D1S80 (pMCT118) allele frequencies in a Malay population sample from Malaysia

Development of an algorithm of satellite markers for monitoring chimerism status in post-allogeneic haematopoietic stem cell transplantation patients

INTRODUCTION

Analysis of variable number tandem repeats (VNTRs) by polymerase chain reaction (PCR) is a common method used to predict engraftment status in post-allogeneic haematopoeitic stem cell transplantation (HSCT) patients. Different populations have different copies of repeated DNA sequence and hence, different percentage of informativeness between patient and donor.

METHODS

PCR amplification of four highly polymorphic VNTR markers (YNZ-22, D1S80, D1S111 and ApoB) was conducted on 60 patient-donor pairs. The informativeness of the markers was analysed using 3% agarose gel electrophoresis.

RESULTS

We developed an algorithm for identification of informative VNTR markers in 60 post-allogeneic HSCT patients. YNZ-22 was the most informative (72%), followed by D1S80 (63%) and D1S111 (60%), while the least informative was ApoB (47%). The degree of informativeness achieved was 95%, which could discriminate 57 patient-donor pairs, when all four markers were combined.

CONCLUSION

Since population genetic studies on VNTR loci are not well established in Southeast Asia, the present study is useful to determine reliable markers during the initial screening step of chimerism analysis. By following this algorithm, we are able to reduce time and cost of finding a suitable VNTR marker in our cohort.

Genetic variability at the D1S80 minisatellite: predominance of allele 18 among some indian populations

BACKGROUND

Hypervariable minisatellites are considered as useful genetic markers in population studies because they are highly polymorphic, multiallelic and co-dominant in nature. The D1S80 minisatellite is one of the well studied markers, and has been used for differentiating population groups of various geographic, linguistic, cultural and genetic origins.

OBJECTIVE

The present study reports the genetic variation observed at the D1S80 minisatellite among seven anthropologically distinct ethnic groups from Kerala state in south India and is compared with other reported Indian and world populations.

SUBJECTS AND METHODS

DNA was isolated from the peripheral blood samples of 282 random, normal and healthy volunteers, PCR amplified and electrophoresed on 4% PAGE followed by silver staining.

RESULTS

A total of 22 alleles (14-39 repeats) were detected with high heterozygosity (0.63-0.84) and Polymorphic Information Content (PIC) values (0.63-0.83). Allele 18 was the predominant allele, except in Ezhavas. The comparison of allele frequency data with world populations including other studied Indian ethnic groups has revealed that the majority of Indian populations possessed allele 18 as the predominant allele. In contrast, allele 24 was reported to be the predominant allele worldwide with a few exceptions.

CONCLUSIONS

This study at the D1S80 minisatellite on seven ethnic groups will provide useful information for the Indian population genetic database. However, the most important observation was the predominance of allele 18 among the majority of Indian ethnic groups. The reason is not clear yet and thus further studies on Indian ethnic groups from different regions are necessary to find out the importance of allele 18 as the predominant allele in Indian population.