Genome-wide association with bone mass and geometry in the Framingham Heart Study

Background

Osteoporosis is defined as the loss of bone mineral density that leads to bone fragility with aging. Population-based case-control studies have identified polymorphisms in many candidate genes that have been associated with bone mass maintenance or osteoporotic fracture. To investigate single nucleotide polymorphisms (SNPs) that are associated with osteoporosis, we examined the genetic variation among Koreans by analyzing 81 genes according to their function in bone formation and resorption during bone remodeling.

Methods

We resequenced all the exons, splice junctions and promoter regions of candidate osteoporosis genes using 24 unrelated Korean individuals. Using the common SNPs from our study and the HapMap database, a statistical analysis of deviation in heterozygosity depicted.

Results

We identified 942 variants, including 888 SNPs, 43 insertion/deletion polymorphisms, and 11 microsatellite markers. Of the SNPs, 557 (63%) had been previously identified and 331 (37%) were newly discovered in the Korean population. When compared SNPs in the Korean population with those in HapMap database, 1% (or less) of SNPs in the Japanese and Chinese subpopulations and 20% of those in Caucasian and African subpopulations were significantly differentiated from the Hardy-Weinberg expectations. In addition, an analysis of the genetic diversity showed that there were no significant differences among Korean, Han Chinese and Japanese populations, but African and Caucasian populations were significantly differentiated in selected genes. Nevertheless, in the detailed analysis of genetic properties, the LD and Haplotype block patterns among the five sub-populations were substantially different from one another.

Conclusion

Through the resequencing of 81 osteoporosis candidate genes, 118 unknown SNPs with a minor allele frequency (MAF) > 0.05 were discovered in the Korean population. In addition, using the common SNPs between our study and HapMap, an analysis of genetic diversity and deviation in heterozygosity was performed and the polymorphisms of the above genes among the five populations were substantially differentiated from one another. Further studies of osteoporosis could utilize the polymorphisms identified in our data since they may have important implications for the selection of highly informative SNPs for future association studies.     

A Note on Including Phenotypic Information from Monozygotic Twins in Variance Components Qtl Linkage Analysis

Williams & Blangero (1999) derived closed form expressions for the power of a univariate variance components test of linkage for a variety of pedigree structures. We have extended their results by investigating the effect of including monozygotic twins in the design on the power to detect linkage. Specifically, we determined the power associated with a pedigree of size three, where individuals one and two were monozygotic twins and individual three was a full sibling to the twins. The power of this sampling unit was uniformly greater than the power obtained from a sib‐pair under the same genetic model. The reason for this was that addition of a second monozygotic twin provided another estimate of the sibling correlation for the particular IBD class. In addition, when the total heritability of the trait was <50%, the number of individuals that needed to be phenotyped was less than that with sib‐pairs alone. However, a pedigree consisting of a monozygotic pair and sibling was never as informative as a sib‐trio, presumably because the sib‐trio provided information about allele sharing between three individuals, whereas the monozygotic twins and sibling unit only provided one such relationship. We conclude that including a monozygotic twin in the analysis is an economical strategy, since only one twin needs to be genotyped.     

Heterozygosities and allelic frequencies of a set of microsatellite markers used for genome-wide scans in a Chinese population

Microsatellite (short tandem repeat) markers are useful tools for genetic linkage analysis because of their high frequency of occurrence in eukaryotic genomes, ease of typing, and high polymorphism content. To establish a panel of microsatellite markers useful for genome-wide screens in the Chinese population, we determined the heterozygosities and allelic frequencies of a widely used set of 285 markers in 208 individuals of Han Chinese descent. Although the median heterozygosity level in our Chinese population was 0.72, only 63.6% of these markers have a heterozygosity of at least 0.7, compared with 90.8% in the original Caucasian sample. The significant difference in heterozygosity and allelic frequencies between populations suggests that markers should be optimally selected for each study population to maximize information content and power. Received: July 1, 2002 / Accepted: August 23, 2002 Acknowledgments This work is partially supported by Singapore National Medical Research Council grant no. SERI/MG/96-01/0001 and by the Singapore Ministry of Defence. We would like to thank the SAF Medical Classification Centre and the Singapore Eye Research Institute Clinic staff for help in recruitment. We also thank S.J. Chew and D. Tan for their support. The first two authors contributed equally to this work. Correspondence to:E. Yap     

