Less clear is how often outcomes will be improved and in which cases interventions might have occurred in the absence of testing. The guideline noted that the causal relationship between many of the genetic abnormalities detected by CGH and autism spectrum disorder is not clear. Regarding its use in ASD, the AAP guidelines for the identification and evaluation of children with ASDs Johnson et al, noted that "[c]omparative genomic hybridization-microarray analysis is a promising tool that may become standard of care in the future, but this technique has not been evaluated systematically in children with ASDs.
The American College of Medical Genetics published practice guidelines for the clinical genetics evaluation in identifying the etiology of ASD Schaefer et al, The guidelines state: "Currently, array comparative genomic hybridization aCGH has emerged as a powerful new tool that promises further revolution of clinical genetic testing. The technology of assessing submicroscopic re-arrangements is evolving at a mind-boggling rate.
New platforms are being developed at rates faster than clinical studies can define their use. The availability of multiple platforms further complicates the ability to compare studies from various sites. Relatively few studies have been published that provide an actual estimate of the diagnostic yield of aCGH in evaluating patients with autism. They noted that, "Until definitive, large-scale studies provide confirmation of the use of aCGH, its role in the evaluation of autism spectrum disorders may not be fully appreciated.
The assessment stated that CGH arrays have the advantage of greatly improved resolution and more exact locus definition of conventionally detectable abnormalities; however, the results are conceptually similar to those obtained by conventional methods.
The assessment found that, while the diagnostic yield represents a vast improvement in identifying a genetic etiology for these patients, very few studies have addressed the impact of testing on patient outcomes; thus, it is not possible to draw evidence-based conclusions regarding the clinical utility of aCGH genetic evaluation. However, the same may be said of conventional cytogenetic testing.
The assessment stated: "Some have called for broader efforts to standardize protocols, define quality criteria for successful analysis, and develop reporting guidelines; in addition, a national multicenter trial to address accuracy, indications, and efficacy has been suggested. This approach has proved useful in identifying abnormalities in individuals with developmental delay and physical abnormalities when results of traditional chromosomal analysis have been normal.
The use of CGH in prenatal diagnosis, at present, is limited because of the difficulty in interpreting which DNA alterations revealed through CGH may be normal population variants. Until there are more data available, use of CGH for routine prenatal diagnosis is not recommended.
An article by Moeschler et al , described the experience of clinical genetics practices in Northern New England Vermont, New Hampshire, and Maine. The genetic practices formed a learning collaborative with the purpose of improving genetic health care and outcomes. The aim was to improve the rate of etiological diagnosis of those with DDs referred to each genetics center by improving the processes of care. Four of 5 sites also evaluated the impact of CGH laboratory testing of such patients and found significant site-to-site variation in the rate of new diagnoses by CGH with the average new diagnosis rate of One source of variation noted was the type of array utilized.
Some sites utilized targeted BAC arrays and others utilized the oligonucleotide arrays. However, the authors stated, "[w]ithout process and outcomes data to contribute to the discussion of how the group might improve the application of such technology, we can only speculate on possible explanations for the variation.
This would be particularly informative and this represents an opportunity for future clinical improvement activities and, perhaps, an impetus to accelerate implementation in the clinical sites.
Sagoo et al updated the diagnostic and false-positive yields of CGH testing from a previously reported systematic review and meta-analysis on patients with learning disability and congenital anomalies in whom conventional cytogenetic analyses had proven negative Subramonia-Iyer et al, Nineteen studies 13, patients were included of which 12 studies 13, patients were published since their previous analysis.
The authors stated that this updated meta-analysis provides new evidence to support the use of CGH in investigating patients with learning disability and congenital anomalies in whom conventional cytogenetic tests have proven negative; however, given that this technology also identifies false positives at a similar rate to causal variants, caution in clinical practice should be advised.
An evaluation of this meta-analysis by the Center for Reviews and Dissemination stated that the reliability of the conclusions of this meta-analysis "is uncertain due to some unclear reporting, potential publication bias, and failure to appropriately consider study quality. A review article on the clinical utility of CGH for the detection of chromosomal imbalances associated with mental retardation and multiple congenital anomalies reported that a number of different array CGH platforms have emerged and are being used as an adjunct test to standard karyotype analysis.
