Deletion/Duplication Analysis

Genes

Various Genes

Test Guide

The Collagen Diagnostic Laboratory offers testing for copy number changes using a custom high-density targeted oligonucleotide array (8x60K Agilent platform).  Targeted array testing is offered for the majority of genes on our test menu.  Genes where deletion/duplication analysis is not yet available are marked with an asterisk on the test requisition form.

The array includes probes covering gene coding sequences, regions 10 kb upstream and downstream of the gene(s) of interest, and selected regions containing regulatory elements associated with the genes(s) of interest.  

Methodology

Microarray:  DNA extracted from the patient and a control DNA sample are labeled separately with contrasting fluorescent dyes. The DNA samples are normalized, mixed and hybridized to the custom high density oligonucleotide microarray targeting the gene(s) of interest. After hybridization, the microarray is scanned and an intensity ratio profile of the fluorescent dye signals is generated. The data are analyzed to identify copy number changes in the patient compared to the normal control.

Specimen Requirements

Stored Sample (Reflex testing)

BLOOD:
2 EDTA (purple top) tubes
Adults: 5-10cc
Children: 3-5cc
Infants: 2-3cc

Whole blood may be stored up to 5-7 days in the refrigerator before shipping.

DNA:
Single Gene, +/- array (del/dup):15 µg DNA at a minimum concentration of ≥200 ng/µl
Gene panels, +/- array (del/dup): 35 µg DNA at a minimum concentration of ≥200 ng/µl

Special Instructions

In some instances, copy number variants are detected incidentally in targeted regions outside of the gene(s) of interest. The Collagen Diagnostic Laboratory makes every effort to alert ordering providers of incidental findings that are of known clinical significance and medically actionable. Please be aware that incidental findings may be detected regardless of the gene(s) ordered.

Frequently Asked Questions on deletion/duplication studies:

Which genes can array CGH be ordered for?

Array CGH testing is available for the majority of individual genes and panels currently offered by the CDL.  Genes where deletion/duplication analysis is not yet available are marked with an asterisk on the test requisition form.

How much does array CGH cost?

The cost is $952.00 for the first gene read on the array (CPT code 81228 or CPT code 81411 for 15 gene vascular panel only), and $112.00 for each additional gene (CPT code G0452) with a maximum charge not to exceed $1288.00.  Please note that the price for testing two genes also applies to genes commonly tested together (e.g. the cost for testing both COL1A1 and COL1A2 is $1064.00)  The cost of deletion/duplication studies for the 6 genes in the core vascular panel is $1288.00 given the ‘do not exceed $1288.00’ policy.

How much do additional interpretations (after array CGH has already been completed and reported) cost ?

If your patient has already had deletion/duplication studies by array CGH performed at the Collagen Diagnostic Laboratory, the price for ordering deletion/duplication studies on additional genes is $112 total (CPT code: G0452), regardless of how many additional genes are requested for analysis.

When is it appropriate to order array CGH?

In general, array CGH is appropriate when there is strong clinical suspicion for a genetic condition but no mutation is identified in the corresponding gene(s) of interest upon genomic sequencing. The likelihood of detecting a copy number change depends on the clinical picture and the specific gene of interest. For further help in determining whether array CGH is an appropriate test for your patient, please visit our Test Guides (see menu at top of page) or contact one of the laboratory genetic counselors (206-543-5464).

Should I order array CGH as a reflex test?

In cases of strong clinical suspicion for a genetic condition, ordering array CGH as a reflex test (to be performed immediately after genomic sequencing if no mutation is found) is a convenient and efficient option. In other instances, such as when the clinical suspicion for a condition is relatively low, it may be beneficial to wait for genomic sequencing results before deciding on added testing.  When interpreting genomic sequencing results, the CDL reports the presence of heterozygous polymorphic variants identified during sequencing.  In many cases, the presence of multiple polymorphic variants reduces the likelihood of finding a partial gene deletion by array CGH.

Can array CGH be ordered by itself?

Yes. While genomic sequencing is often the recommended first step in making a genetic diagnosis, array CGH may be ordered independently of genomic sequencing for any of the genes currently offered as clinical tests.

How to Order

To add on deletion/duplication studies to an existing or stored sample, please complete a new Test Requisiton form (below) and fax it to the CDL at (206) 616-1899.

PDF-Icon.jpg  CDL TEST REQUISITION FORM

PDF-Icon.jpg  (PDF FILLABLE) CDL TEST REQUISITION FORM

  1. Complete Test Requisition Form
  2. Collect Specimen
  3. Ship Specimen

CPT Code & Cost

Deletion/Duplication Analysis:  First Gene

CPT CODEDESCRIPTION
81228Deletion/Duplication Analysis – High-Density Targeted Array, single gene
TOTAL$952.00

Deletion/Duplication Analysis:  Each Additional Gene

CPT CODEDESCRIPTION
G0452*Complex Additional Interpretation, CDL aCGH
TOTAL$112.00

Deletion/Duplication Analysis:  Panel (all Panels except 15-Gene Vascular)

CPT CODEDESCRIPTION
81228Deletion/Duplication Analysis – High-Density Targeted Array, 4 or more genes
G0452*Complex Additional Interpretation, CDL aCGH
G0452*Complex Additional Interpretation, CDL aCGH
G0452*Complex Additional Interpretation, CDL aCGH
TOTAL$1288.00

Deletion/Duplication Analysis:  15-Gene Vascular Panel Only

CPT CODEDESCRIPTION
81411Deletion/Duplication Analysis Panel, must include analyses for TGFBR1, TGFBR2, MYH11, and COL3A1
TOTAL$1288.00
81411; 81228
$952.00 for the first gene read on the array, $112 for each additional gene interpretation with a maximum charge not to exceed $1288.00

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