High Density SNP Microarray

Test description

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 10 Kb to 20 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.1

Test details and complementary testing

  • Recommendations for additional testing differ based on the disorder suspected; contact a laboratory genetic counselor to discuss which testing options are most useful for your patient.
  • 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 may be indicated.

Advantages

  • Evaluates hundreds of different genetic conditions across the genome with one test
  • Detects aneuploidy (including trisomy and sex chromosome abnormalities) and triploidy
  • Identifies 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

Limitations

  • Cannot identify all genetic conditions or the cause of all congenital defects
  • Does not detect changes in the DNA sequence of genes
  • Cannot detect balanced chromosome rearrangements, such as translocations (a complementary test such as Postnatal Chromosome Analysis should be performed to detect balanced chromosome rearrangements)
  • Unable to reliably detect all cases of 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.

  1. 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.