Comparing Genetic Tests

Types of Genetic Tests

Tests that assess sequence variants

Condition-specific tests: Tests for a specific genetic condition of interest, comprehensively, often using multiple methods to detect different variant types associated with the condition (e.g., hereditary ataxia evaluation, sensorineural hearing loss panel, Cowden syndrome testing). They may include testing for one or multiple genes, depending on the condition.

Broad multi-gene tests: Tests for variants in genes associated with a condition or category of conditions (e.g., infantile epilepsy panel, hereditary cancer panel). They may or may not include multiple testing methods to detect different variant types. Includes multiple genes – a few to dozens.

Exome testing: The exome is the portion of the genome containing the protein-coding regions of the genes known as exons. While representing only about 1% of the genome, exome testing has a high diagnostic yield because most variants known to be associated with hereditary conditions are located within the exons, or in the regions immediately flanking them.

Whole genome sequencing: Examines nearly all coding and non-coding DNA, or about 3 billion base pairs of DNA, and results in a very large amount of data that needs to be interpreted. It includes assessment of the non-coding and regulatory regions of the genome, where a variant associated with disease could possibly be located. These regions are not typically assessed by exome testing.

Targeted mutation analysis: Targeted tests that assess specific variants within a gene or genes that have been associated with a condition. For example, a test designed for a specific variant that has been identified as being causal in a close relative. There is also targeted testing based on common variants in certain ethnicities, such as testing for the three most common variants in BRCA1 and BRCA2 found in individuals of Ashkenazi Jewish descent. Some carrier screening panels that inform risk for recessive conditions are targeted to known variants in high risk populations as well.

Tests that assess chromosomal variants

Chromosome analysis (karyotype): Analysis of the structure of chromosomes. It detects extra or missing chromosomes and large structural arrangements. It can detect deletions as small as 3-5 Mb and duplications larger than ~5 Mb.

Chromosomal microarray analysis (CMA): Test that is used to detect copy number variants (CNVs – see description below). CMA can detect chromosome deletions/duplications as small as 100 kb.

Types of Variation

Single nucleotide variants (SNV): Changes to a single nucleotide within the DNA sequence, such as single base substitutions, insertions, or deletions.

Deletions and duplications. Missing or extra genomic information. Both very small (single nucleotides) and very large (whole chromosomes) insertions and deletions of genomic information can impact gene function. Indel (insertion/deletion) is the term typically used for deletions and duplications of less than 1 kb, or 1000 bases (nucleotides). CNV (copy number variation) is typically used for deletions and duplications of more than 1 kb. CNVs can be as large as an entire chromosome (e.g., Down syndrome).

Trinucleotide repeat (TNR) expansion: A type of duplication with an increased number of trinucleotide repeats (three specific nucleotides recurring multiple times in a row) beyond what is normally expected in a given area of a gene (e.g., Friedreich ataxia).

Methylation (Methyl): The addition of methyl groups to DNA can turn the activity of a gene off. Changes to the methylation pattern can cause disease (e.g., imprinting disorders such as Angelman syndrome). These changes do not change the DNA sequence.

Mitochondrial DNA variants (mtDNA): Changes to the DNA in the mitochondria can include single nucleotide variants and deletion/duplications (e.g., mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes or MELAS).

Tests vary significantly among laboratories. The table below indicates variants that are commonly assessed in each of the test types. Check with the lab to determine the variants that can be detected by the specific test.

Table 1: Comparison of tests and the variants commonly assessed in each of the test types

 

SNV

Indel

CNV

TNR

Methyl

mtDNA

Targeted mutation analysis

X    

# #

#    

Condition-specific

X

#

#

#

Broad multi-gene tests

X

X


 

CMA

X* 
   

Exome

X X

     



 

Whole genome sequencing

X

X

 
 

# Variants assessed when appropriate for the condition tested

* CMA is only able to detect deletions and duplications greater than 100kb, and the exact size depends on the specific CMA methodology used.

Test Attributes

The table below is intended to provide an overview of the differences among tests that assess sequence variants. As test offerings vary significantly, it is important to check with the laboratory directly to assess these characteristics for a specific test.

Tests that assess other variant types (i.e., chromosome structural changes, methylation patterns, and mtDNA) are not included.

Table 2: Comparison of test characteristics for tests that assess sequence variants

  Scope Sensitivity Uncertain findings Secondary findings Unexpected findings Cost Turn-around time
Targeted mutation analysis  +  +++++  +  N/A  +  +  +
Condition-specific  ++  ++++  ++  +  ++  +  +
Broad multi-gene tests  +++  +++  +++  ++  +++  ++  +
Exome testing  ++++  ++  ++++  +++  ++++  +++  +++
Whole genome sequencing  +++++  +  +++++  +++  +++++  ++++  ++++

Scope: The specific subset of genetic material the test assesses.

Sensitivity: Includes both whether certain types of variants are detected and, for sequence variants, the read depth (the number of times a particular base is assessed). Read depth can be an important factor impacting the interpretation of wide-scale tests such as exome and whole genome testing, as it indicates the likelihood that the test would have identified a variant if it was present. 

Uncertain findings: Occur when a test detects variants for which their impact and/or specific function remain unknown or unclear.

Secondary findings: Identification of variants in genes unrelated to the presenting condition. These findings may or may not be reported, depending on lab policies and procedures and patient preferences.

Unexpected findings: Identification of variants that indicate misattributed family relationships (e.g., nonpaternity), or variants in genes not previously suspected, but related to the presenting findings.

Turnaround time: Amount of time it takes for tests results to be returned to the ordering provider.

 

 Updated May 2020