SHORT COMMUNICATION Linkage Mapping
of Human Chromosome Polymorphisms
10 Microsatellite
RUTH A. DECKER,* JULIE MOORE, t BRUCE PONDER, t AND JAMES L. WEBER**’ *Marshfield
Medical
Research Foundation, 1000 North Oak Avenue, Marshfield, Department of Pathology, Tennis Court Road, Cambridge Received
September
Ten microsatellite DNA polymorphisms located on human chromosome 10 were regionally mapped using subchromosoma1 somatic cell hybrids and linkage analysis, The resulting order of the markers from pter-qter was [DlOSSS, DlOSlll], DlOS107, DlOS109, [DlOSSl, DlOSllO, DlOS108, DlOS88, DlOS168], and DlOS169. Order of the markers within brackets was uncertain, although the order given was most likely. The microsatellites were distributed along the chromosome from the proximal p arm to near qter, with an unlinked gap between DlOS168 and DlOS169. Q 1992 Academic
Prese. Inc.
Ongoing efforts to develop randomly distributed human microsatellite DNA polymorphisms yielded 10 (dCdA), * (dG-dT), markers that were located on chromosome 10. Two of the 10 markers, DlOS88 and DlOS89, have been described in previous publications (4, 5); the remaining 8 are displayed in Table 1. Estimates of heterozygosity for the chromosome 10 microsatellites ranged from 0.44 to 0.80. Allele frequency estimates for the new markers have been submitted to the Genome Data Base. Assignment of the microsatellites to chromosome 10 was accomplished by amplifying DNA from panels of somatic cell hybrids containing various combinations of human chromosomes (6). DNA samples from four human/rodent somatic cell hybrids (1; Moore and Ponder, unpublished) that contained restricted portions of human chromosome 10 were then used to localize the microsatellites to either the short or the long arm. Two markers, DlOS89 and DlOSlll, were localized to the short arm on the basis of amplification only from hybrids TG3, which contained lOpter-qll.2, and JFl23B13, which contained the lOpter-pll.2 translocation chromosome from the t(10,21) cell line GM06135. All eight other microsatellites could be amplified only using DNA from hybrids 64034~6 (lOcen-qter) and TK2 (lOqll.2-qter) and therefore were localized to the long arm. For linkage mapping, DNA samples from five of the largest CEPH reference families (families 884, 1331, 1332, 1333, and 1362 totaling 81 members) were typed 1 To whom
correspondence
should
12,604-606 (1992) 0888-7543/92 $3.00 Copyright 0 1992 by Academic Press, All rights of reproduction in any form
be addressed.
GENOMICS
604 Inc. reserved.
Wisconsin 54449; and tUniversity CB2 1QP, United Kingdom
of Cambridge,
3, 1991
with each of the microsatellites. For initial incorporation of the microsatellites into the existing chromosome 10 linkage maps (2, 7), the sites of meiotic recombination within the five CEPH families were mapped using the CEPH genotyping data and the consensus order for existing chromosome 10 RFLPs. Boundaries for the locations of each of the microsatellites were then determined by comparing the phase of the microsatellite alleles to the phase of alleles on the existing map. Results are shown in the far right column of Table 2. Two-point lod scores (Table 2) between the microsatellites and RFLPs computed using the MLINK or ILINK programs of the LINKAGE software package also provided indications of the locations of the microsatellites. Further information on the order of the microsatellite polymorphisms was obtained by analysis of the observed recombination events among the microsatellites themselves. The best order obtained using all data was [DlOS89, DlOSlll], DlOS107, DlOS109, [DlOS91, DlOSllO, DlOS108, DlOS88, DlOS1681, and DlOS169. Three or more unambiguous recombination events between each of the pairs [DlOS89, DlOSlll]-DlOS107, DlOS107-DlOS109, DlOS109-[DlOS91, DlOSllO, DlOS108, DlOS88, DlOS1681, and [DlOS91, DlOSllO, DlOS108, DlOS88, DlOS168]-DlOS169 firmly established the relative order of these pairs. For the markers within the brackets, relative order was uncertain, although the order shown is most likely on the basis of single recombination events. Because of the possibility of typing errors or rare double recombination events within relatively small genetic intervals, a single recombination event was not considered sufficient evidence to establish the favored order. Within the group of five closely linked (and bracketed) 1Oq microsatellites, DlOS91 was located proximal to each of DlOS108, DlOS88, and DlOS168 on the basis of two or more recombination events. Cytogenetic and linkage mapping results for the chromosome 10 microsatellites were consistent. On the basis of previous cytogenetic mapping of RFLP markers (2), the microsatellites ranged from the proximal portion of the p arm to the region q26-qter. Sex-specific recombination frequencies between the microsatellites determined using the program CRIMAP (Table 2) confirmed previous findings of an excess of female over male recombi-
SHORT
TABLE Chromosome
605
COMMUNICATION
1
10 Microsatellite
Polymorphisms Genotype”
Locus
Clone name
DlOSlll
Mfd164
DlOS107
Mfd78
DlOS109
Mfd150
DlOS91
Mfd29
DlOSllO
Mifd157
DlOS108
MfdlOO
DlOS168
Mfd175
DlOS169
Mfd187
PIC
133101
133102
0.67
0.62
150,148
148,146
6
144-154
0.53
0.46
159,157
157,157
5
0.71
0.73
86,84
86,84
9
155-167 (157) 82-98
0.67
0.60
125,119
121,119
6
0.58
0.55
188,188
190,188
6
0.64
0.55
139,131
131,131
12
0.44
0.57
167,165
165,165
6
0.73
0.68
107.107
113.99
7
Heterozygosity*
Primers” GAAAAGTCTTAGAATTTTGCAG CCAAAGTGCTGAATTTCAGG GAATCCATAGCTGTACTCCA AATTGTCTATGGTCCCAGCA GAAATCTCAAAAGACAAACAAGT GATCGTTCTTGCTGATTTT AGCTCCCTCGAGATGCACT TTCTTTGCTTTACATGTGGC ATGTCCTTATAAAATGAGGG ATCTTTTCTTGCCTCTTCCA GGAGCCAAATACTAAATTCT TTAGGCACTTTAATCAGGCT CATGGCACTAATAGAGTTAAC TTCACTTGGGATGGAGGCA GATCTGTGACTGCCTTCCT AAGAGGAGGAGTCCATTCAG
of
Size range (bp) (predominant allele)
Number alleles
(148)
(84 115-125 (119) 184-194 (188) 117-147 (131) 159-175
(165) 99-117 (107)
D CA-strand primer is listed first for each marker. * Informativeness estimates were based on the genotypes of 72-90 unrelated Caucasians from CEPH families (parents and grandparents). ’ Genotypes for CEPH family 1331 parents (father, 01; mother, 02) are listed with allele sizes in basepairs. Genotypes for 133101 and 133102, respectively, for DlOS88 (Mfd7) are 217,213 and 217,215 and for DlOS89 (Mfd28) are 150,144 and 152,144.
nation in the centromeric region. Considering location, informativeness, strength of amplification, and readability of genotypes, the markers DlOS89, DlOS107, DlOS109, DlOS108, and DlOS169 constituted the best group for initial coverage of chromosome 10 in linkage
TABLE Linkage
Locus
Mapping
18.3 (0.05,
0.00)
7.6 (0.25,
0.04)
3.0 (0.23,
0.19)
DlOSlll DlOS107
10 Microsatellites
Lod scores between microsatellites and indicated RFLPs i (8) DlOS49-12.0
(0.02)
DlOS49-16.9
(0.00);
DlOS5-3.0
D10S109
2
of Chromosome
Lod scoresa between adjacent microsatellites i 6, e,,
DlOS89
mapping of disease genes. Under the assumption that linkage between a microsatellite polymorphism and a diseasegene can be detected at a distance of ~15 CM, this group of markers provides coverage of approximately 55% of the chromosome.
