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Applications and extensions of subpopulation theory: a caseworkers guide.

This paper extends the calculation of conditional probabilities from those given by Balding and Nichols to casework situations where a series of possible DNA types are possible. Such situations may occur when a sample is identified containing a mixture of DNA from two or more people or where extra information can be determined about the subpopulation under consideration by analysis of additional samples. Using this approach, the error in the estimated likelihood ratios is expected to reduce as the number of additional individuals typed from the subpopulation increases.

Forensic Medicine↗
PubMed2005

Preliminary DNA identification for the tsunami victims in Thailand.

The 2004 Southeast Asia Tsunami killed nearly 5,400 people in Southern Thailand, including foreign tourists and local residents. To recover DNA evidence as much as possible from the seriously decomposed bodies, we explored procedures of sample preparation from both bone and tooth samples as well as both mitochondrial and nuclear markers. Despite having failed to recover enough DNA for nuclear marker typing, we succeeded in obtaining fully informative results for mitochondrial markers (HV1 and HV2) from 258 tooth samples with a success rate of 51% (258/507). Using an organic DNA extraction method coupled with an ultrafiltration step, we obtained 16 STR (including 13 CODIS loci, one sex discrimination locus, and two Identifiler loci) profiles for 834 samples with a success rate of 79% (834/1,062). In addition, by comparing the allelic frequencies between the typed samples as a group and other index populations, we conclude that the Thai tsunami victims are a combined group of several populations. Our results provide valuable evidence and protocols for the future forensic practice.

Bone and Bones↗
PubMed1999

Forensic science.

Explore the source record for details and available documents.

Benzodiazepines↗
PubMed2005

Separation of sperm and epithelial cells in a microfabricated device: potential application to forensic analysis of sexual assault evidence.

Forensic DNA analysis of sexual assault evidence requires separation of DNA from epithelial (victim) and sperm (perpetrator) cells. The conventional method used by crime laboratories, which is termed "differential extraction", is a time-consuming process. To supplant the conventional process, separation of sperm from a biological mixture containing epithelial cells has been demonstrated on a microfluidic device. This separation utilizes the differential physical properties of the cells that result in settling of the epithelial cells to the bottom of the inlet reservoir and subsequent adherence to the glass substrate. As a result, low flow rates can be used to separate the sperm cells from the epithelial cell-containing biological mixture. Following cell separation on the microdevice, DNA extraction, amplification, and separation were performed using conventional laboratory methods, showing that the cell separation product in the outlet reservoir was of male origin. The reported cell separation has the potential to impact the forensic DNA analysis backlog of sexual assault cases by circumventing the time-consuming conventional differential extraction procedure.

Cell Separation↗
PubMed1995

Population structure, stepwise mutations, heterozygote deficiency and their implications in DNA forensics.

In a substructured population the overall heterozygote deficiency can be predicted from the number of subpopulations (s), their time of divergence (t), and the nature of the mutations. At present the true mutational mechanisms at the hypervariable DNA loci are not known. However, the two existing mutation models (the infinite allele model (IAM) and the stepwise mutation model (SMM)) provide some guides to predictions from which the possible effect of population substructuring may be evaluated, assuming that the subpopulations do not exchange any genes among them during evolution. The theory predicts that the loci with larger mutation rate, and consequently showing greater heterozygosity within subpopulations, should exhibit a smaller proportional heterozygote deficiency (GST) and, hence, the effects of population substructuring should be minimal at the hypervariable DNA loci (an order of magnitude smaller than that at the blood group and protein loci). Applications of this theory to data on six Variable Number of Tandem Repeat (VNTR) loci and five short tandem repeat (STR) loci in the major cosmopolitan populations of the USA show that while the VNTR loci often exhibit a large significant heterozygote deficiency, the STR loci do not show a similar tendency. This discordant finding may be ascribed to the limitations, coalescence and nondetectability of alleles associated with the restriction fragment length polymorphism (RFLP) analysis through which the VNTR loci are scored. Such limitations do not apply to the polymerase chain reaction (PCR) method, through which the STR loci are scored. The implications of these results are discussed in the context of the forensic use of DNA typing data.

DNA↗
PubMed2005

Sequential application of interphase-FISH and CGH to single cells.

A comprehensive genomic analysis of single cells is needed for numerous scenarios in tumor genetics, clinical diagnostics and forensic application. PCR protocols were developed which allow an unbiased amplification of the whole genome of a single cell for subsequent analyses by comparative genomic hybridization (CGH). However, verification of single-cell CGH results has been impossible as the procedure naturally involves the destruction of the respective cell. Here we show that the genome of individual cells can be analyzed by two different single cell techniques applied sequentially to the same cell. In a first step, interphase fluorescence in situ hybridization (FISH) is applied. After evaluation of the interphase-FISH signals, cells of interest can be selected for a further analysis. Single cells are collected by laser microdissection, the DNA is amplified by linker-adaptor PCR and subjected to CGH-analysis. This strategy offers new opportunities for a sophisticated selection of cells based on interphase-FISH signals. Furthermore, the sequential application of two different single-cell approaches to the same single-cell represents the only option to control and verify the single-cell CGH results. We demonstrate the feasibility of this approach with a series of experiments including cells from pre- and postnatal diagnostics, for example, cells with trisomies 13, 18, or 21, respectively, leukemia and tumor cells and tissue sections.

In Situ Hybridization, Fluorescence↗
PubMed2004

Inferring the most likely geographical origin of mtDNA sequence profiles.

In a number of practical cases it is important to determine the likely geographical origin of an individual or a biological sample. A dead body, old bones or a sample of semen may be available. Information on where the sample might come from can assist investigation or research. The first part of this paper is independent of specific data structure. We formulate the problem as a classification problem. Bayes' theorem allows different sources of information or data to be reconciled conveniently. The main part of the paper involves high dimensional data for which simple, standard methods are not likely to work properly. Mitochondrial DNA (mtDNA) data is a typical example of such data. We propose a procedure involving essentially two steps. First, principal component analysis is used to reduce the dimension of the data. Next, quadratic discriminant analysis performs the actual classification. A cross validation procedure is implemented to select the optimal number of principal components. The importance of using separate data sets for model fitting and testing is emphasized. This method distinguishes well between individuals with a self reported European (Icelandic or German) origin and SE Africans. In this case the error rate is 2.0%.

Africa↗