ExonArrayDx - a novel service to evaluate one or more genes from a list of >460 genes for partial or full gene deletions or duplications defined at the exon level.

GeneDx now offers ultra-high resolution microarray-based comparative genomic hybridization (array CGH) to detect partial or complete gene deletions and duplications of clinically significant genes. ExonArrayDx gene list (Clinical) The ExonArrayDx test permits deletion/duplication analysis at the exon level for disorders known to be caused by deletions or duplications within a single gene.

Exon-level deletion/duplication testing is also available for disorders due to haploinsufficiency or loss of function for a specific gene for which the frequency of gene deletions/duplications is currently not well established. ExonArrayDx gene list (Research) 
 

There are several categories of disorders for which the relevant genes are tested by ExonArrayDx:

• Autosomal dominant developmental disorders caused by haploinsufficiency
• Multiple congenital anomaly syndromes
• Inherited (familial) cancer and genome instability syndromes
• Autosomal recessive metabolic disorders
• X-linked mental retardation
• Autism spectrum disorders
• Inherited cardiac disorders
• Genetic eye disorders

A total of 484 unique genes are available for analysis on the ExonArrayDx platform. Deletion/duplication analysis by ExonArrayDx may be requested for a single gene or for a custom panel of clinically related genes (up to 10 genes). Please see the ExonArrayDx gene lists for details.

GeneDx offers sequence analysis for a large number of autosomal recessive disorders. For most autosomal recessive disorders, if sequencing is done at GeneDx and only one mutation has been identified in a patient, GeneDx will also perform ExonArrayDx microarray analysis to exclude a deletion of the second allele at no extra cost.

How does deletion/duplication analysis differ from other diagnostic tests done by DNA sequencing?

ExonArrayDx deletion/duplication analysis is a specialized service for the detection of a whole or a partial gene deletion or duplication. The ExonArrayDx test is based on the innovative use of microarray-based comparative genomic hybridization, which has a higher sensitivity for detecting deletions and duplications compared to MLPA and quantitative PCR (qPCR). It can be ordered for:

• Analysis of selected genes on our current test menu in which a deletion/duplication is suspected ( http://www.genedx.com/tests_by_gene.php)
• As a second tier test on a specimen previously sequenced at GeneDx (a discount applies). 

What are the possible indications for ExonArrayDx analysis?

• As a primary test in a Mendelian disorder due to haploinsufficiency when sequence analysis fails to identify a causative mutation; in particular when whole or partial gene deletions are a known cause for the disorder (for example STK11 deletion associated with Peutz-Jeghers syndrome, RAI1 deletion associated with Smith-Magenis syndrome). 

• To evaluate for deletions or duplications when a single mutation has been identified for a recessive disorder. 

• As a confirmation test for deletion or duplication detected by MLPA or qPCR.

• Carrier testing when a specific deletion or duplication has been identified in an affected relative (i.e., testing of carrier status of female relatives of an affected male with X-linked hydrocephalus due to L1CAM deletion).

Deletion/duplication testing using ExonArrayDx sounds very similar to GenomeDx. What are the similarities and differences between these two tests?

• Both ExonArrayDx and GenomeDx use the same technology. The key difference is that ExonArrayDx is intended to detect deletions/duplications within individual exons and introns of targeted genes and therefore can identify whole or partial gene deletions or duplications. The probe spacing on the ExonArrayDx platform is very small – between 100-200bp within exons and 3 probes per intron regardless of size. As a result, the ExonArrayDx test can detect deletions/duplications as small as 250-500bp within a targeted gene. When a whole gene deletion/duplication is found, the ExonArrayDx test cannot determine the breakpoints outside the gene.
• GenomeDx is an oligonucleotide microarray with a cytogenetics focus and designed for evaluating the entire human genome for whole chromosome aneuploidy or segmental aneusomy. The GenomeDx array can detect interstitial imbalances as small as 100 kb genome-wide and approximately 5-20 kb in >150 clinically relevant regions that are targeted with higher probe density. This test can define the breakpoints of deletions or duplications of large chromosomal imbalances as well as of entire genes. Technical limits apply and depend predominantly on the number and density of probes that are used.

How is ExonArrayDx deletion/duplication analysis ordered?

• ExonArrayDx analysis a specialized service intended to interrogate specific clinically significant genes. Please use the submission form link at the top of this page to download. It is necessary to discuss any deletion/duplication analysis request prior to sending a specimen. Please use the Contact Us link on our website, e-mail us at genedx@genedx.com or call GeneDx at (301)-519-2100.

What type of specimen is required?

• Our standard specimen requirement for this analysis is a single tube with 1-5 ml blood in EDTA. Please DO NOT send buccal swabs/brushes. Please see our standard Sample Requirements page.