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GenomeDx: Whole Genome Cytogenetic Array CGH (high-density oligonucleotide array)

For detailed information on this service, including technical design, test method, sensitivity, limitations, reports, and relevant literature, please use the following links:

 Click Here to View the GenomeDx array probe coverage in regions and genes of clinical interest

 Click here for GenomeDx Information Sheet including prices and CPT codes

 Click Here to View an aCGH Technology Comparison Chart

 View a Sample GenomeDx Result Report

 Click here for GenomeDx (oligo aCGH) Submission Form

This diagnostic service has now been improved using version 3 of our GenomeDx array. GenomeDx specifically tests for regions of genomic gain or loss across the known, non-repetitive sequence of the entire genome and is the next generation of chromosome analysis. Changes in DNA dosage, ie., genomic deletions, duplications and amplifications, may be associated with a multitude of pediatric and adult genetic disorders. The technology is also known as Chromosomal Microarray Analysis (CMA) or oligo array Comparative Genomic Hybridization (oligo aCGH).
 

What is the GenomeDx test design?                                                                                   


As of June, 2008, GenomeDx has been improved with the introduction of version 3.0 to provide high-resolution genome-wide oligo aCGH analysis with increased probe density and technical sensitivity across almost 30 regions associated with susceptibility to autism spectrum disorders It consists of a custom-designed, validated oligonucleotide-based microarray with 105,000 probes across the non-repetitive sequence of the genome to evaluate for known as well as novel genomic deletion and duplication syndromes The new GenomeDx version 3 has a genome-wide coverage with average probe spacing of 37 kb and additional probe density (9-17 kb resolution) at over 150 clinically relevant loci. Specific dosage-sensitive genes have also been selected to contain ultra-high probe density (300bp-1 kb resolution). The specifically targeted regions include loci for i) known genomic deletion and duplication syndromes, ii) selected genetic disorders with possible gene deletion/duplication (disease-specific loci), iii) autism susceptibility loci, iv) all subtelomeric and pericentromeric regions, and v) other gene-dense regions, including the entire X chromosome. Based on this design, GenomeDx v.3.0 can identify regions of genomic gain and loss as small as 5-10 kb in the targeted regions and as small as 200 kb in other areas of the genome.

What are the indications for GenomeDx analysis?                                                             
 

  • As a primary screening test for the diagnosis of persons with unexplained dysmorphic features, birth defects, unexplained mental retardation/developmental delay, multiple congenital anomalies, seizures or any suspicion of genomic imbalance
  • As a primary screening test for the diagnosis of persons with autism spectrum disorder
  • As a complementary or replacement test for FISH and BAC-based microarray analysis when a deletion or duplication syndrome (contiguous or single gene) is suspected
  • As a superior alternative to subtelomere FISH in persons with developmental disabilities/mental retardation
  • As a test to precisely determine the breakpoints of chromosomal rearrangements that were previously detected with conventional cytogenetic methods and BAC arrays
  • As a complementary diagnostic test in a Mendelian disorder due to functional loss of one allele (haploinsufficiency), specifically when sequence analysis fails to identify a causative mutation and a whole-gene deletion is suspected


How is GenomeDx analysis done?                                                                                        
(See also our explanatory booklet "Your Guide To Microarray Analysis")                      
 

  • DNA from a proband’s blood specimen is labeled, mixed with a gender-matched, diploid reference and hybridized with 105,000 probes of the microarray. The results are analyzed by comparing the hybridization pattern of the proband’s and reference specimens
  • Significant numeric aberrations are compared to known copy number variable regions in the general population and to previously reported abnormalities
  • Any clinically relevant change in DNA dosage is independently confirmed with the most appropriate method, including FISH, quantitative PCR analysis (CopyDx), and/or array CGH of another design (15K or 60K)

Parental testing policy                                                                                                         

GeneDx recommends parental testing in cases in which the 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 the patient’s results. GeneDx offers free parental analysis in cases in which parental testing can be useful to interpret a result of unclear clinical significance in the patient. When a patient has a clinically well‐characterized genomic imbalance and parental testing is indicated (e.g., to determine if a microdeletion is inherited) or if testing is standard of care to determine recurrence risk and for genetic counseling (e.g., to rule out a balanced chromosomal rearrangement in a parent), FISH or targeted array CGH (FISHonChipDx) testing is available for an additional cost. Please refer to the information sheet for further detail.

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