Figure 2 | Genetics in Medicine

Figure 2

From: The next generation of population-based spinal muscular atrophy carrier screening: comprehensive pan-ethnic SMN1 copy-number and sequence variant analysis by massively parallel sequencing

Figure 2

A novel computational algorithm PGCNARS (paralogous gene copy-number analysis by ratio and sum) for SMN1 copy-number analysis using next-generation sequencing coverage depth data for spinal muscular atrophy carrier screening. PGCNARS involves three major steps for the SMN1 copy-number analysis. First, for each sample in the same capture pool, the copy-number ratio of SMN1 to SMN2 is calculated using the read depth of the paralogous sequence variants in exon 7 (c.840C/T) or exon 8 (c.*233T/A) of SMN1 and SMN2 (step a1–3). The SMN1 and SMN2 total copy number was determined by their exonic coverage data after normalization to the read depth of the median identified in the sample group (step b1–7). Finally, the SMN1 copy number in each sample is calculated based on the SMN1 to SMN2 copy-number ratio and their total copy number (step c).

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