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Rapid microarray (CGH and SNP)
Clinical Genetic Test
Help
offered by
Allele Diagnostics
View lab's test page
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GTR Test Accession: Help GTR000525320.10
CAP
INHERITED DISEASESYNDROMIC DISEASEDYSMORPHOLOGY ... View more
Last updated in GTR: 2024-05-16
View version history
Last annual review date for the lab: 2024-05-16 LinkOut
At a Glance
Test purpose: Help
Diagnosis
Conditions (247): Help
Congenital chromosomal disease; 11p partial monosomy syndrome; 11q partial monosomy syndrome more...
Chromosomal regions/ Mitochondria (58): Help
10p14; 11q23-q25; 12p; 14q13.1-q13.3; 15q11-q13 more...
Genes (173): Help
ABCC8 (11p15.1); ACVRL1 (12q13.13); ADGRG1 (16q21); ADGRV1 (5q14.3); ALX4 (11p11.2) more...
Methods (2): Help
Molecular Genetics - Deletion/duplication analysis: Microarray; ...
Target population: Help
Individuals with developmental delay, intellectual disability, multiple congenital anomalies, dysmorphic …
Clinical validity: Help
Not provided
Clinical utility: Help
Establish or confirm diagnosis; Guidance for management
Ordering Information
Offered by: Help
Allele Diagnostics
View lab's website
View lab's test page
Specimen Source: Help
  • Buccal swab
  • Cell culture
  • Cord blood
  • Fibroblasts
  • Fresh tissue
  • Frozen tissue
  • Isolated DNA
  • Peripheral (whole) blood
  • Product of conception (POC)
  • Skin
  • View specimen requirements
Who can order: Help
  • Genetic Counselor
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
Test Order Code: Help
100
View other test codes
CPT codes: Help
**AMA CPT codes notice

Copyright: 2023 American Medical Association. All rights reserved.

Lab contact: Help
Annie Morton, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
[email protected]
844-255-3532
Contact Policy: Help
Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order: Help
For specimen requirements and handling instructions please visit: https://www.allelediagnostics.com/ordering/sample-requirements/. Allele Diagnostics accepts samples Monday through Saturday, excluding some holidays. Contact Allele Diagnostics regarding holiday schedules. Please include a complete copy of the appropriate Allele Diagnostics Requisition form: https://www.allelediagnostics.com/ordering/requisition/. Our secure online portal allows providers the option of both placing test …
View more
Order URL
Test service: Help
Custom Deletion/Duplication Testing
Test development: Help
Test developed by laboratory (no manufacturer test name)
Informed consent required: Help
Based on applicable state law
Test strategy: Help
After identification of a copy number gain or loss, FISH confirmation/visualization is attempted for majority of findings if specimen is adequate.
View citations (1)
  • Microarray analysis for constitutional cytogenetic abnormalities. Shaffer LG, et al. Genet Med. 2007;9(9):654-62. doi:10.1097/gim.0b013e31814ce3d9. PMID: 17873655.
Pre-test genetic counseling required: Help
No
Post-test genetic counseling required: Help
No
Conditions Help
Total conditions: 247
Condition/Phenotype Identifier
Test Targets
Chromosomal regions/Mitochondria Help
Total chromosomal regions/mitochondria: 58
Chromosomal region/Mitochondrion Associated condition
Genes Help
Total genes: 173
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 2
Method Category Help
Test method Help
Instrument *
Deletion/duplication analysis
Microarray
Detection of homozygosity
SNP Detection
* Instrument: Not provided
Clinical Information
Test purpose: Help
Diagnosis
Clinical utility: Help
Establish or confirm diagnosis
View citations (2)
  • Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Manning M, et al. Genet Med. 2010;12(11):742-5. doi:10.1097/GIM.0b013e3181f8baad. PMID: 20962661.
  • Ellison JW, Ravnan JB, Rosenfeld JA, Morton SA, Neill NJ, Williams MS, Lewis J, Torchia BS, Walker C, Traylor RN, Moles K, Miller E, Lantz J, Valentin C, Minier SL, Leiser K, Powell BR, Wilks TM, Shaffer LG. Clinical utility of chromosomal microarray analysis. Pediatrics. 2012;130(5):e1085-95. doi:10.1542/peds.2012-0568. Epub 2012 Oct 15. PMID: 23071206.

