Instructions for use

• Ask for confidentiality • Statistics and graphs • Complex alleles

 

• Ask for confidentiality

In some circumstances, you may not be willing to submit a variant to Infevers in order not to jeopardize further publication in a scientific journal.
However, it happened many times that we heard about a variant that was eventually submitted to Infevers by another contributor before being published by the initial discoverer. Indeed, our policy is to favor dissemination of information.
To avoid these uncomfortable situations, we now offer the possibility that your sequence variant remains confidential for a while.
If you ask for confidentiality, your data will not be visible, but you will be credited with the date of submission when it becomes visible.
After submission you will be reminded every 6 months to allow or not your variant to become publicly available.
After three reminders (18 months), the variant will automatically become visible.
In the event that another contributor submits the same variant in the meantime, you will be warned and this duplicated data submission will automatically activate publication of your data.

 

• Statistics and graphs
Several novel applications are now available through the "search entire database module".

Tabular list:
Provides a complete list of validated (and not confidential) sequence variants currently recorded in Infevers.
A complete detailed tabular list can also be downloaded as an excel file.
All data can be cross-queried by selecting values in each item. For example [location:"exon1"] + [alteration: "substitution"] + [technique: "sequencing"] extracts the list of sequence variants matching these 3 parameters among the complete list.
Details on each variant are available as a specific "detailed variant form" by simply clicking on "see details"
This detailed variant form contains all available information on the variant, and shows the upstream and downstream 15bp surrounding the first base mutated (in red).

Gene graph:
A schematic figure of the gene, with exons and introns roughly on scale is provided. The distribution of the sequence variants along the gene is represented, and the "detailed variant form" is available by simply clicking on the variant name.

Statistics:
Histograms depicting the current number of sequence variants recorded in Infevers are provided per alteration type, location and ancestry . Data are shown as the total number of sequence variants, or according to the phenotype associated with the variant (red: number of variants with a defined associated phenotype, orange: number of variants with unknown phenotype, green: number of variants with no associated phenotype).

Sequences:
The cDNA sequence and the genomic sequence of the gene are shown.
You can download as a doc file the sequence of gene including 1000 bp 5' and 3' of the gene.
Exons are in upper case, introns are in lower case.
The ATG of the first translated Met codon, and the termination codon are highlighted.

Note: Any table or illustration from this module is freely available, however you are kindly requested to quote Infevers.
The following citation format is appropriate: Infevers: an online database for autoinflammatory mutations. Copyright. Available at http://fmf.igh.cnrs.fr/ISSAID/infevers/ Accessed (date of access) together with the following references:

Milhavet F, Cuisset L, Hoffman H, El-Shanti H, Slim R, Aksentijevich I, Lesage S, Waterham H, Wise C, Sarrauste de Menthière C, Touitou I.
2008 - Hum Mutat.

Touitou I, Lesage S, McDermott M, Cuisset L, Hoffman H, Dode C, Shoham N, Aganna E, Hugot JP, Wise C, Waterham H, Pugnere D, Demaille J, Sarrauste de Menthière C.
2004 - Hum Mutat. 24(3):194-8.

Sarrauste de Menthière C, Terrière S, Pugnère D, Ruiz M, Demaille J, Touitou I.
2003 - Nucleic Acids Res.31(1):282-5.

 

• Complex alleles
Complex alleles (more than one change in one allele) are now listed, and a new specific form is available for their submission.

List of complex alleles:
When one change participates in one or more complex allele(s), this information is indicated in the "complex allele" column, available at the right end of the tabular list of the "search entire database" module. All recorded complex alleles including the specific change are then detailed through the "see details" button.

Submission of complex alleles:
When you wish to contribute a novel sequence variant, you will now be given the choice to submit either a simple variant, or a complex allele.
The sequence changes constituting the complex allele:

  • Must be already recorded in the database
  • Must appear sequentially from 5' to 3'
    Example p.[S108R; M694V] and not p.[M694V; S108R]

Nomenclature :

Description of the nucleotidic change
Two variations in one allele, separated by at least one nucleotide, are described as "[first change; second change]". Consequently, the description c.76_77delinsTT is preferred over c.[76A>T; 77G>T].

  • c.[76A>C; 83G>C] denotes two changes in one allele; A to C change at nucleotide 76 and a G to C change at nucleotide 83
Description of the protein change
Two variations in one allele
  • deriving from two independent changes at DNA level are described as "[first change;second change]"
  • p.[Ala25Thr;Gly28Val] denotes two changes in one allele; amino acid Alanine-25 to Threonine and Glycine-28 to Valine
  • deriving from one change at DNA level that has more than one effect on RNA/protein level are described as "[first change, second change]"
  • p.[Ala5Thr, Ala5_Gly30delfsX] denotes two protein changes deriving from a change in one allele at DNA level (c.13G>A, resulting in two transcripts (r.[13g>a, 13_88del]); amino acid Alanine-5 to Threonine and a deletion of amino acids Alanine-5 to Glycine-30 followed by a frame shift