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GenomeDx: High-density, Genome-wide Oligonucleotide Microarray Analysis


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

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
View a table of genomic deletion and duplication syndromes that are densely covered
View a table for disease-specific loci that are densely covered
Click here for GenomeDx (oligo aCGH) Submission Form

This diagnostic service has now been improved using version 2 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 January 1, 2008, GenomeDx has been improved with the introduction of version 2.0 to provide high-resolution genome-wide oligo aCGH analysis with increased probe density and technical sensitivity. 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. Probes are placed at 35 kb intervals across the genome, thus more than doubling the probe density compared to GenomeDx array version 1.0. An even higher (2-10 times) density of probes increases the sensitivity at over 120 targeted genomic regions of clinical significance. These regions include loci for i) known genomic deletion and duplication syndromes, ii) selected genetic disorders with possible gene deletion/duplication (disease-specific loci), iii) all subtelomeric regions, and iv) other gene-dense regions, including the entire X chromosome. Based on this design, GenomeDx v.2.0 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, autism, seizures or any suspicion of genomic imbalance
  • 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 telomere FISH in persons with developmental disabilities/mental retardation
  • As a test to precisely determine the breakpoints of genomic alterations that were previously detected with conventional cytogenetic methods and BAC arrays
  • As a test to determine the presence or absence of a specific gene within a known region of genomic imbalance (contiguous gene deletion/duplication syndrome)
  • As a complementary diagnostic test in a Mendelian disorder due to functional loss of one allele
    • (haploinsufficiency), in particular when sequence analysis failed to identify a causative mutation and a whole gene deletion
  • is a possible cause

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 quantitative PCR analysis (CopyDx), microarray, or microsatellite marker genotyping.
  • In certain cases, interpretation of results depends on whether the copy number change is inherited or de novo. Therefore samples from parents will be analyzed free of charge.
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