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Method Detail
Submitter Method Handle: KRIBB_YJKIM
Submitter Method ID: ILLUMINA
Submitted method description:
The GoldenGate genotyping assay is based on a highly multiplexed, allele-discriminating, extension reaction.
Two allele-specific oligos (ASOs) and a locus-specific oligo (LSO) are used to query each SNP.
The pooled assay oligos are hybridized to genomic DNA in a carefully controlled process.
ASOs whose 3' end base pairs with the SNP position are efficiently extended by a DNA polymerase.
ASOs whose 3' end mismatches the SNP position are not efficiently extended.
Thus, extension by DNA polymerase imparts allele selectivity to the assay.
The successfully extended ASOs terminate at the 5' phosphate of their cognate LSOs.
Upon addition of DNA ligase, the successfully extended ASOs are ligated to the LSOs.
The ligation process combines information carried by the allele-specific extension product (as determined by the DNA polymerase) with information for hybridization to a bead type in the Sentrix array matrix (through the unique address sequence in each LSO
After thermocycling, the PCR product is captured on a solid support, and single stranded fluorescently labeled material is eluted and hybridized to the Sentrix array matrix.
The unique address sequences in the LSOs will hybridize to complementary sequences on the beads in the Sentrix array matrix.
This last process de-multiplexes the information about the genotype calls generated in solution by separation on a Sentrix array matrix.
Illumina's Sentrix array matrix consists of 96 array bundles configured in a microplate-compatible format.
Each array bundle contains nearly 50,000 individual light-conducting fiber strands..
The fiber strands are chemically etched to create a microscopic well at the end of each strand.
Most of the wells are filled, each with a single 3-micron bead. Covalently attached to each bead are several hundred thousand copies of an oligonucleotide probe.
Consequently, each SNP genotype determination is the result of data averaged from multiple beads, greatly reducing the possibility of error.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
KRIBB_YJKIM Genotype KHB2007_2_ILLUMINA 129
KRIBB_YJKIM Frequency KHB2006_1 126
KRIBB_YJKIM Frequency KHB2007_2_ILLUMINA 129
KRIBB_YJKIM Assay KHB2007_2_ILLUMINA 129
KRIBB_YJKIM Assay KHB2007_1_ILLUMINA 129
KRIBB_YJKIM Assay KHB2008_1_ILLUMINA 129
KRIBB_YJKIM Assay KHB2008_2_ILLUMINA 130