European Council of Legal Medicine (ECLM) on-site inspection forms for forensic pathology, anthropology, odontology, genetics, entomology and toxicology for forensic and medico-legal scene and corpse investigation: the Parma form.

Further to a previous publication by the European Council of Legal Medicine (ECLM) concerning on-site forensic and medico-legal scene and corpse investigation, this publication provides guidance for forensic medical specialists, pathologists and, where present, coroners' activity at a scene of death inspection and to harmonize the procedures for a correct search, detection, collection, sampling and storage of all elements which may be useful as evidence, and ensure documentation of all these steps. This ECLM's inspection form provides a checklist to be used on-site for the investigation of a corpse present at a crime or suspicious death scene. It permits the collection of all relevant data not only for the pathologist, but also for forensic anthropologists, odontologists, geneticists, entomologists and toxicologists, thus supporting a collaborative work approach. Detailed instructions for the completion of forms are provided.

Global genetic variation of select opiate metabolism genes in self-reported healthy individuals.

CYP2D6 is a key pharmacogene encoding an enzyme impacting poor, intermediate, extensive and ultrarapid phase I metabolism of many marketed drugs. The pharmacogenetics of opiate drug metabolism is particularly interesting due to the relatively high incidence of addiction and overdose. Recently, trans-acting opiate metabolism and analgesic response enzymes (UGT2B7, ABCB1, OPRM1 and COMT) have been incorporated into pharmacogenetic studies to generate more comprehensive metabolic profiles of patients. With use of massively parallel sequencing, it is possible to identify additional polymorphisms that fine tune, or redefine, previous pharmacogenetic findings, which typically rely on targeted approaches. The 1000 Genomes Project data were analyzed to describe population genetic variation and statistics for these five genes in self-reported healthy individuals in five global super- and 26 sub-populations. Findings on the variation of these genes in various populations expand baseline understanding of pharmacogenetically relevant polymorphisms for future studies of affected cohorts.

Temporal variation in coat colour (genotypes) supports major changes in the Nordic cattle population after Iron Age.

Variation in coat colour genotypes of archaeological cattle samples from Finland was studied by sequencing 69 base pairs of the extension locus (melanocortin 1-receptor, MC1R) targeting both a transition and a deletion defining the three main alleles, such as dominant black (E(D) ), wild type (E(+) ) and recessive red (e). The 69-bp MC1R sequence was successfully analysed from 23 ancient (1000-1800 AD) samples. All three main alleles and genotype combinations were detected with allele frequencies of 0.26, 0.17 and 0.57 for E(D) , E(+) and e respectively. Recessive red and dominant black alleles were detected in both sexes. According to the best of our knowledge, this is the first ancient DNA study defining all three main MC1R alleles. Observed MC1R alleles are in agreement with calculated phenotype frequencies from historical sources. The division of ancient Finnish cattle population into modern Finnish breeds with settled colours was dated to the 20th century. From the existing genotyped populations in Europe (43 breeds, n = 2360), the closest match to ancient MC1R genotype frequencies was with the Norwegian native multicoloured breeds. In combined published genotype data of ancient (n = 147) and genotypes and phenotypes of modern Nordic cattle (n = 738), MC1R allele frequencies showed temporal changes similar to neutral mitochondrial DNA and Y-chromosomal haplotypes analysed earlier. All three markers indicate major change in genotypes in Nordic cattle from the Late Iron Age to the Medieval period followed by slower change through the historical periods until the present.

Post-mortem analysis of lactate concentration in diabetics and metformin poisonings.

Lactate is produced in carbohydrate metabolism under anaerobic conditions. Lactic acidosis occurs when the production of lactate exceeds its removal. In post-mortem (PM) context, the lactic acidosis is difficult to interpret due to unknown pathophysiological factors prior to death and PM changes that may affect the lactate levels. We evaluated 1865 medico-legal autopsy cases where the quantitation of glucose, lactate, and ketone bodies was performed as a part of the cause of death (CoD) investigation. Lactate was shown to ascend in a logarithmic manner as the PM interval increased until a plateau was achieved approximately after 8-10 days PM, and the elevation was caused mainly by PM changes. The lactate level was higher than the mean in cases where the CoD was diabetes mellitus type 2 (DM2) or metformin poisoning. Although there was a correlation between metformin and lactate levels, our findings suggest the DM2 and its complications were the cause for elevated lactate levels rather than metformin, since the lactate levels were similar in DM2-associated deaths where no metformin was detected. Elevated lactate levels in PM samples rather referred to metabolic disturbances often caused by DM2. An assay to detect D-lactate in PM samples was described.

What really happened with pneumonia mortality in Finland in 2000-2008?: a cohort study.

