Accession Numbers?
Recently a deathly ill child in Wisconsin became the beneficiary of a Next Gen sequence diagnosis for Leptospira santarosi
http://www.nytimes.com/2014/06/05/he...ness.html?_r=0
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.
Recently a deathly ill child in Wisconsin became the beneficiary of a Next Gen sequence diagnosis for Leptospira santarosi
http://www.nytimes.com/2014/06/05/he...ness.html?_r=0
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.
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