How to submit an order for targeted genotyping marker design

Name used for identifying and reporting markers. Each candidate marker must have an entry in this column. All marker names must be unique within the marker set.

Defined allele sequences with flanking sequence on both sides.

See the document Format_Instructions_For_Marker_Submission_With_Examples_v0.9.xlsx for examples of the required format.

• DNA strand orientation must be 5' to 3', with allele variants and flanking sequence defined on the same strand.
• Flanking sequence consists of DNA nucleotides bases, including IUPAC ambiguity codes, in upper case, with no spaces or line breaks allowed.
• "Reference allele" and "Alternative allele" are defined at the appropriate position in the TargetSequence in square brackets [REF/ALT], as per the example [C/A].
• Non ACGT IUPAC symbols cannot be present within the square brackets except for '-' when used for deletion variant of indel markers.
• Indel type markers may be represented as a standard insertion and deletion pair such as [T/-] or [-/TTA], or may be represented by a pair of   distinct sequences such as [GA/AAT] or [GGAC/TGGAT].
• Indel type allele definitions must not contain any common prefix or suffix bases, for example [TAGTGA/TAGA] is not permitted, as it contains common prefix and suffix.
• Only a single instance of '-' can be present within the square brackets and cannot be combined with other characters to make an allele sequence.
• If possible, provide 150bp nucleotide sequences from right and left ends of the Variant - ATCGAACGTT….150bp [REF/ALT]ACTTGCA…... 150bp 
• Provide a minimum of 100bp total sequence length to allow a proper probe design

Note: Allow only a single variant specified within the sequence - i.e. only a single pair of square brackets [REF/ALT], and only 2 alleles within the brackets. Definitions with more than 2 alleles [REF/ALT/ALT] cannot be processed. These can be represented as separate markers with one [REF/ALT] combination per marker submission row.

Optional. When available, provide the name, including version information, of the Reference genome used to provide position information for the marker.For the Reference genomes(s) included here, provide a download link in the accompanying specifications section at the end of this document.

Specify here the Ref and Alt alleles of the marker in the same format used in the TargetSequence in Column 2, [REF/ALT]. Check that the defined Ref and Alt alleles correspond exactly the definition included in Column 2, and that the defined alleles are on the same strand as the flanking sequence.

Optional. Indicate those markers which are considered to be essential, and should be included in the selected marker panel regardless of design quality or other selection and optimisation criteria. Markers which are considered essential should be marked with YES in this column, otherwise NO

Optional. If applicable, a MAF value can be provided for use in marker selection. If MAF values are provided, they must be given for all candidate markers with the exception of those marked as essential in Column 9.

Optional. If applicable, include a quality score for use in marker selection. The quality score should consist of values between 1.0 and 10.0, with 1.0 indicating the best quality. If quality scores values are provided, they must be given for all candidate markers with the exception of those marked as essential in Column 9.