Approximate linkage map position b DlOS28-RBP3
DlOS34-5.2
(0.00)
DlOS28-RBP3
(0.00)
DlOSll-DlOS45
DlOS14-4.2
(0.00);
DlOS29-7.7
(0.03);
DlOS62-8.3
(0.06)
DlOS62-8.8
(0.06);
DlOS4-4.1
(0.00)
DlOS62-DlOS20
DlOS20-5.4
(0.00);
DlOS4-3.5
(0.00)
DlOS62-DlOS12
DlOS29-4.9
(0.04);
DlOS62-7.7
(0.03);
DlOS48-3.0
(0.00);
DlOS40-3.4
(0.11)
DlOS62-3.1
(0.14)
DlOS47-5.4
(0.07);
DlOS16-DlOS29
7.6 (0.25,0.08) DlOS91 7.6 (0.05,
0.00)
6.8 (0.12,
0.00)
DlOSllO D10S108
DlOS20-4.8
(0.00)
DlOS4-DlOS12
3.1 (0.00,0.11) DlOS88 2.4 (0.00,
DlOS20-DlOSl2
0.11)
DlOS168
DlOS20-DlOSl2
Unlinked DlOS169 a Listed are maximum lod scores (2) along with and male, respectively). For the lod scores between * Map intervals are based on the sites of meiotic
DlOSlO-5.0
(0.00)
DlOS44-qter
the sex-specific maximum likelihood estimates of recombination frequency the microsatellites and RFLPs, only sex-averaged recombination fractions recombination. Intervals were determined using only phase known data.
(jr,, 8,) (female are listed.
606
SHORT
COMMUNICATION
ACKNOWLEDGMENTS This work was and by a program We thank Scott Carol Jones, Sue matic cell hybrids.
supported by NIH Grant ROl-HG00248 (J.L.W.) grant from the Cancer Research Campaign (B.P.). Bennesch for help with the computer analysis and Povey, and Robert Norum for making available so-
3.
Simpson, N. E., and Cann, on the genetic constitution Genet. 55: 142-152.
4.
Weber, J. L., and May, P. E. (1989). Abundant DNA polymorphisms which can be typed using chain reaction. Am. J. Hum. Genet. 44: 368-396.
5. Weber, morphism
REFERENCES 1.
2.
6. Weber,
Mathew, C. G. P., Wakeling, W., Jones, E., Easton, D., Fisher, R., Strong, C., Smith, B., Chin, K., Little, P., Nakamura, Y., Shows, T. B., Jones, C., Goodfellow, P. J., Povey, S., and Ponder, B. A. J. (1990). Regional localization of polymorphic markers on chromosome 10 by physical and genetic mapping. Ann. Hum. Genet. 54: 121-129. Morton, N. E., and Collins, A. (1990). Standard some 10. Ann. Hum. Genet. 54: 235-251.
maps of chromo-
7.
H. (1990). Report of the committee of chromosome 10. Cytogenet. Cell. class of human the polymerase
J. L., and May, P. E. (1990). Dinucleotide at the DlOS89 locus. Nucleic Acids Res.
repeat
poly-
18: 4637.
J. L., Polymeropoulos, M. H., May, P. E., Kwitek, A. E., Xiao, H., McPherson, J. D., and Wasmuth, J. J. (1991). Mapping of human chromosome 5 microsatellite DNA polymorphisms. Genomics 11:695-700. White, R. L., Lalouel, J. M., Nakamura, Y., Donis-Keller, H., Green, P., Bowden, D. W., Mathew, C. G. P., Easton, D. F., Robson, E. B., Morton, N. E., Gusella, J. F., Haines, J. L., Retief, A. E., Kidd, K. K., Murray, J. C., Lathrop, G. M., and Cann, H. M. (1990). The CEPH consortium primary linkage map of human chromosome 10. Genomics 6: 393-412.
