Population specificity of minisatellite MS32
Lineages of structurally related alleles at minisatellite MS32 (D1S8) in human populations show considerable differentiation at the continental level. Here we provide the data obtained from a series of studies to determine inter-population variation within minisatellite MS32 to varying degrees.
Minisatellites and allele mapping
Minisatellites are regions of repetitive DNA with repeats units of typically 6-100 bp in length tandemly repeated 10-1000 times. The number of repeats and therefore the overall length of the minisatellite varies between alleles which often makes minisatellites highly variable within a population. In addition to length variation, not all repeat units are identical. Minor sequence variations between repeat units results in a range of variant repeat units throughout a minisatellite array. Characterization of the distribution of variant repeat units produces highly informative maps of minisatellite structure which allow similarities and differences between alleles to be examined in far more detail by simply analyzing the varying lengths of the alleles.
To determine the genetic variations inherent in diverse populations, we have extensively analyzed variant repeat distribution within alleles of MS32 using the technique of minisatellite variant repeat mapping by PCR (MVR-PCR) (Jeffreys et al., 1991).
Dot-matrix analysis method
To date 1269 alleles have been mapped(ethnic breakdown is shown in Table 1). In order to identify alleles that share regions of map similarity, MVR codes were compared with one another via heuristic dot matrix analysis using modified Microsoft Excel software originally written by AJJ (Jeffreys et al. 1991; Tamaki et al. 1995).Comparisons searched for perfect 9-repeat matches, and allele pairs showing scores of 22 or more over the best two diagonals (i.e. having the greatest allelic similarity) were selected. The authenticity of these selected matches and the final alignment of allele groups were checked by eye, with gaps inserted to improve alignments.
The full range of MS32 alleles analyzed by MVR-PCR is as follows:
Table1.Ethnic group codes and registered number of alleles
| Code | Ethnic group | No. | Code | Ethnic group | No. | |
|---|---|---|---|---|---|---|
| a | Armish | 4 | f | French | 40 | |
| b | Bangladeshi | 27 | j | Japanese | 325 | |
| ee | East European | 4 | mel | Melanesian | 6 | |
| in | Indian | 4 | th | Thai | 119 | |
| m | Mormon | 102 | af | African | 14 | |
| png | Papua New Guinean | 18 | e | English | 236 | |
| zim | Zimbabwean | 43 | g | German | 35 | |
| ac | Afro-Caribbean | 196 | kar | Karitiana | 14 | |
| ch | Han Chinese | 73 | p | Polish | 3 | |
| v | Venezuelan | 6 |
Table 2. MVR and sequences
| MVR code | sequence |
|---|---|
| a | 5′- GGCCAGGGGTGACTCAGAATGGAGCAGGY -3′ |
| t | 5′- GACCAGGGGTGACTCAGAATGGAGCAGGY -3′ |
| 0 | common code of the ‘null’ repeat which fail to be amplified by either a- or t-type MVR-specific primers |
| N | 5′- GRCC-GGGGTGACTCAGAATGGAGCAGGY -3′ (one of the ‘null’ repeats) |
| U | null repeat confirmed (N-type repeat ruled out) |
| ? | unable to be typed |
MVR codes of all alleles from the populations specified can be found on the following pages:
Aligned MS32 alleles
References:
Jeffreys AJ, MacLeod A, Tamaki K, etal. Minisatellite repeat coding as a digital approach to DNA typing. Nature. 1991Nov 21; 354(6350):204-9.
Acknowledgements:
These Databases draw upon data collected and analyzed by AJJ.