This cohort study examines trends in pneumonia mortality in Finland and the effects of a WHO recommendation restricting the registering of pneumonia as the underlying cause of death (COD) for several chronic diseases. All cases having pneumonia in any COD fields in 2000-2008 were extracted from the COD statistics. We examined trends in underlying-cause pneumonia mortality where pneumonia was also the immediate COD. Results are presented as age-specific and age-standardized rates. In the study period 2000-2008, there were 90 626 deaths with pneumonia in COD fields, while the underlying-cause pneumonia mortality rate decreased from 32 to 6/100 000 person-years. Immediate-cause pneumonia was less often chosen as underlying-cause towards 2008 suggesting an effect from changing coding practices. Changes in coding practices need to be considered when comparing different countries or time periods in pneumonia mortality.

The genetical archaeology of the human genome.

Palaentology and archaeology are disciplines that traditionally deal with the reconstruction of human origins and history. Recently, however, molecular genetics has come to make increasing contributions to this area. In particular, several data sets indicate that variation of the human gene pool originated in Africa within the last 200,000 years. Furthermore, the study of DNA sequences allows the detection of expansions in population size. Here we briefly summarize and exemplify how DNA sequences can be used to reconstruct the history of populations.

Minisatellite diversity supports a recent African origin for modern humans.

In a study of human diversity at a highly variable locus, we have mapped the internal structures of tandem-repetitive alleles from different populations at the minisatellite MS205 (D16S309). The results give an unusually detailed view of the different allelic structures represented on modern human chromosomes, and of the ancestral relationships between them. There was a clear difference in allelic diversity between African and non-African populations. A restricted set of allele families was found in non-African populations, and formed a subset of the much greater diversity seen on African chromosomes. The data strongly support a recent African origin for modern human diversity at this locus.

Homozygosity for a HERG potassium channel mutation causes a severe form of long QT syndrome: identification of an apparent founder mutation in the Finns.

OBJECTIVES: We studied the clinical characteristics and molecular background underlying a severe phenotype of long QT syndrome (LQTS). BACKGROUND: Mutations of cardiac ion channel genes cause LQTS, manifesting as increased risk of ventricular tachycardia and sudden death. METHODS: We studied two siblings showing prolonged QT intervals corrected for heart rate (QTc), their asymptomatic parents with only marginally prolonged QTc intervals and their family members. The potassium channel gene HERG was screened for mutations by deoxyribonucleic acid sequencing, and the electrophysiologic consequences of the mutation were studied in vitro using the whole-cell patch-clamp technique. RESULTS: A novel missense mutation (L552S) in the HERG channel, present in the homozygous state in the affected siblings and in the heterozygous state in their parents, as well as in 38 additional subjects from six LQTS families, was identified. One of the homozygous siblings had 2:1 atrioventricular block immediately after birth, and died at the age of four years after experiencing unexplained hypoglycemia. The other sibling had an episode of torsade de pointes at the age of two years. The mean QTc interval differed significantly (p < 0.001) between heterozygous symptomatic mutation carriers (500 +/- 59 ms), asymptomatic mutation carriers (452 +/- 34 ms) and noncarriers (412 +/- 23 ms). When expressed in vitro, the HERG-L552S formed functional channels with increased activation and deactivation rates. CONCLUSIONS: Our data demonstrate that homozygosity for a HERG mutation can cause a severe cardiac repolarization disorder without other phenotypic abnormalities. Absence of functional HERG channels appears to be one cause for intrauterine and neonatal bradycardia and 2:1 atrioventricular block.

Bones hold the key to DNA virus history and epidemiology.

DNA in human skeletal remains represents an important historical source of host genomic information and potentially of infecting viruses. However, little is known about viral persistence in bone. We searched ca. 70-year-old long bones of putative Finnish casualties from World War II for parvovirus B19 (B19V) DNA, and found a remarkable prevalence of 45%. The viral sequences were exclusively of genotypes 2 (n = 41), which disappeared from circulation in 1970´s, or genotype 3 (n = 2), which has never been reported in Northern Europe. Based on mitochondrial and Y-chromosome profiling, the two individuals carrying B19V genotype 3 were likely from the Soviet Red Army. The most recent common ancestor for all genotypes was estimated at early 1800s. This work demonstrates the forms of B19V that circulated in the first half of the 20(th) century and provides the first evidence of the suitability of bone for exploration of DNA viruses.

Glucose metabolism in identical twins discordant for obesity. The critical role of visceral fat.

