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PubMed2005

Genotypic probabilities for pairs of inbred relatives.

Expressions for the joint genotypic probabilities of two related individuals are used in many population and quantitative genetic analyses. These expressions, resting on a set of 15 probabilities of patterns of identity by descent among the four alleles at a locus carried by the relatives, are generally well known. There has been recent interest in special cases where the two individuals are both related and inbred, although there have been differences among published results. Here, we return to the original 15-probability treatment and show appropriate reductions for relatives when they are drawn from a population that itself is inbred or when the relatives have parents who are related. These results have application in affected-relative tests for linkage, and in methods for interpreting forensic genetic profiles.

Breeding↗

PubMed1993

Genetic analysis using polymerase chain reaction-amplified DNA and immobilized oligonucleotide probes: reverse dot-blot typing.

The reverse dot-blot method is a simple and rapid diagnostic procedure that allows screening of sample for a variety of mutations/polymorphisms in a single hybridization reaction. Several methods of immobilizing the oligonucleotide probes are discussed. The reverse dot-blot method has several unique properties that are valuable in a diagnostic setting: (1) the typing results from a single sample can be located on a single strip. This facilitates scanning and interpretation of the probe reactivity patterns and minimizes the potential for user error. (2) The test can utilize premade typing strips. This minimizes user labor as well as error potential and allows the use of standardized reagents. (3) Unlike dot-blot/oligonucleotide typing, only the PCR product is labeled, eliminating the potential problem of probes labeled to different specific activities. This method has already been used in the areas of forensic genetic typing (the HLA-DQ alpha Amplitype test), tissue typing for transplantation (the HLA-DR beta) test, cystic fibrosis screening, as well as in a variety of research applications.

Amino Acid Sequence↗

PubMed2006

Dissection of mitochondrial superhaplogroup H using coding region SNPs.

Haplogroup H (hg H) includes about 40-50% of the West Eurasian mitochondrial DNA (mtDNA) samples investigated so far. In order to enhance discrimination within this haplogroup we selected 45 coding region SNPs that allow to ascribe samples to the main phylogenetic branches of super hg HV (that embraces hg H) and, in particular, to H sublineages with a much finer resolution than previous studies. SNP selection was carried out using the most up-to-date available literature on population and forensic genetics and extended by means of phylogenetic analysis of complete or coding region genomes (<430) and control region sequences. A meticulous inspection of the H phylogeny led us to the observation of various but uncharacterized subclades of hg H. The selected SNPs were amplified in two PCR-multiplex reactions and subsequently targeted in three single-base extension multiplex reactions. A total of 2214 West Eurasian samples were screened for hg H specific loci 2706 and 7028, of which 859 fell in hg H and were further subjected to subhaplogroup typing. We observed 35 different subhaplogroups in total, 33 of which were found at frequencies below 5%. This assay can be used as a prescreening tool in forensic casework for rapid discrimination between divergent lineages (very effective for high-volume crime cases) or as discriminatory assay, when identical hg H haplotypes were obtained by control region sequencing.

Adolescent↗

PubMed2006

Successful RNA extraction from various human postmortem tissues.

Recently, several authors described the observation that RNA degradation does not correlate with the postmortem interval (PMI), but rather with other parameters like environmental impact and the circumstances of death. Therefore, the question arose if the analysis of gene expression could be a valuable tool in forensic genetics to contribute to the determination of the cause of death. In our study, six human tissues obtained from six individuals with PMI varying between 15 and 118 h were used for total RNA extraction. Quantification was performed using a GAPDH real-time assay, and the quality of mRNA was checked by amplification of different fragment lengths of the GAPDH transcript. In our set of samples, nearly all tissues in all PMI revealed satisfactory results, while skeletal muscle, followed by brain and heart, gave the best results. No correlation between PMI and RNA degradation could be detected, as very good results were observed for all tissues from the individual with the longest PMI. The highly promising results obtained in this study raise hopes that in the near future several fields of forensic investigation may profit from additional information about gene expression patterns and their correlation with pathological findings.

