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  • exome sequencing can detect fusion genes?

    Solitary fibrous tumors (SFTs) are rare mesenchymal tumors. Here, we describe the identification of a NAB2-STAT6 fusion from whole-exome sequencing of 17 SFTs. Analysis in 53 tumors confirmed the presence of 7 variants of this fusion transcript in 29 tumors (55%), representing a lower bound for fusi …


    This research says it did. Is it because the junction point lies with exons of both genes?

  • #2
    Sure, you can still pick up chromosomal and other structural rearrangements with exome sequencing, just not 100% of the time. You're correct that the reason this worked was due to the genes rearranging and effectively merging in the genome. Because of that, the capture kit still got reads that mapped to the end of one or the other of the genes (with the remainder mappable to the other gene).

    This would be in contrast to detecting fusion transcripts arising from neighboring genes being coexpressed and spliced together. Those sorts of situations wouldn't be detectable with exome sequencing.

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    • #3
      The answer is that it depends on:
      - where fusion junction point lies (it is "well" inside an exon which should be 'captured' properly and both genes involved in fusion should captured properly),
      - coverage of sequencing

      Whole genome sequencing and RNA-seq are ones of the most used for finding fusion genes and/or translocations.

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      • #4
        Originally posted by ymc View Post
        http://www.ncbi.nlm.nih.gov/pubmed/23313954

        This research says it did. Is it because the junction point lies with exons of both genes?
        Hi,
        Have you detected fusions using Exome tumor data?
        Thanks,
        Sachin

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        • #5
          For anyone interested: They used dRanger (not publicly available) and Breakpointer in order to detect the fusion from exome data.

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