Screening of intracerebral hemorrhage associated allele combinations at different loci using a novel association analysis

BACKGROUND

Genetic research has progressed along with scientific and technological developments. However, it is difficult to identify frequency differences in the allele combination at cross-loci.

OBJECTIVE

The purpose of this study was to examine the relationship between the presence of specific allele combinations of short tandem repeat (STR) loci and the onset of intracerebral hemorrhage (ICH) using a novel methodology.

METHODS

DNA samples were collected from patients with ICH, who were adult population. There were a total of 51 Chinese patients (102 chromosomes), comprising 30 males and 21 females. Alleles from short tandem repeat (STR) loci were determined using the STR Profiler Plus PCR amplification kit (15 STR loci). Statistically significant differences between observed and expected frequencies of allele combinations were identified. To further determine allele combinations related to the disease, analyses of patient age at disease onset for those carrying a specific allele combination were conducted. Finally, cross-validation of the two sets of analytical results was carried out.

RESULTS

A total of 1550 pairwise combinations were obtained by computer counting, of which eight pairs of alleles showed significant differences between the observed and expected frequencies (p<0.05, from 0.006 to 0.042). The p value for the cross-validation analysis was less than 0.05 for two pairs of alleles (D13S317-11 and vWA-17, p=0.021; D7S820-13 and D2S1338-18, p=0.023).

CONCLUSIONS

The study identified each population had a unique gene distribution and that distribution followed certain rules. ICH onset may be associated with this allele combinations (D13S317-11 and vWA-17; D7S820-13 and D2S1338-18). The new methodology used in this study could enable additional discoveries pertaining to the relationship between specific allele combinations at different loci and the onset of complex diseases.

Screening of longevity-associated genes based on a comparison between dead and surviving populations

AIM

To investigate longevity-associated genes based on a comparison between dead and surviving populations.

METHODS

A total of 71 cases of dead individuals were treated as the death group, and healthy volunteers who were matched with the dead individuals based on sex and age were recruited as the survival group. Alleles of 13 CODIS STR loci were determined using the AmpFLSTR Profiler Plus PCR Amplification Kit. The cross-validation was performed based on differences between the two groups in both frequency values and ages.

RESULTS

The frequency value of the D18S51-17 alleles was significantly higher in the dead group than in the survival group (p<0.05), and the frequency value of the D2S1338-18 allele was statistically lower in the dead group than in the survival group (p<0.05). The mean age of the subjects with the D2S1338-18 allele was also significantly higher than that of the subjects without D2S1338-18, and no significant difference was observed with respect to the other three alleles.

CONCLUSIONS

The results suggest that D2S1338-18 is associated with longevity.

Novel association analysis between 9 short tandem repeat loci polymorphisms and coronary heart disease based on a cross-validation design

OBJECTIVE

To investigate genes associated with coronary heart disease (CHD) screened with a novel cross-validation design.

METHODS

On the basis of age at the onset of the first episode of CHD, stratified sampling by age (<50 years, 50-59 years, 60-69 years, 70-79 years and >80 years) was performed. Alleles of the nine CODIS STR loci including D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820, were determined using the STR Profiler Plus PCR amplification kit. Allele frequencies were compared with a control population. The mean age of patients with and without the alleles was compared. Cross-validation was based on differences in both frequency values and ages instead of adjustment procedure for multiple testing.

RESULTS

There were statistical differences in frequency values between the CHD group and the control population for three alleles, and also statistical differences in the age at first onset of CHD for two alleles; at least one allele, D21S11-28.2, was statistically different with regards to both frequency values and age. It was confirmed that D21S11-28.2 is truly related with CHD.

CONCLUSIONS

A single true CHD-related allele could be discriminated from the sampling errors through cross-validation. It appears that CHD-related genes may be located near to loci D21S11.

