When comparing genotyping data, it is important to use the same DNA
strand designation. For Infinium array data analyzed using
GenomeStudio, sample genotypes can be reported in several formats,
including Plus Strand, Top Strand, and/or Forward Strand. The strand
designations are based on information provided in the product manifest
file, and are relative to the nucleotides reported in the SNP column.
Note: The first nucleotide listed for the SNP is Allele A, and
the second nucleotide is Allele B. Alleles A and B are determined by
the Top/Bottom, A/B designation (for more details, see the bulletin Simple
Guidelines for Identifying Top/Bottom TOP/BOT Strand and A/B
Allele and the Technical Note "TOP/BOT"
Strand and "A/B" Allele).
DNA strand designations
Top/Bottom (TOP/BOT, T/B): This designation was developed by
Illumina to allow unambiguous specification of the strand, based on
the variant and surrounding DNA sequence, without reference to any
database (dbSNP, genomic reference, etc.). The T/B annotation within
the IlmnID provides the strand designation of the SNP column in the
manifest. It is useful when no reference is available, or when
comparing to data generated prior to a reference being
Plus/Minus (+/-): Plus strand corresponds to the genomic
sequence as reported in the FASTA for the genomic reference. The +/-
strand designation for the SNP column is provided in the RefStrand
column of the manifest for commercial arrays, and for custom arrays
by request. These designations can change with NCBI Genome Build
Forward/Reverse (FWD/REV, F/R): The Illumina designation of
Forward strand indicates that the alleles in the SNP column match
the RefSNP alleles displayed in dbSNP. The F/R annotation is found
within the IlmnID. Neither this Illumina strand designation nor a
Forward strand report from GenomeStudio are expected to correspond
to the FWD/REV strand designation in dbSNP, which provides the
orientation of the RefSNP alleles relative to the genomic reference.
For custom content, the customer defines this annotation.
GenomeStudio final report strand options
Allele1, 2 – Top, Plus, and/or Forward: Allele 1 and 2
nucleotides correspond to Allele A and B, and are reported on the
Top, Plus, or Forward strand as described above.
Allele1, 2 – Design: Allele 1 and 2 nucleotides correspond to
Allele A and B, and are reported on the strand on which the probe
was designed. This is generally not a useful convention for sharing
data; however, may be useful for investigation of data in which
multiple designs have been created for the same variant.
ILMN Strand: The strand used to design each probe is
designated as TOP/BOT for SNPs or PLUS/MINUS for indels as indicated
in the ‘IlmnStrand’ column of the manifest. The alleles in the ‘SNP’
column are on the IlmnStrand.
Customer Strand: The strand submitted to the Illumina
designer by Illumina or a customer is designated as TOP/BOT for SNPs
or PLUS/MINUS for insertion/deletion (indel), as indicated in the
‘SourceStrand’ column of the manifest.
Plus/Minus Strand: The +/- strand designation for the SNP
column is indicated if provided in the ‘RefStrand’ column of the
Example strand annotations for rs10000030
The rs10000030 strand designations for the [T/C] SNP reported in the
SNP column can be determined by referencing the IlmnStrand and
RefStrand columns in the manifest.
- [T/C] strand = BOT (IlmnID and IlmnStrand), Minus
(RefStrand), and R (IlmnID, SNP is on the opposite
strand of the dbSNP entry)
- Therefore, the [A/G] strand =
TOP, Plus, F (SNP matches dbSNP entry)
- The SNPs are listed
in A/B allele order according to the TOP/BOT convention, rather than
the Ref/Alt allele order.
In summary, the following relationships hold true for dbSNP variants
within the Illumina manifest, except in cases of unmapped