High-Resolution Rapid Microarray (CGH and SNP)
Clinical Genetic Test
Help
offered by
GTR Test Accession: Help GTR000560671.2
CAP
INHERITED DISEASESYNDROMIC DISEASEDYSMORPHOLOGY ... View more
Last updated in GTR: 2019-06-20
Last annual review date for the lab: 2023-05-18 LinkOut
At a Glance
Diagnosis
Congenital chromosomal disease; 11p partial monosomy syndrome; 11q partial monosomy syndrome; ...
10p14; 11q23-q25; 12p; 14q13.1-q13.3; 15q11-q13; ...
ABCC8 (11p15.1), ACVRL1 (12q13.13), ADGRG1 (16q21), ADGRV1 (5q14.3), ALX4 (11p11.2), ...
Molecular Genetics - Deletion/duplication analysis: Comparative Genomic Hybridization; ...
Individuals with pregnancies that have abnormal ultrasound, abnormal karyotype, abnormal …
Not provided
Establish or confirm diagnosis; Guidance for management; Reproductive decision-making
Ordering Information
Offered by: Help
Specimen Source: Help
  • Amniocytes
  • Amniotic fluid
  • Cell culture
  • Chorionic villi
  • Cord blood
  • Cystic hygroma fluid
  • Fetal blood
  • Fresh tissue
  • Frozen tissue
  • Isolated DNA
  • Product of conception (POC)
  • Skin
  • View specimen requirements
Who can order: Help
  • Genetic Counselor
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
Test Order Code: Help
CPT codes: Help
**AMA CPT codes notice
Lab contact: Help
Annie Morton, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
info@allelediagnostics.com
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-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/.
Order URL
Test service: Help
Custom Balanced Chromosome Rearrangement Studies
    Comment: After identification of a copy number gain or loss, FISH confirmation/visualization is attempted for majority of findings if specimen is adequate.
Custom Deletion/Duplication Testing
    Comment: After identification of a copy number gain or loss, FISH confirmation/visualization is attempted for majority of findings if specimen is adequate.
Maternal cell contamination study (MCC)
    Comment: Maternal cell contamination studies are recommended but not required for all prenatal microarrays.
    OrderCode: 7500
Cell culturing
    Comment: Backup cell culturing performed with all prenatal microarrays. CPT code 88233 for POC, 88235 for amnio or CVS.
Test development: Help
Test developed by laboratory (no manufacturer test name)
Informed consent required: Help
Based on applicable state law
Test strategy: Help
Microarray analysis reported within 2-4 business days if specimen is adequate. If not adequate, client will be contacted and plan established.
After identification of a copy number gain or loss, FISH confirmation/visualization is attempted for majority of findings if specimen is adequate. If parental specimens are submitted with prenatal …
View more
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
Comparative Genomic Hybridization
Detection of homozygosity
SNP Detection
* Instrument: Not provided
Clinical Information
Test purpose: Help
Diagnosis
Clinical utility: Help
Establish or confirm diagnosis
View citations (3)
  • Shaffer LG, Dabell MP, Fisher AJ, Coppinger J, Bandholz AM, Ellison JW, Ravnan JB, Torchia BS, Ballif BC, Rosenfeld JA. Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies. Prenat Diagn. 2012;32(10):976-85. doi:10.1002/pd.3945. Epub 2012 Aug 02. PMID: 22865506.
  • Chromosomal microarray versus karyotyping for prenatal diagnosis. Wapner RJ, et al. N Engl J Med. 2012;367(23):2175-84. doi:10.1056/NEJMoa1203382. PMID: 23215555.
  • Committee Opinion No. 581: the use of chromosomal microarray analysis in prenatal diagnosis. , et al. Obstet Gynecol. 2013;122(6):1374-7. doi:10.1097/01.AOG.0000438962.16108.d1. PMID: 24264715.

Guidance for management
View citations (3)
  • Shaffer LG, Dabell MP, Fisher AJ, Coppinger J, Bandholz AM, Ellison JW, Ravnan JB, Torchia BS, Ballif BC, Rosenfeld JA. Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies. Prenat Diagn. 2012;32(10):976-85. doi:10.1002/pd.3945. Epub 2012 Aug 02. PMID: 22865506.
  • 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.
  • Committee Opinion No. 581: the use of chromosomal microarray analysis in prenatal diagnosis. , et al. Obstet Gynecol. 2013;122(6):1374-7. doi:10.1097/01.AOG.0000438962.16108.d1. PMID: 24264715.

Reproductive decision-making
View citations (3)
  • Shaffer LG, Dabell MP, Fisher AJ, Coppinger J, Bandholz AM, Ellison JW, Ravnan JB, Torchia BS, Ballif BC, Rosenfeld JA. Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies. Prenat Diagn. 2012;32(10):976-85. doi:10.1002/pd.3945. Epub 2012 Aug 02. PMID: 22865506.
  • Chromosomal microarray versus karyotyping for prenatal diagnosis. Wapner RJ, et al. N Engl J Med. 2012;367(23):2175-84. doi:10.1056/NEJMoa1203382. PMID: 23215555.
  • Committee Opinion No. 581: the use of chromosomal microarray analysis in prenatal diagnosis. , et al. Obstet Gynecol. 2013;122(6):1374-7. doi:10.1097/01.AOG.0000438962.16108.d1. PMID: 24264715.

Target population: Help
Individuals with pregnancies that have abnormal ultrasound, abnormal karyotype, abnormal maternal serum screen (MSS) results, abnormal non-invasive prenatal testing (NIPT)/cell-free fetal DNA (cffDNA) test results, family history of chromosomal abnormality, and/or desire testing based on advanced maternal age or maternal anxiety. Testing is also appropriate for pregnancies resulting in stillbirth … View more
View citations (3)
  • Lee CN, Lin SY, Lin CH, Shih JC, Lin TH, Su YN. Clinical utility of array comparative genomic hybridisation for prenatal diagnosis: a cohort study of 3171 pregnancies. BJOG. 2012;119(5):614-25. doi:10.1111/j.1471-0528.2012.03279.x. Epub 2012 Feb 07. PMID: 22313859.
  • Shaffer LG, Dabell MP, Fisher AJ, Coppinger J, Bandholz AM, Ellison JW, Ravnan JB, Torchia BS, Ballif BC, Rosenfeld JA. Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies. Prenat Diagn. 2012;32(10):976-85. doi:10.1002/pd.3945. Epub 2012 Aug 02. PMID: 22865506.
  • Committee Opinion No. 581: the use of chromosomal microarray analysis in prenatal diagnosis. , et al. Obstet Gynecol. 2013;122(6):1374-7. doi:10.1097/01.AOG.0000438962.16108.d1. PMID: 24264715.
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:
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 frozen tissue 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 frozen tissue 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 https://www.allelediagnostics.com/services/tests/4/high-resolution-rapid-microarray-cgh-and-snp/
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.
Recommended fields not provided:
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
Additional Information

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.