methods provide powerful tools to bridge the technical divide between these related areas. One such hybrid method is microarray-based comparative genomic hybridization. Chromosomal microarray analysis has been applied to clinical testing for unbalanced gains or losses of genomic regions associated with genetic disorders. This technology is poised to have a substantial impact on clinical genetics, including prenatal genetic testing.

Sonographic imaging of fetal tympanic rings

OBJECTIVE

To examine the feasibility of ultrasonographic imaging of fetal tympanic rings.

METHODS

This was an observational cohort study of 80 healthy fetuses in low-risk pregnancies, divided into four gestational-age subgroups (12, 16, 23 and 32 weeks), each comprising 20 consecutive fetuses. Tympanic ring visualization was achieved by two-dimensional and three-dimensional (3D) sonography. A standard algorithm for tympanic ring examination was constructed using 3D multiplanar reconstruction. The volume acquisition plane was directed to the inferolateral aspect of the fetal temporal bone. Transvaginal scans were carried out in the 12-week and 16-week subgroups, and transabdominal scans in the 23-week and 32-week subgroups. Study parameters included the inferomedial inclination angle (IMIA) of the tympanic ring relative to the vertical skull axis, the anteromedial inclination angle (AMIA) of the tympanic ring relative to the anteroposterior skull axis and the longest (LTRD) and shortest (STRD) tympanic ring diameter, the latter measured perpendicular to the LTRD. The feasibility of tympanic ring demonstration was assessed in each gestational-age subgroup.

RESULTS

Tympanic rings appeared as round-oval, thin, echogenic structures in a plane tangential to the inferolateral surface of the fetal skull below the inferior border of the squamous part of the temporal bone. Higher demonstration rates were achieved in the 16-week and 23-week subgroups (90% and 80%, respectively) than in the others. LTRD and STRD each showed a linear correlation with gestational age (r = 0.96 for both measurements; P < 0.01). Mean IMIA ranged from 41.0 to 60.4° and mean AMIA from 17.3 to 23.4° across the different gestational-age subgroups. The malleal manubrium was observed only in examinations in the second half of pregnancy, appearing as a bright echo within the upper area of the tympanic ring in 56% (9/16) and 82% (9/11) of cases with tympanic ring imaging appropriate for measurement of the study parameters in the 23-week and 32-week subgroups, respectively.

CONCLUSION

This is the first report of sonographic imaging of fetal tympanic rings and shows that this is feasible in the second trimester. We discuss the possible implications of our findings for the prenatal diagnosis of congenital hearing loss.

Narrowing the critical region for congenital vertical talus in patients with interstitial 18q deletions

Interstitial deletions of 18q lead to a number of phenotypic features, including multiple types of foot deformities. Many of these associated phenotypes have had their critical regions narrowly defined. Here we report on three patients with small overlapping deletions of chromosome 18q determined by microarray analysis (chr18:72493281-73512553 hg19 coordinates). All of the patients have congenital vertical talus (CVT). Based on these findings and previous reports in the literature and databases, we narrow the critical region for CVT to a minimum of five genes (ZNF407, ZADH2, TSHZ1, C18orf62, and ZNF516), and propose that TSHZ1 is the likely causative gene for CVT in 18q deletion syndrome.

CGH protocols: chronic lymphocytic leukemia

Array-based comparative genomic hybridization (aCGH) is a powerful assay to identify copy number abnormalities underlying the pathogenesis of cancer. aCGH has become the gold standard for whole genome copy number analysis in medium and large cohorts in clinical and research laboratories. Identifying the best workflow is critical to achieving the optimal performance for this assay. Here we describe the aCGH protocol used by our group in the study of B-chronic lymphocytic leukemia (CLL). We also describe some initial applications of aCGH in association with clinical outcome for CLL.

Abnormal myelination in ring chromosome 18 syndrome

Partial deletion of genetic material from the long arm of chromosome 18 results in a syndrome with multisystemic involvement, including dysmorphic features, intellectual disability, cardiac malformations, endocrine abnormalities, immunodeficiency, musculoskeletal deformities, and variable neurologic manifestations. Hypomyelination has been reported in patients with chromosome 18q- and postulated to be secondary to deletion of the gene coding for myelin basic protein found at 18q23. Little however is reported on cerebral anomalies seen in patients with ring chromosome 18, an analogous syndrome but with expectedly more severe phenotype secondary to the combined deletions of genetic material from both the short (p-) and long arm (q-) of chromosome 18. We are reporting a case of a girl with ring chromosome 18 and deletions involving 18p11.32-18p11.21 and 18q21.31-18q23. The abnormalities observed on magnetic resonance imaging are discussed with a specific focus on the evolution and significance of associated white matter changes.

