Determination of sibship by PCR-amplified short tandem repeat analysis in Taiwan

Development of a new screening method for faster kinship analyses in mass disasters: a proof of concept study

Kinship analysis in forensics is based on the calculation of the respective kinship indices. However, this calculation is only possible when the subject under identification has been associated with a particular population, whose allele frequency data is available for the particular set of STR markers used in the forensic practices. In the case of mass disasters, where a large number of individuals are to be identified, gathering the population frequency data and calculating the kinship indices can be an intricate process which requires a lot of time and huge resources. The new method of allele matching cut off score (AMCOS) developed in this study is based on the allele sharing approach. This approach simply refers to the number of shared alleles (1 or 2) between the two individuals; also known as identical by state (IBS) alleles which might have been inherited from a recent common ancestor in which the alleles are identical by descendent (IBD). In case of mass disasters, this method can be used to narrow down the number of pairs (dead and alive) to be matched for kinship without using the allele frequency data. The results obtained from this method could further be confirmed by LR based method, which uses the allele frequency data of the respective population of the pairs being tested for kinship. AMCOS method has been tested for its sensitivity, specificity and various other statistical parameters and has shown promising values for the same in various types of kinship analyses. This ascertains the authenticity and potential use of this method in forensic practice but only after its validation in a larger sample size. AMCOS method has been tested on siblings and grandparent-grandchildren by using autosomal and X-STR markers both, as the reference samples from the parents cannot always be available for the identification. The present study also compared the results shown by the autosomal and X-STR markers in siblings and grandparent-grandchildren identification, thereby suggesting the use of better set of markers on the basis of obtained values of various statistical parameters.

Evaluation of the allele-sharing approach, known as the IBS method, in kinship analysis

To infer relatedness from genetic data based on short tandem repeats, the exact method, in which shared allele frequencies are applied to relevant equations, has been conventionally used. An alternative approach is the IBS method that is based on the number of shared alleles between individuals. In the present study, the performance of the IBS method in pairwise kinship analysis was compared with the exact method using simulated data of 10,000 genotype pairs for 15 loci in the ABI Identifiler system. The likelihood ratio in allele-sharing of zero, one and two was calculated from joint probabilities based on allele frequencies of the Japanese population. Whereas the IBS method generally produced lower values of combined indices, smaller deviations of the distributions were evident. The threshold for identification of full siblings relative to non-relatives was comparable with that of the exact method, indicating that both inference powers were almost identical. The likelihood ratio in the IBS method depends on the heterozygosity at a locus, and heterozygosities of the 15 loci were consistent across various population groups, particularly in East Asians. The convenience of fixed LR values in the IBS method is beneficial for cases with uncertain allele frequencies and rare alleles.

Determination of combined sibship indices "gray zone" using 15 STR loci for central Bosnian human population

In our previous population studies of Bosnia and Herzegovina human population, we have used autosomal STR, Y-STR, and X-STR loci, as well as Y-chromosome NRY biallelic markers. All obtained results were included in Bosnian referent database. In order of future development of applied population molecular genetics researches of Bosnia and Herzegovina human population, we have examined the effectiveness of 15 STR loci system in determination of sibship by using 15 STR loci and calculating different cut-off points of combined sibship indices (CSI) and distribution of sharing alleles. From the perspective of its application, it is very difficult and complicated to establish strict CSI cut-off values for determination of the doubtless sibship. High statistically significant difference between the means of CSI values and in distribution of alleles sharing in siblings and non-siblings was noticed (P < 0.0001). After constructing the "gray zone", only one false positive result was found in three CSI cut-off levels with the highest percent of determined sibship/non-sibship at the CSI = 0.067, confirming its practical benefit. Concerning the distribution of sharing alleles, it is recommended as an informative estimator for its usage within Bosnia and Herzegovina human population.

