Quick Order
Welcome, Guest

Genotyping Glossary

Bookmark and Share

Summary

Displays the fundamental description of an SNP sensing Probe Set.

  • Product Name – The name of the GeneChip® probe array or Targeted Genotyping panel name where the given Probe Set or SNP is located. Documentation of the GeneChip® probe array may be found in the Support section.


  • Probe Set ID/Assay ID – A unique Affymetrix identifier for the probe set or SNP.


  • TSC ID – The SNP Consortium (TSC) ID that corresponds to this probe set. The SNP Consortium is a nonprofit organization that sequences and records single nucleotide polymorphism records in a public domain database. An Affymetrix SNP array probe set may be designed around an SNP record from TSC, but as the genomic sequence shifts in subsequent genome versions, a probe set may no longer be associated with a TSC ID. The TSC ID may not be available for SNPs if they are not yet part of the TSC database.


  • dbSNP RS ID – The dbSNP ID that corresponds to this probe set or SNP. The dbSNP at the National Center for Biotechnology Information (NCBI) attempts to maintain a unified and comprehensive view of known single nucleotide polymorphisms (SNPs), small scale insertions/deletions, polymorphic repetitive elements, and microsatellites from TSC and other sources. The dbSNP is updated periodically, and the dbSNP version used for mapping is given in the dbSNP version field.

    • http://www.ncbi.nlm.nih.gov/SNP/index.html


    • The genome build may change or nullify the relationship between the SNPs detected by Affymetrix genotyping arrays if the genome sequence, which is assigned to it, changes subsequent to the design of the array.

  • Allele A/B – The alternative nucleotides at the SNP position that occur in the population and can be identified by the probeset. All the SNPs measured by the Affymetrix mapping arrays are biallelic. Note: When comparing the allele data on NetAffx to the allele data for the corresponding RefSNP record in dbSNP, the alleles reported here could be different from the alleles reported for the corresponding RefSNP on the dbSNP web site. This difference arises mainly from the reference genomic strand that was chosen to define the alleles by Affymetrix. To choose the reference genomic strand, we follow a convention based on the alphabetic ordering of the sequence surrounding the SNP. Sometimes the reference strand on the dbSNP is different from NetAffx, and the alleles could represent reverse complement of those provided on dbSNP.


  • Fragment Length – The size of the restriction fragment containing the SNP detected by the probeset. Please refer to the assay manual for details on the GeneChip mapping assay strategy.


  • Fragment Enzyme – The enzyme that yields the restriction fragment containing the SNP. The Whole Genome Assay protocol detects SNPs that are contained within the genomic restriction fragments to simplify the sequence background for genotyping arrays.


  • Flanking Sequence – The nucleotide sequence surrounding the SNP. This is a 33-mer sequence with 16 nucleotides on either end of the SNP position. The alleles at the SNP position are provided in the brackets. For the Targeted Genotyping panels, these are variable length sequence surrounding the SNP.

Physical Map

The current genomic context of the SNP, with the Allele sequence at the center.

  • Genome Version – The genome build or version on which the NetAffx annotations are based. The NetAffx site attempts to provide the mappings of the most current genome build available, although mappings for a newly released genome build will take some time to become available on NetAffx.


  • dbSNP Version – NetAffx SNP annotations are primarily derived from the dbSNP refSNP annotations. Here we provide the build number of the dbSNP database used to generate NetAffx annotations for mapping arrays.


  • Chromosome – The chromosome on which the SNP is located on the current Genome Version (See Glossary entry)


  • Genomic Strand – The reference genomic strand used to define the alleles. We use a convention based on the alphabetic ordering of the sequence including and surrounding the SNP position to choose the reference genomic strand. The alleles are defined from the reference strand.


  • Physical Position – The nucleotide base position where the SNP is found. The genomic coordinates given are in relation to the current genome version and may shift as subsequent genome builds are released.


  • Cytoband – Cytoband location of the SNP derived from the SNP physical map and the chromosome band data provided by UCSC.

Associated Genes

Describes transcripts and their association with the SNP. Although some redundant transcripts are removed from our library, NetAffx incorporates several transcript sources that may still describe the same record or its variants.

