SBEprimer:")?>
Primer-Design for multiplexed, minisequencing-based Genotyping
Single-nucleotide polymorphism (SNP) analysis is a powerful tool for mapping and
diagnosing disease-related alleles. Mutation analysis by polymerase mediated
single-base primer extension (minisequencing) can be massively parallelized using
DNA microchips or flow cytometry with microspheres as solid support. By adding a
unique oligonucleotide tag to the 5' end of the minisequencing primer and
attaching the complementary anti-tag to the array or bead surface, the assay
can be "demultiplexed". Such high-throughput scoring of SNPs requires a high
level of primer multiplexing in order to analyze multiple loci in one assay, thus
enabling inexpensive and fast polymorphism scoring.
Publication:")?>
This work has been published in Nucleic Acids Research
Kaderali,L., Deshpande,A., Nolan,J.P. and White,P.S. (2003): Primer-Design for
Multiplexed Genotyping, Nucleic Acids Research 31 (6), 1796-1802
Software:")?>
The software is available for free for academic use, please cite the Nucleic Acids Research Publication. Commercial entities, please contact
Lars Kaderali before downloading and using the code.
The following programs are available for Unix systems:
45-Plex Genotyping PCR Primers for the 15 Amplicons | ||
Gene | Forward | Reverse |
LMP2 exon 3 | 5'-TAACTTGGTGACTGTTGACTCC-3' | 5'-CCATTTCCCAGTGTCCAG-3' |
LMP7 exon 1b | 5'-GTCATGGCGCTACTAGATGT-3' | 5'-CTCCTCTCAGGCGACC-3' |
TAP1 Exon 4 | 5'-ACTCTCTTCTCCCCAACCCT-3' | 5'-CTGTGTAGAGCGGGCCAACT-3' |
TAP1 exon 5 | 5'-ATTAGTGTCCCTGATGGTTT-3' | 5'-TGGAGTCACGGCATCTTA-3' |
TAP1 exon 6,7 | 5'-TTCTCTACCTCAGTCCCTTT-3' | 5'-TGAAGGCAGGAAGAAAAT-3' |
TAP1 exon 10 | 5'-GTGGCTATACCGTTCTCATC-3' | 5'-AGCAAGATTGGGTGGGA-3' |
TAP2 exon 1 | 5'-CTGTTCTGAGCCCTCCTG-3' | 5'-TTACCACCTCCAACTCACAAC-3' |
TAP2 exon 6 | 5'-GAAGATTCCCAGCCTCAT-3' | 5'-GGTAGATCATAAAGGAAAGCA-3' |
TAP2 exon 7 | 5'-GGGTGGTTTCTGGTAGAAGT-3' | 5'-TCTCAGAGGCAAATGAACTATA-3' |
TAP2 exon 9 | 5'-CCTTGGGGGTTTACACA-3' | 5'-CGACCTTCACCACTAAGAGT-3' |
TAP2 exon 10 | 5'-TTGTATCTGAGGAAGGGAAT-3' | 5'-CTCTCACGGTACTCACGG-3' |
TAP2 exon 11 | 5'-CTTCAGCTGCAGGACTGGA-3' | 5'-GAGAAGAGGGCCCAGTATC-3' |
Tapasin ex-int 2 | 5'-GGGCAGGTCACCAGACA-3' | 5'-GGGGATACCGCCTGAAG-3' |
Tapasin exon 4 | 5'-CCTCATCTCCCTGTCTTCC-3' | 5'-GCAGGTATGGCAGGTGTA-3' |
Tapasin exon 6 | 5'-CTGGAGGTAGCAGGTAAGA-3' | 5'-GATGGGTGTCAGGCTCT-3' |