Phenotypic and molecular characterization of partial trisomy 2q resulting from insertion-duplication in chromosome 18q: a case report and review of literature

Trisomy 2q is a well-documented chromosomal anomaly with considerable variation in the phenotype depending upon the breakpoints and the co-existing chromosomal aberrations. The case of a dysmorphic male infant found to have trisomy of the 2q31.1-q37.3 segment, resulting from insertion-duplication of this segment in chromosome 18q23 is reported here. The rearrangement was resolved in detail by cytogenetic microarray and whole chromosome paint-based fluorescence in situ hybridization studies. There is some overlap of the phenotypic features in the reported patient with those described in previously reported cases with partial trisomy 2q. A detailed review of the available literature on 2q trisomy has also been presented and delineation of the phenotypic characteristics common to all patients with 2q trisomy has been attempted.

Familial 4.8 MB deletion on 18q23 associated with growth hormone insufficiency and phenotypic variability

The deletion of the long arm of chromosome 18 causes a contiguous gene deletion syndrome with a highly variable phenotype, usually related to the extent of the deleted region. The most commonly reported clinical features include: decreased growth, microcephaly, facial abnormalities, hypotonia, developmental delay, intellectual disability, congenital aural atresia with hearing impairment and limb anomalies. Here we report on a familial terminal deletion of 18q23 region transmitted from a mother to two daughters, resulting in a remarkable phenotypic variability. The deletion was first detected by conventional cytogenetic analysis in one daughter and subsequently characterized using fluorescence in situ hybridization (FISH) and array-CGH. FISH analysis using subtelomeric 18p and 18q probes confirmed the 18qter deletion in the three patients, and FISH with a whole chromosome painting probe specific for chromosome 18 excluded rearrangements with other chromosomes. Array-CGH analysis allowed us to precisely define the extent of the deletion, which spans 4.8 Mb from 71,236,891 to 76,093,303 genomic positions and includes GALR1 and MBP genes, among others. High-resolution analysis of the deletion, besides a detailed clinical assessment, has provided important data for phenotype-genotype correlation and genetic counseling in this family. Furthermore, this study adds valuable information for phenotype-genotype correlation in 18q- syndrome and might facilitate future search for candidate genes involved in each phenotypic trait.

Congenital aural atresia: bone-anchored hearing aid vs. external auditory canal reconstruction

OBJECTIVE

To compare the audiologic outcome and feasibility of bone-anchored hearing aid (BAHA) and external auditory canal reconstruction (EACR) surgeries in pediatric patients presenting a congenital aural atresia (CAA).

METHODS

A retrospective chart review of 40 patients operated in our tertiary pediatric care center between 2002 and 2010 was performed. 20 patients underwent EACR, whereas another 20 patients were implanted with a BAHA device. Air conduction (AC), bone conduction (BC), pure tone average (PTA) and speech discrimination score (SDS) were compared preoperatively, and hearing gain (HG) postoperatively at 6 and at 12 months at frequencies of 500, 1000, 2000 and 4000 Hz. Operative time, complications and associated microtia were documented as well. EACR patients were graded retrospectively upon Jahrsdoerfer's classification.

RESULTS

Preoperative AC were significantly different between groups, at 500, 1000 and 2000 Hz but not at 4000 Hz. BAHA group compared postoperatively to EACR group showed significantly a superior HG of 46.9 ± 7.0 dB (p<0.001) and of 39.8(7) ± 7.2(6.9)dB (p<0.001) at 6 months and at 1 year, respectively. Moreover, aided air thresholds from the EACR group revealed an audiologic status similar to those of the BAHA group patients, at 6 months and one year postoperatively. Both groups had a similar evolution of their BC, as well as of the incidence of complications. We report one case of transient facial paralysis in the EACR group. Total operative time is significantly lower (p<0.001) for a BAHA implantation (56 ± 21 min) than for EACR surgery (216 ± 174 min). No preoperative or postoperative correlation (Pearson correlation test; p>0.05) was found between patient's Jahrsdoerfer's score and their audiologic outcome. HG does not seem to be influenced by the presence of microtia.

CONCLUSION

EACR, although constituting an attractive option, does not give acceptable results alone. It can however, when combined to conventional air conduction hearing aids, provide excellent audiologic outcomes comparable to BAHA. BAHA implantation is a reliable, safe and efficient therapeutic option that allows a significantly better audiologic outcome when compared to unaided EACR for patients with CAA.

