Table 4

Comparisons of results from using single-end and paired-end reads for finding fusions

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.

Kim and Salzberg Genome Biology 2011 12:R72   doi:10.1186/gb-2011-12-8-r72

Open Data