> 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/000001521.md).

# Simple guidelines for identifying top/bottom (TOP/BOT) strand and A/B allele

It can be challenging to determine the DNA strand and allele designations for a single nucleotide polymorphism (SNP) because strand designations and orientation can differ depending on the database or assembly referenced (eg, NCBI genome build updates).

To address this issue, Illumina developed the top/bottom (TOP/BOT) strand and A/B Allele nomenclature using sequence-based context to assign DNA strand orientation that allows the same allele calls over time regardless of database or genome build used.

**Unambiguous SNPs \[A/(G or C)] or \[T/(G or C)]**

For SNPs that are not \[A/T] or \[G/C], A is always on the top strand and T is always the bottom strand. A and T nucleotides are the Allele A”; G and C nucleotides are the Allele B”.

**Ambiguous SNPs \[A/T] or \[G/C]**

If the SNP is \[A/T] or \[G/C]: Use sequence walking to determine TOP/BOT strands, then assign A/B Alleles.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-57ab3fb1449323ad982382cbb566b03b32cfca94%2Fimage1.png?alt=media)

**Figure 1**. Sequence walking convention to determine TOP/BOT strands.

**How to use sequence walking to assign strands for ambiguous SNPs**

1. The ambiguous SNP position is “n” (Figure 1). Nucleotides one position upstream and one downstream from “n” are “n-1” and “n+1.” Nucleotides two positions upstream and two downstream from “n” are “n-2” and “n+2.” , etc.
2. Examine n-1|n+1. Is one of the pair either an “A” **or** “T” and the other a “G” **or** “C”?
   1. If no: Examine n-2|n+2. If needed, continue sequence walking until you find an n-*x*|n+*x* pairing in which one of the pair is either an “A” or “T” and the other is a “G” or “C.” Then proceed to Step b.
   2. If yes: Is the “A” or “T” in this unambiguous pair 5′ of the SNP position (“n”) or 3′ of the SNP position (“n”)?
      * If 5′: This is the TOP Strand.
      * If 3′: This is the BOT Strand.

**Note:** In Figure 1, an unambiguous pairing is present at n-1|n+1: \[C/T]. T is present 3' of the SNP positions, thus, this is the BOT Strand.

1. 1.

**How to assign nucleotide designations A or B Allele**

* **For \[A/T] SNPs**
  * when the Strand is TOP: Allele A = A and Allele B = T
  * when the Strand is BOT: Allele A = T and Allele B =A
* **For \[C/G] SNPS**
  * when the Strand is TOP: Allele A = C and Allele B = G.
  * when the Strand is BOT: Allele A = G and Allele B = C

**Note:** In Figure 1, the Strand is BOT and the SNP is \[A/T], thus Allele A = T and Allele B = A.

**Reference:**

[“TOP/BOT” Strand and “A/B” Allele](https://www.illumina.com/documents/products/technotes/technote_topbot.pdf)

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #1521), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001521%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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