Disruption of teashirt zinc finger homeobox 1 is associated with congenital aural atresia in humans

Congenital aural atresia (CAA) can occur as an isolated congenital malformation or in the context of a number of monogenic and chromosomal syndromes. CAA is frequently seen in individuals with an 18q deletion, which is characterized by intellectual disability, reduced white-matter myelination, foot deformities, and distinctive facial features. Previous work has indicated that a critical region for CAA is located in 18q22.3. We studied four individuals (from two families) with CAA and other features suggestive of an 18q deletion, and we detected overlapping microdeletions in 18q22.3 in both families. The minimal region of deletion overlap (72.9-73.4 Mb) contained only one known gene, TSHZ1, which was recently shown to be important for murine middle-ear development. Sequence analysis of the coding exons in TSHZ1 in a cohort of 11 individuals with isolated, nonsyndromic bilateral CAA revealed two mutations, c.723G>A (p.Trp241X) and c.946_947delinsA (p.Pro316ThrfsX16), and both mutations predicted a loss of function. Together, these results demonstrate that hemizygosity of TSHZ1 leads to congenital aural atresia as a result of haploinsufficiency.

Strategies for genotyping

The identification of genomic loci linked to or associated with human disease has been greatly facilitated by the evolution of genotyping strategies and techniques. The success of these strategies continues to be based upon clear clinical assessment, accurate sample handling, and careful data management, but also increasingly upon experimental design. Technological advances in the field of genotyping have permitted increasingly complex and large population studies to be performed. An understanding of publicly available genetic variation databases, including an awareness of the limitations of these data, and an appreciation of the strategic approaches that should be used to exploit this information will provide tremendous insight for researchers are aiming to utilize this accessible technology. As genome-wide association studies (GWAS) and Next Generation (NextGen) sequencing become the mainstays of genetic analyses, it is important that their technical strengths and limitations, as well as their impact on study design, be understood before use in a linkage or genetic association study.

The 18q deletion syndrome and analysis of the critical region for orofacial cleft at 18q22.3

INTRODUCTION

The 18q deletion syndrome (18q-) is a multiple-anomaly disorder associated with mental retardation, white matter anomalies in the brain, growth hormone deficiency, congenital aural atresia, orofacial cleft (OFC), and palate abnormalities. The aims of this study were to determine the frequency of different forms of OFC in 18q- individuals: cleft palate with or without cleft lip (CP/L), cleft lip (CL), and palate abnormalities. We also sought to map a potential critical region for OFC within chromosome 18q22.3 region.

PATIENTS

The study presents an overview of selected 18q- individuals from 11 published reports and one presented poster.

RESULTS

The frequency of CP/L and CL among 18q- individuals is about 25%; when high/arched palate cases are included, the frequency rises to about 43%.

CONCLUSION

Orofacial abnormalities are characteristic features of 18q- syndrome patients and potential CP/L critical region could be assumed at 18q22.3 between markers D18S879 and D18S1141. In addition, gene deficient mouse models for Sall3 or Tshz1 genes, which are located at the 18q22.3 critical region, displayed palate abnormality phenotype.

Application of metaphase HR-CGH and targeted Chromosomal Microarray Analyses to genomic characterization of 116 patients with mental retardation and dysmorphic features

Recent advances in molecular cytogenetics enable identification of small chromosomal aberrations that are undetectable by routine chromosome banding in 5-20% of patients with mental retardation/developmental delay (MR/DD) and dysmorphism. The aim of this study was to compare the clinical usefulness of two molecular cytogenetic techniques, metaphase high-resolution comparative genomic hybridization (HR-CGH) and targeted array CGH, also known as Chromosomal Microarray Analysis (CMA). A total of 116 patients with unexplained mild to severe MR and other features suggestive of a chromosomal abnormality with apparently normal or balanced karyotypes were analyzed using HR-CGH (43 patients) and/or CMA (91 patients). Metaphase HR-CGH detected seven interstitial deletions (16.3%). Rare deletions of chromosomes 16 (16p11.2p12.1) and 8 (8q21.11q21.2) were identified. Targeted CMA revealed copy-number changes in 19 of 91 patients (20.8%), among which 11 (11.8%) were clinically relevant, 6 (6.5%) were interpreted as polymorphic variants and 2 (2.1%) were of uncertain significance. The changes varied in size from 0.5 to 12.9 Mb. In summary, our results show that metaphase HR-CGH and array CGH techniques have become important components in cytogenetic diagnostics, particularly for detecting cryptic constitutional chromosome imbalances in patients with MR, in whom the underlying genetic defect is unknown. Additionally, application of both methods together increased the detection rates of genomic imbalances in the tested groups.