Decreasing amplification bias associated with multiple displacement amplification and short tandem repeat genotyping

Although multiple displacement amplification (MDA) is being used increasingly to amplify genomes, the amplification bias generated by the varphi29 polymerase can be a concern with genotyping applications. It has been noted that the bias is pronounced with small template amounts, particularly with single nucleotide polymorphism (SNP) and short tandem repeat (STR) genotyping. Bias may occur between loci, or between alleles within a locus, and may differ between sample donors at the same loci. Previous research has suggested that omitting denaturation of the template prior to amplification can reduce the observed bias significantly. Comparison of the two methods (with and without denaturation) has found that nondenaturation of template reverses the direction of bias observed between allelic pairs following MDA. By combining two MDA reactions, one denatured and one nondenatured, the bias was found to be reduced significantly, aiding copy number analysis and subsequent genotyping.

Molecular crowding increases the amplification success of multiple displacement amplification and short tandem repeat genotyping

Multiple displacement amplification (MDA) can generate large quantities of genomic DNA product from small amounts of template. We investigated the ability of MDA to amplify samples containing very small amounts of target DNA (5 pg to 1 ng) in the presence of a second, larger DNA sample for downstream short tandem repeat (STR) multiplex genotyping. We observed that STR amplification success of the minor fraction was increased in these mixed samples when compared with standard PCR only or MDA containing only the single trace DNA sample. Increased numbers of alleles were detected, with less amplification bias between loci than in single source samples undergoing the same protocol. To improve the STR genotyping accuracy, animal DNA was substituted for the additional human DNA, maintaining the increase in the number and quality of human-specific STR loci amplified. Polyethylene glycol 400, a commonly used crowding agent, was used as a replacement for the added genomic DNA in the MDA reaction and produced very similar results. Therefore, we suggest that additional DNA is acting as a molecular crowding agent during MDA. Performing MDA on trace amounts of DNA under crowded conditions results in greater numbers of alleles being amplified and more balanced amplification occurring between alleles.

Possible pitfalls in motherless paternity analysis with related putative fathers

Nowadays, more and more paternity cases are carried out investigating only child and putative father, mostly for economical or private reasons. Usually, reliable results can be obtained and the putative father can be included or ruled out with a high certainty. Considerable problems might arise when a relative of the biological father is investigated as being the putative father. In this study, we investigated 164 persons from 27 families creating artificial deficiency cases using the AmpFlSTRIdentifiler kit, which amplifies 15 STRs simultaneously. We analyzed 93 child/biological father pairs and the corresponding uncles, respectively the brothers of the biological fathers. The average paternity probability for the biological father was 99.9699% (paternity index (PI): 3321.26); only in three cases the results were under 99.9%. In five out of 125 child/uncle pairs no STR mismatches were found and paternity probabilities between 99.9726% (PI 3652) and 99.9970% (PI 33,545) were calculated. The average number of excluding loci was 3.4, but in 31.2% of the cases only zero, one or two mismatches were found. When both putative fathers were genetically typed, the biological father usually had a statistically higher paternity probability. Nevertheless, the differences between probabilities for father and uncle were only small. These results show that a reliable investigation of deficiency cases (i.e. child and putative father) seems to be more difficult than generally assumed. Especially in cases with an unknown familiar background and/or when investigating foreigners for immigration purposes, the laboratory expert should include the mother, increase the number of investigated loci or include a second method such as RFLP-analysis, some serological systems or typing of X-chromosome specific STRs to further ascertain the results.

Recent advances in the applications of CE to forensic sciences (2001–2004)

The present article reviews the applications of CE in forensic science covering the period from 2001 until the first part of 2005. The overview includes the most relevant examples of analytical applications of capillary electrophoretic and electrokinetic techniques in the following fields: (i) Forensic drugs and poisons, (ii) explosive analysis and gunshot residues, (iii) small ions of forensic interest, (iv) forensic DNA and RNA analysis, (v) proteins of forensic interest, and (vi) ink analysis.

