How does depth of sequencing influence detection of mosaicism and low-level CNVs in NGS data?

• A. Lower depth improves detection of mosaicism and small CNVs.
• B. Not increasing depth has any impact on detection.
• C. Higher depth improves detection of mosaicism and small CNVs.
• D. Depth affects only sequencing speed, not detection.

Answer: (C)

Sequencing depth directly influences how reliably we can spot signals that are present in only a subset of cells or in a small genomic region. When a mosaic variant exists in a fraction of cells, the number of reads carrying the alternate allele is proportional to that fraction. If the overall depth is low, those a few alternate reads can be lost in random sampling noise or mistaken for sequencing error. As depth increases, the true signal scales up with the number of reads, making it easier to distinguish a real mosaic variant from noise and to estimate its fraction more accurately.

The same idea applies to small CNVs. Detecting a copy-number change relies on observing a deviation in read depth across a genomic interval. Low depth has high variability in read counts, so small changes can be masked by normal fluctuation. Increasing depth reduces this noise and provides a clearer, more consistent signal of a copy-number gain or loss, enabling detection of smaller or lower-level CNVs that would be missed at shallower depths.

Thus, deeper sequencing improves sensitivity for both mosaicism and small CNVs, though it comes with higher cost and data handling requirements.