Autopsy↗

PubMed1997

A dedicated internal standard in fragment length analysis of hyperpolymorphic short tandem repeats.

Some of the most polymorphic short tandem repeats (STRs) have alleles differing in size by as little as one basepair. Since sizing precision with commercially available internal standards ordinarily does not allow safe discrimination at this level, typing is accomplished through comparisons with allelic ladders run on each gel. Here we introduce the use of optimally spaced sequenced alleles as a dedicated internal standard for measurement and typing of hyperpolymorphic STRs. We have constructed such a dedicated internal standard for HUMACTBP2 ([1]; Moos and Gallwitz, EMBO I., 5 (1983) 757-761) typing, including 25 sequenced, ROX labelled HUMACTBP2 alleles spanning the size range for alleles at this locus (233-333 basepairs (bp)). Comparisons of inter-gel runs of selected alleles with this dedicated standard and the commercial GS500 internal standard demonstrate that only the presently described internal standard is suited for direct typing based on fragment length measurements only. Obvious advantages of this typing procedure are that fragment measurements are precise and in accordance with sequenced lengths, and that the typing procedure via an external allelic ladder is avoided. Sequences of the alleles used in the internal standard as well as of selected alleles for allelic ladders in two other hyperpolymorphic AAAG-repeat STRs, D11S554 (Phromchotikul et al., Hum. Mol. Genet., 3 (1991) 21) and HUMAPOA11 (Kimpton et al., PCR Methods Appl., 3 (1993) 13-22) are also presented. To allow fragment length analysis of these two STRs, five D11S554 alleles, spanning from 176 to 225 basepairs, were added to the dedicated internal standard. Performing similar comparisons as for HUMACTBP2, it is demonstrated that even if sizing accuracy is not as good as with HUMACTBP2, typing based on measured fragment size only may be achieved with both other STRs as well. Selecting different colours for the three STRs, triplex electrophoretic runs were performed of a Norwegian population database of 300 unrelated individuals. The probability that two unrelated individuals have the same type in all three STRs is 5 x 10(-7), and the combined paternity exclusion power 99.77%, indicating that this STR selection may represent a good choice for forensic genetic casework.

Base Composition↗

PubMed2005

Decision analysis in forensic science.

Forensic scientists are routinely faced with the problems of making decisions under circumstances of uncertainty (i.e., to perform or not perform a test). A decision making model in forensic science is proposed, illustrated with an example from the field of forensic genetics. The approach incorporates available evidence and associated uncertainties with the assessment of utilities (or desirability of the consequences). The paper examines a general example for which identification will be made of the decision maker, the possible actions, the uncertain states of nature, the possible source of evidence and the kind of utility assessments required. It is argued that a formal approach can help to clarify the decision process and give a coherent means of combining elements to reach a decision.

Bayes Theorem↗

PubMed2003

Mixed stains from sexual assault cases: autosomal or Y-chromosome short tandem repeats?

We analyzed forensic DNA samples from four cases of sexual assault, using the Y-chromosome-specific human DNA markers and a panel of autosomal short tandem repeats (STRs). The presence of male contribution was evaluated by the analysis of the Amelogenin locus. A panel of tetrameric Y-STR (DYS19, DYS390, DYS391, DYS392, DYS385, DYS389I and II) was used in further analysis of samples, increasing the efficiency of the forensic genetic analyses. It was possible to identify a partial or full Y-profile of the rapists in different DNA mixtures when genetic profile could not be detected by autosomal STRs. However, in the case of male/male DNA mixture, only the victim's Y-profile could be obtained because the DNA of the offenders was present in low amounts. When the mixture contained different male/male proportion of DNA, only the full profile of the major component could be detected. In cases where male/female DNA mixed stains contained a sufficient amount of male DNA, the analysis of autosomal STRs was adequate enough to identify the full profile of the rapist. Our experience shows that the main advantage of the Y-STR approach is its ability to detect the male component in the mixed stains when the DNA of the male contributor is present only in a very small amount.

