DEPARTMENT: CYTOGENETICS
DIRECTOR: Athena Milatovich Cherry, Ph.D.
NEW TEST
Array Comparative Genomic Hybridization (aCGH)
Test Description and Clinical Indications: Array comparative genomic hybridization (aCGH) is a new method using existing array technology to detect some chromosomal abnormalities that are too small to be appreciated by high-resolution chromosomal analysis. Typically, high-resolution chromosomal analysis can detect chromosomal abnormalities of between 5 to 10 Mb in size. Depending upon the type of array and the spacing of the features on the array, the size of detectable anomalies can be anywhere from a few hundred kilobases of DNA to less than 5 Mb.
Our method utilizes a microarray carrying 44,000 oligonucleotide (Agilent) sequences from known genomic locations at an average spatial resolution of 35 kb of DNA. Patient and control DNA samples are labeled using different fluorescent tags. These DNA samples are then hybridized to the array. The arrays are scanned and the intensities of the fluorescence are plotted as a ratio at each oligonucleotide probe. These ratios can then be interpreted as representing either a loss or a gain of DNA. A copy number change is considered only when three or more adjacent oligonucleotides are shown to be duplicated or deleted (with an average size of ~ 100 kb).
Please note: This array cannot detect polyploidy, balanced chromosomal rearrangements; mosaicism, small duplications or deletions below the resolution of this array or point mutations. Blood on the patient AND his/her parents are requested at the initiation of testing. This is to confirm by FISH (where possible) any anomalies detected by aCGH, as well as to determine if the difference (s) found are unreported copy number variants (CNV’s).
Array-based Comparative Genome Hybridization, Genetic Dx. |
Order Code:CGH GEN |
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Synonyms: |
aCGH, CGH, array CGH |
Specimen Type: |
Peripheral blood. Note: blood specimens of both parents at the initiation of testing are also requested. See note in Test Description. |
Container Type: |
Green-top tube (sodium heparin) |
Required Volume: |
10 mL |
Minimum Volume (Pediatric): |
2 mL |
Special Handling: |
Room temperature; blood specimens of both parents also requested. Note: blood specimens of both parents at the initiation of testing are also requested. See note in Test Description. |
Methodology: |
Array-based comparative genome hybridization |
| TAT |
21 days |
CPT Codes: |
88386 x 4, 83891, 83892 x 2 |
Report: |
Interpretation and report |
| Causes For Rejection: |
Improperly labeled specimen, incorrect specimen, hemolyzed or coagulated specimen. |
NEW TEST
CHIC2 Deletion (or FIP1L1/PDGFRA fusion)
Test Description and Clinical Indications: Interphase fluorescence in situ hybridization (FISH) is performed using a set of differentially labeled probes specific for three different loci – CHIC2, FIP1L1 and PDGFRA. Loss of the CHIC2 probe is used as a surrogate for fusion of FIP1L1 and PDGRFA. CHIC2 deletion (or FIP1L1/PDGFRA fusion) can be observed in individuals with hypereosinophillic syndrome (HES) or systemic mast cell disease (SMCD). The FIP1L1/PDGFRA fusion creates a novel tyrosine kinase which can be a therapeutic target for imatinib mesylate (or Gleevec).
FISH CHIC2 |
Order Code: CGFi CHIC2 |
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Synonyms: |
FISH, FIP1L1/PDGFRA gene rearrangement; FIP1L1; PDGFRA; deletion 4q12; del(4q12) |
Specimen Type: |
Whole blood, bone marrow, or other cellular fluid |
Container Type: |
Green-top tube (sodium heparin), or sterile container for other fluid |
Required Volume: |
2 mL |
Minimum Volume (Pediatric): |
1 mL |
Special Handling: |
Transport at Room Temperature. |
Methodology: |
Fluorescence in situ hybridization, deletion probes, interphase analysis |
TAT: |
12-14 days |
CPT Codes: |
88271 x 3, 88275 |
| Report: |
Interpretation and report |
| Causes For Rejection: |
Improperly labeled specimen, incorrect specimen, hemolyzed or coagulated specimen. |
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