Evaluation of allelic alterations in short tandem repeats in different kinds of solid tumors--possible pitfalls in forensic casework

Archival pathology specimens are nowadays a frequently used source in forensic identification or paternity testing, if no other material is available. A greater part of this archived material, however, consists of solid tumors known for aberrations in coding and non-coding regions of the genome. Therefore, alterations of short tandem repeats (STRs) used in forensic casework are also possible. In our study of 118 solid tumors, 46 lymph node metastases, and 16 distant metastases with the AmpFlSTR trade mark Profiler Plus PCR amplification kit comprising nine STR loci, we detected four kinds of changes between normal and tumor tissue: partial loss of one allele (pLOH), complete loss of one allele (LOH), occurrence of an additional allele and occurrence of a new allele instead of that found in normal tissue. Twenty-two percent of the tumor lesions displayed pLOH, but only in 14% one allele was completely lost. New alleles could be demonstrated in 18% of tumors, and in 8% the new allele in the tumor tissue replaced the one found in normal tissue. The changes were distributed over all nine STRs, but the STRs mostly affected were FGA, D3S1558, D18S51 and D21S11. The occurrence of new alleles in the tetra-nucleotide repeats correlated mainly with microsatellite instability in di-nucleotide and mono-nucleotide repeats. The occurrence of new alleles was most frequent in primary tumors of colon carcinomas and HNSCC metastases. In melanomas, only loss of alleles could be found. Our results demonstrate that the use of tumor tissue in forensic identification and paternity testing is questionable, especially if only tumors with known microsatellite instability are available.

STR typing of ductal adenocarcinomas of the pancreas and healthy control tissue in 18 individuals

Recently, different work groups have demonstrated that short tandem repeat (STR) typing of various tumor tissues may lead to erroneous results due to tumor microsatellite instability (MSI). This may have considerable implications for genetic profiling of tumor tissue, e.g. in paternity testing or sample individualization. To elucidate whether this is true for ductal adenocarcinomas (DAC) of the pancreas, we genetically investigated tumor and corresponding healthy tissue from 18 patients using a commercially available multiplex PCR kit commonly used in forensic laboratories. STR typing of the samples revealed no differences between tumor and healthy tissue in 17 out of 18 samples. One sample, however, showed an allele expansion at locus D21S11. In heterozygous cases, peak heights varied strongly at different loci, mocking a loss of heterozygozity. This investigation shows that even though tetranucleotide MSI in pancreatic DAC is a rare event, the interpretation of genetic profiles obtained from cancerous samples can be difficult and lead to misinterpretations.

Effects of electron-beam irradiation on buccal-cell DNA

Buccal cells were collected from 29 participants, by use of mouthwash rinses, and were split into equal aliquots, with one aliquot irradiated by electron-beam (E-beam) irradiation equivalent to the sterilizing dosage used by the U.S. Postal Service and the other left untreated. Aliquots were extracted and tested for DNA yields (e.g., TaqMan assay for quantifying human genomic DNA), genomic integrity, and amplification-based analysis of genetic variants (e.g., single-nucleotide polymorphisms [SNPs] and single tandem repeats [STRs]). Irradiated aliquots had lower median DNA yields (3.7 microg/aliquot) than untreated aliquots (7.6 microg/aliquot) (P<.0005) and were more likely to have smaller maximum DNA fragment size, on the basis of genomic integrity gels, than untreated aliquots (P<.0005). Irradiated aliquots showed poorer PCR amplification of a 989-bp beta-globin target (97% for weak amplification and 3% for no amplification) than untreated aliquots (7% for weak amplification and 0% for no amplification) (P<.0005), but 536-bp and 268-bp beta-globin targets were amplified from all aliquots. There was no detectable irradiation effect on SNP assays, but there was a significant trend for decreased detection of longer STRs (P=.01) in irradiated versus untreated aliquots. We conclude that E-beam irradiation reduced the yield and quality of buccal-cell specimens, and, although irradiated buccal-cell specimens may retain sufficient DNA integrity for some amplified analyses of many common genomic targets, assays that target longer DNA fragments (>989 bp) or require whole-genome amplification may be compromised.