Obesity, especially intraabdominally deposited fatness, is associated with reduced insulin sensitivity. However, it is not well established whether this association is confounded by genetic factors. We studied 23 monozygous twin pairs (14 female, 9 male), 33-59 yr old, who had, on the average, 18 kg intrapair difference in body weight. A 75-g oral glucose tolerance test with glucose and insulin measurements at 30-min intervals was performed, and fat distribution was determined with magnetic resonance imaging. The pairs were divided into two groups by the gender-specific median of the abdominal visceral fat area (AVF) in the obese co-twins. In the high-AVF pairs, the mean area under curve (AUC) for glucose (mmol x min/L) was 758 vs. 968 (P = 0.001), AUC for insulin (mU x min/L) was 4320 vs. 8741 (P = 0.001), and insulin sensitivity index (mg x L x L/mmol x mU x min) was 71.5 vs. 45.9 (P < 0.001) in the lean and obese co-twins, respectively. In the low AVF pairs, the mean AUC for glucose was 669 vs. 706 (not significant), AUC for insulin was 3323 vs. 4241 (not significant), and the sensitivity index was 85.2 vs. 73.7 (P = 0.04) in the lean and obese co-twins, respectively. In subjects who are genetically identical but who are discordant for body mass, only those who differ most in visceral fat level are characterized by major alterations in insulin sensitivity and glucose tolerance.

Analysis of mtDNA HVRII in several human populations using an immobilised SSO probe hybridisation assay.

Several populations were typed for the hypervariable region II (HVRII) of the mitochondrial DNA (mtDNA) control region using immobilised sequence-specific oligonucleotide (SSO) probes. A total of 16 SSO probes was used to type 1081 individuals from eight different ethnic groups (African Americans, Somali, US Europeans, US Hispanics, Bosnians, Finns, Saami and Japanese). Data was compared with already published sequence data by analysis of principal components, genetic distances and analysis of the molecular variance (AMOVA). The analyses performed group the samples in several clusters according to their geographical origins. Most of the variability detected is assigned to differences between individuals and only 7% is assigned to differences among groups of populations within and between geographical regions. Several features are patent in the samples studied: Somali, as a representative East African population, seem to have experienced a detectable amount of Caucasoid maternal influence; different degrees of admixture in the US samples studied are detected; Finns and Saami belong to the European genetic landscape, although Saami present an outlier position attributable to a strong maternal founder effect. The technique used is a rapid and simple method to detect human variation in the mtDNA HVRII in a large number of samples, which might be useful in forensic and population genetic studies.

Experimentally observed germline mutations at human micro- and minisatellite loci.

We have analysed close to 30,000 human germline transmission events at five microsatellite loci (D3S1359, HumTH01, HumvWA, HumTPO and HumFES) and four minisatellite loci (D1S80, ApoB, Col2A1 and D17S30). At these loci the mutation rates are similar at the microsatellite and the minisatellite loci, varying from 0.2 x 10(-3) to < 3.3 x 10(-3) and from 0.5 x 10(-3) to 1.5 x 10(-3), respectively. Interestingly, paternal mutations appeared to be dominant at the microsatellite loci, whilst maternal mutations are dominant at minisatellite loci. Based on our data, no unequivocal support for a strict strand-slippage mutation mechanism (gain or loss of a single repeat) was found, although the vast majority of the mutational events were small gains or losses of one to three repeats, and only few unequivocal large gains or losses were observed.

Population genetic comparisons among eight populations using allele frequency and sequence data from three microsatellite loci.

Eight different population samples (Moroccans, Ovambos, Papuans, Australian aborigines, Germans, Turks, Japanese and Chinese) were studied using the tetranucleotide short tandem repeat systems HumTHO1 (THO1), Hum VWFA31 (VWA) and HumACTBP2 (ACTBP2). Ten alleles were differentiated in THO1, 11 alleles in VWA and 28 alleles in ACTBP2. THO1 showed 1 bp deletions in the repeat region, VWA sequence and structure variations of the 4-bp repeat motif and ACTBP2 sequence, structure and length variations in the repeat array and deletions/insertions (1-6 bp) in the flanking regions. A phylogenetic tree was constructed (UPGMA method) leading to branches which grouped Germans and Turks, Japanese and Chinese, and Papuans and Australian aborigines.

Y chromosomal polymorphisms reveal founding lineages in the Finns and the Saami.

