Overview
Chromosomal microarray hybridizes patient DNA to probes spanning the genome to detect copy-number variants (CNVs) and, on SNP arrays, absence of heterozygosity.
Clinical Importance
Evaluate developmental delay, autism, and congenital anomalies
Detect CNVs below karyotype resolution
Specimen Requirements
- Specimen: whole blood or plasma as validated for the assay
- Tube: lavender-top K₂EDTA (preferred for many viral load and germline DNA assays)
- Handling: mix gently; separate plasma promptly when required; avoid heparin for many PCR assays (inhibition)
- Storage: refrigerate or freeze plasma per IFU; extract nucleic acid within validated windows
Analytical Method
Labeled patient (± reference) DNA hybridizes to oligonucleotide/SNP arrays; intensity and allele patterns yield CNV calls after bioinformatic analysis and laboratory interpretation.
Instruments Used
Automated analyzers
- Affymetrix / Thermo Fisher SNP array platforms
- Agilent and other CGH array scanners
- Array hybridization ovens and wash stations
Manual methods
- Manual DNA labeling and hybridization workflows
Reference Values
Molecular cutoffs, units (IU/mL, copies/mL, Ct), reportable ranges, and variant classifications are assay- and laboratory-specific. Always interpret against the performing laboratory report, manufacturer IFU, and current CLSI / CAP / AMP / ACMG guidance as adopted locally. Limit of detection and inhibition controls are essential for negative results.
No numeric clinical interval. CNVs classified by size, gene content, and databases (e.g., benign vs pathogenic). Balanced rearrangements are not detected.
Interpretation
Common Causes of Increased Results
- Pathogenic/likely pathogenic CNV; correlate with phenotype and genetic counseling
Common Causes of Decreased Results
- No clinically significant CNV detected; does not exclude sequence-level or balanced rearrangements
Clinical Significance
- Pediatric constitutional cytogenomic testing
- Selected prenatal evaluations per guideline pathways
Factors Affecting Results
Pre-analytical
- Wrong specimen type or transport medium for the validated assay
- Delayed transport degrading RNA targets
- Contamination during collection (especially amplicon-rich environments)
- Inadequate volume or low cellularity/tumor content
Analytical
- PCR inhibition (heparin, humic acids, excess hemoglobin; assay-dependent)
- Extraction failure or pipetting/contamination in amplification areas
- Probe/primer mismatch with sequence variants causing false negatives
- Calibration/QC failure; expired reagents
Post-analytical
- Reporting Ct or raw copies without assay-specific interpretive rules
- Misapplying another laboratory’s LOD or units
- Variant classification without current ACMG/AMP framework when required
Advantages and Limitations
Advantages
- Higher CNV resolution than karyotype
- Genome-wide
Limitations
- Misses balanced translocations
- VUS CNVs common
Clinical Pearls
Microarray finds missing or extra DNA segments; it will not see a balanced swap of chromosome arms.
References
Authoritative textbooks, guidelines, and reviews supporting this laboratory test reference. Verify reference intervals, critical limits, and method details against institutional protocols and current guideline editions.
Textbooks
- McPherson RA, Pincus MR. Henry's Clinical Diagnosis and Management by Laboratory Methods. 24th ed. Elsevier; 2021. (Molecular diagnostics chapters, verify current edition.)
- Buckingham L. Molecular Diagnostics: Fundamentals, Methods, and Clinical Applications. 3rd ed. F.A. Davis; 2019. (Verify current edition and institutional adoption.)
CLSI and Professional Guidelines
- Clinical and Laboratory Standards Institute (CLSI). Consult current CLSI molecular method documents available through your laboratory, document numbers and editions change; do not treat any single CLSI title as universal.
- Institutional molecular laboratory standard operating procedures (SOPs), assay manufacturer instructions for use (IFU), and locally adopted accreditation requirements. Always verify current local practice.
- Clinical and Laboratory Standards Institute (CLSI). Molecular method evaluation and related documents (verify current CLSI editions applicable to the assay).
- College of American Pathologists. Molecular pathology accreditation and proficiency testing expectations (verify current CAP checklist requirements).
- Association for Molecular Pathology (AMP). Practice guidelines and position statements for molecular diagnostics (verify current AMP documents for the assay).
- American College of Medical Genetics and Genomics (ACMG). Standards and guidelines for interpretation of sequence variants and related genetic testing practice (verify current ACMG documents).
WHO Publications
- World Health Organization. Laboratory and diagnostic guidance relevant to molecular testing (verify current WHO publication for the assay/pathogen).
Frequently Asked Questions
Common questions about using this Chromosomal Microarray laboratory test Medical Laboratory Library reference in Medical Laboratory Science education.
What is the Chromosomal Microarray laboratory test reference used for?
This Medical Laboratory Library page summarizes the clinical importance of Chromosomal Microarray. Review the Clinical Importance section for why the test is ordered in laboratory medicine practice.
Where can I find Chromosomal Microarray specimen requirements?
See the Specimen Requirements section on this page for specimen information related to Chromosomal Microarray. Confirm collection details against your laboratory protocol.
Where are Chromosomal Microarray reference values listed?
See the Reference Values section on this Laboratory Library page. Reference ranges can vary by method and population, so verify intervals with your laboratory.
How do I interpret Chromosomal Microarray results?
Use the Interpretation section for laboratory interpretation framing, including increased and decreased result patterns when provided. Do not treat educational text as a patient-specific diagnosis.
What analytical method is used for Chromosomal Microarray?
See the Analytical Method section for principle and method notes. Method details may differ by instrument and institutional SOP.
Are related laboratory tests linked from Chromosomal Microarray?
Yes. The Related Laboratory Tests section lists connected references for continued lookup in the Medical Laboratory Library.
How can I continue learning after reading Chromosomal Microarray?
Use Continue learning links on this page for related Academy lessons, medical laboratory quizzes, or laboratory case studies when available for this Molecular Diagnostics topic.
What are the clinical pearls for Chromosomal Microarray?
See the Clinical Pearls section for concise laboratory practice notes associated with Chromosomal Microarray. Apply pearls alongside institutional protocols.
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