Discovery of recurrent structural variants in nasopharyngeal carcinoma.
We present the discovery of genes recurrently involved in structural variation in nasopharyngeal carcinoma (NPC) and the identification of a novel type of somatic structural variant. We identified the variants with high complexity mate-pair libraries and a novel computational algorithm specifically designed for tumor-normal comparisons, SMASH. SMASH combines signals from split reads and mate-pair discordance to detect somatic structural variants. We demonstrate a >90% validation rate and a breakpoint reconstruction accuracy of 3 bp by Sanger sequencing. Our approach identified three in-frame gene fusions (YAP1-MAML2, PTPLB-RSRC1, and SP3-PTK2) that had strong levels of expression in corresponding NPC tissues. We found two cases of a novel type of structural variant, which we call "coupled inversion," one of which produced the YAP1-MAML2 fusion. To investigate whether the identified fusion genes are recurrent, we performed fluorescent in situ hybridization (FISH) to screen 196 independent NPC cases. We observed recurrent rearrangements of MAML2 (three cases), PTK2 (six cases), and SP3 (two cases), corresponding to a combined rate of structural variation recurrence of 6% among tested NPC tissues.
Division of Bioinformatics, Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California 90087, USA;
Anton
A
Valouev
Ziming
Z
Weng
Robert T
RT
Sweeney
Sushama
S
Varma
Quynh-Thu
QT
Le
Christina
C
Kong
Arend
A
Sidow
Robert B
RB
West
D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics; D002277:Carcinoma; D004268:DNA-Binding Proteins / Q000235:genetics; D051417:Focal Adhesion Kinase 1 / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic; D050939:Gene Fusion / Q000235:genetics; D056914:Genomic Structural Variation; D006801:Humans; D006836:Hydro-Lyases; D017404:In Situ Hybridization, Fluorescence; D008565:Membrane Proteins / Q000235:genetics; D000077274:Nasopharyngeal Carcinoma; D009303:Nasopharyngeal Neoplasms / Q000235:genetics* / Q000473:pathology; D009687:Nuclear Proteins / Q000235:genetics; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D010750:Phosphoproteins / Q000235:genetics; D017027:Protein Tyrosine Phosphatases / Q000235:genetics; D051705:Sp3 Transcription Factor / Q000235:genetics; D015534:Trans-Activators; D014157:Transcription Factors / Q000235:genetics; D000091102:YAP-Signaling Proteins
D048868:Adaptor Proteins, Signal Transducing; D004268:DNA-Binding Proteins; C471297:MAML2 protein, human; D008565:Membrane Proteins; D009687:Nuclear Proteins; D015514:Oncogene Proteins, Fusion; D010750:Phosphoproteins; C542463:RSRC1 protein, human; C497121:SP3 protein, human; D015534:Trans-Activators; D014157:Transcription Factors; D000091102:YAP-Signaling Proteins; C088374:YAP1 protein, human; D051705:Sp3 Transcription Factor; D051417:Focal Adhesion Kinase 1; C496050:PTK2 protein, human; D017027:Protein Tyrosine Phosphatases; D006836:Hydro-Lyases; C484872:HACD2 protein, human