Genetics > Genetics (General Principles) > Genetic testing

Applications of common genetic tests
Test	Applications	Limitations
Gene sequencing	Detects mutations within a single gene (eg, point mutation)	Cannot detect whole gene deletion
Fluorescence in situ hybridization (FISH)	Identifies targeted chromosomal abnormalities (eg, deletion, duplication, trisomy) Specific probe(s) used for a suspected diagnosis (eg, BCR-ABL fusion in CML)	Cannot detect chromosomal abnormalities other than those specified by labeled probe
Chromosomal microarray	Identifies targeted chromosomal abnormalities (eg, microdeletion, microduplication) Many probes allow for simultaneous assessment of multiple abnormalities for a broad diagnosis (eg, autism)	Cannot detect chromosomal abnormalities other than those specified by labeled probe Cannot detect balanced translocations
Karyotype (cytogenetic analysis)	Detects large chromosomal abnormalities (eg, aneuploidy)	Cannot detect small chromosomal abnormalities
CML = chronic myeloid leukemia.

In this study, the affected patients have varying and unknown point mutations within a particular gene. The initial genetic test for identifying an unknown mutation in a given gene is single gene sequencing. This technique typically involves isolating and amplifying the target gene (eg, via PCR) and then determining the specific nucleotide order. Subsequent comparison to a normal sequence allows for identification of a potentially pathogenic variant.

The patients in this study likely have Li-Fraumeni syndrome, an autosomal dominant disorder involving a tumor suppressor gene on chromosome 17 (TP53). This gene plays an important role in preventing cell cycle progression in cells with damaged DNA. Because patients with Li-Fraumeni syndrome have only 1 functional gene, they are at a greater risk for malignancy due to uncontrolled cell proliferation if the remaining gene spontaneously mutates during the cell's lifetime.

Multiple pathogenic variants, most commonly missense point mutations, have been identified at various loci within the gene, making single gene sequencing the ideal tool for identifying patients with Li-Fraumeni syndrome. However, this method has limitations, including the inability to detect whole gene deletions (the remaining normal allele will still be sequenced, so the absence of the deleted allele cannot be directly ascertained).

(Choices A and C) Chromosomal microarrays and fluorescence in situ hybridization (FISH) identify known targeted chromosomal abnormalities using oligonucleotide probes (at least 20 bases long) that bind complementary sequences; neither can reliably detect the presence of unknown point mutations at various locations. Microarrays are typically used to screen for many mutations or genetic polymorphisms simultaneously, whereas FISH is typically used to identify a suspected condition (eg, BCR-ABL1 fusion in chronic myeloid leukemia).

(Choice B) Cytogenetic analysis, or karyotyping, can detect large abnormalities in chromosomal size (eg, long arm deletion) or number (eg, trisomy) but not small chromosome abnormalities or point mutations.

(Choice D) DNA methylation is an epigenetic modification that results in suppressed gene expression via the addition of a methyl group to a base. Because methylation patterns can be specific to the parental origin of the chromosome, methylation analysis is useful for suspected imprinting disorders (eg, Prader-Willi syndrome) in which a patient may inherit two genes derived from the same parent.

Educational objective:
Single gene sequencing is the initial genetic test for disorders caused by an unknown mutation in a single gene (eg, Li-Fraumeni syndrome). A limitation includes the inability to detect whole gene deletions.

Clinical Genetics

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