Table 5.
CNV Detection with CFseq
| Data set | Sample and region | CNV type | ExomeDepth24 | CONTRA25 | Coverage ratio plot | qPCR agreement | Primer region sequencing |
|---|---|---|---|---|---|---|---|
| 51 samples | S8 (exon_5) | Loss | N | Y | Y | N | N |
| S23 (exon_4)∗ | Loss | Y | Y | Y | N | c.274-60C>T† | |
| S42 (exon_26) | Gain | Y | Y | N | Y | NA | |
| S50 (exon_2-3)∗ | Loss | Y | Y | Y | Y-e3, N-e2 | NA | |
| 48 samples | S6 (intron_12)∗ | Loss | Y | Y | Y | Y | N |
| S16 (exon_25-26)∗ | Loss | Y | Y | Y | Y-e25, e26 | NA |
Analysis using three computational algorithms predicted CNVs in six samples, four of which were concordant among all three methods. qPCR quantitatively confirmed four of six CNV samples, with the exception of exon 2 in sample S50, which was a known exon 2,3 deletion sample based on Luminex panel testing. Sanger sequencing of primer annealing regions identified a rare variant under primer 4F in S23 (primer base position 18, marked with an underline below) as a possible cause of an allele-specific amplification failure. The CNV in sample 8 that was predicted by only two of the three methods was not confirmed.
CNV, copy number variant; NA, not available; qPCR, real-time quantitative PCR.
Predicted CNVs for which all three prediction algorithms agreed.
Located 8 bp from the 3′ end of primer 4F (5′-AGTCTTGTGTTGAAATTCTCAGGGT-3′).