Table 1. NGS identification of an internal tandem duplication in the BCOR gene.
| Sample | Contig Length | Conting start | Conting end | Transcript start | Transcript end | BLASTN E-val | ITD |
|---|---|---|---|---|---|---|---|
| CCSK1 | 67 | 1 | 30 | 5237 | 5266 | 1.00E-08 | c.5171_5266dup |
| 29 | 67 | 5169 | 5207 | 5.00E-14 | |||
| CCSK3 | 54 | 1 | 17 | 5250 | 5266 | 1.00E-05 | |
| 16 | 54 | 5169 | 5207 | 4.00E-14 | |||
| CCSK5 | 77 | 1 | 40 | 5227 | 5266 | 2.00E-14 | |
| 39 | 77 | 5169 | 5207 | 6.00E-14 | |||
| CCSK6 | 67 | 1 | 30 | 5237 | 5266 | 1.00E-08 | |
| 29 | 67 | 5169 | 5207 | 5.00E-14 | |||
| CCSK2 | 58 | 1 | 22 | 5204 | 5225 | 6.00E-04 | c.5136_5225dup |
| 20 | 58 | 5133 | 5171 | 4.00E-14 | |||
| CCSK4 | 75 | 1 | 39 | 5187 | 5225 | 6.00E-14 | |
| 37 | 75 | 5133 | 5171 | 6.00E-14 | |||
| CCSK7 | 69 | 1 | 33 | 5193 | 5225 | 2.00E-10 | |
| 31 | 69 | 5133 | 5171 | 6.00E-14 | |||
| CCSK8 | 51 | 1 | 22 | 5191 | 5212 | 5.00E-04 | c.5099_5212dup |
| 23 | 51 | 5099 | 5127 | 3.00E-08 |
The analysis detected three different breakpoints on exon 15 of BCOR transcript (ENST00000378444). For each sample the BLASTN algorithm locally aligns the contigs in two different regions mapping on exon15 of BCOR: the first portion of the sequence overlaps a BCOR region closer to 3′-end with respect to the last portion, suggesting a duplication and insertion event.