Causation of permanent unilateral and mild bilateral hearing loss in children

Children with permanent unilateral or mild bilateral hearing loss have been a focus of concern by audiologists, educators, and physicians for at least 2 decades. These children are known to be at risk for psychoeducational difficulties. However, despite this concern, little has been learned about the causative factors of these hearing losses and how those factors might be contributing to child development. This review of known causes of permanent unilateral and mild bilateral hearing loss in children is meant to draw attention to the importance of the search for etiologic factors. That is, the identification of the hearing loss should not signal the end of the diagnostic process but, rather, the beginning of a search for causation. With the combined efforts of audiologists, otolaryngologists, pediatricians, geneticists, and other medical professionals, we may enhance our understanding of the primary causes of unilateral and mild bilateral hearing loss and, perhaps, create links between causative factors and psychosocial and psychoeducational outcomes.

Identification and characterization of a new type of asymmetrical dicentric chromosome derived from a single maternal chromosome 18

Molecular cytogenetic analysis identified a new type of dicentric chromosome involving different breakpoints at 18q in a female fetus. The chromosome anomaly was designated as an asymmetrical pseudoisodicentric chromosome 18, 46,XX,psu dic(18)(pter-->q11.2::q21.3-->pter)mat. A series of BAC clones for 18q11.2 and q21.3 regions were used to identify one breakpoint within the region q11.2 between 19.8 and 21.6 Mb from the telomere of 18p and another breakpoint within q21.3 between 55.4 and 56.9 Mb from the telomere of 18p by FISH analysis. Real-time quantitative PCR and microsatellite analysis further verified that the dicentric chromosome was maternal in origin and resulted from a break-reunion between sister chromatids of a single maternal chromosome. We propose that a loop-type configuration of sister chromatids took place and that the break-reunion occurred at cross sites of the loop to form an asymmetrical isodicentric chromosome during either mitosis or meiosis. In this case, the asymmetrical pseudoisodicentric resulted in an 18pter--> q11.2 duplication and an 18q21.3-->qter deletion, which could have led to certain dysmorphic features of 18q- syndrome in this fetus.

In utero exposure to mycophenolate mofetil: a characteristic phenotype?

Mycophenolate mofetil (MMF) is a widely prescribed immunosuppressive agent after solid organ transplantation. Potential teratogenic effects after in utero exposure to MMF in experimental studies and clinical observations in humans has been postulated in recent literature. However, a specific pattern of malformation has not been identified yet. We present a newborn patient, born to a recipient of renal transplantation, who became pregnant while taking MMF as immunosuppressive therapy. The newborn exhibited cleft lip and palate, bilateral microtia and atretic external auditory canals, chorioretinal coloboma, hypertelorism, and micrognathia. An extensive review of the literature documented six other cases with similar malformations after in utero exposure to MMF. A consistent pattern of malformations comprising cleft lip and palate, microtia and external auditory canals could be observed in five of the six cases. A different malformative pattern observed in one of the patients could be attributed to a different agent rather than MMF. The possible teratogenic effects of other immunosuppressive drugs, such as tacrolimus and prednisone, to which this patient was also exposed, are discussed herein. In addition, the differential diagnosis with other dysmorphic syndromes that can present with a similar phenotype, such as CHARGE syndrome, 18q deletion and hypertelorism-microtia-clefting (HMC) syndrome, is presented. We conclude that in utero exposure to MMF can cause a characteristic phenotype and propose the existence of a mycophenolate-associated embryopathy whose main features are: cleft lip and palate, microtia with atresia of external auditory canal, micrognathia and hypertelorism. Ocular anomalies, corpus callosum agenesis, heart defects, kidney malformations, and diaphragmatic hernia may be part of the phenotypic spectrum of MMF embryopathy. The human teratogenicity of MMF is reinforced by this report, and the current contraceptive recommendations about its use in fertile women are stressed.

Genotype-phenotype mapping of chromosome 18q deletions by high-resolution array CGH: an update of the phenotypic map

Partial deletions of the long arm of chromosome 18 lead to variable phenotypes. Common clinical features include a characteristic face, short stature, congenital aural atresia (CAA), abnormalities of the feet, and mental retardation (MR). The presence or absence of these clinical features may depend on the size and position of the deleted region. Conversely, it is also known that patients whose breakpoints are localized within the same chromosome band may exhibit distinct phenotypes. New molecular techniques such as array CGH allow for a more precise determination of breakpoints in cytogenetic syndromes, thus leading to better-defined genotype-phenotype correlations. In order to update the phenotypic map for chromosome 18q deletions, we applied a tiling resolution chromosome 18 array to determine the exact breakpoints in 29 patients with such deletions. Subsequently, we linked the genotype to the patient's phenotype and integrated our results with those previously published. Using this approach, we were able to refine the critical regions for microcephaly (18q21.33), short stature (18q12.1-q12.3, 18q21.1-q21.33, and 18q22.3-q23), white matter disorders and delayed myelination (18q22.3-q23), growth hormone insufficiency (18q22.3-q23), and CAA (18q22.3). Additionally, the overall level of MR appeared to be mild in patients with deletions distal to 18q21.33 and severe in patients with deletions proximal to 18q21.31. The critical region for the 'typical' 18q-phenotype is a region of 4.3 Mb located within 18q22.3-q23. Molecular characterization of more patients will ultimately lead to a further delineation of the critical regions and thus to the identification of candidate genes for these specific traits.