Association of ulcerative colitis with the inflammatory bowel disease susceptibility locus IBD2 in non-Jewish Caucasians and evidence of genetic heterogeneity among racial and ethnic populations with Crohn disease

Genomewide scanning has been used to identify chromosomal regions encoding susceptibility loci to inflammatory bowel disease (IBD). The greatest evidence for linkage to IBD has been reported for a region of chromosome 12q14 surrounding the microsatellite marker D12S83, with a logarithm of odds score of 5.47 and a positive transmission disequilibrium test, and which was subsequently named IBD2. We wished to confirm this locus by genotyping the highly polymorphic microsatellites D12S1022, D12S1056, and D12S83, spanning a continuous region on chromosome 12 of 342 kb, in a cohort of nonrelated individuals with ulcerative colitis (89 patients), Crohn disease (121 patients), and population-based control subjects (100 patients). In non-Jewish Caucasians, one D12S1022 allele, one D12S1056 genotype, and three D12S83 alleles were found to have statistically significant differences in distribution between the two disease groups and the control population. These data support a significant association of IBD with the IBD2 locus in close vicinity to the three markers studied. The replication of genetic risk loci in a case control association study may indicate susceptibility genes in this region and may facilitate identification of candidate genes for IBD. Subgroup analysis revealed a notable difference in genotype distribution among Jewish Caucasian and African American patients affected with Crohn disease when compared with similarly affected non-Jewish Caucasians. Using Fisher exact test, statistically significant distribution differences were observed for D12S1022 and D12S83. These data indicate that there may be significant genetic heterogeneity between different ethnic and racial IBD populations or may simply reflect differences in marker allele frequencies among populations.     

Heterozygosities and allelic frequencies of 358 dinucleotide-repeat marker loci in the Japanese population

We examined 64 normal Japanese chromosomes to determine the heterozygosities and allelic frequencies of 358 dinucleotide-repeat marker loci spanning the whole human genome. Comparisons of the data for each marker in the Japanese population sample with data for the same markers among Caucasian samples in the Genome Database (GDB) revealed a slightly lower average of heterozygosity in Japanese (71% vs 79%). Although the majority of the markers were as informative as in Caucasians, some in our sample were uninformative due to low heterozygosity; 38 loci revealed heterozygosities lower than 50% and 11 of these were less than 30%. Furthermore, allelic distributions at many of the marker loci were quite different in the two racial groups. Since such differences will influence statistical analyses between markers and disease loci, our data will be essential for linkage analyses, sib-ship pair analyses, and association studies involving the Japanese population. Therefore we have archived this database on a home page on the Internet (http://www.ims.u-tokyo.ac.jp/nakamura/Yamane.html). Received: March 11, 1998 / Accepted: April 11, 1998     

Testing of human homologues of murine obesity genes as candidate regions in Finnish obese sib pairs

