David N. Stivers

The utility of short tandem repeat loci beyond human identification: Implications for development of new DNA typing systems

Since the first characterization of the population genetic properties of repeat polymorphisms, the number of short tandem repeat (STR) loci validated for forensic use has now grown to at least 13. Worldwide variations of allele frequencies at these loci have been studied, showing that variations of interpopulation diversity at these loci do not compromise the power of identification of individuals. However, data collected for validation of these loci for forensic use has utility beyond human identification; the origin and past migration history of modern humans can be reconstructed from worldwide variations at these loci. Furthermore, complex forensic cases previously unresolvable can now be investigated with the help of the validated STR loci. Here, we provide the absolute power of the validated set of 13 STR loci for addressing these issues using multilocus genotype data on 1,401 individuals belonging to seven populations (US European‐American, US African‐American, Jamaican, Italian, Swiss, Chinese and Apache Native‐American). Genomic research is discovering new classes of polymorphic loci (such as the single nucleotide polymorphisms, SNPs) and lineage markers (such as the mitochondrial DNA and Y‐chromosome markers); our aim, therefore, was to determine how many SNP loci are needed to match the power of this set of 13 STR loci. We conclude that the current set of STR loci is adequate for addressing most problems of human identification (including interpretations of DNA mixtures). However, if suitable number of SNPs are used that would match the power of the STR loci, they alone cannot resolve more complex cases unless they are supplemented by the validated STR loci.

Association of microsatellite markers near the fibrillin 1 gene on human chromosome 15q with scleroderma in a Native American population

OBJECTIVE To localize disease genes for scleroderma, or systemic sclerosis (SSc), in a population of Choctaw Native Americans with a high prevalence of SSc, in which there is evidence of a possible founder effect. METHODS A candidate gene approach was used in which microsatellite alleles on human chromosomes 15q and 2q, homologous to the murine tight skin 1 (tsk1) and tsk2 loci, respectively, were analyzed in Choctaw SSc cases and race-matched normal controls for possible disease association. Genotyping first-degree relatives of the cases identified potential disease haplotypes, and haplotype frequencies were obtained by expectation-maximization and maximum-likelihood estimation methods. Simultaneously, the ancestral origins of contemporary Choctaw SSc cases were ascertained using census and historical records. RESULTS A multilocus 2-cM haplotype was identified on human chromosome 15q homologous to the murine tsk1 region, which showed a significantly increased frequency in SSc cases compared with controls. This haplotype contains 2 intragenic markers for the fibrillin 1 (FBN1) gene. Genealogical studies demonstrated that the SSc cases were distantly related, and their ancestry could be traced back to 5 founding families in the mid-eighteenth century. The probability that the SSc cases share this haplotype due to familial aggregation effects alone was calculated and found to be very low. There was no evidence of any microsatellite allele disturbances on chromosome 2q in the region homologous to the tsk2 locus or the region containing the interleukin-1 family. CONCLUSION A 2-cM haplotype on chromosome 15q that contains FBN1 is associated with scleroderma in Choctaw Native Americans from Oklahoma. This haplotype may have been inherited from common founders about 10 generations ago and may contribute to the high prevalence of SSc that is now seen.

PATERNITY EXCLUSION BY DNA MARKERS : EFFECTS OF PATERNAL MUTATIONS

In parentage testing when one parent is excluded, the distribution of the number of loci showing exclusion due to mutations of the transmitting alleles is derived, and it is contrasted with the expected distribution when the exclusion is caused by nonpaternity. This theory is applied to allele frequency data on short tandem repeat loci scored by PCR analysis, and VNTR data scored by Southern blot RFLP analysis that are commonly used in paternity analysis. For such hypervariable loci, wrongly accused males should generally be excluded based two or more loci, while a true father is unlikely to be excluded based on multiple loci due to mutations of paternal alleles. Thus, when these DNA markers are used for parentage analysis, the decision to infer non-paternity based on exclusions at two or more loci has a statistical support. Our approach places a reduced weight on the combined exclusion probability. Even with this reduced power of exclusion, the probability of exclusion based on combined tests on STR and VNTR loci is sufficiently large to resolve most paternity dispute cases in general populations.

Microsatellites and intragenic polymorphisms of transforming growth factor β and platelet‐derived growth factor and their receptor genes in Native Americans with systemic sclerosis (scleroderma): A preliminary analysis showing no genetic association