From microscopes to microarrays: dissecting recurrent chromosomal rearrangements

Submicroscopic chromosomal rearrangements that lead to copy-number changes have been shown to underlie distinctive and recognizable clinical phenotypes. The sensitivity to detect copy-number variation has escalated with the advent of array comparative genomic hybridization (CGH), including BAC and oligonucleotide-based platforms. Coupled with improved assemblies and annotation of genome sequence data, these technologies are facilitating the identification of new syndromes that are associated with submicroscopic genomic changes. Their characterization reveals the role of genome architecture in the aetiology of many clinical disorders. We review a group of genomic disorders that are mediated by segmental duplications, emphasizing the impact that high-throughput detection methods and the availability of the human genome sequence have had on their dissection and diagnosis.

Oligonucleotide arrays for high-resolution analysis of copy number alteration in mental retardation/multiple congenital anomalies

Genetic diseases arising from microdeletions and microduplications lead to copy number alterations of genomic regions containing one or more genes. Clinically, these rearrangements may be detected by routine cytogenetic testing, which may include karyotype analysis, subtelomeric analysis with fluorescence in situ hybridization, and/or fluorescence in situ hybridization directed at known chromosomal rearrangement-based disorders. The major limitations of these tests are low resolution and limited coverage of the genome. Array-based comparative genomic hybridization has recently become a widely used approach in the genome-wide analysis of copy number alterations in children with mental retardation and/or multiple congenital anomalies. Oligonucleotide-based arrays provide a genome-wide coverage at a much higher resolution than microarrays currently used in clinical diagnostics, greatly improving the rate of detection of submicroscopic copy number alterations in children with mental retardation and/or multiple congenital anomalies.

Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation

The clinical implementation of array comparative genomic hybridization has revolutionized the diagnosis of patients with syndromic or nonsyndromic mental retardation. Multiple studies of hundreds of patients with idiopathic mental retardation, and normal karyotype and/or subtelomeric testing using genome-wide microarray platforms with approximately 2000 to >30,000 (tiling-path) interrogating BAC/PAC probes have detected chromosome abnormalities in up to 17% of cases. Surprisingly, some of the pathogenic changes are mosaic and not detectable in conventional karyotyping. Commercially available genome-wide microarrays with >300,000 synthesized oligonucleotide probes enable higher resolution and sensitivity and will probably replace the BAC/PAC arrays in clinical laboratories.

Role of cytogenetics and molecular cytogenetics in the diagnosis of genetic imbalances

Five decades ago, Tijo and Levan (1956) first recognized the correct chromosome number in man to be 46. Shortly thereafter, several chromosome aneuploid syndromes were identified. In the early 1970s, various chromosomal-banding techniques were developed that allowed the recognition of individual chromosomes and deletions and duplications as etiologies for numerous chromosome syndromes. Slightly more than 10 years ago, fluorescence in situ hybridization (FISH) procedures, using fluorescent-labeled DNA sequences were developed and clinical use of this technique allowed for the identification of cryptic chromosome abnormalities associated with microdeletions and microduplications. The use of subtelomere region-specific FISH probes further led to the identification of deletions and other unbalanced rearrangements in individuals with mental retardation with an apparently normal karyotype. More recently, microarray comparative genomic hybridization was developed, and the technique has recently become incorporated into the clinical cytogenetics laboratory for the identification of submicrosopic deletions and duplications that are associated with developmental delay. The intent of this article is to review the cytogenetic and molecular cytogenetic techniques currently available for the diagnosis of individuals with neurologic disease and genetic imbalances that result in neurologic disturbances and to summarize the most efficient and appropriate use of these techniques in clinical practice.

Array-based comparative genomic hybridization in clinical diagnosis

The sequencing of the human genome and development of high-throughput microarray technologies have enhanced the detection of copy number alterations in cancer research and the study of constitutional chromosomal abnormalities. Microarray-based comparative genomic hybridization (array CGH) has integrated molecular and traditional cytogenetics and has begun to impact the clinician's approach to medical genetics. Clinical applications of array CGH may define new genetic syndromes, expand the phenotype of existing syndromes and characterize a genomic signature of some cancers. As array CGH becomes the initial diagnostic approach for the investigation of constitutional and acquired chromosomal abnormalities, the combination of bioinformatics, robotics and microarray technology will set the stage for a new generation of high-resolution and high-throughput tools for genetic analysis, diagnosis and gene discovery.

