Table 3

Predicted Rearrangments involving PTPN12 in GBM.

Recurrent Gene PTPN12

Gene

Genomic Location

# Patients


PTPN12

chr7.77004708-77106533

16


Intrachromosomal Fusion Gene Predictions

5' End Gene

3' End Gene

# Patients

RMS


PTPN12

chr7.77005287-77106533

RSBN1L

chr7.77163678-77246421

8

0.1081

PTPN12

chr7.77004708-77106533

LUC7L2

chr7.138695173-138757626

8

0.2605


Interchromosomal Fusion Gene Predictions

5' End Gene

3' End Gene

# Patients

RMS


TMEM30A

chr6.76019357-76051074

PTPN12

chr7.77005287-77106533

6

0.1306

RNF150

chr4.142006174-142273412

PTPN12

chr7.77005287-77106533

5

0.1409

PTPN12

chr7.77005287-77106533

MED13

chr17.57374747-57497348

9

0.1906

CLK1

chr2.201425977-201434830

PTPN12

chr7.77005287-77106533

8

0.3168

ZRANB2

chr1.71301561-71319266

PTPN12

chr7.77005287-77106533

9

0.3250

PTPN12

chr7.77005287-77106533

UBR1

chr15.41022389-41185512

9

0.3475

PTPN12

chr7.77005287-77106533

LINGO1

chr15.75692423-75711712

8

0.3787

PPIL3

chr2.201443923-201460583

PTPN12

chr7.77004708-77106533

6

0.4741


The phosphatase PTPN12 appears in 10 predicted fusion genes, and is also a predicted gene truncation for 16 patients. The predictions are ranked according to the root mean squared difference (RMS) of the copy number on either side of the fusion point.

Ritz et al. BMC Bioinformatics 2011 12:114   doi:10.1186/1471-2105-12-114

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