Table 4 |
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|
Comparisons of results from using single-end and paired-end reads for finding fusions |
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|
Read type |
Fusion genes (left-right) |
Chromosomes (left-right) |
5' position |
3' position |
Spanning reads (RPM) |
Spanning pairs |
|
|
||||||
|
Single |
GAS6-RASA3 |
13-13 |
114529968 |
114751268 |
15 (0.267) |
|
|
Paired |
GAS6-RASA3 |
13-13 |
114529968 |
114751268 |
10 (0.198) |
43 |
|
Single |
BCR-ABL1 |
22-9 |
23632599 |
133655755 |
6 (0.107) |
|
|
Single |
BCR-ABL1 |
22-9 |
23632599 |
133729450 |
3 (0.053) |
|
|
Paired |
BCR-ABL1 |
22-9 |
23632599 |
133655755 |
2 (0.040) |
7 |
|
Paired |
BCR-ABL1 |
22-9 |
23632599 |
133729450 |
3 (0.059) |
10 |
|
Single |
ARFGEF2-SULF2 |
20-20 |
47538548 |
46365683 |
17 (0.302) |
|
|
Paired |
ARFGEF2-SULF2 |
20-20 |
47538545 |
46365686 |
10 (0.198) |
30 |
|
Single |
BCAS4-BCAS3 |
20-17 |
49411707 |
59445685 |
25 (0.445) |
|
|
Paired |
BCAS4-BCAS3 |
20-17 |
49411707 |
59445685 |
13 (0.257) |
145 |
|
|
||||||
|
Comparisons of single-end and paired-end reads as evidence for gene fusions in the Universal Human Reference (UHR) cell line (a mixture of multiple cancer cell lines), using the known fusions GAS6-RASA3, BCR-ABL1, ARFGEF2-SULF2, and BCAS4-BCAS3. With TopHat-Fusion's ability to align a read across a fusion, the single-end approach is competitive with the paired-end-based approach. RPM is the number of reads that span a fusion per millon reads sequenced. For instance, the RPM of single-end reads in GAS6-RASA3 is 0.267, which is slightly better than the RPM for paired-end reads. Single-end reads may show higher RPM values than paired-ends in part because single-end reads are longer (100 bp) than paired-end reads (50 bp) in these data, and therefore they are more likely to span fusions. |
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|
Kim and Salzberg Genome Biology 2011 12:R72 doi:10.1186/gb-2011-12-8-r72 |
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