Cytogenetics
Cytogenetics and Chromosomal Microarray at GeneDx
GeneDx provides comprehensive molecular cytogenetic testing. We offer a high-resolution whole-genome chromosomal microarray (CMA) to evaluate the entire genome for copy number changes, to detect uniparental disomy (UPD), and to detect single-gene deletions or duplications. Traditional chromosome analysis and FISH studies can also be ordered as stand-alone tests or in conjunction with CMA or gene-specific DNA sequencing tests.
Parental testing is often recommended when a patient is found to have a genomic imbalance. This testing is standard of care in many circumstances and also helps interpret findings of unclear significance in a proband.
For more information, click on the appropriate tab below:
GeneDx offers a custom-designed postnatal chromosomal microarray (CMA) for detection of pathogenic copy number changes. The whole-genome CMA uses 182,000 probes to evaluate the entire genome for chromosomal aneuploidy and intrachromosomal deletions and duplications. In addition, SNP genotyping probes on all chromosomes allows detection of large blocks of homozygosity, which may represent uniparental disomy. Lastly, this array also contains exon-level probe coverage to detect single-exon deletions or duplications in approximately 65 genes associated with developmental disorders.
*Chromosomal microarray testing is also available for prenatal samples. For more information regarding prenatal cytogenetic testing services at GeneDx, please click here.
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| Whole-Genome Chromosomal Microarray (CMA) for Product of Conception (POC) |
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GeneDx participates in the International Standards for Cytogenomic Arrays (ISCA) consortium. Anonymized CMA data and clinical information may be submitted to a HIPAA-compliant, de-identified database as part of the National Institutes of Health's effort to improve diagnostic testing and enhance our understanding of the relationships between genetic changes and clinical symptoms. Visit the consortium website here. Confidentiality and full anonymity of each submission is maintained. Please use the current GeneDx cytogenetics test requisition and consent forms when requesting testing. If these GeneDx forms are not sent with the submitted specimen, CMA data will be anonymized and submitted to the ISCA database. If you wish not to have genomic information derived from your submitted sample sent to the database, please email iscaoptout@genedx.com.
GeneDx offers traditional cytogenetic testing including chromosome analysis and FISH studies. Karyotyping by G-banding is available for analysis of the number and structures of individual chromosomes. Additionally, individual FISH assays are available for several genomic disorders, and also for intrachromosomal abnormalities, such as terminal deletions or duplications, subtelomeric rearrangements, and for pericentromeric imbalances (supernumerary marker chromosomes).
*Chromosome analysis and FISH studies are also available for prenatal samples. For more information regarding prenatal cytogenetic testing services at GeneDx, please click here.
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Postnatal chromosome analysis
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Fish Analysis
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Parental testing policy: GeneDx recommends parental testing when a patient is found to have a genomic imbalance. Parental analysis is used to evaluate the inheritance of an abnormality (familial or de novo) and may also clarify the clinical significance of copy number changes. GeneDx uses FISH, quantitative PCR (qPCR), targeted CMA or G‐band chromosome analysis, as appropriate, for parental analysis.
* For clinically well‐characterized genomic imbalances, parental analysis is available as a separate test for an additional cost. Additionally, testing other family members is available as a separate test for an additional cost. Price and CPT codes for known familial deletion/duplication test are provided below.
* For genomic imbalances of unclear significance, GeneDx offers free parental analysis. The turn-around time for an updated report including parental results is 4-6 weeks.
Known Familial Deletion/Duplication Testing
Array CGH Guide for Physicians and Patients
Click here to view the online version of our “Genome-Wide Microarray Analysis” flipbook, or to order a printed copy of the flipbook please send an email to zebras@genedx.com with your request.
Genome Analysis Tool
Array CGH reports from GeneDx contain data that can be used to explore genomic regions of interest in the UCSC genome browser. Click here to sign in with the username "GenomeDx" and password "report". Enter the sequence coordinates from the report in the format "chr#:xxxxx-xxxxx". Array probes are shown on the top half. Questions about array probe coverage or interpretation of findings can be directed to our genetic counselors or clinical cytogeneticists.
The ISCA consortium
GeneDx participates in the International Standards for Cytogenomic Arrays (ISCA) consortium. Anonymized CMA data and clinical information may be submitted to a HIPAA-compliant, de-identified database as part of the National Institutes of Health's effort to improve diagnostic testing and enhance our understanding of the relationships between genetic changes and clinical symptoms. Visit the consortium website here to find out more information. Confidentiality and full anonymity of each submission is maintained. Please use the current GeneDx cytogenetics test requisition and consent forms when requesting testing. If these GeneDx forms are not sent with the submitted specimen, CMA data will be anonymized and submitted to the ISCA database. If you wish not to have genomic information derived from your submitted sample sent to the database, please email iscaoptout@genedx.com.
Genomic Oligoarray and SNP Array Evaluation Tool v1.0
Significant absence of heterozygosity (AOH) suggests identity by descent (IBD) (e.g. parental consanguinity). Regions of AOH in an individual may have clinical significance if both parents are heterozygous carriers of an autosomal recessive mutation in the same gene located within one of these genomic regions. A list of recessive disorders mapping to any identified homozygous blocks can be obtained using the online resource provided here.
References and other resources
- Ming, JE et al., (2006) Rapid detection of submicroscopic chromosomal rearrangements in children with multiple congenital anomalies using high density oligonucleotide arrays. Hum Mutat. 27(5):467-473.
- Aradhya, S and Cherry, AM (2007) Array-based comparative genomic hybridization: clinical contexts for targeted and whole-genome designs. Genet Med. 9(9):553-559.
- Thuresson, AC et al., (2007) Whole-genome array-CGH for detection of submicroscopic chromosomal imbalances in children with mental retardation. Cytogenet Genome Res 118(1):1-7.
- Aradhya, S et al., (2007) Whole-genome array-CGH identifies novel contiguous gene deletions and duplications associated with developmental delay, mental retardation, and dysmorphic features. Am J Med Genet A. 143A(13):1431-1441.
- Toruner, GA et al., (2007) An oligonucleotide based array-CGH system for detection of genome wide copy number changes including subtelomeric regions for genetic evaluation of mental retardation. Am Je Med Genet A. 143A(8):824-829.
- Shaikh, TH (2007) Oligonucleotide arrays for high-resolution analysis of copy number alteration in mental retardation/multiple congenital anomalies. Genet Med 9(9):617-625.
- Baris, HN et al., (2007) Diagnostic utility of array-based comparative genomic hybridization in a clinical setting. Am J Med Genet A. 143A(21):2523-2533.
- McMullan et al., (2009) Molecular karyotyping of patients with unexplained mental retardation by SNP arrays: a multicenter study. Hum Mutat. 30(7):1082-1092.
- Miller et al., (2010) Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 86(5):749-764.
- Kearney et al., (2011) American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med. 13(7):680-685.
- Sanders et al., (2011) Multiple Recurrent De Novo CNVs, Including Duplications of the 7q11.23 Williams Syndrome Region, Are Strongly Associated with Autism. Neuron. 70(5):863-885.
- Bremer et al., (2011) Copy number variation characteristics in subpopulations of patients with autism spectrum disorders. Am J Med Genet B Neuropsychiatr Genet. 156(2):115-124.
- American College of Medical Genetics (ACMG) Practice Guidelines: Microarray / CMA/ CGH
- Genome.gov
