Finding the Needle in the Genomic Haystack With DRAGEN - Seite 2

One way to tackle this is to perform longer reads. If the fragments are long enough to bridge the homologous region, reads can be mapped unambiguously to different copies of that region in the reference genome. For example, Illumina Complete Long Reads can create reads up to about 10,000 base pairs. But some homologous regions are still longer than that.

Luckily, Illumina scientists have developed solutions to this problem even for short reads. Targeted callers are tailor-made to quickly and accurately detect the copy number (and other variants) of genes associated with specific diseases. Read on to learn about three of them-congenital adrenal hyperplasia, alpha thalassemia, and atherosclerosis-and how DRAGEN Secondary Analysis software version 4.2 pierces the fog to locate their genetic origin.

CYP21A2 and congenital adrenal hyperplasia

Our adrenal glands, located atop our kidneys, help regulate the levels of sodium and potassium in our blood. They do this by synthesizing the hormones cortisol and aldosterone, with the help of the protein 21-hydroxylase.

That protein is coded by the gene CYP21A2, which unfortunately sits in just one of two copies of the highly homologous RCCX region. The other copy of RCCX contains a very similar "pseudogene," CYP21A1P, which has no function. This homology confuses not just gene sequencing, but human reproduction: When parental chromosomes recombine to form their child's DNA, they might mistakenly mix genetic material between the functional CYP21A2 and the nonfunctional CYP21A1P, impairing the resulting gene's ability to code for 21-hydroxylase… or they might delete the gene entirely.

As with many inherited diseases, a child usually shows no symptoms as long as they have one functioning copy of CYP21A2-they're only a carrier for the condition. But having two nonfunctional copies leads to congenital adrenal hyperplasia (CAH).

CAH caused by 21-hydroxylase deficiency occurs about once in 10,000 to 15,000 live births. If a developing fetus's adrenal glands have a decreased level of 21-hydroxylase, they can't synthesize as much cortisol and aldosterone as their body needs. Then, the excess materials they would've used for synthesis accumulate and instead form androgens, or male sex hormones. This is called "simple virilizing CAH." Girls with excessive androgens may develop ambiguous genitalia; boys may not show any external signs and require targeted screening to diagnose.

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