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    Nomenclature

    fs-tool in all inputs expects a certain level on nomenclature standards being maintained.

    HLA Class I

    HLA alllele nomenclature can vary substantially across tools, laboratories or even agencies.
    There are certain times where it will take a considerable time to standardize the names where the benefit is not obvious. Example is the HLA Prefix or the * separator, however the field separator : and maintaining the Gene (A0201 vs 0201) as part of the allele name ensure certain safeguards.

    An obvious one, is that using different programs and dealing with values as 0201 or A0201 could lead to unwanted removal of the 0 digit as well as cause problems during parsing when such inputs are supplied to various programs.

    For this reason in all inpus to fs-tool, the : (colon) field separator must be present in both the --index allele supplied and in the cohort HLA genotype columns. This means that the following is true:

    ExampleValid
    A0201No
    0201No
    A02:01Yes
    A*02:01Yes
    HLA-A*02:01Yes
    HLA-A*24:09NYes
    A30:14LYes

    For further information on HLA nomenclature, please visit http://hla.alleles.org/nomenclature/naming.html.

    KIR

    KIR alleles supplied are valid with or without acronym and with or without allele specifed. However, alleles speciefed have to have at least the three letter series specified (KIR2DL1*003 vs KIR2DL1*3).
    The KIR acronym is not required and can be ommited in the column names of cohort data.

    ExampleValid
    2DL1*03No
    KIR2DL1Yes
    2DL1Yes
    KIR2DL5AYes
    2DL5BYes
    2DL1*0030202Yes

    The following KIR genes are currently supported:

    • 2DL1
    • 2DL2
    • 2DL3
    • 2DL4
    • 2DL5A/2DL5B
    • 2DS1
    • 2DS2
    • 2DS3
    • 2DS4
    • 2DS5
    • 3DL1/3DS1
    • 3DL2
    • 3DL3
    • 2DP1
    • 3DP1

    For more information, on the KIR gene/alelle nomenclature, please visit https://www.ebi.ac.uk/ipd/kir/alleles.html