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Genetic Marker Analysis

This page contains a list of mouse genetic markers suitable for multiplex PCR (see Table 1.)

Ref: Vandenbergh, D. J. et al. "Simple Tests to Detect Errors in High Throughput Genotype Data in the Molecular Lab" J.  Biomolecular Techniques [14(1)9-16].

There are also links to files relevant to error detection when using
high-throughput systems to generate genotype data. The first file is a short Readme.doc file with information about the template file so
that you have an easier time adapting the template to your needs.

The second file is a downloadable Excel file that serves as a template to aid in detecting typical errors in high throughput genotype analysis when there are only two alleles at each marker (in our case a B6 and a D2 allele). The file is called  ErrorDetectionTemplate.xls

Below is a table of 97 markers used to analyze mice from a C57BL/6J by DBA2/J cross.  The file shows the markers that were pooled in multiplex PCR amplifications for fluorescent fragment size analysis.

Send comments and suggestions by email to David Vandenbergh (djv4@psu.edu).

Table 1: Markers for multiplexed genotyping to distinguish C57BL/6J and DBA2/J mouse alleles.a

Markerb CMc Sepd B6 allele Observed (bp)e B6 allele Published (bp) DBA allele Observed (bp)f B6 allele Published (bp) Dye label
D1Mit68 9   176 172 180 176 HET
D1Mit236 25.7 16.7 149 143 133 136 HET
D1Mit46 43.1 17.4 254 256 259 264 HET
D1Mit87 62.1 19 201 204 197 198 TET
D1Mit16 87.2 25.1 183 186 196 197 FAM
D1Mit221 102 14.8 114 119 120 125 TET
with 16   18.6        

 
D2Mit149 7   199 195 201 197 HET
D2Mit323 31.7 24.7 126 126 124 128 TET
D2Mit300 50.3 18.6 101 108 99 106 FAM
D2Mit304 73 22.7 118 120 196 186 FAM
D2Mit343 84.2 11.2 149 183 141 173 FAM
D2Mit266 109 24.8 126 130 135 138 HET
with 7   20.4        

 
D3Mit264 2.4   103 109 101 107 FAM
D3Mit46 13.8 11.4 160 166 155 160 HET
D3Mit25 29.5 15.7 130 134 124 127 FAM
D3Mit29 45.2 15.7 145 150 182 184 FAM
D3Mit42 58.8 13.6 150 154 142 146 TET
D3Mit194 67.6 8.8 144 146 139 142 HET
D3Mit59 84.1 16.5 203 208 201 206 FAM
with 18  

13.6

        

 
D4Mit104 1.9   244 243 242 241 HET
D4Mit214 17.9 16 121 126 137 152 HET
D4Mit255 48.5 30.6 251 238 244 234 TET
D4Mit204 61.9 13.4 104 104 82 82 FAM
D4Mit190 79 17.1 143 145 150 151 FAM
with 13   19.3          
D5Mit227 9   97 92 102 102 FAM
D5Mit81 28 19 206 210 192 194 TET
D5Mit10 54 26 189 196 197 203 FAM
D5Mit137 68 14 149 152 144 148 HET
D5Mit167 78 10 120 121 116 125 HET
with X   17.3          
D6Mit116 5.5   117 123 110 114 FAM
D6Mit188 32.5 27 127 130 156 155 HET
D6Mit149 46.3 13.8 199 189 208 199 TET
D6Mit111 63.7 17.4 139 146 142 148 FAM
D6Mit15 74 10.3 255 260 195 195 FAM
with 12   17.1          
D7Mit76