The authors noted that the current limitations of the technology include the inability to detect balanced chromosome rearrangements and the equivocal nature of copy number alterations of unknown significance that may be identified Edelmann and Hirschhorn, The ACOG's Committee Opinion on array CGH in prenatal diagnosis stated that the widespread use of array CGH for the diagnosis of genomic re-arrangements in children with idiopathic mental retardation, developmental delay, and multiple congenital anomalies has spurred interest in applying array CGH technology to prenatal diagnosis.
The use of array CGH technology in prenatal diagnosis is currently limited by several factors, including the inability to detect balanced chromosomal re-arrangements, the detection of copy number variations of uncertain clinical significance, and significantly higher costs than conventional karyotype analysis. Although array CGH has distinct advantages over classic cytogenetics in certain applications, the technology is not currently a replacement for classic cytogenetics in prenatal diagnosis.
Furthermore, the Committee Opinion stated that targeted array CGH may be useful as a screening tool; however, further studies are needed to fully determine its utility and limitations. Roesser reviewed genetic testing guidelines in the evaluation of children with ASDs.
The clinical report published by the AAP recommended individualizing the work-up, including karyotype and specific DNA testing for fragile X syndrome. The medical records of children seen through the Kirch Developmental Services Center were abstracted for genetic testing and factors associated with this testing.
Abnormalities were found on karyotype in 2. The author concluded that the diagnostic yield of the genetic testing was low in this population. Furthermore, their findings supported the theory that CMA can be considered as part of the initial genetic screening in children with ASD in most situations. They stated that prospective studies will need to be performed to evaluate children in a standard fashion.
Single nucleotide polymorphism-based chromosomal microarray of products of conception yields a higher rate of results compared with karyotyping, and it can identify maternal cell contamination, which is important in decreasing false-negative results. Additional information is needed regarding the clinical use and cost-effectiveness in cases of recurrent miscarriage and structurally normal pregnancy losses at less than 20 weeks of gestation.
There are currently insufficient published reports on the use of CGH in recurrent miscarriage. Available guidelines for genetic evaluation and counseling of couples with recurrent miscarriage Laurino et al, stated: "The use of specialized chromosomal studies such as comparative genome hybridization, subtelomeric studies, interphase studies on sperm and assays for skewed X-inactivation patterns are not warranted at this time, as their clinical utility has yet to be determined.
Bartnik et al noted that there are only few studies of the role of CNVs in epilepsy and genetic etiology in the vast majority of cases remains unknown. These researchers applied whole-genome exon-targeted oligonucleotide array CGH to a cohort of patients with various types of epilepsy with or without additional neurodevelopmental abnormalities.
Chromosomal microarray analysis revealed 24 non-polymorphic CNVs in 23 patients, among which 10 CNVs are known to be clinically relevant. Two rare deletions in 2q The authors concluded that these findings further support the notion that rare CNVs can cause different types of epilepsy, emphasize the efficiency of detecting novel candidate genes by whole-genome array CGH, and suggest that the clinical application of array CGH should be extended to patients with unexplained epilepsies.
These results need tobe validated by well-designed studies. The American College of Medical Genetics and Genomics ACMG standards and guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications revision states that "microarray methodologies, including array comparative genomic hybridization and single-nucleotide polymorphism-detecting arrays, are accepted as an appropriate first-teir test for the evaluation of imbalances associated with intellectual disability, autism, and multiple congenital anomalies.
Bauer and Bastian stated that cancer typically results in loosened control over genomic integrity, resulting in alterations of the genome of cancer cells. Comparative genomic hybridization CGH is a method that can be used on DNA extracted from routinely fixed tissue to assess the entire genome for the presence of changes in DNA copy number.
CGH analysis has revealed that melanoma differs from melanocytic nevi by the presence of frequent chromosomal aberrations. In contrast, melanocytic nevi typically show no chromosomal aberrations, or have a restricted set of alterations with basically no overlap to melanoma.