Amelogenin↗

PubMed2002

[Genetic investigations in forensic medicine].

Scientific research of the last decade including the introduction of new molecular biological methods and mapping of the human genome allowed the development of a revolutionary new molecular biological approach in forensic medicine. The traditional serological methods study proteins, the new DNA analysis goes further down to study DNA structures to analyze unique individual features. The two main areas of DNA application in forensic medicine are inheritance studies and personal identification in criminal cases using biological traces. Using this new, reliable and reproducible method we can answer questions they were almost impossible in the past. This article reviews how molecular techniques used to detect genetic polymorphism in forensic medicine.

DNA↗

PubMed1996

Rapid detection of sequence polymorphisms in the human mitochondrial DNA control region by polymerase chain reaction and single-strand conformation analysis in mutation detection enhancement gels.

The article describes a rapid approach for the detection of sequence polymorphisms in the mitochondrial (mt)DNA control region that involves enzymatic amplification of each entire mtDNA control region (HV1 and HV2) and the subsequent analysis of the PCR products by single-strand conformation analysis (SSCA) in mutation detection enhancement (MDE) gels, followed by silver stain detection. HV1 and HV2 SSC reference ladders were developed to standardize the classification of the different mtDNA types. Twenty-five mtDNA types were observed among the 45 Spanish individuals analyzed: 11 types were observed in the HV1 region as compared with 10 types in the HV2 region. This mutation scanning strategy could be a promising method of potential use not only in forensic genetics but also in population and evolutionary studies.

DNA, Mitochondrial↗

PubMed2006

Unknown biological mixtures evaluation using STR analytical quantification.

Allelic quantification of STRs, where the presence of three or more alleles represents mixtures, provides a novel method to identify mixtures from unknown biological sources. The allelic stutters resulting in slightly different repeat containing products during fragment amplification can be mistaken for true alleles complicating a simple approach to mixture analysis. An algorithm based on the array of estimated stutters from known samples was developed and tuned to maximize the identification of true non-mixtures through the analysis of three pentanucleotide STRs. Laboratory simulated scenarios of needle sharing generated 58 mixture and 38 non-mixture samples that were blinded for determining the number of alleles. Through developing and applying an algorithm that additively estimates stuttering around the two highest peaks, mixtures and non-mixtures were characterized with sensitivity of 77.5, 82.7 and 58% while maintaining the high specificity of 100, 97.4 and 100 for the W, X, and Z STRs individually. When all three STRs were used collectively, the resulting sensitivity and specificity was 91.4 and 97.4%, respectively. The newly validated approach of using multiple STRs as highly informative biomarkers in unknown sample mixture analyses has potential applications in genetics, forensic science, and epidemiological studies.

Algorithms↗

PubMed2007

Sub-populations within the major European and African derived haplogroups R1b3 and E3a are differentiated by previously phylogenetically undefined Y-SNPs.

Single nucleotide polymorphisms on the Y chromosome (Y-SNPs) have been widely used in the study of human migration patterns and evolution. Potential forensic applications of Y-SNPs include their use in predicting the ethnogeographic origin of the donor of a crime scene sample, or exclusion of suspects of sexual assaults (the evidence of which often comprises male/female mixtures and may involve multiple perpetrators), paternity testing, and identification of non- and half-siblings. In this study, we used a population of 118 African- and 125 European-Americans to evaluate 12 previously phylogenetically undefined Y-SNPs for their ability to further differentiate individuals who belong to the major African (E3a)- and European (R1b3, I)-derived haplogroups. Ten of these markers define seven new sub-clades (equivalent to E3a7a, E3a8, E3a8a, E3a8a1, R1b3h, R1b3i, and R1b3i1 using the Y Chromosome Consortium nomenclature) within haplogroups E and R. Interestingly, during the course of this study we evaluated M222, a sub-R1b3 marker rarely used, and found that this sub-haplogroup in effect defines the Y-STR Irish Modal Haplotype (IMH). The new bi-allelic markers described here are expected to find application in human evolutionary studies and forensic genetics.

