Copy number variation (CNV) refers to deletions or duplications of DNA segments. Which testing methods detect CNVs?

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CNVs are deletions or duplications of DNA segments that can range from kilobases to megabases in size, so detecting them requires methods that measure copy number rather than just sequence sequence changes. Chromosomal microarray analysis (CMA) compares patient DNA to a reference across the genome using probes, revealing gains and losses at many loci with resolution determined by probe density. Multiplex Ligation-dependent Probe Amplification (MLPA) uses targeted probes to quantify copies at specific regions, making it very useful for known or suspected CNVs in particular genes or intervals. Sequencing-based approaches detect CNVs by looking at how many sequencing reads map to a region; a higher read depth suggests a duplication, while a lower depth suggests a deletion, enabling genome-wide or targeted CNV detection through depth-of-coverage analysis. Quantitative PCR (qPCR) compares the amount of DNA amplified from a region to a reference, providing a straightforward validation or targeted CNV assessment.

Karyotyping mainly detects large chromosomal alterations but lacks the resolution to reliably identify many CNVs, which is why it’s not as central for CNV detection. Sequencing can detect CNVs when analyzed for depth of coverage, so the statement that CNVs aren’t detectable by sequencing-based approaches isn’t correct. CNVs refer to segments of DNA, not single-nucleotide changes, so D is also inaccurate.