These marked differences between aberration patterns in melanomas and melanocytic nevi can be exploited diagnostically to classify melanocytic tumors that are ambiguous based on histopathologic assessment.
In addition to potential diagnostic applications, detailed analyses of recurrent aberrations can lead to the identification of genes relevant in melanocytic neoplasia. Ali et al stated that melanocytic neoplasms with spitzoid features including spitz nevi, spitz tumors and spitzoid melanomas are commonly encountered in the practice of dermatopathology.
Although many cases can be accurately diagnosed on the basis of morphology and histology, a significant number of cases may be difficult to accurately classify.
Several studies have now shown that chromosomal copy number aberrations are typical of melanoma while present in only a small percent and to a limited degree in spitz nevi. In this study, these researchers correlated the clinical, histologic and array CGH findings of 10 spiztoid melanocytic neoplasms. This study showed that the clinical and histologic changes correlate well with the molecular findings by array CGH.
Further that array CGH can be used to help classify and predict behavior of spitzoid melanocytic neoplasms. A limited variety of copy number aberrations including gains of 11p and much more rarely 7q may be seen in spitz nevi. Additionally in this report these investigators presented the first case of a typical spitz nevus with copy number gains involving both 7q and 11p.
Conversely, melanomas with spitzoid features typically have multiple chromosomal copy number aberrations involving a variety of loci. A smaller number of chromosomal aberrations, possibly a single aberrant locus, may be present in spitz tumors, but their presence may predict more aggressive behavior. Ahmadi et al stated that melanocytic proliferations with Spitz differentiation present a difficult clinicopathologic dilemma, as their spectrum ranges from benign to malignant.
Distinct entities include Spitz nevus, atypical Spitz nevus, and Spitzoid melanoma. Their histopathologic differentiation can be challenging, and cases of Spitzoid melanoma initially diagnosed as benign Spitz nevi were reported in the literature. The goal of this study was to discuss the diagnostic tools including CGH , which may be helpful in differentiating benign Spitz nevi from malignant melanoma with Spitzoid features, and to propose an appropriate management strategy for each entity.
Medical records of patients referred for suspicious nevi were reviewed. Data regarding demographics, site, pathology reports, and treatment were reviewed. A total of 4 patients with 3 distinct diagnoses involving Spitz differentiation were identified. The pathologic interpretation of these biopsies was difficult and multiple dermatopathologists were involved. All 4 patients underwent excision with or without sentinel node biopsy.
The authors concluded that otolaryngologists, plastic surgeons and dermatopathologists will encounter patients who have melanocytic lesions with Spitz differentiation at some point in their career. The management of these patients is significantly impacted by the histopathologic diagnosis, and should not be undertaken until it is confirmed, possibly with CGH. They believed that a team approach between the surgeon and the dermatopathologist is crucial when diagnosing and managing patients with Spitz lesions.
Busam et al noted that Spitz tumors represent a group of melanocytic neoplasms that typically affect young individuals. Microscopically, the lesions are composed of cytologically distinct spindle and epithelioid melanocytes, with a range in the architectural display or the cells, their nuclear features, and secondary epidermal or stromal changes.
Recently, kinase fusions have been documented in a subset of Spitz tumors, but there is limited information on the clinical and pathologic features associated with those lesions. These investigators reported a series of 17 patients 9 males, 8 females with spitzoid neoplasms showing ALK fusions 5 Spitz nevi and 12 atypical Spitz tumors.
The patients' ages ranged from 2 years to 35 years mean of 17 years; median of 16 years. Most lesions were located on the lower extremities and presented clinically as polypoid nodules.
All tumors were compound melanocytic proliferations with a predominant intra-dermal growth. Tumor thickness ranged from 1. The most characteristic histopathologic feature of the tumors seen in all but 2 lesions was a plexiform dermal growth of intersecting fascicles of fusiform melanocytes.