  1. Relationship – Describes the relationship of the listed feature to the SNP described. Four possible entries to this field are:


  2. 3UTR – SNP is located in the 3' UTR of the transcript.
    5UTR – SNP is located in the 5' UTR of the transcript.
    CDS – SNP is located in the CDS of the transcript.
    Intron – SNP is located in the intron.
    Exon – SNP is located in the exon.
    Upstream – The 3' end of the transcript lies some distance upstream from the SNP.
    Downstream – The 5' end of the transcript lies some distance downstream of the SNP.
    If you need to retrieve all the SNPs in exon, you will have to perform a search against the relationship field with the following keyword that combines multiple relationship attributes separated by "|" operator: "3UTR|5UTR|CDS|Exon"

  3. Distance – Describes the distance between the SNP and the transcript in nucleotide bases. A distance of 0 means that the SNP falls within the outer boundaries of the transcript record. There may be more than one transcript at the same distance from the SNP if there are multiple records describing the same locus.
  4. Gene – Displays a gene name derived from NCBI UniGene/Gene records when available.
  5. Transcript – The accession and link that goes out to the full entry record.
  6. Entrez Gene – The identifier from the NCBI Entrez Gene database and the link that goes out to the Locus description.
  7. Description – mRNA sequence description. This is derived from GenBank or Ensembl.

Genetic Map

Describes the genetic location of the SNP derived from three separate linkage maps (deCODE, Marshfield, or SLM). The physical distance between the markers is assumed to be linear with their genetic distance. The genetic location is computed using the linkage maps from the latest physical location of the SNP and the neighboring microsatellite markers.

Marshfield reference: Broman KW, Murray JC, Sheffield VC, et.al., (1998) Comprehensive human genetic maps: Individual and sex-specific variation in recombination. Am J Human Genetics, 63(3):861-869.

Decode Reference: Kong A, Gudbjartsson DF, Sainz J, et.al., (2002) A high-resolution recombination map of the human genome. Nat Genet. Jul;31(3):241-7. Epub 2002 Jun 10.

SLM is a Genetic Map accumulated in house at Affymetrix. It is described in the technical note: SNP Selection Criteria for the GeneChip® Human Mapping 10K Array Xba 131.

  • Source – Original source of the linkage map (deCODE, Marshfield, or SLM).
  • Sex-averaged (cM) – Genetic distance of the SNP derived from the sex-averaged linkage map.
  • Female (cM) – Genetic distance of the SNP derived from the female-specific linkage map.
  • Male (cM) – Genetic distance of the SNP derived from the male-specific linkage map.
  • STR Upstream – Microsatellite marker (upstream of the SNP) used to derive the original linkage map.
  • STR Downstream – Microsatellite marker (downstream of the SNP) used to derive the original linkage map. The marker was used in this study to derive the genetic location of the SNP.
  • SNP Upstream – SNP marker (upstream of the SNP) used to derive the original linkage map.
  • SNP Downstream – SNP marker (downstream of the SNP) used to derive the original linkage map. The marker was used in this study to derive the genetic location of the SNP.

Neighboring Microsatellite

Describes the nearest microsatellite markers (upstream, downstream and overlapping) for the SNP.

  • Relationship – The relative location of the marker from the SNP (upstream, downstream or overlapping).
  • Distance – Distance in nucleotide bases of the marker from the SNP.
  • Alias – Gives the microsatellite ID. Microsatellites data are derived from various sources (UniSTS, Genethon, decode, and etc.) as collected in UCSC's Genome STS record.

Population Frequency Data From Affymetrix Validation Studies

Describes the frequency of the allele from studies using the Affymetrix genotyping arrays. The data are described in the following reference:

  1. Population – The Ethnic group used in the genotyping study. The following is a description of the population groups:
  2. Yoruba – Yoruba in Ibadan, Nigeria
    Japanese – Japanese in Tokyo, Japan
    Han Chinese – Han Chinese in Beijing, China
    CEPH – CEPH (Utah residents with ancestry from northern and western Europe)

  3. p(N) – Major allele frequency. The actual allele is provided in parenthesis.
  4. q(N) – Minor allele frequency. The actual allele is provided in parenthesis.
  5. H(2pq) – Heterozygosity frequency.
  6. # of individuals counted – The number of individuals included in the study to derive the genotype. This is an indication of the total number of individuals included in the study and the SNP call rate.

Back to Top >