The human homologues of recently discovered murine obesity genes provide relevant candidates to study the genetic component of obesity in humans. We analysed the human counterparts to murine obesity genes ob, db, agouti, tub, melanocortin 4-receptor (MC4-R) and mitochondrial uncoupling proteins 2 and 3 (UCP2 and UCP3), as well as two other chromosomal regions reported to be linked to obesity-related phenotypes in restricted populations. We found no significant evidence for linkage to any analysed loci in our total study material of 105 affected sib pairs collected from the genetically homogenous population of Finland. However, several markers on 14 cM chromosomal region flanking the MC4-R gene showed sharing of alleles identical-by-descent (IBD) more frequently than expected. A selected subset of non-diabetic obese sib pairs strengthened the P values down to 0.003 in this particular region. The smallest P value (P = 0.001) was obtained with a marker D18S487 in a subgroup containing only sib pairs with one lean and one obese parent. We therefore screened seven obese subjects included in our sib pair material for sequence changes in their MC4-R gene, but no mutations of apparent causal relationship were found. In conclusion, we could not find evidence for significant contribution of the chromosomal loci corresponding to the murine single gene obesity genes for human morbid obesity, but additional studies are still needed to clarify whether DNA alterations within or adjacent to the MC4-R gene play some role.     

Association of ulcerative colitis with the inflammatory bowel disease susceptibility locus IBD2 in non‐Jewish Caucasians and evidence of genetic heterogeneity among racial and ethnic populations with Crohn disease

Genomewide scanning has been used to identify chromosomal regions encoding susceptibility loci to inflammatory bowel disease (IBD). The greatest evidence for linkage to IBD has been reported for a region of chromosome 12q14 surrounding the microsatellite marker D12S83, with a logarithm of odds score of 5.47 and a positive transmission disequilibrium test, and which was subsequently named IBD2. We wished to confirm this locus by genotyping the highly polymorphic microsatellites D12S1022, D12S1056, and D12S83, spanning a continuous region on chromosome 12 of 342 kb, in a cohort of nonrelated individuals with ulcerative colitis (89 patients), Crohn disease (121 patients), and population‐based control subjects (100 patients). In non‐Jewish Caucasians, one D12S1022 allele, one D12S1056 genotype, and three D12S83 alleles were found to have statistically significant differences in distribution between the two disease groups and the control population. These data support a significant association of IBD with the IBD2 locus in close vicinity to the three markers studied. The replication of genetic risk loci in a case control association study may indicate susceptibility genes in this region and may facilitate identification of candidate genes for IBD. Subgroup analysis revealed a notable difference in genotype distribution among Jewish Caucasian and African American patients affected with Crohn disease when compared with similarly affected non‐Jewish Caucasians. Using Fisher exact test, statistically significant distribution differences were observed for D12S1022 and D12S83. These data indicate that there may be significant genetic heterogeneity between different ethnic and racial IBD populations or may simply reflect differences in marker allele frequencies among populations. © 2002 Wiley‐Liss, Inc.     

Evidence of linkage of the inflammatory bowel disease susceptibility locus on chromosome 16 (IBD1) to ulcerative colitis.

Crohn's disease (CD) and ulcerative colitis (UC) are inflammatory bowel diseases (IBD) of unknown aetiology which are characterised by chronic inflammation of the gastrointestinal tract. Epidemiological studies suggest the presence of a genetic component in the aetiology of both CD and UC. A susceptibility gene for Crohn's disease has recently been mapped to the pericentromeric region of chromosome 16 (IBD1), and this finding has been replicated in two subsequent studies. Although CD and UC are distinct clinical entities, the fact that both disorders occur in a significant proportion of families with multiple cases of IBD suggests that overlapping sets of susceptibility genes may be involved. We have addressed this question for IBD1 by typing eight microsatellite markers from the locus in 70 kindreds affected with either UC only or with both UC and CD and analysing the data for linkage by both non-parametric and parametric methods. Evidence for linkage was detected in families affected with only UC, with a mean proportion of 0.70 affected sib pairs sharing alleles identical by descent at D16S3136 (p=0.01), and a peak non-parametric linkage score of 2.02 at D16S3120 with the GENEHUNTER program (p=0.02). The estimated sib relative risk attributable to IBD1 in these families was 1.46. Surprisingly, no evidence of linkage was detected in the families affected with both UC and CD (p>0.2). The data suggest that IBD1 may also contribute to susceptibility to ulcerative colitis, and that it is likely to be located in the 12 cM interval between D16S419 and D16S409.     

