High Density SNP Microarray

TEST NAME:   High Density SNP Microarray - Postnatal
Also known as:   Copy Number + SNP Array

INDICATIONS FOR TESTING:   Due to the increased diagnostic yield of microarray, this assay is recommended as a first tier test1 for individuals with:

  • Intellectual disabilities
  • Autism spectrum disorders
  • Multiple congenital anomalies

In addition, the High Density SNP Array can be helpful in the identification of an underlying genetic etiology for patients with other significant concerns:

  • Seizure disorders
  • Vision/hearing problems
  • Low muscle tone
  • Neurodevelopmental and neuromuscular disorders
  • Suspicion of a well-known microdeletion or microduplication syndrome
  • An abnormal, unbalanced karyotype
  • Imprinting associated disorders
  • Suspicion of consanguinity
  • A family history of a structural chromosomal anomaly

TEST INFORMATION:   Our postnatal microarray is a high density single nucleotide polymorphism (SNP) platform designed to interrogate the whole genome at resolution much higher than is possible using traditional karyotyping or fluorescence in situ hybridization (FISH) methodologies. Our High Density SNP array contains a total of 2.6 million markers distributed throughout the genome for the detection of both genomic dosage anomalies (deletions and duplications) and regions of homozygosity (ROH; regions lacking typical amounts of genetic variation). This marker density provides a global resolution of 5 Kb to 10 Kb for copy number changes and 5 Mb resolution for ROH. Due to the increased diagnostic yield of microarray, the American College of Medical Genetics (ACMG) recommends microarray as a first tier test for individuals with intellectual disabilities, autism spectrum disorders, and/or multiple congenital anomalies.


  • Evaluates hundreds of different genetic conditions, including aneuploidy, with one test
  • Detects large and small deletions and duplications, many of which are undetectable by traditional chromosome analysis
  • Detects ROH, which cannot be identified using other testing methodologies
  • Allows for enhanced breakpoint detection and refinement in patients with a structural chromosome anomaly
  • Offers a more comprehensive and cost-effective approach to testing for microdeletion or microduplication syndromes than ordering multiple FISH tests
  • Allows for testing on limited amounts of specimen, including DNA extracted from non-invasive buccal swabs


  • This test cannot identify all genetic conditions or the cause of all congenital defects.
  • The High Density SNP Array does not detect changes in the DNA sequence of genes.
  • This test cannot detect balanced chromosome rearrangements, such as translocations, or low level mosaicism.
  • Despite dense marker distribution throughout the genome, this assay is limited in its detection of genetic aberrations by the probe density at a given locus.


  • A normal result indicates no clinically-significant chromosome anomalies were identified.
  • An abnormal or pathogenic result indicates that the assay identified a genomic dosage anomaly (deletion or duplication) or ROH that likely provides an explanation for the individual’s clinical findings.
  • In some cases, the clinical significance of an identified chromosomal anomaly may not be well understood. These anomalies will be reported as variants of uncertain clinical significance.
  • Parental testing may be recommended in order to clarify whether the result is de novo or familial for the purpose of recurrence risk calculation.


  • The Autism / Intellectual Disability / Multiple Anomalies Panel can be ordered as comprehensive testing or in a tiered fashion to evaluate for common single gene causes of autism spectrum disorders, intellectual disabilities, or multiple congenital anomalies.
  • If trisomy 13, 18, or 21 (Down syndrome) is suspected, Chromosome Analysis is recommended.
  • If an imprinting disorder, such as Angelman syndrome is suspected, additional testing such as Methylation Analysis or Targeted Gene Sequencing may be indicated. Recommendations for additional testing differ based on the disorder suspected.

For assistance determining which testing options are most useful for your patient, please call our laboratory at 402-559-5070 and ask to speak with a laboratory genetic counselor.

REQUIRED FORMS:   Postnatal Test Request Form

OTHER FORMS:   Request for Pre-Authorization for Genetic Testing (Postnatal Diagnoses on peripheral blood)


  • Blood > 3 mo of age: 3-5 ml blood in an EDTA tube (purple top)
  • Blood (newborn minimum): 1 ml in an EDTA tube (purple top)
  • Buccal swab: kits available upon request
  • Extracted DNA: 5 µg


CPT CODES:   81229, 88230

PRICING:   Contact the laboratory billing staff for current costs.

TURN-AROUND-TIME:   Results are typically available in 1-2 weeks; 1 week for newborn studies.


  • Manning M, Hudgins L; Professional Practice and Guidelines Committee. Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genet Med 2010;12:742–745.
  • GeneReviews™

1. ARTICLE: Miller DT, Adam MP, Aradhya S, et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 2010;86:749–764. 


CAP Accredited
CAP Graphic

CLIA Accredited
CMS Centers for Medicare & Medicaid Services Logo

contact us
Phone:  402-559-5070 
1-800-656-3937 x95070
Fax:  402-559-7248