L'hybridation génomique comparative sur microréseau d'ADN (puces à ADN) en pathologie chromosomique constitutionnelle

Chromosomal aberrations are the first cause of mental impairment and dysmorphism. Rearrangements involving large chromosomal segments can be detected by standard chromosome analysis using GTG-banding, but this technique is not suited for the detection of small chromosome abnormalities. Array comparative genomic hybridisation (array-CGH) is a method used to detect segmental DNA copy number alterations. Recently, advances in this technology have enabled high-resolution examination for identifying genetic alterations and copy number variations on a genome-wide scale. This review describes the current genomic array platforms and CGH methodologies and highlights their applications for studying constitutional disease.

Detection of low-level mosaicism by array CGH in routine diagnostic specimens

The advent of microarray-based comparative genomic hybridization (array CGH) promises to revolutionize clinical cytogenetics because of its ability to rapidly screen the genome at an unprecedented resolution. Yet, the ability of array CGH to detect and evaluate low-level mosaicism is not known. Our laboratory has analyzed over 3,600 clinical cases with the SignatureChip which we developed for the detection of microdeletions, microduplications, aneuploidy, unbalanced translocations, and subtelomeric and pericentromeric copy number alterations. Here, we report 18 cases of mosaicism detected by array CGH in a routine diagnostic setting, 14 of which were not known to us at the time of the analysis. These 14 cases represent approximately 8% of all abnormal cases identified in our laboratory. For each case, fluorescence in situ hybridization (FISH) analysis was performed on PHA-stimulated cultures after mosaic chromosome abnormalities were suspected by array CGH. In all cases, FISH confirmed the mosaic chromosome abnormalities which included a variety of marker chromosomes, autosomal trisomies, terminal and interstitial deletions, and derivative chromosomes. Interestingly, confirmatory FISH analyses on direct blood smears indicated that the percentage of abnormal cells in unstimulated cultures was in some cases different than that found in PHA-stimulated cells. We also report the detection of a previously unsuspected case of an isochromosome 12p (associated with Pallister-Killian syndrome) by array CGH using genomic DNA extracted from peripheral blood. These results support a growing body of data that suggests that stimulated peripheral blood cultures likely distort the percentage of abnormal cells and may, for some chromosome abnormalities, make their detection unlikely by conventional analysis. Thus, array CGH, which is based on genomic DNA extracted directly from uncultured peripheral blood, may be more likely to detect low-level mosaicism for unbalanced chromosome abnormalities than traditional cytogenetic techniques.

Application of array-based comparative genomic hybridization to clinical diagnostics

Microarray-based comparative genomic hybridization (array CGH) is a revolutionary platform that was recently adopted in the clinical laboratory. This technology was first developed as a research tool for the investigation of genomic alterations in cancer. It allows for a high-resolution evaluation of DNA copy number alterations associated with chromosome abnormalities. Array CGH is based on the use of differentially labeled test and reference genomic DNA samples that are simultaneously hybridized to DNA targets arrayed on a glass slide or other solid platform. In this review, we examine the technology and its transformation from a research tool into a maturing diagnostic instrument. We also evaluate the various approaches that have shaped the current platforms that are used for clinical applications. Finally, we discuss the advantages and shortcomings of "whole-genome" arrays and compare their diagnostic use to "targeted" arrays. Depending on their design, microarrays provide distinct advantages over conventional cytogenetic analysis because they have the potential to detect the majority of microscopic and submicroscopic chromosomal abnormalities. This new platform is poised to revolutionize modern cytogenetic diagnostics and to provide clinicians with a powerful tool to use in their increasingly sophisticated diagnostic capabilities.

Cytogenetic genotype-phenotype studies: improving genotyping, phenotyping and data storage

High-resolution molecular cytogenetic techniques such as genomic array CGH and MLPA detect submicroscopic chromosome aberrations in patients with unexplained mental retardation. These techniques rapidly change the practice of cytogenetic testing. Additionally, these techniques may improve genotype-phenotype studies of patients with microscopically visible chromosome aberrations, such as Wolf-Hirschhorn syndrome, 18q deletion syndrome and 1p36 deletion syndrome. In order to make the most of high-resolution karyotyping, a similar accuracy of phenotyping is needed to allow researchers and clinicians to make optimal use of the recent advances. International agreements on phenotype nomenclature and the use of computerized 3D face surface models are examples of such improvements in the practice of phenotyping patients with chromosomal anomalies. The combination of high-resolution cytogenetic techniques, a comprehensive, systematic system for phenotyping and optimal data storage will facilitate advances in genotype-phenotype studies and a further deconstruction of chromosomal syndromes. As a result, critical regions or single genes can be determined to be responsible for specific features and malformations.

Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders

Genomic disorders are a group of human genetic diseases caused by genomic rearrangements resulting in copy-number variation (CNV) affecting a dosage-sensitive gene or genes critical for normal development or maintenance. These disorders represent a wide range of clinically distinct entities but include many diseases affecting nervous system function. Herein, we review selected neurodevelopmental, neurodegenerative, and psychiatric disorders either known or suggested to be caused by genomic rearrangement and CNV. Further, we emphasize the cause-and-effect relationship between gene CNV and complex disease traits. We also discuss the prevalence and heritability of CNV, the correlation between CNV and higher-order genome architecture, and the heritability of personality, behavioral, and psychiatric traits. We speculate that CNV could underlie a significant proportion of normal human variation including differences in cognitive, behavioral, and psychological features.

Application of multicolor banding for identification of complex chromosome 18 rearrangements

Multicolor chromosome banding (mBAND) is a recently developed technique that allows the delineation of chromosomal regions with a resolution of a few megabase pairs. The resolution of mBAND is slightly below that of conventional chromosome banding; however, the color bands have a great value in identifying chromosomal abnormalities, particularly complex chromosome rearrangements, and intrachromosome exchanges (ie, inversions, deletions, duplications, and insertions). These abnormalities cannot be defined easily by conventional cytogenetic analysis or chromosome paint. In this report, we present the application of the mBAND analysis for identification of complex intrachromosome rearrangements of chromosome 18 in a child with dysmorphic features.

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.

Identification of novel genomic markers related to progression to glioblastoma through genomic profiling of 25 primary glioma cell lines

Identification of genetic copy number changes in glial tumors is of importance in the context of improved/refined diagnostic, prognostic procedures and therapeutic decision-making. In order to detect recurrent genomic copy number changes that might play a role in glioma pathogenesis and/or progression, we characterized 25 primary glioma cell lines including 15 non glioblastoma (non GBM) (I-III WHO grade) and 10 GBM (IV WHO grade), by array comparative genomic hybridization, using a DNA microarray comprising approx. 3500 BACs covering the entire genome with a 1 Mb resolution and additional 800 BACs covering chromosome 19 at tiling path resolution. Combined evaluation by single clone and whole chromosome analysis plus 'moving average (MA) approach' enabled us to confirm most of the genetic abnormalities previously identified to be associated with glioma progression, including +1q32, +7, -10, -22q, PTEN and p16 loss, and to disclose new small genomic regions, some correlating with grade malignancy. Grade I-III gliomas exclusively showed losses at 3p26 (53%), 4q13-21 (33%) and 7p15-p21 (26%), whereas only GBMs exhibited 4p16.1 losses (40%). Other recurrent imbalances, such as losses at 4p15, 5q22-q23, 6p23-25, 12p13 and gains at 11p11-q13, were shared by different glioma grades. Three intervals with peak of loss could be further refined for chromosome 10 by our MA approach. Data analysis of full-coverage chromosome 19 highlighted two main regions of copy number gain, never described before in gliomas, at 19p13.11 and 19q13.13-13.2. The well-known 19q13.3 loss of heterozygosity area in gliomas was not frequently affected in our cell lines. Genomic hotspot detection facilitated the identification of small intervals resulting in positional candidate genes such as PRDM2 (1p36.21), LRP1B (2q22.3), ADARB2 (10p15.3), BCCIP (10q26.2) and ING1 (13q34) for losses and ECT2 (3q26.3), MDK, DDB2, IG20 (11p11.2) for gains. These data increase our current knowledge about cryptic genetic changes in gliomas and may facilitate the further identification of novel genetic elements, which may provide us with molecular tools for the improved diagnostics and therapeutic decision-making in these tumors.

Identification of 2.3-Mb Gene Locus for Congenital Aural Atresia in 18q22.3 Deletion

OBJECTIVE

18q deletion syndrome is a multiple-anomaly mental retardation syndrome associated with congenital aural atresia. The purpose of this study was to determine the frequency of the congenital aural atresia phenotype in 18q deletion syndrome patients and to delineate a potential critical region for congenital aural atresia at the 18q22.3-18q23 region.

STUDY DESIGN AND PATIENTS

The study describes one 18q deletion syndrome clinical report (Patient 15) with an overview of 19 other selected 18q deletion syndrome patients presenting congenital aural atresia from 18 published articles and one presented poster on 18q deletion syndrome.

RESULTS

Our investigation, together with the results of published 18q deletion syndrome reports, shows that the average frequency of congenital aural atresia is approximately 52%. A combination of three 18q deletion syndrome probands defines a chromosomal deletion site for congenital aural atresia at 18q22.3-18q23 in the region between markers D18S489 and D18S554. These polymorphic markers outline a putative critical interval of approximately 2.3 Mb, including the genes ZNF407, ZADH2, SDCCAG33, ZNF516, FLJ44881, ZNF236, MBP-Golli, and GALR1. The haploinsufficiency of these genes is suggested to be a primary cause of congenital aural atresia phenotype in 18q deletion syndrome individuals.

