Microsatellite Typing

There are currently two separate microsatellite testing protocols that have been approved for use in IHWG projects. The first has been developed by Dr. Benedicte Lie of the Institute of Immunology, Oslo and is being used by laboratories participating in the HLA and Disease Component, chaired by Dr. Thorsby. The second has been developed by Dr. Mary Carrington of the National Cancer Institute, Frederick, MD and is being used by laboratories participating in the Hematopoietic Cell Transplant Component, chaired by Dr. Petersdorf. If you have any questions about these protocols or about which is most appropriate for your laboratory, please contact the project leader for further information.

Laboratories submitting microsatellite data will also be asked to type a set of DNA samples selected from the IHWG Microsatellite Reference Panel as validation of their testing results.

Protocols Available:

OSLO
for the Disease Component Genetics of Disease Susceptibility: Strategies for Analyzing Polygenic HLA Associations Using Microsatellite Markers, by Benedicte Lie, Dag Undlien and Erik Thorsby

NCI
used by the Hematopoietic Cell Transplantation and the Genomic Analysis of Human MHC Haplotypes Components
pdf file or (MS Word) download
by Mary Carrington

 




  The tables below list the MHC- related microsatellite loci that can be defined with these protocols and show a comparison of microsatellite fragment sizes generated by each protocol when tested on the microsatellite reference cell panel.

Microsatellite Markers in the Human MHCa

Microsatelliteb Approximate Location Heterozygosity No. Allelesc Referencesd
D6S291 3.6-4cM centromeric of DPB1 0.72 7 1,2
Ring3CA 36.4Kb centromeric of DMB 0.73 9 3
TAP1CA 4.8Kb centromeric of TAP1 0.58 9 4
G51152 37.2Kb centromeric of DQB1 0.81 9-11 3
DQCAR 1134 bp telomeric of DQB1 0.78 13 5,6
DQCARII 13.8Kb telomeric of DQB1 0.88 15 7
D6S273 96Kb telomeric of HSP70 0.78 8 8,1
BAT2CA 30Kb centromeric of TNFa 0.77 12 9
TNFd 10Kb centromeric of TNFa   6 10
MIB 24.9Kb centromeric of HLA-B 0.82 15 11
HLABC-CA 39.4Kb centromeric of HLA-C     12
HLAC-CA 88.4Kb telomeric of HLA-C     12
D6S265 115Kb centromeric of HLA-A 0.76 14 13,14,15
D6S510 37Kb centromeric of HLA-A 0.74 8 16
MOGCA 262Kb telomeric of HLA-A 0.77 15 17
D6S105 2-3cM telomeric of HLA-A 0.81 10-12 18
D6S276 3-4cM telomeric of HLA-A 0.79 16 1
D6S2222 ~2cM telomeric of HLA-F 0.5   19
D6S2223 ~2.5cM telomeric of HLA-F 0.5   19
D6S2239 Telomeric of HLA-F, near HFE 0.6   19
These microsatellite markers are also being used for studies in other 13th IHWS projects including the HLA and Disease Component and the Hematopoietic Stem Cell Transplantation Component.

See map for precise location

aAdditional information about these markers is available from
  • the Genome Database at http://www.gdb.org/;
  • "Microsatellites in the HLA region: 1998 update" Tissue Antigens 52:318, 1998.


    • bTable of Primer Sequences specific for each microsatellite locus
    cAll microsatellites selected are dinucleotide (CAn") repeats.
    Size range of fragments may vary according to technique and protocol used.






    References

    1 The 1993-94 Genethon human genetic linkage map.Nat Genet. 1994 Jun;7:246-339.
    2 Recombination rates across the HLA complex: use of microsatellites as a rapid screen for recombinant chromosomes.Hum Mol Genet. 1995 Mar;4(3):423-8.
    3 Evolutionary dynamics of non-coding sequences within the class II region of the human MHC. J Mol Biol. 1996 Jan 12;255(1):1-13
    4 A polymorphic dinucleotide repeat in the third intron of TAP1.Hum Mol Genet. 1994 Jan;3(1):218.
    5 DQ microsatellite association studies in three ethnic groups.Tissue Antigens. 1997 Nov;50(5):507-20.
    6 Extensive polymorphism of a (CA)n microsatellite located in the HLA-DQA1/DQB1 class II region. Hum Immunol. 1995 Mar;42(3):209-20.
    7 Extensive HLA class II studies in 58 non-DRB1*15 (DR2) narcoleptic patients with cataplexy. Tissue Antigens. 1997 Apr;49(4):329-41
    8 Strong genetic association between HLA-DR3 and a polymorphic variation in the regulatory region of the HSP70-1 gene.Immunogenetics. 1993;37(3):177-82.
    9 A highly polymorphic microsatellite marker in the human MHC class III region, close to the BAT2 gene. Immunogenetics. 1997;46(4):357-8.
    10 Highly informative typing of the human TNF locus using six adjacent polymorphic markers. Genomics. 1993 Apr;16(1):180-6.
    11 New highly polymorphic microsatellite marker in linkage disequilibrium with HLA-B. Hum Immunol. 1996 Dec;51(2):89-94
    12 Twenty-six new polymorphic microsatellite markers around the HLA-B, -C and -E loci in the human MHC class I region .Tissue Antigens. 1998 Apr;51:337-46.
    13 Alleles at D6S265 and D6S105 define a haemochromatosis-specific genotype. Br J Haematol. 1994 Apr;86(4):863-6.
    14 A precise meiotic map in the class I region of the human major histocompatibility complex. Genomics. 1995 Dec 10;30(3):486-92.
    15 New polymorphic microsatellite markers place the haemochromatosis gene telomeric to D6S105. Hum Mol Genet. 1995 Oct;4(10):1869-74.
    16 Dinucleotide repeat polymorphism at the D6S510 locus. Hum Mol Genet. 1994 Jul;3(7):1210
    17 Three highly polymorphic microsatellites at the human myelin oligodendrocyte glycoprotein locus, 100 kb telomeric to HLA-F. Characterization and relation to HLA haplotypes. Hum Immunol. 1995 Aug;43(4):276-82.
    18 Dinucleotide repeat polymorphism at the D6S105 locus.Nucleic Acids Res. 1991 Feb 25;19(4):968
    19 A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis. Nat Genet. 1996 Aug;13(4):399-408.




    The table below illustrates the value of using a standard reference panel to compare microsatellite fragment sizes obtained from the use of different protocols. Protocols employing different primer pairs to amplify microsatellite variants at a given locus will produce fragment sizes of different lengths. The only way to compare the variable fragment lengths is to test a common, standardized reference panel. The comparative table below shows that different fragment sizes are obtained for nine of twelve microsatellite loci using the Oslo and NCI protocols, while those of three loci are identical.



    The different fragment sizes were derived from testing the IHW Microsatellite Reference Panel (N=50 cells) using the NCI and OSLO protocols.