OBJECTIVE Abnormalities of transforming growth factor beta (TGFbeta) and platelet-derived growth factor (PDGF) alpha and beta and/or their receptors have been demonstrated in systemic sclerosis (SSc). This study aimed to determine whether genetic polymorphisms in or near the TGFbeta and PDGF gene families were associated with susceptibility to SSc in a Native American population with a high disease prevalence. METHODS Genotyping of 5 intragenic polymorphisms within the TGFbeta1 gene and mapping of 35 microsatellites near the genes for TGFbeta1, latent TGFbeta1 binding protein (LTBP1), TGFbeta receptors I and II, PDGFalpha, PDGFbeta, PDGF receptor alpha, and PDGF receptor beta was performed in 19 SSc patients, 76 controls, and 42 family members. Allele distributions and frequencies were examined between SSc patients and controls, and marker haplotypes were examined in families when allele frequencies appeared to be different between patients and controls. RESULTS Although 1 polymorphism within the TGFbeta1 gene (TGFbeta1) was modestly increased in the SSc patients, this did not maintain statistical significance after correction. Similarly, 1 microsatellite (D9S120) near the TGFbeta receptor I gene (TGFBR1) showed a significant disturbance of allele frequencies between patients and controls; however, it did not form a disease-associated haplotype with other nearby markers. Weak disturbances of markers near PDGFalpha (PDGFA) and PDGFbeta, (PDGFB) also failed to maintain significance after correction. Both PDGF receptor genes (PDGFRA and PDGFRB) also showed no disease associations. CONCLUSION The results of these preliminary analyses suggest that genetic anomalies of the TGFbeta1 and PDGF gene families are not likely to explain the dysregulation seen in SSc or to account for the susceptibility to SSc in this population.

Estimation of mutation rates from parentage exclusion data: applications to STR and VNTR loci

Nonpaternity is a common source of bias in estimating mutation rates when they are obtained from family data showing discordance of parental and childrens genotypes. With the availability of hypervariable DNA markers, this source of bias can be largely eliminated. However, the proportion of cases where parentage exclusion is caused by presumed mutation(s) of parental alleles must be adjusted to obtain a valid mutation rate estimate. The present work derives the basis of this adjustment factor, called the proportional bias. This proportional bias depends upon the allele frequency distribution at the locus. The maximum and minimum bounds of the proportional bias depend on the number of alleles at the locus. Using data from Caucasian populations at tandem repeat loci commonly used for parentage testing and forensic identification purposes, we show that when mutation rates are estimated at these loci, the proportional bias is generally very close to the maximum possible value for the observed number of alleles (or binned fragment sizes) at each locus. The expected proportional bias decreases with increasing mutation rate at a locus. For the short tandem repeat loci, without bias correction, the direct count method can result in an underestimation of up to 60% of their true value. In contrast, for the minisatellite VNTR loci, even with crude measurements on allele sizes, we show that the absolute proportional bias is generally below the coefficient of variation of the direct estimates.

Poly(ADP)-ribose polymerase and susceptibility to systemic lupus erythematosus and primary antiphospholipid syndrome: comment on the article by Delrieu et al

Several genome-wide scans for systemic lupus ery-thematosus (SLE) susceptibility genes have shown linkage to aregion on human chromosome lq41-42 (1–3). Poly(ADP-ribose) polymerase (PARP) is one of the candidates in thisregion implicated by a transmission disequilibrium study of 124multiethnic (primarily Caucasian) SLE families, suggestingthat PARP alleles may be (or be close to) the SLE suscepti-bility gene within lq41-q42 (4). Therefore, we read withinterest the article by Delrieu et al (5) reporting a lack ofassociation of PARP alleles with SLE among French Cauca-sians. Our data described below suggest that PARP alleles maybe in linkage disequilibrium with an SLE susceptibility gene.The incidence of SLE in African Americans is 2–4times greater than that in Caucasians (6). Our study usedbanked DNA obtained from consecutive African AmericanSLE patients (n 5 91) at the Division of Rheumatologyand Immunogenetics, University of Texas–Houston MedicalSchool and from normal controls (n 5 53) recruited fromamong medical center personnel. All SLE patients fulfilledthe American College of Rheumatology criteria for thedisease (7).Consistent with the findings reported by Delrieu et al(5), no specific PARP promoter allele was found to besignificantly associated with SLE or with any subset of SLE(patients stratified by the presence of lupus nephritis, anti–double-stranded DNA [by

A discrete-time, multi-type generational inheritance branching process model of cell proliferation

Mammalian cell populations, such as tumors, may contain subpopulations differing in parameters such as cell lifetimes, even if the populations are derived from single cells. The mode of inheritance of cell lifetimes has previously been the subject of experimental and mathematical investigation. To obtain data on cell lifetimes over more cell generations then previously available, Axelrod et al. [Cell Prolif. 26:235-249(1988)] measured the number of cells in primary colonies and secondary colonies derived form the primary colonies. The experimental results indicated large variance of cells per colony and highly significant correlations between the numbers of cells in primary and secondary colonies. To mathematically model these results we derive, for previously uninvestigated multi-type Galton-Watson branching process models, the covariance of the cell counts in the primary and secondary colonies. As a result, we are able to successfully model the data with two subpopulations having differing proliferation rates, in which the proliferation rate of a daughter cell is primarily determined by the proliferation rate of its mother. Interestingly, simulations display a trade-off between high values of variances and correlation coefficients. The values obtained from experiment are located on the boundary of the region attainable by simulation.