<pcrAssay>

This type describes a PCR assay, which is broadly defined as an assay that uses two primers to amplify and query a unique location in the genome.

The results of a PCR assay are reported within a sequencingResult element. If no variants are reported for a sample on which this assay was performed, the genotype for the sample in the amplified region is assumed to be the same as the reference sequence. Consult the sequencingResult element for details on how to handle incomplete reads.

The relationship between the primers and the reference sequence depends on the coordinate system that is used. The forward primer's annealing positions will always be less than the annealing positions of the reverse primer since the forward primer should fall to the logical left of the reverse primer in the coordinate system. This means that if the coordinate system is in the forward orientation and on the plus strand, then:

• the forward primer must anneal to the left of the reverse primer in the reference sequence, and the annealing portion of the sequence must match some substring of the reference sequence, and
• the reverse primer must anneal to the right of the forward primer in the reference sequence, and the annealing portion of the sequence must match some substring of the reverse compliment of the reference sequence.

If the coordinate system is in the reverse orientation and on the minus strand, just swap the forward and reverse primers in the statements above.

Note that it is an error for the coordinate system to be in the forward orientation and on the minus strand or in the reverse orientation and on the plus strand for PCR assays.

Attributes

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.
amplicon	The region of the reference sequence amplified by this PCR assay.
forwardPrimer	The forward sequencing primer that anneals 5' with respect to the reverse primer.
reversePrimer	The reverse sequencing primer that anneals 3' with respect to the forward primer.
method	The experimental method used to perform this assay.

Validation Rules

Content validation performed on this element:

• The start and stop positions of the amplicon must lie on the reference sequence.
• If primers are defined, the primers must not have regions that overlap.
• If primers are defined, they must be defined in the correct order -- the forward primer must be upstream of the reverse primer.
• If primers are defined, the amplicon must lie within the outermost extent of the primers. For example, if the primers start and stop at positions (5, 10) and (20, 25) respectively, the largest amplicon region can be (5, 25).
• (Warning) The forwardPrimer and the reversePrimer should be defined.

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