Black People↗

PubMed2003

Pitfalls in molecular diagnosis in a family with severe factor VII (FVII) deficiency--misdiagnosis by direct sequence analysis using a PCR product.

Molecular diagnostic tests are becoming a routine analysis in many laboratories. These modern analyses are widely used in clinical medicine, forensic, genetic and prenatal diagnosis and also in preimplantation genetic diagnosis. The accuracy of analysis is highly dependent on the success achieved in minimising genotyping errors. The pitfalls in molecular diagnostic tests can be due to a simple technique such as the polymerase chain reaction (PCR) used universally. This technique is routinely used for its apparent accuracy, but it is also a well-known source of errors. We report an error introduced during PCR reaction that leads to a wrong sequence result and consequently to a 'false' molecular result in a next prenatal diagnosis in a family with severe factor VII (FVII) deficiency. This error was verified using an unsuitable primer design in a rich repetitive sequence of the FVII gene that leads to a false annealing and then to a wrong molecular diagnosis. It is essential to link closely molecular data with clinical and phenotype analysis in order to avoid false-negative or false-positive results, which is of great importance to diagnosis and molecular prevention.

Adult↗

PubMed2003

Population study of eight novel Y-chromosome STRs (DYS460, DYS461, GATA-A10, GATA-C4, GATA-H4, DYS434, DYS437, DYS439) in a southeast Iberian population: looking for highly informative Y-chromosome haplotypes.

The present study analyses 8 recently described tetranucleotide microsatellites (DYS460, DYS461, GATA-A10, GATA-C4, GATA-H4, DYS434, DYS437, DYS439) in southeast Spain and out of a total of 76 individuals 67 showed different haplotypes. Out of the 67 different haplotypes, 63 were present once, 3 were found 2 times, and 1 was found 7 times (9.21%). By combining the allelic states of the present eight Y-chromosome STRs with those previously carried out on the same individuals, highly informative haplotypes could be obtained. The haplotype diversity using the basic set of Y-STRs (DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS385 and DYX156Y) previously analyzed is 0.9844. For the same individuals, this value using the new set of Y-STRs is slightly lower (0.8949), while the haplotype diversity combining the two sets of primers significantly increase to 0.9868. The results obtained in the present work show the usefulness of these microsatellites for individual identification and paternity testing in forensic genetics.

Chromosomes, Human, Y↗

PubMed2000

Sequence variation of two hypervariable short tandem repeats at the D22S683 and D6S477 loci.

For two short tandem repeats at the D22S683 and D6S477 loci, 30 and 22 selected alleles, respectively were sequenced. A total of 20 different alleles were found for the D22S683 locus and 12 alleles for the D6S477 locus. In both systems the alleles were designated according to the total number of repeats. D22S683 is a hypervariable STR consisting of blocks of (TATC) repeats with a basic sequence structure (TATATC)n (TATC)n (ATC)0-1 (TATC)n. The D6S477 locus consists of blocks of (TCTA) repeats with a basic sequence structure (TCTA)n (TA)1 (TCTA)0-2 (TA)0-1 (TCTA)n. Population data showed a heterozygosity of 0.89 for D22S683 and 0.75 for D6S477. These STRs are promising markers for forensic genetics as they are robust and can be easily included in multiplexes.

Alleles↗

PubMed2005

Mitochondrial DNA error prophylaxis: assessing the causes of errors in the GEP'02-03 proficiency testing trial.