of Human Chromosome Polymorphisms
10 Microsatellite
RUTH A. DECKER,* JULIE MOORE, t BRUCE PONDER, t AND JAMES L. WEBER**’ *Marshfield
Medical
Research Foundation, 1000 North Oak Avenue, Marshfield, Department of Pathology, Tennis Court Road, Cambridge Received
September
Ten microsatellite DNA polymorphisms located on human chromosome 10 were regionally mapped using subchromosoma1 somatic cell hybrids and linkage analysis, The resulting order of the markers from pter-qter was [DlOSSS, DlOSlll], DlOS107, DlOS109, [DlOSSl, DlOSllO, DlOS108, DlOS88, DlOS168], and DlOS169. Order of the markers within brackets was uncertain, although the order given was most likely. The microsatellites were distributed along the chromosome from the proximal p arm to near qter, with an unlinked gap between DlOS168 and DlOS169. Q 1992 Academic
Prese. Inc.
Ongoing efforts to develop randomly distributed human microsatellite DNA polymorphisms yielded 10 (dCdA), * (dG-dT), markers that were located on chromosome 10. Two of the 10 markers, DlOS88 and DlOS89, have been described in previous publications (4, 5); the remaining 8 are displayed in Table 1. Estimates of heterozygosity for the chromosome 10 microsatellites ranged from 0.44 to 0.80. Allele frequency estimates for the new markers have been submitted to the Genome Data Base. Assignment of the microsatellites to chromosome 10 was accomplished by amplifying DNA from panels of somatic cell hybrids containing various combinations of human chromosomes (6). DNA samples from four human/rodent somatic cell hybrids (1; Moore and Ponder, unpublished) that contained restricted portions of human chromosome 10 were then used to localize the microsatellites to either the short or the long arm. Two markers, DlOS89 and DlOSlll, were localized to the short arm on the basis of amplification only from hybrids TG3, which contained lOpter-qll.2, and JFl23B13, which contained the lOpter-pll.2 translocation chromosome from the t(10,21) cell line GM06135. All eight other microsatellites could be amplified only using DNA from hybrids 64034~6 (lOcen-qter) and TK2 (lOqll.2-qter) and therefore were localized to the long arm. For linkage mapping, DNA samples from five of the largest CEPH reference families (families 884, 1331, 1332, 1333, and 1362 totaling 81 members) were typed 1 To whom
correspondence
should
12,604-606 (1992) 0888-7543/92 $3.00 Copyright 0 1992 by Academic Press, All rights of reproduction in any form
be addressed.
GENOMICS
604 Inc. reserved.
Wisconsin 54449; and tUniversity CB2 1QP, United Kingdom
of Cambridge,
3, 1991
with each of the microsatellites. For initial incorporation of the microsatellites into the existing chromosome 10 linkage maps (2, 7), the sites of meiotic recombination within the five CEPH families were mapped using the CEPH genotyping data and the consensus order for existing chromosome 10 RFLPs. Boundaries for the locations of each of the microsatellites were then determined by comparing the phase of the microsatellite alleles to the phase of alleles on the existing map. Results are shown in the far right column of Table 2. Two-point lod scores (Table 2) between the microsatellites and RFLPs computed using the MLINK or ILINK programs of the LINKAGE software package also provided indications of the locations of the microsatellites. Further information on the order of the microsatellite polymorphisms was obtained by analysis of the observed recombination events among the microsatellites themselves. The best order obtained using all data was [DlOS89, DlOSlll], DlOS107, DlOS109, [DlOS91, DlOSllO, DlOS108, DlOS88, DlOS1681, and DlOS169. Three or more unambiguous recombination events between each of the pairs [DlOS89, DlOSlll]-DlOS107, DlOS107-DlOS109, DlOS109-[DlOS91, DlOSllO, DlOS108, DlOS88, DlOS1681, and [DlOS91, DlOSllO, DlOS108, DlOS88, DlOS168]-DlOS169 firmly established the relative order of these pairs. For the markers within the brackets, relative order was uncertain, although the order shown is most likely on the basis of single recombination events. Because of the possibility of typing errors or rare double recombination events within relatively small genetic intervals, a single recombination event was not considered sufficient evidence to establish the favored order. Within the group of five closely linked (and bracketed) 1Oq microsatellites, DlOS91 was located proximal to each of DlOS108, DlOS88, and DlOS168 on the basis of two or more recombination events. Cytogenetic and linkage mapping results for the chromosome 10 microsatellites were consistent. On the basis of previous cytogenetic mapping of RFLP markers (2), the microsatellites ranged from the proximal portion of the p arm to the region q26-qter. Sex-specific recombination frequencies between the microsatellites determined using the program CRIMAP (Table 2) confirmed previous findings of an excess of female over male recombi-
SHORT
TABLE Chromosome
605
COMMUNICATION
1
10 Microsatellite
Polymorphisms Genotype”
Locus
Clone name
DlOSlll
Mfd164
DlOS107
Mfd78
DlOS109
Mfd150
DlOS91
Mfd29
DlOSllO
Mifd157
DlOS108
MfdlOO
DlOS168
Mfd175
DlOS169
Mfd187
PIC
133101
133102
0.67
0.62
150,148
148,146
6
144-154
0.53
0.46
159,157
157,157
5
0.71
0.73
86,84
86,84
9
155-167 (157) 82-98
0.67
0.60
125,119
121,119
6
0.58
0.55
188,188
190,188
6
0.64
0.55
139,131
131,131
12
0.44
0.57
167,165
165,165
6
0.73
0.68
107.107
113.99
7
Heterozygosity*
Primers” GAAAAGTCTTAGAATTTTGCAG CCAAAGTGCTGAATTTCAGG GAATCCATAGCTGTACTCCA AATTGTCTATGGTCCCAGCA GAAATCTCAAAAGACAAACAAGT GATCGTTCTTGCTGATTTT AGCTCCCTCGAGATGCACT TTCTTTGCTTTACATGTGGC ATGTCCTTATAAAATGAGGG ATCTTTTCTTGCCTCTTCCA GGAGCCAAATACTAAATTCT TTAGGCACTTTAATCAGGCT CATGGCACTAATAGAGTTAAC TTCACTTGGGATGGAGGCA GATCTGTGACTGCCTTCCT AAGAGGAGGAGTCCATTCAG
of
Size range (bp) (predominant allele)
Number alleles
(148)
(84 115-125 (119) 184-194 (188) 117-147 (131) 159-175
(165) 99-117 (107)
D CA-strand primer is listed first for each marker. * Informativeness estimates were based on the genotypes of 72-90 unrelated Caucasians from CEPH families (parents and grandparents). ’ Genotypes for CEPH family 1331 parents (father, 01; mother, 02) are listed with allele sizes in basepairs. Genotypes for 133101 and 133102, respectively, for DlOS88 (Mfd7) are 217,213 and 217,215 and for DlOS89 (Mfd28) are 150,144 and 152,144.
nation in the centromeric region. Considering location, informativeness, strength of amplification, and readability of genotypes, the markers DlOS89, DlOS107, DlOS109, DlOS108, and DlOS169 constituted the best group for initial coverage of chromosome 10 in linkage
TABLE Linkage
Locus
Mapping
18.3 (0.05,
0.00)
7.6 (0.25,
0.04)
3.0 (0.23,
0.19)
DlOSlll DlOS107
10 Microsatellites
Lod scores between microsatellites and indicated RFLPs i (8) DlOS49-12.0
(0.02)
DlOS49-16.9
(0.00);
DlOS5-3.0
D10S109
2
of Chromosome
Lod scoresa between adjacent microsatellites i 6, e,,
DlOS89
mapping of disease genes. Under the assumption that linkage between a microsatellite polymorphism and a diseasegene can be detected at a distance of ~15 CM, this group of markers provides coverage of approximately 55% of the chromosome.
