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  • where are the accession numbers?

    Accession Numbers?

    Recently a deathly ill child in Wisconsin became the beneficiary of a Next Gen sequence diagnosis for Leptospira santarosi



    The diagnosing laboratory sequenced samples of fluid from the patient and hooked up to the open access NCBI database to search for pathogen DNA matches via methods published recently in Genome Research. see
    A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples Published in
    Advance June 4, 2014, doi: 10.1101/gr.171934.113 Genome Res. 2014.

    Unfortunately, while the genome of this bacterial species had been published as of 2012--see Sequence of Leptospira santarosai serovar Shermani genome
    and prediction of virulence-associated genes
    Gene
    Volume 511, Issue 2, 15
    December 2012, Pages
    364-370

    the sequences had NOT been deposited into GenBank as of August 2013
    when the bioinfo analysis was run on behalf of the severely ill patient and so the bioinformatics answer had to be supplemented with additional wet laboratory procedures in order to nail the exact identity of the obscure pathogen. http://www.genomeweb.com/clinical-ge...l-boys-disease

    The published article on Leptospira santarosi does not show an accession number even though the journal instructs all authors to do so. "Gene requires all new nucleotide and amino acid sequences to be deposited. Obtain and include an accession number with all sequences. The most convenient method for submitting sequence data is by World Wide Web:
    EMBL
    GenBank
    DDBJ"

    It is especially important to deposit new sequences of obscure organisms into accessible databases as expected upon peer reviewed publication because culturing pathogenic organisms in vitro can present huge challenges that can be readily overcome by unbiased next gen sequencing in a manner timely enough to save a patient's life.

  • #2
    It is indeed really annoying when people don't deposit the things they should into repositories. While journals technically require this, the editors seem to never check and the reviewers seem not to half the time.

    Comment


    • #3
      Checking "Sequence of Leptospira santarosai serovar Shermani genome and prediction of virulence-associated genes" (http://europepmc.org/abstract/MED/23041083), the details of the submission are covered in "2.4. Nucleotide sequence accession number":

      The genome sequence of L. santarosai serovar Shermani has been deposited at DDBJ/EMBL/GenBank under the accession ADOR00000000. The version described in this paper is the first version, ADOR01000000.
      Checking in ENA this project exists in the INSDC databases and is associated with a set of whole genome shotgun entries, see http://www.ebi.ac.uk/ena/data/view/ADOR00000000

      So it looks like the sequence data has been submitted.

      However the paper does mention that an assembly and annotation was performed, which suggests there should also be a CON entry for the genome. This appears to be absent, although that may be based on the assembly and annotation being a draft and the authors preferring to finalise it before submitting that data.

      Comment


      • #4
        For those of you who are unable to see the GenomeWeb link that Joann included, the effective treatment ended up being penicillin.

        Comment


        • #5
          Please take note: Many thanks for the correct information

          Many thanks for posting the correct information about this matter which indicates that the relevant sequences for Leptospira santarosai were submitted on April 7, 2011 to INSDC. And also for posting the article text reference to the accession number from Gene journal. My desktop access to this journal only shows the first (abstract) page of the article and there is no accession numbers indicated by the publisher on that page. (I believed it was customary to display accession numbers below the abstract for the sake of text and data curation efforts and that publishers complied with this.) It is my hope that this discussion clears up some confusion concerning sequence databases and their importance as an open access resource in healthcare situations globally.

          Comment

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