CONCLUSION

Congenital aural atresia is a relevant diagnostic clue and a major recognizable feature of 18q deletion syndrome. Early diagnosis of 18q deletion syndrome may enable application of hearing aids. Knockout studies on the congenital aural atresia mouse gene homolog may add further insight into the genes responsible for this condition.

A multiplex PCR predictor for aCGH success of FFPE samples

Formalin-fixed, paraffin-embedded (FFPE) tissue archives are the largest and longest time-spanning collections of patient material in pathology archives. Methods to disclose information with molecular techniques, such as array comparative genomic hybridisation (aCGH) have rapidly developed but are still not optimal. Array comparative genomic hybridisation is one efficient method for finding tumour suppressors and oncogenes in solid tumours, and also for classification of tumours. The fastest way of analysing large numbers of tumours is through the use of archival tissue samples with first, the huge advantage of larger median follow-up time of patients studied and second, the advantage of being able to locate and analyse multiple tumours, even across generations, from related individuals (families). Unfortunately, DNA from archival tissues is not always suitable for molecular analysis due to insufficient quality. Until now, this quality remained undefined. We report the optimisation of a genomic-DNA isolation procedure from FFPE pathology archives in combination with a subsequent multiplex PCR-based quality-control that simply identified all samples refractory to further DNA-based analyses.

18q deletions: Clinical, molecular, and brain MRI findings of 14 individuals

We studied 14 individuals with partial deletions of the long arm of chromosome 18, including terminal and interstitial de novo and inherited deletions. Study participants were examined clinically and by brain MRI. The size of the deletion was determined by segregation analysis using microsatellite markers. We observed that the phenotype was highly variable, even in two families with three 1st degree relatives. Among the 14 individuals, general intelligence varied from normal to severe mental retardation. The more common features of 18q-deletions (e.g., foot deformities, aural atresia, palatal abnormalities, dysmyelination, and nystagmus) were present in individuals lacking only the distal portion 18q22.3-qtel. Interstitial deletions exerted very heterogeneous effects on phenotype. In individuals with distal 18q22.3-q23 deletions, brain MRI was very distinctive with poor differentiation of gray and white matter on T2-weighted images.

Novel candidate tumour suppressor gene loci on chromosomes 11q23–24 and 22q13 involved in human insulinoma tumourigenesis

Insulinomas represent the predominant syndromic subtype of endocrine pancreatic tumours. Previous molecular studies have shown that gain of chromosome 9q rather than MEN1 gene mutation is an important early event in tumour development and that chromosomal instability is associated with metastatic disease. In order to identify new gene loci and to define further the critical genetic events in insulinoma tumourigenesis, 27 insulinomas were investigated by array-based comparative genomic hybridization (array CGH) on 3.7 k genomic BAC arrays (resolution < or =1 Mb). Fluorescence in situ hybridization was used to validate alterations in a subset of tumours. Array CGH most frequently detected loss of chromosomes 11q and 22q and gains of chromosome 9q. The chromosomal regions of interest (CRI) included 11q24.1 (56%), 22q13.1 (67%), 22q13.31 (56%), and 9q32 (63%). Evaluation of the simultaneous occurrence of these aberrations in the individual tumours revealed that gain of 9q32 and loss of 22q13.1 are early genetic events in insulinomas, occurring independently of the other alterations. In tumours with increased genomic complexity, these alterations were often detected simultaneously, occurring in the same tumour cells. Losses of 11q24.1 and 22q13.31 were also associated with these more advanced tumour cases. The CRIs identified most likely harbour crucial candidate genes important in insulinoma tumourigenesis.

Microarray-based comparative genomic hybridization and its applications in human genetics

Through the years, several techniques capable of detecting DNA copy number changes have been developed. A number of those, such as karyotyping and fluorescence in situ hybridization (FISH), have proven to be valuable tools in both research and diagnostics. Recently, a new technique, called microarray-based comparative genomic hybridization (array CGH), has been introduced. Array CGH has proven to be a specific, sensitive, and fast technique, with considerable advantages compared to other methods used for the analysis of DNA copy number changes. Array CGH enables analysis of the whole genome in a single experiment. Until now, its applications have been mainly directed at detecting genomic abnormalities in cancer. However, array CGH is also suitable for the analysis of DNA copy number aberrations that cause human genetic disorders. This review gives an overview of array CGH and its applications in human genetics. Advantages, limitations, and future perspectives of array CGH are discussed.