Minttu Hedman

Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs.

A number of applications of analysis of human Y-chromosome microsatellite loci to human evolution and forensic science require reliable estimates of the mutation rate and knowledge of the mutational mechanism. We therefore screened a total of 4,999 meioses from father/son pairs with confirmed paternity (probability >/=99. 9%) at 15 Y-chromosomal microsatellite loci and identified 14 mutations. The locus-specific mutation-rate estimates were 0-8. 58x10-3, and the average mutation rate estimates were 3.17x10-3 (95% confidence interval [CI] 1.89-4.94x10-3) across 8 tetranucleotide microsatellites and 2.80x10-3 (95% CI 1.72-4.27x10-3) across all 15 Y-chromosomal microsatellites studied. Our data show a mutational bias toward length increase, on the basis of observation of more repeat gains than losses (10:4). The data are in almost complete agreement with the stepwise-mutation model, with 13 single-repeat changes and 1 double-repeat change. Sequence analysis revealed that all mutations occurred in uninterrupted homogenous arrays of >/=11 repeats. We conclude that mutation rates and characteristics of human Y-chromosomal microsatellites are consistent with those of autosomal microsatellites. This indicates that the general mutational mechanism of microsatellites is independent of recombination.

A Comprehensive Survey of Human Y-Chromosomal Microsatellites

We have screened the nearly complete DNA sequence of the human Y chromosome for microsatellites (short tandem repeats) that meet the criteria of having a repeat-unit size of > or = 3 and a repeat count of > or = 8 and thus are likely to be easy to genotype accurately and to be polymorphic. Candidate loci were tested in silico for novelty and for probable Y specificity, and then they were tested experimentally to identify Y-specific loci and to assess their polymorphism. This yielded 166 useful new Y-chromosomal microsatellites, 139 of which were polymorphic, in a sample of eight diverse Y chromosomes representing eight Y-SNP haplogroups. This large sample of microsatellites, together with 28 previously known markers analyzed here--all sharing a common evolutionary history--allowed us to investigate the factors influencing their variation. For simple microsatellites, the average repeat count accounted for the highest proportion of repeat variance (approximately 34%). For complex microsatellites, the largest proportion of the variance (again, approximately 34%) was explained by the average repeat count of the longest homogeneous array, which normally is variable. In these complex microsatellites, the additional repeats outside the longest homogeneous array significantly increased the variance, but this was lower than the variance of a simple microsatellite with the same total repeat count. As a result of this work, a large number of new, highly polymorphic Y-chromosomal microsatellites are now available for population-genetic, evolutionary, genealogical, and forensic investigations.

Forensic osteological investigations in Kosovo

A team of Finnish forensic experts performed investigations of alleged mass graves in Kosovo under the mandate of the European Union (EU). Human skeletal remains from two locations were examined. The remains contained three almost complete skeletons, and individual bones and bone fragments, part of which were burned. Injuries, pathological changes, and findings for identification purposes were examined and documented using standard methods of forensic pathology and osteology. Gunshot injuries were found in some cases, but reliable determination of the cause and manner of death was not possible. A discrepancy arose between the number of victims reported in information received from the presiding district court, and results of the investigations. The estimation of the minimum number of victims was mostly acquired by DNA analysis.

Discrimination power of Investigator DIPplex loci in Finnish and Somali populations

In this study, the suitability of the Investigator DIPplex insertion/deletion polymorphism (indel) kit for forensic casework was assessed through the genotyping of 151 Finns and 175 Somalis. Allele frequency and heterozygosity (H) of this 30-indel marker set were determined, and forensic efficacy was evaluated through estimation of discrimination power (DP), match probability (MP), typical paternity index (TPI), power of paternity exclusion (PE), and polymorphic information content (PIC). A high level of discrimination power was observed for the marker set in both sample groups (CDP>0.9999). East-west population substructure found previously in uniparental markers within Finland was not evident for this autosomal set (E-W F(ST)=0.003). High exclusion probability and low subdivision together demonstrate that these markers are well-suited for identification of individuals in Finland. However, values for typical paternity index and power of paternity exclusion were low (TPI range Finns=0.750-1.190, PE=0.996; TPI Somalis=0.680-1.090, PE=0.986) in comparison to standard STR sets, and thus indels are not recommended for use in paternity or kinship investigations, except as a supplement to other more powerful tools.

Analysis of 9p24 and 11p12-13 regions in autism spectrum disorders: rs1340513 in the JMJD2C gene is associated with ASDs in Finnish sample.

