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Deletion/Duplication Analysis

Info Sheet   

ExonArrayDx – a novel, specialized service to evaluate one or more genes for partial or full gene deletions or duplications defined at the exon level. The ExonArrayDx test is based on the use of a ultra-high resolution microarray-based comparative genomic hybridization (array CGH), which has a higher sensitivity for detecting deletions and duplications compared to MLPA and quantitative PCR (qPCR), to detect partial or complete gene deletions and duplications of clinically significant genes. 

GeneDx offers this service for disorders known to be caused by deletions or duplications within a single gene as well as 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.

In addition to deletion/duplication analysis of a single gene from our test menu, Custom ExonArrayDx testing of any gene(s) in the exome (up to 20) is available.

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
  • Inherited eye disorders

It can be ordered for:

  • Analysis of selected gene(s) on our current test menu in which a deletion/duplication is suspected (Tests by Gene)
  • As a second tier test on a specimen, in which previous sequence analysis or whole exome sequence analysis, did not identify a disease-associated mutation.
     

Other possible indications for ExonArrayDx analysis include:
 

  • 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 (i.e., STK11 deletion associated with Peutz-Jeghers syndrome or 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).

 

*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.

ExonArray Testing (Test codes, CPT codes and TATs)

Custom ExonArrayDX Testing: Gene(s) Not on GeneDx Menu (Test codes, CPT codes and TAT)

Requirements:

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.

 

Info Sheet       Informed Consent

 

Deletion/duplication analysis is a specialized service for the detection of a whole or partial gene deletion or duplication in a single known gene of interest. Our deletion/duplication analysis is based on the innovative use of quantitative PCR-technology, which has a higher sensitivity for detecting deletions and duplications compared to FISH.

It can be ordered for:

  1. Analysis on any gene on our current test menu in which a deletion/duplication is suspected (Tests By Gene)
  2. As a second tier test on a specimen previously sequenced at GeneDx (a discount applies).
  3. For any gene not on our test menu; GeneDx will custom design a quantitative PCR assay for any gene in which a deletion/duplication is suspected in a patient.
     

Other possible indications for deletion/duplication analysis include:
 

  • As a complementary test or substitute for FISH and quantitative microarray analysis when a deletion or duplication syndrome (contiguous or single gene) is suspected.
  • As a confirmation test for a genomic gain or loss identified by genome-wide microarray analysis, such as GenomeDx.
  • To determine the presence or absence of a specific gene within a deleted chromosomal segment (contiguous gene deletion).
  • As second tier 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-Jegher syndrome, RAI1 deletion associated with Smith-Magenis syndrome).
  • Carrier testing for deletion/duplication syndromes when the specific region is known 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).
  • Using certain MLPA tests, contiguous gene deletion or duplication syndromes may also be detected (i.e. WAGR syndrome can be identified with the PAX6 MLPA testing kit).
     

Deletion/duplication analysis for a custom gene (gene not currently on our test menu) is a specialized service. Therefore, it is necessary to discuss these requests prior to sending a specimen. You can use the Contact Us link on our website, e-mail us at genedx@genedx.com or call GeneDx at (301)-519-2100.

CopyDx/MLPA Testing (Test codes, CPT codes and TATs)

 

Requirements: 

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

 

 

 

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