Your father and I

Genomewide scanning has been used to identify chromosomal regions encoding susceptibility loci to inflammatory bowel disease (IBD). The greatest evidence for linkage to IBD has been reported for a region of chromosome 12q14 surrounding the microsatellite marker D12S83, with a logarithm of odds score of 5.47 and a positive transmission disequilibrium test, and which was subsequently named IBD2. We wished to confirm this locus by genotyping the highly polymorphic microsatellites D12S1022, D12S1056, and D12S83, spanning a continuous region on chromosome 12 of 342 kb, in a cohort of nonrelated individuals with ulcerative colitis (89 patients), Crohn disease (121 patients), and population‐based control subjects (100 patients). In non‐Jewish Caucasians, one D12S1022 allele, one D12S1056 genotype, and three D12S83 alleles were found to have statistically significant differences in distribution between the two disease groups and the control population. These data support a significant association of IBD with the IBD2 locus in close vicinity to the three markers studied. The replication of genetic risk loci in a case control association study may indicate susceptibility genes in this region and may facilitate identification of candidate genes for IBD. Subgroup analysis revealed a notable difference in genotype distribution among Jewish Caucasian and African American patients affected with Crohn disease when compared with similarly affected non‐Jewish Caucasians. Using Fisher exact test, statistically significant distribution differences were observed for D12S1022 and D12S83. These data indicate that there may be significant genetic heterogeneity between different ethnic and racial IBD populations or may simply reflect differences in marker allele frequencies among populations. © 2002 Wiley‐Liss, Inc.     

Effects of age at onset on the power of the affected sib pair and transmission/disequilibrium tests

Information on the age of a patient at disease onset, an important feature of complex diseases, is often collected in studies designed to map the disease genes. Penetrance-model-free methods, requiring no specification of penetrance functions, have been used extensively for detecting linkage and association between marker and disease loci. In this paper, we conduct an analytical study to examine the effects of incorporation of age at onset information on the power of two commonly used penetrance-model-free methods, the affected sib-pair (ASP) and transmission/disequilibrium tests (TDT). Assuming a Cox model with a major gene effect for the age at onset, we quantify analytically how age at onset affects the identity by descent (IBD) probabilities, the mean IBD values, and the expected numbers of alleles transmitted from heterozygous parents to affected children under various genetic models. We show that the power of the mean IBD test and the TDT can be greatly affected by the ages at onset of affected siblings or children used in the study. Generally, the most powerful test for ASPs is that based on affected sib pairs both having early disease onset and for TDT analyses is that based on trios with early-onset children. Naively combining affected sib pairs with different ages at onset or parent-children trios with different ages at onset of affected children can result in reduced power for detecting linkage or association. These results may be used to guide collection and analysis of sib pairs or families for diseases with variable age at onset.     

Linkage analysis of peripheral neurofibromatosis to DNA markers on chromosome 8.

Linkage relationships of the gene for peripheral neurofibromatosis (NF) were assessed in a large American Caucasian pedigree using two DNA markers located on chromosome 8. Linkage to the thyroglobulin locus, located at 8q24, was excluded (lod less than or equal to -2.0) to 21 cM. Data obtained for the tissue plasminogen activator locus, located at 8p12, excluded linkage to 4 cM. These results exclude between 20 to 30% of chromosome 8 as a possible map location for the NF gene in this family. Comparison of the two DNA markers excluded their linkage to 0.5 cM.     

Genetic linkage of bipolar disorder to chromosome 6q22 is a consistent finding in Portuguese subpopulations and may generalize to broader populations.

