SNP Array

A SNP (single nucleotide polymorphism) array is a genetic test that looks for differences in a person’s chromosomes.

It is also called a chromosomal SNP microarray.

Chromosomes are like tiny packages inside cells that have a person’s genetic information (called “genes” or “DNA”). This genetic information tells a person’s body how to grow and function.

The SNP array test looks for differences in a person’s chromosomes, like extra copies (gains) or missing parts (losses). These gains or losses result in extra or missing copies of genetic material. Differences in a person’s chromosomes may be associated with known genetic conditions or may cause problems with health and development.

Yes, a SNP array also looks for genetic similarity (called “homozygosity”). Genetic similarity happens when parts of the chromosomes inherited from each parent are the same. If there are multiple areas of similarity, it could mean that a person’s parents might be more closely related (for example, cousins). Genetic similarity can be the cause of some genetic conditions.

A SNP array cannot find all differences in your chromosomes or DNA. For example, it cannot detect rearrangements in the chromosomes that do not cause extra or missing copies of genetic material (balanced chromosome rearrangements) and cannot detect small changes in the DNA (error in 1, or a few, letters of the DNA sequence).

• Negative or normal result: No detectable differences in genetic material were identified. There are also no unusual patterns of genetic similarity. However, many genetic conditions cannot be found by this test, especially those caused by a difference in a single gene.
• Positive or abnormal result: A gain or loss of genetic material or genetic similarity was found. Sometimes this result will diagnose a well-described genetic condition or suggest it is the cause of a person’s health problems.
• Variant of uncertain significance: A difference in genetic material was found but there is not enough information to know if it will cause a genetic condition or is benign. Testing genetic parents can sometimes help understand if this change is inherited or new in a person. However, even if genetic parents have testing, the laboratory may not be able to say for sure if these are causing health problems or are benign.
  
  A variant of uncertain significance could also mean that an area of genetic similarity was found. This can sometimes suggest a genetic abnormality called uniparental disomy (UPD). UPD happens when more chromosome material is passed down (inherited) from one parent than the other. If an area of genetic similarity is found, it could give us a clue to a specific genetic condition and more genetic testing may be recommended.
• Unexpected findings: This test could also show results that are not directly related to the reason the test was ordered. For example, the test could show that a person is at risk for genetic condition that happens later in life, or that a person is at risk for developing cancer, or that a person is a carrier for a genetic condition.

Genetic tests, like a SNP array, can be expensive and may not be covered by insurance. Insurance plans want to know if the genetic test is medically necessary and how it could affect your child’s care before they approve coverage. This is called pre-authorization. Without pre-authorization, you may have to pay for the cost of SNP array.

For more information, read our handout “Insurance Coverage for Genetic Testing,” seattlechildrens.org/pdf/PE2051.pdf.

A genetic counselor can explain this information in more detail. Please contact Seattle Children’s Genetics Scheduling team at 206-987-2056, and select option 1, to make an appointment with a genetic counselor.

Genetic counselors are healthcare providers who talk with families about how genetics affect health. Genetic counselors explain tests and test results, helping families decide which tests are right for them.