Approximate linkage map position b DlOS28-RBP3
DlOS34-5.2
(0.00)
DlOS28-RBP3
(0.00)
DlOSll-DlOS45
DlOS14-4.2
(0.00);
DlOS29-7.7
(0.03);
DlOS62-8.3
(0.06)
DlOS62-8.8
(0.06);
DlOS4-4.1
(0.00)
DlOS62-DlOS20
DlOS20-5.4
(0.00);
DlOS4-3.5
(0.00)
DlOS62-DlOS12
DlOS29-4.9
(0.04);
DlOS62-7.7
(0.03);
DlOS48-3.0
(0.00);
DlOS40-3.4
(0.11)
DlOS62-3.1
(0.14)
DlOS47-5.4
(0.07);
DlOS16-DlOS29
7.6 (0.25,0.08) DlOS91 7.6 (0.05,
0.00)
6.8 (0.12,
0.00)
DlOSllO D10S108
DlOS20-4.8
(0.00)
DlOS4-DlOS12
3.1 (0.00,0.11) DlOS88 2.4 (0.00,
DlOS20-DlOSl2
0.11)
DlOS168
DlOS20-DlOSl2
Unlinked DlOS169 a Listed are maximum lod scores (2) along with and male, respectively). For the lod scores between * Map intervals are based on the sites of meiotic
DlOSlO-5.0
(0.00)
DlOS44-qter
the sex-specific maximum likelihood estimates of recombination frequency the microsatellites and RFLPs, only sex-averaged recombination fractions recombination. Intervals were determined using only phase known data.
(jr,, 8,) (female are listed.
606
SHORT
COMMUNICATION
ACKNOWLEDGMENTS This work was and by a program We thank Scott Carol Jones, Sue matic cell hybrids.
supported by NIH Grant ROl-HG00248 (J.L.W.) grant from the Cancer Research Campaign (B.P.). Bennesch for help with the computer analysis and Povey, and Robert Norum for making available so-
3.
Simpson, N. E., and Cann, on the genetic constitution Genet. 55: 142-152.
4.
Weber, J. L., and May, P. E. (1989). Abundant DNA polymorphisms which can be typed using chain reaction. Am. J. Hum. Genet. 44: 368-396.
5. Weber, morphism
REFERENCES 1.
2.
6. Weber,
Mathew, C. G. P., Wakeling, W., Jones, E., Easton, D., Fisher, R., Strong, C., Smith, B., Chin, K., Little, P., Nakamura, Y., Shows, T. B., Jones, C., Goodfellow, P. J., Povey, S., and Ponder, B. A. J. (1990). Regional localization of polymorphic markers on chromosome 10 by physical and genetic mapping. Ann. Hum. Genet. 54: 121-129. Morton, N. E., and Collins, A. (1990). Standard some 10. Ann. Hum. Genet. 54: 235-251.
maps of chromo-
7.
H. (1990). Report of the committee of chromosome 10. Cytogenet. Cell. class of human the polymerase
J. L., and May, P. E. (1990). Dinucleotide at the DlOS89 locus. Nucleic Acids Res.
repeat
poly-
18: 4637.
J. L., Polymeropoulos, M. H., May, P. E., Kwitek, A. E., Xiao, H., McPherson, J. D., and Wasmuth, J. J. (1991). Mapping of human chromosome 5 microsatellite DNA polymorphisms. Genomics 11:695-700. White, R. L., Lalouel, J. M., Nakamura, Y., Donis-Keller, H., Green, P., Bowden, D. W., Mathew, C. G. P., Easton, D. F., Robson, E. B., Morton, N. E., Gusella, J. F., Haines, J. L., Retief, A. E., Kidd, K. K., Murray, J. C., Lathrop, G. M., and Cann, H. M. (1990). The CEPH consortium primary linkage map of human chromosome 10. Genomics 6: 393-412.