We recently reported genome-wide significant linkage to chromosome 6q for bipolar disorder, in a study of 25 Portuguese families, using the Human Mapping Assay Xba 131 (HMA10K). To explore the generalizability of this finding, we reanalyzed our SNP linkage data according to the families' geographic origin. Specifically, the 25 families included 20 families from the Portuguese island collection (PIC; 15 families from the Azores Islands and 5 from the Madeira Islands) and 5 families from continental Portugal. Non-parametric linkage analysis (NPL) was performed as previously described and indicated that each of these subpopulations showed evidence of linkage for the same region. To further address the potential generalizability of these findings to other populations, we have also examined allelic heterozygosity in our subpopulations and in three reference populations (Caucasian, East Asian, and African-American). This analysis indicated that the PIC population is highly correlated to the Caucasian reference population (R = 0.86) for all of chromosome 6. In contrast allelic heterozygosity was more weakly correlated between PIC and both East Asian (R = 0.37) and African-American (R = 0.32) reference populations. Taken together these observations suggest a shared genetic liability among Portuguese populations for bipolar disorder on chromosome 6q, and that the PIC population is likely representative of Caucasians in general.     

Microsatellite typing for DRB1 alleles: application to the analysis of HLA associations with rheumatoid arthritis

The current methods for molecular typing of HLA-DR alleles incur a substantial financial burden when performing large population studies. In the current study, we aimed to provide much less expensive typing approach with high predictability for DRB1 genotype. We have used a panel of three microsatellite markers in the class II region (D6S2666, D6S2665 and D6S2446) for genotyping and haplotype reconstruction in a total of 1687 Caucasian (1313 RA patients and 374 controls) and 1364 Korean individuals (744 RA patients and 620 controls), all of whom were previously genotyped for DRB1. We found that a total of 88.4 and 87.4% of all observed three-marker haplotypes could determine the DR type with a positive predictive value >0.8 with high sensitivity and specificity. There was a high degree of haplotype conservation when comparing Caucasian and Asian populations. Interestingly, we found that the majority of DRB1*09 and DRB1*10 alleles share a common three-marker haplotype in both Caucasian and Asian populations. This is unexpected, since these two alleles are found on very different haplotype families. In addition, these two alleles are both associated with rheumatoid arthritis, making the elucidation of these haplotype relationships potentially important for understanding disease susceptibility.     

Analysis of 168 short tandem repeat loci in the Japanese population, using a screening set for human genetic mapping

We devised a multiplex polymerase chain reaction (PCR) amplification and loading system for the convenient typing of 168 short tandem repeat (STR) polymorphic markers in a commercially available screening primer set for human linkage analysis. We genotyped all these 168 STR loci with 32 healthy unrelated Japanese, calculated allele frequencies at each STR locus, and performed three kinds of tests for Hardy-Weinberg equilibrium (HWE). Significant deviations from HWE in all three tests were observed at only three loci, and the average heterozygosity in the Japanese (0.733) was slightly lower than that in Caucasians (0.773). We also examined 32 Caucasians at some selected loci, to be compared with Japanese. Some markers showed greatly different heterozygosities or allelic distributions in Japanese and Caucasian populations. In two groups of STRs, those with and without irregular alleles (or inter-alleles), the former had a higher proportion of bimodal allelic distribution and possessed more alleles per locus than the latter. However, no significant differences in the observed and expected heterozygosities, or in the powers of discrimination, were found between the two groups. The present basic study of allele frequency databases of these STRs will contribute to further applications in forensic science and human genetics. Received: March 26, 2001 / Accepted: April 25, 2001     