All but 2 tumors were amelanotic. All tumors were strongly immunoreactive for ALK. None of the 8 tumors that were analyzed by FISH for copy number changes of 6p, 6q, 9p, or 11q met criteria for melanoma. Two patients underwent a sentinel lymph node biopsy, and in both cases melanocyte nests were found in the subcapsular sinus of the node. Array CGH of these 2 tumors revealed no chromosomal gains or losses. The 11p amplification is characteristic of Spitz tumors and is not commonly seen in melanoma.
A study of 16 atypical Spitz tumors with array CGH showed that almost all of the chromosomal aberrations present in these lesions were not those commonly seen in conventional melanoma. These findings provide support for atypical Spitz tumor as a group of lesions distinct from both conventional Spitz tumors and conventional melanoma ….
Histopathologic diagnosis -- The initial step in diagnosis is histopathologic examination of the excised tumor to determine whether a clear-cut Spitz tumor or melanoma is present. Atypical lesions should be systematically evaluated for histopathologic and immunohistochemical features.
For ambiguous lesions, investigation of genetic aberrations by comparative genomic hybridization or fluorescence in situ hybridization may be performed if available …. Immunostaining may be helpful in the evaluation of ambiguous lesions. Molecular analysis with comparative genomic hybridization or fluorescence in situ hybridization can be performed if the diagnosis remains uncertain.
The absence of genetic aberrations or the demonstration of an isolated copy gain in chromosome 11p favors a diagnosis of benign lesion.
Bestetti and associates stated that primary ovarian insufficiency POI describes the progression toward the cessation of ovarian function before the age of 40 years. Genetic causes are highly heterogeneous and despite several genes being associated with ovarian failure, most of genetic basis of POI still needs to be elucidated. These researchers determined whether high resolution array-CGH analysis on a cohort of women showing a POI phenotype in young age can identify CNVs with a deleterious effect on ovarian function.
Results of patients and female controls were analyzed to search for rare CNVs. All variants were validated and subjected to a gene content analysis and disease gene prioritization based on the present literature to find out new ovary candidate genes. Characterization of particular CNVs with molecular and functional studies was carried out to examine their pathogenic involvement in POI.
These investigators identified 37 ovary-related CNVs involving 44 genes with a role in ovary in 32 patients. All except 1 of the selected CNVs were not observed in the control group. Disease gene prioritization identified both previously reported POI genes e. The authors concluded that their array-CGH screening turned out to be efficient in identifying different CNVs possibly implicated in disease onset, thus supporting the extremely wide genetic heterogeneity of POI. The authors stated that this study had several limitations.
This was a descriptive analysis for almost all of the CNVs identified. Inheritance studies of CNVs in some non-familial sporadic cases was not performed as the parents' DNA samples were not available. Furthermore, real-time quantitative polymerase chain reaction RT-qPCR analyses were performed in few cases as RNA samples were not always available and the genes were not expressed in blood.
Venturella and colleagues noted that several causes for POI have been described, including iatrogenic and environmental factor, viral infections, chronic disease as well as genetic alterations. In a systematic review, these researchers collected all the genetic mutations associated with non-syndromic POI.
All studies, including gene screening, genome-wide study and assessing genetic mutations associated with POI, were included and analyzed. Syndromic POI and chromosomal abnormalities were not evaluated. Future strategies include linkage analysis of families with multiple affected members, array CGH for analysis of copy number variations, NGS technology and genome-wide data analysis.
These investigators stated that this review included almost all genetic abnormalities and genes linked with non-syndromic POI. Its occurrence is not associated with an increase in maternal age, but whenever the additional chromosome complement is of paternal origin, the placenta exhibits histological characteristics of a partial hydatidiform mole Brancati et al.
In fact, in one of the cases with triploid karyotype, in which the anatomic-pathological study showed hydropic degeneration of the villi, we were able to demonstrate the paternal origin of the additional chromosome complement data not shown.
The anatomic-pathological findings show that hydropic degeneration of villi is not a feature exclusive of hydatidiform moles complete or partial. Although half of the cases in which it was observed presented a chromosome alteration, inferences regarding the karyotype based on pathological examination should be avoided Lescoat et al.
