Paula E. May

Mapping of human chromosome 5 microsatellite DNA polymorphisms

Thirteen moderately to highly informative microsatellite DNA polymorphisms based on (dC-dA)n.(dG-dT)n repeats were mapped to segments of human chromosome 5 using both linkage analysis and a panel of somatic cell hybrids which contained rearranged chromosomes. The markers were distributed throughout most of the length of the chromosome from the regions p15.3-p15.1 to q33.3-qter. Maps of the sites of meiotic recombination within the reference families proved particularly useful for the purpose of integrating new polymorphisms into the existing linkage map.

Dinucleotide repeat polymorphisms at the DXS453, DXS454 and DXS458 loci

Frequency: Mfd66: Estimated from 87 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.63. Allele (bp) Frequency Allele (bp) Frequency 170 0.21 164 0.01 168 0.48 160 0.12 166 0.18 Mfd72: Estimated from 73 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.59. Allele (bp) Frequency Allele (bp) Frequency 152 0.07 146 0.49 148 0.16 144 0.27 Mfd79: Estimated from 103 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.62. Allele (bp) Frequency Allele (bp) Frequency 190 0.05 182 0.08 188 0.52 180 0.13 186 0.20 178 0.01 184 0.01 Chromosomal Localization: Mfd66 was provisionally assigned to Xpl 1.23-q21.1, and Mfd72 and Mfd79 were both provisionally asigned to Xq21. 1-q23 using DNA templates isolated from panels of chromosomal and subchromosomal somatic cell hybrids (1, 2).

Dinucleotide repeat polymorphisms at the D5S107, D5S108, D5S111, D5S117 and D5S118 loci

Frequency: Mfd27: Estimated from 120 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.78. Allele (bp) 155 153 151 149 147 Frequency 0.01 0.07 0.12 0.31 0.25 Allele (bp) 143 141 139 135 133 Frequency 0.10 0.04 0.02 0.01 0.07 Mfd34: Estimated from 122 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.45. Allele (bp) Frequency Allele (bp) Frequency 93 0.01 87 0.02 91 0.34 83 0.04 89 0.59 Mfd40: Estimated from 102 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC =0 .51 Allele (bp) Frequency Allele (bp) Frequency 171 0.59 167 0.22 169 0.20 Mfd48: Estimated from 112 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.62. Allele (bp) Frequency Allele (bp) Frequency 163 0.05 155 0.05 161 0.01 153 0.33 159 0.08 151 0.02 157 0.45 147 0.01 Mfd63: Estimated from 122 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.48. Allele (bp) Frequency Allele (bp) Frequency 92 0.02 84 0.02 90 0.08 82 0.01 88 0.05 80 0.04 86 0.70 78 0.08

Dinucleotide repeat polymorphisms at the D8S85, D8S87, and D8S88 loci

Frequency: Mfdl8: Estimated from 116 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.69. Allele (bp) Frequency Allele (bp) Frequency 84 0.01 76 0.22 82 0.36 74 0.22 80 0.19 Mfd39: Estimated from 96 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.65. Allele (bp) Frequency Allele (bp) Frequency 157 0.02 149 0.14 155 0.18 147 0.04 153 0.06 145 0.05 151 0.51 Mfd45: Estimated from 120 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.82. Allele (bp) Frequency Allele (bp) Frequency 100 0.02 88 0.15 98 0.04 86 0.25 96 0.10 84 0.12 92 0.04 82 0.03 90 0.21 76 0.03 Chromosomal Localization: The three markers were assigned to chromosome 8 using DNA templates isolated from panels of somatic cell hybrids.

Dinucleotide repeat polymorphisms at the D16S260, D16S261, D16S265, D16S266, and D16S267 loci

Frequency: Mfdl2: Estimated from 152 chromosomes of unrelated CEPH family parents (Caucasians). PIC = 0.43. Allele (bp) Frequency Allele (bp) Frequency 240 0.01 236 0.58 238 0.04 234 0.37 Mfd23: Estimated from 104 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.75. Allele (bp) 117 115 113 111 109 107 Frequency 0.01 0.01 0.03 0.05 0.11 0.07 Allele (bp) 105 103 101 99 95 89 Frequency 0.01 0.18 0.05 0.07 0.01 0.41 Mfd24: Estimated from 122 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.66. Allele (bp) Frequency Allele (bp) Frequency 100 0.01 94 0.40 98 0.07 92 0.25 96 0.25 88 0.02 Mfd62: Estimated from 118 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.54. Allele (bp) Frequency Allele (bp) Frequency 104 0.02 98 0.08 102 0.06 96 0.57 100 0.26 94 0.01 Mfd65: Estimated from 120 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.45. Allele (bp) Frequency Allele (bp) Frequency 170 0.01 166 0.21 168 0.12 154 0.67

Dinucleotide repeat polymorphisms at the D11S419 and CD3D loci.

Source/Description: For Mfd58, a human genomic Sau3A IDNA fragment was cloned into mpl9 and selected by hybridization to poly(dC-dA) • poly(dG-dT). Sequencing of the clone provided the information necessary for polymerase chain reaction primer synthesis. For Mfd69, a (dC-dA)n • (dG-dT)n sequence was found within an intron of the human gene encoding the delta subunit of the CD3 T-cell receptor complex by computer search of GenBank (Accession numbers M12727 and X03934). Polymerase chain reaction primers were selected from this sequence.

Dinucleotide repeat polymorphisms at the D7S435 and D7S440 loci

Frequency: Mfd20: Estimated from 112 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.53. Allele (bp) Frequency Allele (bp) Frequency 134 0.01 126 0.57 132 0.27 122 0.03 128 0.12 Mfd50: Estimated from 112 chromosomes of unrelated CEPH family grandparents (Caucasians). PIC = 0.70. Allele (bp) 191 189 187 185 183 Frequency 0.02 0.13 0.23 0.04 0.03 Allele (bp) 181 179 177 175 169 Frequency 0.02 0.04 0.04 0.44 0.01 Chromosomal Localization: Mfd20 and Mfd50 were assigned to chromosome 7 by using DNA templates isolated from panels of somatic cell hybrids.

Linkage mapping of the highly informative DNA marker D21S156 to human chromosome 21 using a polymorphic GT dinucleotide repeat

A (GT)n repeat within the anonymous DNA sequence D21S156 was shown to be highly polymorphic in DNA from members of the 40 CEPH families. At least 12 alleles of this locus were recognized by electrophoresis on polyacrylamide gels of DNA amplified by the polymerase chain reaction (PCR) using primers flanking the (GT)n repeat. The polymorphism information content was 0.82. PCR amplification of DNA from somatic cell hybrid lines mapped D21S156 to human chromosome 21 and linkage analysis localized this marker close to the loci ETS2, D21S3, and HMG14 on chromosomal band 21q22.3. This polymorphism is highly informative and can serve as an anchor locus for human chromosome 21.