内蒙古蒙古族人群杀伤细胞免疫球蛋白样受体基因簇多态性研究

目的 研究中国蒙古族人群杀伤细胞免疫球蛋白样受体(killer cell immunoglobulin-like receptors,KIR)基因的携带频率、KIR基因型及其遗传规律.方法 采集90名内蒙古农牧区蒙古族个体的血样,应用序列特异性引物聚合酶链反应(polymerase chain reaction-sequence specific primer,PCR-SSP)方法分别扩增KIR基因簇16个基因,依据实验结果计算各基因的携带频率并查询样本的基因型,和已报道的24个其他人群的相关数据进行主成分分析、计算Nei氏遗传距离并绘制遗传树.结果 (1)蒙古族人群KIR 2DL2、2DS2携带率高于蒙古利亚人,低于高加索人.(2)蒙古族KIR基因单倍型AA为37.78%,高于高加索人,低于蒙古利亚人.(3)系统进化树显示蒙古利亚人和高加索人分别聚类,蒙古族人群则介于两者之间.结论 蒙古族其成因似与受到高加索人和蒙古利亚人的双重影响有关,表现为介于高加索人和蒙古利亚人之间的中间形式.

Abstract：

Objective To investigate the killer cell immunoglobulin-like receptor (KIR) gene frequencies and genotypes distributions in the Inner Mongolian population. Methods Ninety genomic DNA samples were extracted from blood samples of randomly chosen Mongolian individuals. Gene-specific PCR amplification was used to identify genes present or absent for 16 KIR loci. KIR genotype distributions were obtained and compared to that of 24 populations published in literatures using principal component analysis by SAS8.0 software. Genetic tree was constructed by the calculate Nei's genetic distance. Results (1) The frequency of KIR 2DL2,2DS2 in Mongolian individual is higher than that in north Mongoloid and less than that in Caucasian. (2) Haplotype AA was identified in 37.78% of individuals, which is higher than that in north Mongoloid and lower than that in Caucasian. (3) Mongolian was considered between north Mongoloid and Caucasian by principal component and genetic tree analysis. Conclusion Mongolian might be affected by the north Mongoloid and Caucasian, and showed intermediate between the two populations.     

An Analysis-of-Variance (ANOVA) Approach for Sib-pair Linkage Analysis of Complex Ordinal Human Diseases

INTRODUCTION　　Analysis of Variance(ANOVA) is a versatile and efficient statistical approachfor studying the relation between a dependent variable and one or more independentvariables.One characteristic of this analysis is thatthere is no requirementfor …     

Genome-wide scanning for type 2 diabetes susceptibility in Canadian Oji-Cree, using 190 microsatellite markers

We undertook a genome-wide scan using 190 markers with an average separation of 20 cM in 49 Canadian Oji-Cree sib pairs affected with type 2 diabetes. Four of these markers, one each on chromosomes 6, 8, 16, and 22, showed both suggestive linkage and suggestive association with type 2 diabetes in the Oji-Cree. None of these markers corresponded to any chromosomal region or marker that has so far been linked with type 2 diabetes in other populations. Thus, there might be several genetic loci that confer susceptibility to type 2 diabetes in this study sample. We are following up on these preliminary leads by increasing the density of the markers within these linked and associated regions, and also by increasing the number of study subjects. Also, we found instances in which there were wide disparities between the Oji-Cree and reference Caucasians with respect to marker heterozygosity. This suggests that a particular set of markers for genome-wide scanning will have different informativeness in different ethnic groups. Thus, different marker sets will likely be required for different ethnic groups in order to maximize their information content for linkage calculations. Received: July 17, 1998 / Accepted: September 16, 1998     

Linkage between bronchial responsiveness to methacholine and gene markers of IL-4 cytokine gene cluster and T-cell receptor α/δ gene complex in Korean nuclear families