Mutations and polymorphisms in hemoglobin genes and the risk of pulmonary hypertension and death in sickle cell disease

Pulmonary hypertension is a common complication of sickle cell disease (SCD) and a risk factor for early death. Hemolysis may participate in its pathogenesis by limiting nitric oxide (NO) bioavailability and producing vasculopathy. We hypothesized that hemoglobin mutations that diminish hemolysis in SCD would influence pulmonary hypertension susceptibility. Surprisingly, coincident alpha-thalassemia (Odds Ratio [OR]=0.95, 95% CI=0.46-1.94, P=NS) was not associated with pulmonary hypertension susceptibility in homozygous SCD. However, pulmonary hypertension cases were less likely to have hemoglobin SC (OR=0.18, 95% confidence interval [CI]=0.06-0.51, P=0.0005) or Sbeta(+) thalassemia (OR=0.25, 95% CI=0.06-1.16, P=0.10). These compound heterozygotes may be protected from pulmonary hypertension because of reduced levels of intravascular hemolysis, but develop this complication at a lower rate possibly due to the presence of non-hemolytic risk factors such as renal dysfunction, iron overload and advancing age. Despite this protective association, patients with SC who did develop pulmonary hypertension remained at significant risk for death during 49 months of follow-up (Hazard Ratio=8.20, P=0.0057).

Hair follicle: a reliable source of recipient origin after allogeneic hematopoietic stem cell transplantation

Blood, buccal swab and hair follicles are among the most commonly used sources for forensic science, parentage testing and personal identification. A total of 29 patients who have had a sustained engraftment from 15 months to 21.5 years after allogeneic hematopoietic stem cell transplantation (HSCT) without rejection, relapse or chronic GVHD involving oral mucosa were enrolled for a chimerism study. PCR-amplified short tandem repeat analyses were conducted per patient every 3 months for at least three consecutive times. The results for blood were all donor type except one who had a mixed chimerism, 14.5 years after receiving a transplant for lymphoma. As for buccal swab, mixed chimerism ranging from 10 to 96% donor origin was noted for 28 recipients except the one who had mixed chimerism of blood and retained total recipient type. In contrast, hair follicles were 100% recipient type for the entire group. It is concluded that the hair follicle is devoid of adult stem cell plasticity and may serve as a reliable source of recipient's origin when pre-transplant DNA fingerprinting or reference DNA is not available for people who have successfully received allogeneic HSCT while in need of a personal identification.

A grey zone approach for evaluation of 15 short tandem repeat loci in sibship analysis: A pilot study in Indian subjects

The evaluation of 15 STR loci Applied Biosystems Identifiler kit for sibship determination in Indian subjects is reported. Cumulative sibship indices (CSIs) calculated following standard methods in sibling pairs and non-sibling pairs, showed mean values comparable to other reports. Mean CSI value in sibling group was higher than in corresponding non-sibling group. Moderately high value of CSI in one of the non-sibling pairs and a very low likelihood ratio favoring non-relatedness in a known sibling pair did not allow binary decision about sibship status. To deal with this problem a grey zone approach has been applied to sibship test. It is concluded that the 15 loci STR kit can be reliably used for inferring sibship between pairs of individuals by defining a grey zone of a sibship test as an area of likelihood ratio values where the discriminatory performance is insufficient.

Mixed chimerism and graft failure following conditioning with the fludarabine and cyclophosphamide nonablative regimen; conversion to full donor chimerism

Twenty-one patients with hematologic malignancies were treated with the fludarabine (120-125 mg/m(2)) and cyclophosphamide (120 mg/kg) nonmyeloablative conditioning regimen. Graft versus host disease (GVHD) and graft rejection prophylaxis was with tacrolimus and mycophenolate mofetil. Thirteen of the 21 patients (62%) had mixed chimerism (< or = 90% donor cells) at day 60 and 11 (52%) of these patients had mixed chimerism which persisted until day 100. Immunosuppression was discontinued in 12 of 13 patients and two of them converted to full chimerism by day 100. Eight patients received a donor lymphocyte infusion (DLI) and five of them converted to full donor chimerism with DLI alone. Two patients were given GM-CSF in addition to a DLI with conversion to full donor chimerism. Three patients (14%) had graft failure requiring a second transplant using fludarabine (125 mg/m(2)) and melphalan (140 mg/m(2)). With a median followup of 2.8 years, 15 patients are alive - one with disease and 14 with no disease. Two patients died of acute GVHD, one of chronic GVHD, and three due to progressive disease. We conclude that the nonmyeloablative fludarabine/cyclophosphamide regimen results in a significant incidence of mixed chimerism and graft rejection but is well tolerated. We suggest a more intense regimen, such as fludarabine and melphalan, be used in patients with a high risk of early disease progression to establish early engraftment and graft versus tumor effect.

Y-chromosome short tandem repeats analysis to complement paternal lineage study: a single institutional experience in Taiwan

BACKGROUND

Highly polymorphic autosomal short-tandem-repeat (STR) analysis can be useful in most kinship testing. Y-chromosome-specific STRs, in contrast, have been increasingly applied for the verification of equivocal paternal genetic transmissions.

