New approaches toward discovery of novel translocations

Chromosome rearrangements that result in gene fusions have important roles in the initial steps of tumorigenesis, especially in leukemias and lymphomas, but the biological and clinical impact of gene fusions in common solid tumors are less understood.

Researchers at the Mayo Clinic set out to discover novel translocations that could result in gene fusions in oropharyngeal squamous cell carcinomas (OPSCCs). They identified translocations using 2 different bioinformatics pipelines, SnowShoes-FTD and FusionHunter, examining data from 11 paired-end RNA sequencing (RNA-Seq) data in OPSCC. Translocations were validated by RT-PCR and Sanger sequencing analysis. Two novel cancer-specific translocations involving MGST3-ZMAT5 and MS4A7-C2CD3 were found in 2 of the tumor samples tested. However, these translocations were found only in the single tumor.

  • Wang VW, Laborde RR, Asmann YW, Li Y, Ma J, Eckloff BW, Tombers NM, Olsen SM, Moore EJ, Olsen KD, Smith DI. (2012) Search for chromosome rearrangements: New approaches toward discovery of novel translocations in head and neck squamous cell carcinoma. Head Neck [Epub ahead of print]. [abstract]