Guidance for management
View citations (2)
  • Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Manning M, et al. Genet Med. 2010;12(11):742-5. doi:10.1097/GIM.0b013e3181f8baad. PMID: 20962661.
  • Ellison JW, Ravnan JB, Rosenfeld JA, Morton SA, Neill NJ, Williams MS, Lewis J, Torchia BS, Walker C, Traylor RN, Moles K, Miller E, Lantz J, Valentin C, Minier SL, Leiser K, Powell BR, Wilks TM, Shaffer LG. Clinical utility of chromosomal microarray analysis. Pediatrics. 2012;130(5):e1085-95. doi:10.1542/peds.2012-0568. Epub 2012 Oct 15. PMID: 23071206.

Target population: Help
Individuals with developmental delay, intellectual disability, multiple congenital anomalies, dysmorphic features, autistic spectrum disorder, behavioral abnormalities, and/or other features consistent with chromosomal disorders.
View citations (1)
  • Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Manning M, et al. Genet Med. 2010;12(11):742-5. doi:10.1097/GIM.0b013e3181f8baad. PMID: 20962661.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
Copy number variants detected by microarray analysis are investigated to determine gene content, gene number, size of alteration, publications involving similar deletions and duplications, and whether similar copy gains and losses are present in existing databases. Genes are further evaluated for function, known mutations, evidence of haploinsufficiency and animal models. … View more

Will the lab re-contact the ordering physician if variant interpretation changes? Help
.
Recommended fields not provided:
Clinical validity, Are family members with defined clinical status recruited to assess significance of VUS without charge?, Is research allowed on the sample after clinical testing is complete?, Sample negative report, Sample positive report
Technical Information
Test Procedure: Help
FISH confirmation/visualization of the majority of copy number abnormalities. If submitting a specimen that cannot be cultured, such as a buccal swab or extracted DNA, a secondary specimen may be recommended for follow-up by FISH visualization (at no extra charge). Molecular studies may be recommended depending on specific test results.
Test Confirmation: Help
FISH confirmation/visualization of the majority of copy number abnormalities. If submitting a specimen that cannot be cultured, such as a buccal swab or extracted DNA, a secondary specimen may be recommended for follow-up by FISH visualization (at no extra charge). Molecular studies may be recommended depending on specific test results.
Test Comments: Help
For more information about this test, please see the description at http://www.allelediagnostics.com/services/tests/1/
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
This test is evaluated for analytical validity using an established validation process utilizing abnormal and normal specimens as per CAP, ACMG, and CLIA guidelines. For the CGH component, regions known to be involved in cytogenetic abnormalities are covered, including over 255 recognized genetic syndromes, over 980 gene regions of functional … View more
View citations (2)
Assay limitations: Help
Although microarray detects microscopic and submicroscopic deletions and duplications undetectable by karyotyping, microarray will not detect balanced chromosome rearrangements, such as balanced translocations or inversions. It will not detect alterations in chromosome structure at areas of the genome not covered by the array. This technology will not detect sequence alterations … View more
View citations (1)
  • Stankiewicz P, Beaudet AL. Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation. Curr Opin Genet Dev. 2007;17(3):182-92. doi:10.1016/j.gde.2007.04.009. Epub 2007 Apr 30. PMID: 17467974.
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Formal PT program

PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
VUS:
Software used to interpret novel variations Help
Review of internal and external databases of previously identified genomic variants.

Laboratory's policy on reporting novel variations Help
Reports are faxed to the ordering physician and other providers indicated on the requisition form or uploaded to our secure online portal, for clients that indicate that preference. Telephone calls are made for critical results and as per internal protocols.
Recommended fields not provided:
Description of internal test validation method, Description of PT method, Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
Additional Information
Practice guidelines:
Consumer resources:

IMPORTANT NOTE: NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.