The data of abortion investigations reported so far show an encouraging picture as to the applicability of array-CGH, at least as a complementary method to the traditional cytogenetic techniques. The results of the present study, confirm that the use of array-CGH to complement classical cytogenetics in the chromosome analyses of abortion material is highly recommended. The authors thank Nicole S. Grosso for reviewing the manuscript. Abrir menu Brasil. Genetics and Molecular Biology.
Abrir menu. Borovik Ana Beatriz A. Perez Luciana R. Krepischi-Santos Silvia S. Costa Carla Rosenberg About the authors. Key words: spontaneous abortion, chromosomal aberrations, array-CGH. Cytogenetic analysis Whenever the material contained chorionic villi, both short according to the technique described by Simoni et al.
Results Of the 54 cases referred initially, five 9. Prenat Diagn Fertil Steril Eur J Hum Genet Daniely M, Aviram-Goldring A, Barkai G and Goldman B Detection of chromosomal aberration in fetuses arising from recurrent spontaneous abortion by comparative genomic hybridization.
Hum Reprod Am J Hum Genet Pathologica Abstract in English. Greenwold N and Jauniaux E Collection of villous tissue under ultrasound guidance to improve the cytogenetic study of early pregnancy failure. Mol Hum Reprod Fluorescence in situ hybridization as a confirmatory technique. J Obstet Gynaecol Res Mod Pathol Nucleic Acids Res e Acta Obstet Gynecol Scand J Med Genet Clin Genet Am J Med Genet A Hum Genet Med Sci Abstract in English.
J Histochem Cytochem Abstract Background Array CGH is widely used in cytogenetics centres for postnatal constitutional genome analysis, and is now recommended as a first line test in place of G-banded chromosome analysis. Conclusions Array CGH is a robust and cost-effective alternative to traditional cytogenetic methodology; it provides a higher diagnostic detection rate than G-banded chromosome analysis, and adds to the sum of information and understanding of the role of genomic imbalance in disease.
Background Array CGH aCGH has a much higher resolution than G-banded chromosome analysis and most cytogenetic departments are now using this approach either as an adjunct to G-banded chromosome analysis, or as a first-line test for selected patient groups [ 1 , 2 ]. Methodology Genomic DNA extracted from peripheral blood or saliva, or DNA provided by external laboratories, was processed as previously described [ 3 ].
Turn-around times and success rates The average reporting time for first-line tests over the entire period was 21 days from receipt of sample.
Open in a separate window. Patients may carry more than one pathogenic imbalance. Table 2 Established genomic disorders detected. Interpretation The size of imbalances with potential clinical significance generally correlated with severity of phenotype, although there were exceptions.
Structural information aCGH does not give information on the location in the genome of, for instance, duplicated regions, or on the structure of chromosomes. Incidental findings These are unavoidable for any whole genome test and can be difficult to deal with clinically, especially with late onset conditions and cancer-susceptibility genes where little may be known of the prevalence or penetrance of clinical features associated with imbalances.
Balanced rearrangements Despite the increase in resolution and the higher diagnostic yield associated with aCGH testing, there may be concern that without visualisation of chromosomes by traditional cytogenetic techniques, balanced rearrangements will not be detected.
Summary This report describes 8, first line aCGH tests in a state-funded diagnostic laboratory. Competing interests The authors declare that they have no competing interests. Acknowledgements We are grateful to our clinical colleagues for supporting this work and to the other members of the Cytogenetics Department for their enthusiastic participation.
Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. Clinical implementation of whole-genome array CGH as a first-tier test in pre and postnatal cases. Validation and implementation of array comparative genomic hybridisation as a first line test in place of postnatal karyotyping for genome imbalance.
Detection of mosaicism for genome imbalance in a cohort of 3, clinical cases using an oligonucleotide array CGH platform. Eur J Med Genet. Detection of large-scale variation in the human genome. Nat Genet. Strategies for the rapid prenatal diagnosis of chromosome aneuploidy.
Eur J Hum Genet. The causality of de novo copy number variants is overestimated. De novo rates and selection of large copy number variation. Genome Res. Further delineation of the 15q13 microdeletion and duplication syndromes: a clinical spectrum varying from non-pathogenic to a severe outcome.
J Med Genet.
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