3.4

   226 228 223 226 FAM
D7Mit69

24.5

21.1

 237 236 239 238 HET
D7Mit253

52.8

28.3

 81.4 90 83 92 TET
D7Mit12

66

13.2

 199 197 206 206 TET
with 2   20.9          
D8Mit281 11   122 123 115 117 FAM
D8Mit191 21 10 138 144 127 132 FAM
D8Mit249 37 16 145 148 187 172 HET
D8Mit211 49 12 151 154 163 166 TET
D8Mit215 59 10 174 182 168 176 FAM
with 10   12          
D9Mit64 7   187 190 183 184 FAM
D9Mit229 28 21 122 122 135 142 HET
D9Mit196 48 20 143 148 150 156 FAM
D9Mit212 61 13 99 108 106 118 FAM
D9Mit52 72 11 170 172 174 176 HET
with 19   16.3          
D10Mit212 9   117 123 125 131 HET
D10Mit36 29 20 140 146 142 148 FAM
D10Mit117 48 19 122 142 120 126 TET
D10Mit95 51 3 196 201 176 179 TET
D10Mit14 65 14 191 192 185 182 TET
with 8   14          
D11Mit227 2   165 170 157 166 HET
D11Mit86 28 26 119 126 126 134 HET
D11Mit36 47.6 19.6 237 234 219 220 FAM
D11Mit99 59.5 11.9 121 124 105 108 TET
D11Mit291 70 10.5 92 94 95 96 TET
with 17   17          
D12Mit153 15   142 142 158 158 TET
D12Mit190 28 13 122 128 109 114 TET
D12Mit194 45 17 104 108 96 100 HET
D12Mit8 58 13 167 168 177 179 HET
with 6   15          
D13Mit198 16   132 136 134 140 TET
D13Mit125 44 28 188 191 183 185 FAM
D13Mit230 62 18 150 154 147 151 TET
D13Mit35 75 13 194 190 180 182 HET
with 4   19.7          
D14Mit11 0.7   151 152 159 158 FAM
D14Mit122 21.5 20.8 141 144 127 132 HET
D14Mit203 28.3 6.8 151 158 169 176 HET
D14Mit194 44.4 16.1 91 89 77 81 TET
D14Mit75 54 9.6 177 178 178 190 TET
with 15   13.3          
D15Mit179 10.8   140 148 149 152 TET
D15Mit183 23 12.2 125 129 123 127 FAM
D15Mit105 47.9 24.9 123 125 110 113 HET
D15Mit39 56.6 8.7 130 130 123 124 TET
D15Mit35 61.7 5.1 116 142 110 136 FAM
with 14   12.7          
D16Mit131 4.3   141 144 181 180 TET
D16Mit4 27.3 23 128 132 118 123 HET
D16Mit191 57.8 30.5 116 122 118 124 FAM
D16Mit71 70.7 12.9 156 159 162 163 FAM
with 1   22.1          
D17Mit16 18.2   117 118 104 106 FAM
D17Mit177 24 5.8 107 110 113 116 HET
D17Mit93 44.5 20.5 155 156 170 168 TET
D17Mit123 56.7 12.2 128 133 149 155 FAM
with 11   12.8          
D18Mit60 16   203 186 211 194 TET
D18Mit123 31 15 117 116 123 122 HET
D18Mit142 47 16 115 121 127 133 TET
D18Mit144 57 10 177 180 173 177 HET
with 3   13.7          
D19Mit68 6   131 136 127 132 FAM
D19Mit40 25 19 106 112 100 106 TET
D19Mit8 47 22 196 178 164 168 TET
D19Mit71 54 7 132 137 128 135 TET
with 9   16        

 
DXMit89 3   146 149 153 157 FAM
DXMit166 15.5 12.5 113 114 126 126 FAM
DXMit95 43 27.5 139 151 133 137 TET
DXMit79 50.5 7.5 138 139 136 137 HET
DXMit135 69 18.5 113 118 115 122 TET
with 14   16.5          

 

a This table is also available on the web as a tab-delimited file at http://cdhg.ssri.psu.edu/GeneticMarkerAnalysis/table1.txt

b *Marker*, name of polymorphism used from Research Genetics (resgen.com).  The markers are listed numerically by chromosome (the
number following the “D” in each name).  To make multiplex reactions,
markers from each chromosome were paired with a second chromosome
indicated at the end of each chromosome set (i.e. chromosome 1 paired
with 16; 2 with 7, etc.).

c *cM*, centiMorgan position on the chromosome based on consensus
committee map (www.informatics.jax.org). [See reference 11 for details about the database.]

d *Sep*, distance in cM from previous marker.  The average separation
of markers on a chromosome is in bold at the end of each chromosome list.

e *B6*, actual allele size in basepairs (bp) from c57BL/6 mice.
Published sizes are from the MIT website
www-genome.wi.mit.edu/cgi-bin/mouse/index

f *Dye labels*: Three fluorescent dyes, FAM, HET, and TET, from Applied
Biosystems, Inc. were used to label forward primers.  Primers were pooled keeping dyes in separate multiplex PCR reactions.

 

 

 

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