BACKGROUND: Several candidate genes have been reported to be linked to intermediate phenotypes of asthma in Caucasian populations. OBJECTIVE: To evaluate linkage between phenotypes of asthma and gene markers of high affinity IgE receptor-beta gene (D11S97), IL-4 cytokine gene cluster (IL-4R1), and T-cell receptor alpha/delta gene complex (D14S50) in Korean nuclear families. METHODS: Nuclear families (127 probands and their 130 siblings) for the linkage analysis were ascertained through asthmatic children. Linkages between total serum IgE response, skin responses to common aeroallergens, and bronchial responsiveness to methacholine were performed using a sib-pair approach. RESULTS: The square difference of the slope of the dose-response curve (DRS) between sib-pairs with two IL-4R1 identical alleles was smaller than with one or with neither IL-4R1 identical allele (P = 0.004). As for D14S50, the differences of DRS between sib-pairs with two identical alleles and with one identical allele were smaller than with neither identical alleles (P = 0.01). As for D11S97, no significant differences were observed among the groups with identical alleles of two, one or zero. With regard to total serum IgE levels, no significant linkage was found between this phenotype and the above three gene markers. As for skin responses to common aeroallergens, significant evidence was obtained to establish a linkage between this phenotype and the marker IL-4R1 (P = 0.01). However, no significant linkage was found between this phenotype and the markers D11S97 and D14S50. CONCLUSION: The expression of bronchial responsiveness to methacholine may be influenced by genetic factors in the IL-4 cytokine gene cluster and/or T-cell receptor alpha/delta gene complex, but the genetic influence of the FcepsilonRI-beta gene may be minimal in the expression of bronchial responsiveness in Korean nuclear families.     

Genetic and physical mapping of the Treacher Collins syndrome locus: refinement of the localization to chromosome 5q32-33.2.

Treacher Collins syndrome (TCOF1) is an autosomal dominant disorder of craniofacial development, the locus for which has been chromosomally localized to 5q31-34. We have isolated four hypervariable microsatellite markers (heterozygosity values range from 0.70 to 0.89) which have been mapped to distal 5q. Fifteen unrelated TCOF1 families have been analyzed for linkage to these markers. There is strong evidence demonstrating linkage to all of these markers; the strongest support for positive linkage being provided by the marker IG52, with a maximum pairwise lod score of 9.77 at a recombination fraction of 0.055. Analysis of recombinant individuals, physical mapping by fluorescence in situ hybridization and genetic linkage analysis demonstrated that the TCOF1 locus was flanked proximally by the loci 2C7 and 2D10, and distally by the loci IG26 and IG52 with a maximum lod score of 14.4, as assessed by multipoint linkage analysis. The refinement of the localization of the TCOF1 locus to 5q32-33.2, with flanking markers, represents an important step towards the identification of the mutated gene itself.     

Population genetic study of the STR loci (HUMCSF1PO,HUMTPOX, HUMTHO1, HUMLPL,HUMF13A01, HUMF13B,HSFESFPS and HUMVWA) in North Indians

BACKGROUND: Highly polymorphic genetic markers like short tandem repeats (STRs) have been used successfully in disease analysis and studies of human evolution and population genetic diversity. However, DNA-based population genetic studies of Indian populations are limited. SUBJECTS AND METHODS: To enlarge our understanding of genetic variation in Indian populations, a population genetic study was carried out on Jat Sikh (Punjab, North India) individuals (n = 150) using a battery of the STR loci. The STR loci analysed by means of PCR amplification followed by electrophoresis and silver staining included HUMCSF1PO, HUMTPOX, HUMTHO1, HUMLPL, HUMF13A01, HUMF13B, HUMFESFPS and HUMVWA loci. RESULTS: The overall pattern of allele frequencies was similar to many Caucasian and Indian populations and heterozygosity varied from 65% (HUMLPL) to 85% (HUMVWA). For all eight loci, no deviations from the Hardy-Weinberg equilibrium hypothesis were detected. Significant differences were observed between Jat Sikhs and African, Chinese and Indian tribes. The mean exclusion probability ranged from 35% to 70%, and the power of discrimination from 81% to 93%, indicating the potential of these loci for forensic and paternity investigations. CONCLUSION: The allele frequency spectrum, heterozygosity, probability of exclusion, match probability and discrimination probability estimates show interesting variation and suggest the usefulness of these loci for anthropogenetic, paternity and forensic investigations in Indian populations.