Y chromosomal polymorphisms were studied in 502 males from 16 Eurasian ethnic groups including the Finns, Saami (Inari Lake area and Skolt Saami), Karelians, Mari, Mokshas, Erzas, Hungarians (Budapest area and Csángós), Khanty, Mansi, Yakuts, Koryaks, Nivkhs, Mongolians, and Latvians. The samples were analysed for polymorphisms in the Y chromosome specific Alu insertion (YAP) and six microsatellites (DYS19, DYS389-I and II, DYS390, DYS392, DYS393). The populations were also screened for the recently described Tat polymorphism. The incidence of YAP+ type was highest in the Csángós and in other Hungarians (37.5% and 17.5%, respectively). In the Karelians and the Latvians it was present at approximately the same level as commonly found in other European populations, whilst absent in our further samples of Eurasian populations, including the Finns and the Saami. Aside from the Hungarians, the C allele of the Tat polymorphism was common in all the Finno-Ugric speaking populations (from 8.2% to 63.2%), with highest incidence in the Ob-Ugrian Khanty. The C allele was also found in the Latvians (29.4%). The haplotypes found associated with the Tat C allele showed consistently lower density than those associated with the T allele, indicating that the T allele is the original form. The computation of the age of the Tat C suggested that the mutation might be a relatively recent event giving a maximum likelihood estimate of 4440 years (95% confidence interval about 3140-6200 years). The distribution patterns of the 222 haplotypes found varied considerably among the populations. In the Finns a majority of the haplotypes could be assigned to two distinct groups, one of which harboured the C allele of the Tat polymorphism, indicating dichotomous primary source of genetic variation among Finnish males. The presence of a bottleneck or founding effect in the male lineages of some of the populations, namely in the Finns and the Saami, would appear to be one likely interpretation for these findings.

Golli-MBP gene in multiple sclerosis susceptibility.

Multiple sclerosis (MS) is an oligo- or polygenic disease but no specific susceptibility genes have been identified so far. In the Finnish population we have previously found evidence for linkage between MS and the myelin basic protein gene (here called Golli-MBP gene) suggesting that either Golli-MBP or another gene in its vicinity contributes to MS suceptibility. Here we have screened the Golli-MBP gene for nucleotide variations and carried out multipoint association analyses in a Finnish case-control data-set as well as in an independent data-set composed of 151 MS families from Finland and Sweden. In both data-sets we found association between MS and alleles in the 1.27 kilobase (kb) range at a tetranucleotide repeat element (TGGA)n which is located 1 kb upstream of the MBP exon 1. Haplotype analyses suggested that the MS-associated 1.27 kb alleles can be split into predisposing and non-predisposing variants and provided evidence that the candidate DNA region contributing to MS susceptibility should be located at the Golli-MBP gene within a 20-25 kb segment that was conserved in the predisposing haplotypes. These findings suggest a role for the Golli-MBP locus in MS susceptibility, at least in a subset of patients, and serve as a basis for highly focused attempts to identify predisposing mutation(s).

Amplification of reproducible allele markers for amplified fragment length polymorphism analysis.

A procedure for amplification by PCR of reproducible allele markers for amplified fragment length polymorphism (Amp-FLP) analysis is presented. We have prepared markers for the allelic products of the VNTR loci D1S80 (MCT118) and D17S30 (YNZ22) and for the hypervariable VNTR locus close to the 3' end of the apolipoprotein B gene (apoB) by re-amplifying a mixture of PCR products from individuals with known alleles. These allele markers allow precise and discrete determination of the VNTR alleles at these loci using the Amp-FLP technique that should prove suitable in forensic analyses, paternity testing and population studies.

Forensic DNA typing by the solid-phase minisequencing method.

We describe a method for DNA-typing, in which a panel of biallelic markers are detected by the solid-phase minisequencing method (Syvänen et al., 1990). This method identifies single nucleotide variations in DNA fragments amplified by the PCR. Determination of the panel of 12 markers selected in this study proved to be an efficient and reliable method for forensic identification of individuals. We also introduce a novel approach for rapid determination of allele frequencies by quantitative analysis of pooled DNA samples.

Mutations at Y-STR loci: implications for paternity testing and forensic analysis.

Knowledge about mutation rates and the mutational process of Y-chromosomal short-tandem-repeat (STR) or microsatellite loci used in paternity testing and forensic analysis is crucial for the correct interpretation of resulting genetic profiles. Therefore, we recently analysed a total of 4999 male germline transmissions from father/son pairs of confirmed paternity (probability > or = 99.9%) at 15 Y-STR loci which are commonly applied to forensics. We identified 14 mutations. Locus specific mutation rate estimates varied between 0 and 8.58 x 10(-3), and the overall average mutation rate estimate was 2.80 x 10(-3) (95% CIL 1.72 x 10(-3)-4.27 x 10(-3)). In two confirmed father/son pairs mutation at two Y-STRs were observed. The probability of two mutations occurring within the same single germline transmission was estimated to be statistically not unexpected. Additional alleles caused by insertion polymorphisms have been found at a number of Y-STRs and a frequency of 0.12% was estimated for DYS19. The observed mutational features for Y-STRs have important consequences for forensic applications such as the definition of criteria for exclusions in paternity testing and the interpretation of genetic profiles in stain analysis. In order to further enrich our knowledge of Y-STR mutations we suggest the establishment of a Y-STR mutation database and ask the forensic community for data contribution.