STUDY DESIGN AND METHODS

A total of 338 unrelated males were first typed for the 9-loci Y-STR European minimal haplotype (minHt). Samples with haplotypes that were found at least two times were subject to further study by a commercially available 17-Y-STR multiplex set (AmpFlSTR Yfiler). A separate clinical study for 113 various kinship identifications of male genetic transmission were then conducted by a panel consisting of 18 autosomal STRs and complemented by both Y-STR multiplex sets and their respective results compared.

RESULTS

For the 338 individuals, a total of 270 haplotypes were identified after the minHt study, of which 234 were unique. Among the rest of the 104 samples, AmpFlSTR Yfiler identified 82 other unique haplotypes. Altogether, 324 different haplotypes were observed; 316 (97.5%) were unique whereas 8 were shared by two to seven times. The haplotype diversities for the minHt and the AmpFlSTR Yfiler were 99.75 and 99.96 percent, respectively, whereas the powers of discrimination (PDs) were 79.88 and 95.86 percent, respectively. Despite a lower PD for minHt, there was no discrepancy on the clinical setting for personal identification between the two Y-STR sets in an allegedly true male lineage transmission involving 66 cases with 24 father-son, 19 siblings, 9 uncle-nephew, 8 grandfather-grandson, 3 cousins, and 3 half-siblings. For 47 other cases with a false allegation of paternity, exclusion was made for all without ambiguity by either Y-STR panel.

CONCLUSION

The 9-loci minHt Y-STR set is adequate to complement conventional autosomal STRs for kinship studies where Y-lineage transmission is concerned.

Genetic relatedness analysis: modern data and new challenges

Individuals who belong to the same family or the same population are related because of their shared ancestry. Population and quantitative genetics theory is built with parameters that describe relatedness, and the estimation of these parameters from genetic markers enables progress in fields as disparate as plant breeding, human disease gene mapping and forensic science. The large number of multiallelic microsatellite loci and biallelic SNPs that are now available have markedly increased the precision with which relationships can be estimated, although they have also revealed unexpected levels of genomic heterogeneity of relationship measures.

Determination of twin zygosity using a commercially available STR analysis of 15 unlinked loci and the gender-determining marker amelogenin – a preliminary report

BACKGROUND

The aim of this preliminary study was to estimate the accuracy of the zygosity determination in twin pregnancies.

METHODS

Seventy-three sets of twin pregnancies were enrolled in this study, including 48 sets of twins resulting from assisted reproductive techniques (ART) and 25 sets of spontaneously conceived twins. Determination of zygosity was made by PCR-amplified short tandem repeat (STR) analysis with a commercially available panel, comprising 15 autosomal, codominant, unlinked loci and the gender-determining marker, amelogenin. Monozygotic (MZ) twins were determined when all these unlinked loci and the gender-determining marker were identical. Chorionicity and placenta were examined after delivery of the newborns to check their relationships to the twin zygosities.

RESULTS

Three of 48 (6.25%) sets of twins produced by ART and 18 of 25 (72%) sets of spontaneously conceived twins were MZ. Monozygosity could be evaluated based on 'like sex' in spontaneously conceived twins, because they had a greater incidence of MZs than those produced by artificial reproductive techniques. The MZ prediction rate was 78.6%, and the overestimated rate was 21.4% if the monochorionic like-sexed twins (LST) had a grossly single placenta. The underestimated rate of MZs was 26.7% when the dichorionic LST had apparently separate placentas.

CONCLUSION

With the DNA-based 15 STR analysis amplified in a multiplex PCR, the determination of the zygosity in multifetal pregnancies is not only cost and time saving but also yields greater sensitivity and precision than conventional methods.

Advances ofcapillary electrophoresis in clinical and forensic analysis (1999-2000)

In this paper, capillary electrophoresis in clinical and forensic analysis is reviewed on the basis of the literature of 1999, 2000 and the first papers in 2001. An overview of progress relevant examples for each major field of application, namely (i) analysis of drug seizures, explosives residues, gunshot residues and inks, (ii) monitoring of drugs, endogenous small molecules and ions in biofluids and tissues, (iii) general screening for serum proteins and analysis of specific proteins (carbohydrate deficient transferrin, alpha1-antitrypsin, lipoproteins and hemoglobins) in biological fluids, and (iv) analysis of nucleic acids and oligonucleotides in biological samples, including oligonucleotide therapeutics, are presented.