> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000001489.md).
# How to interpret DNA strand and allele information for Infinium genotyping array data
When comparing genotyping data, it is important to use the same DNA strand designation. For Infinium array data analyzed using GenomeStudio 2.0, 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.
The first nucleotide listed for the SNP corresponds to Allele A, and the second nucleotide corresponds to Allele B. The designation of Alleles A and B is determined based on the Top/Bottom (TOP/BOT), A/B strand system. This is described in detail in [Simple guidelines for identifying top/bottom (TOP/BOT) strand and A/B allele](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000001521?utm_source=agent\&utm_medium=email\&utm_campaign=kb) . [Simple guidelines for identifying top/bottom (TOP/BOT) strand and A/B allele](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Simple-guidelines-for-identifying-top-bottom-TOP-BOT-strand-and-A-B-allele-support-bulletin/README.md)
**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 established.
* **Plus/Minus (+/-):** Plus strand corresponds to the genomic sequence as reported in the FASTA for the genomic reference. The 5′ end of the (+) strand is at the tip of the short arm (p arm) of the chromosome and the 5′ end of the (-) strand is at the tip of the long arm (q arm). 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 versions.
* **Forward/Reverse (FWD/REV, F/R):** The Illumina designation of Forward strand indicates that the alleles in the SNP column match the RefSNP (rs) alleles displayed in dbSNP, if dbSNP was the reference for the design; for non-rs SNPs, derived from resources such as the Thousand Genomes project (KGP), Forward strand refers to the sequence as it exists in the resource. Custom SNPs submitted by the customer can be designated as forward or reverse by the submitter of the design. 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.
**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 manifest.
**Example of Strand Annotations for rs10000030**
**Illumina Manifest File**\
**Figure 1.** Excerpt from an Illumina manifest file showing annotation details for SNP *rs10000030.*
* The Manifest file includes the Illumina ID (*rs10000030-131\_B\_R\_rs10000030*), SNP name (*rs10000030*), and strand designation (*BOT*), indicating that allele assignment follows the bottom strand convention.
* The SNP is defined as a bi-allelic variant \[T/C], where the first nucleotide (T) represents Allele A and the second nucleotide (C) represents Allele B.
* The genomic position is based on genome build 37, located on chromosome 4 at approximately 1 × 10⁸ base pairs.
* The source strand is indicated as TOP, and the probe sequence is shown as AGC\*\[A/G]\*GGC, where the polymorphic site is denoted within brackets.
* The reference strand is indicated as negative (-).
**dbSNP Database**
**Figure 2.** Screenshot of the dbSNP database entry for SNP *rs10000030* (*Homo sapiens*).
* The polymorphic site is displayed within the flanking sequence as *\[A/G]*, indicating a single nucleotide variant with alleles A and G.
* The SNP is located on chromosome 4 at position 102,452,997 and is annotated within the gene *LOC105377621*.
* The functional consequence is classified as an intron variant.
* Validation information includes multiple supporting datasets (e.g., 1000 Genomes Project and HapMap).
* The global minor allele frequency (MAF) is reported, and the variation class is identified as a single nucleotide variant (SNV). The reference SNP alleles are listed as A/G on the forward (FWD) strand.
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 reported in A/B allele order according to the TOP/BOT convention, rather than reference/alternate (Ref/Alt) allele order.\
**Figure 3.** Screenshot illustrating interpretation of strand designations for SNP *rs10000030* using Illumina manifest conventions.
**Figure 4.** Summary table illustrating the relationships between strand designations for dbSNP variants within the Illumina manifest, except in cases of unmapped probes.
**Resources:**
* Technical Note: ["TOP/BOT" Strand and "A/B" Allele](https://www.illumina.com/documents/products/technotes/technote_topbot.pdf)
* Recorded Webinar: [Infinium Genotyping: Strandology - Strand Designations in Infinium Manifests](https://www.youtube.com/watch?v=L96_y1_w-_s\&list=PLKRu7cmBQlahpXlnrrXlQw9itVJ8yHwUZ\&index=58)
* [DNA strand designations](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/DNA-strand-designations-support-bulletin/README.md)
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