Objective Autism spectrum disorders (ASD) often show obsessive repetitive symptoms that are characteristic to obsessive-compulsive disorder (OCD). Aberrant glutamate function has been suggested to a risk for both ASDs and OCD. Considering the common metabolic pathway and recent results from association studies both in OCD and ASDs, a question, whether there is common molecular background in ASDs and OCD, was raised. Methods Ten single nucleotide polymorphisms (SNPs) at 9p24 and 11p12-p13 containing glutamate transporter genes SLC1A1 and SLC1A2 and their neighboring regions in 175 patients with ASDs and 216 controls of Finnish origin were analyzed using real-time-PCR or direct sequencing. Results The strongest association was detected with rs1340513 in the JMJD2C gene at 9p24.1 (P=0.007; corrected P=0.011) that is the same SNP associated with infantile autism (P=0.0007) in the autism genome project consortium (2007). No association was detected at 11p12-p13 with ASD. Interestingly, the strongest association in OCD has been found at rs301443 (P=0.000067) residing between SLC1A1 and JMJD2C at 9p24. Conclusion In summary, our results give evidence for a possible common locus for OCD and ASDs at 9p24. We speculate that the area may represent a special candidate region for obsessive repetitive symptoms in ASDs.

X-STR diversity patterns in the Finnish and the Somali population

Autosomal and Y-chromosomal STR markers have been routinely used in kinship analyses already for over a decade, augmented by mitochondrial DNA in more complex cases questioning the maternal relationships of the samples. Recently, a commercial X-chromosome typing kit Mentype Argus X-8 was introduced to supplement the existing forensic toolkit. In this study, X-STR allele frequencies and population diversity indices in two ethnic groups, the Finnish and the Somali, are reported. Several previously unreported alleles and features in the allelic distribution were observed, some of which were further investigated with a small set of family data. Most notably, several alleles showed significant frequency differences between sexes, yet no obvious explanation for this discrepancy was found. As a demonstration of X-chromosome analysis in practice, we describe two family reunion cases, where the X-STR data was successfully utilized.

High degree of Y-chromosomal divergence within Finland—forensic aspects

Among the Finns, the levels of autosomal STR and mtDNA variation have been reported to be relatively high and evenly distributed throughout the country. In contrast, the Y-STR variation is markedly lower than observed in most other European populations, showing notable geographical substructure within Finland. There are striking interregional differences--the western, middle and eastern parts of Finland segregate clearly, with phiST values comparable to the highest divergences among European populations. The low Y-STR diversity reduces the discriminative power of Y-chromosomal markers among Finns, and, furthermore, the geographical substructure complicates the assessment of profile probabilities in forensic settings. Here, the Y-STR diversity pattern in Finland is for the first time evaluated from the forensic viewpoint.

Factors affecting the STR amplification success in poorly preserved bone samples

BackgroundFactors affecting the success of short tandem repeat (STR) amplification of poorly preserved samples are generally known, but as of yet, they have seldom been systematically assessed. Using two different maximum likelihood-based methods, the relative importance of DNA quantity, degradation and inhibition in STR genotyping was studied with DNA extracts from a set of old bone samples. First, the effects of different factors related to PCR amplification were estimated with a generalized linear mixed model. Second, error rates of allelic drop-out and drop-in were estimated on the basis of the frequency and nature of mismatches between replicates.ResultsIn autosomal STR analyses, the most important factor was the DNA quantity, followed by the degradation, whereas in Y-chromosomal STR analysis, the most important factor was the degradation. Inhibition was a minor concern in STR analyses of poorly preserved bones.ConclusionsThe success of PCR amplification depends largely on the template DNA quality (amount and degradation), but these problems can be partly compensated for by different primer design and amplification chemistry. Consequently, the relative roles of the compromising factors differ according to the kit used.

Typing of XY (male) genotype from malignant neoplastic tissue by the amelogenin-based sex test

DNA profiling of a cancer tissue can be problematic because of genomic instability. Here we have analyzed gastrointestinal cancer specimens from 46 males, of which seven (15%) showed aberrations in determination of gender by the widely used amelogenin test. The X-type amelogenin allele in all cases remained intact. All male tumor samples showing frequent autosomal loss of heterozygosity had a decreased signal of the Y allele from the amelogenin marker. When tested with an alternate set of primers for the amelogenin locus, the Y-type allele showed loss of heterozygosity in the same seven cases. However, when amplified with 15 Y-specific STR primers, all the cancerous tissue Y chromosomes seemed to be intact. These results indicate when malignant neoplastic tissue specimens are used, that amelogenin-based gender determination should be carefully interpreted.

Long D13S317 variant allele: A cautionary case report

Exclusion at locus D13S317 between a father and child was observed in a kinship case, which at first glance appeared as a silent allele. However, a closer inspection using three commercial kits showed that the observed pattern is due to a long variant allele overlapping with different loci in different kits. Sequencing of the variant revealed a duplication within D13S317, that had also created an additional binding site for short amplicon reverse primer. If ignored, genotyping results including this variant may be wrongly interpreted.