PharmGKB Schema Documentation: <referenceSequence>

This element defines a DNA reference sequence. This sequence is primarily used to align positions reported against it on the gene. More specifically, the dnaSequence will be either be BLATed or BLASTed against the Golden Path sequence so that alleles that are reported against it can be properly positioned on the gene.

For some assays (e.g. PCR and DHPLC assays), this sequence is also used to figure out what the default allele is for any given assayed position for a subject so that submitters only need to report variants against the reference sequence. For example:

If a PCR assay is performed and no variants are reported for a subject, the genotype for that subject within the assay's interrogatedRange is the same as the reference sequence.
If a DHPLC assay is performed and it is reported that a subject is sameAsMajority, the genotype for the subject in the assay's analyzedRegion is the same as the reference sequence.

Please refer to the documentation for the individual assays for more details.

As a result of this, while IUPAC ambiguity codes are allowed in the reference sequence, they are not allowed at any interrogated position.

pharmgkbId	A unique identifier assigned by the PharmGKB (the PharmGKB Accession Id). This attribute is used to refer to data that is already in the PharmGKB and is only supplied when editing or adding to such data. See the FAQ for details.
localId	A unique identifier for this element assigned by the submitter. The only rule it must follow is that no two XML elements can be assigned the same localId within a single XML document. See the FAQ for details.

note	A note.
submitter	This element's submitter.
name	A name for this reference sequence.
organism	The type of organism this reference sequence is from. If this is not defined, it defaults to Human unless a gene is cross-referenced, in which case this defaults to the gene's organism.
geneXref	A cross-reference to the gene this reference sequence is for. While it is recommended that this element be specified, it is not required as PharmGKB will attempt to align the sequence to determine the gene it is for, if any.
dnaSequence	The DNA sequence of this reference sequence. The minimum length is 100 bases and the maximum length is 25,000 bases. The sequence must be composed of `A`'s, `G`'s, `C`'s, `T`'s and the IUPAC ambiguity codes.
dnaSequenceSource	The source of this reference sequence: genomic cDNA mitochondria chloroplast This element maps to dbSNP's `MOLTYPE` tag.
xref	A cross-reference to a resource with more information on this reference sequence.
featureSet	A set of features on this reference sequence.
experiment	An experiment performed on this reference sequence.

cannot be filled in by submitters:
required when defining a new element:
at least one required when defining a new element:
only one allowed, required when defining a new element:
details ...