We report the results of the Spanish and Portuguese working group (GEP) of the International Society for Forensic Genetics (ISFG) Collaborative Exercise 2002-2003 on mitochondrial DNA (mtDNA) analysis. Six different samples were submitted to the participating laboratories: four blood stains (M1-M2-M3-M4), one mixture blood sample (M5), and two hair shaft fragments (M6). Most of the labs reported consensus results for the blood stains, slightly improving the results of previous collaborative exercises. Although hair shaft analysis is still carried out by a small number of laboratories, this analysis yielded a high rate of success. On the contrary, the analysis of the mixture blood stain (M5) yielded a lower rate of success; in spite of this, the whole results on M5 typing demonstrated the suitability of mtDNA analysis in mixture samples. We have found that edition errors are among the most common mistakes reported by the different labs. In addition, we have detected contamination events as well as other minor problems, i.e. lack of standarization in nomenclature for punctual and length heteroplasmies, and indels. In the present edition of the GEP-ISFG exercise we have paid special attention to the visual phylogenetic inspection for detecting common sequencing errors.

Blood Stains↗

PubMed2005

Results of the 2003-2004 GEP-ISFG collaborative study on mitochondrial DNA: focus on the mtDNA profile of a mixed semen-saliva stain.

We report here a review of the seventh mitochondrial DNA (mtDNA) exercise undertaken by the Spanish and Portuguese working group (GEP) of the International Society for Forensic Genetics (ISFG) corresponding to the period 2003-2004. Five reference bloodstains from five donors (M1-M5), a mixed stain of saliva and semen (M6), and a hair sample (M7) were submitted to each participating laboratory for nuclear DNA (nDNA; autosomal STR and Y-STR) and mtDNA analysis. Laboratories were asked to investigate the contributors of samples M6 and M7 among the reference donors (M1-M5). A total of 34 laboratories reported total or partial mtDNA sequence data from both, the reference bloodstains (M1-M5) and the hair sample (M7) concluding a match between mtDNA profiles of M5 and M7. Autosomal STR and Y-STR profiling was the preferred strategy to investigate the contributors of the semen/saliva mixture (M6). Nuclear DNA profiles were consistent with a mixture of saliva from the donor (female) of M4 and semen from donor M5, being the semen (XY) profile the dominant component of the mixture. Strikingly, and in contradiction to the nuclear DNA analysis, mtDNA sequencing results yield a more simple result: only the saliva contribution (M4) was detected, either after preferential lysis or after complete DNA digestion. Some labs provided with several explanations for this finding and carried out additional experiments to explain this apparent contradictory result. The results pointed to the existence of different relative amounts of nuclear and mtDNAs in saliva and semen. We conclude that this circumstance could strongly influence the interpretation of the mtDNA evidence in unbalanced mixtures and in consequence lead to false exclusions. During the GEP-ISFG annual conference a validation study was planned to progress in the interpretation of mtDNA from different mixtures.

Clinical Laboratory Techniques↗

PubMed2001

Sequence structure of 12 novel Y chromosome microsatellites and PCR amplification strategies.

In this work, we present sequencing data for 12 recently reported Y STR loci (DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, GATA A10, GATA 7.1, GATA 7.2, GATA C4, GATA H4, GATA A4), as well as the PCR multiplex strategies we implemented for their detection. Sequenced allelic ladders were constructed and a nomenclature for these new systems is proposed based on the sequence structure and following ISFG recommendations.GATA A4 and DYS439 are likely the same STR. They have the same STR structure and the alleles are always the same in the same individuals.Sequence polymorphisms were observed in the GATA C4 and DYS437 STRs. The variation in DYS437 was associated with a specific population group and is very interesting not only for forensic genetics but also for anthropological studies.

Alleles↗

PubMed2002

Sequence variation and allele nomenclature for the X-linked STRs DXS9895, DXS8378, DXS7132, DXS6800, DXS7133, GATA172D05, DXS7423 and DXS8377.

X-linked DNA markers are increasingly used in forensic kinship testing. This paper presents sequencing data of the short tandem repeats (STRs) DXS9895, DXS8378, DXS7132, DXS6800, DXS7133, GATA172D05, DXS7423, DXS8377 and proposes an allele nomenclature. Alleles were assigned according to the recommendations of the International Society of Forensic Genetics (ISFG) Commission.

Alleles↗