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Search Results: 1 - 10 of 4235 matches for " Bruce Budowle "
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Editors’ Pick: Normal aging versus Alzheimer’s disease – expression patterns may discern the differences
Bruce Budowle
Investigative Genetics , 2012, DOI: 10.1186/2041-2223-3-11
Abstract:
ENCODE and its first impractical application
Budowle Bruce
Investigative Genetics , 2013, DOI: 10.1186/2041-2223-4-4
Abstract:
Kinship Index Variations among Populations and Thresholds for Familial Searching
Jianye Ge, Bruce Budowle
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0037474
Abstract: Current familial searching strategies are developed primarily based on autosomal STR loci, since most of the offender profiles in the forensic DNA databases do not contain Y-STR or mitochondrial DNA data. There are generally two familial searching methods, Identity-by-State (IBS) based methods or kinship index (KI) based methods. The KI based method is an analytically superior method because the allele frequency information is considered as opposed to solely allele counting. However, multiple KIs should be calculated if the unknown forensic profile may be attributed to multiple possible relevant populations. An important practical issue is the KI threshold to select for limiting the list of candidates from a search. There are generally three strategies of setting the KI threshold for familial searching: (1) SWGDAM recommendation 6; (2) minimum KI≥KI threshold; and (3) maximum KI≥KI threshold. These strategies were evaluated and compared by using both simulation data and empirical data. The minimum KI will tend to be closer to the KI appropriate for the population of which the forensic profile belongs. The minimum KI≥KI threshold performs better than the maximum KI≥KI threshold. The SWGDAM strategy may be too stringent for familial searching with large databases (e.g., 1 million or more profiles), because its KI thresholds depend on the database size and the KI thresholds of large databases have a higher probability to exclude true relatives than smaller databases. Minimum KI≥KI threshold strategy is a better option, as it provides the flexibility to adjust the KI threshold according to a pre-determined number of candidates or false positive/negative rates. Joint use of both IBS and KI does not significantly reduce the chance of including true relatives in a candidate list, but does provide a higher efficiency of familial searching.
Developing criteria and data to determine best options for expanding the core CODIS loci
Jianye Ge, Arthur Eisenberg, Bruce Budowle
Investigative Genetics , 2012, DOI: 10.1186/2041-2223-3-1
Abstract: The performance of current and newly proposed CODIS core loci sets were evaluated with simplified analyses for adventitious hit rates in reasonably large datasets under single-source profile comparisons, mixture comparisons and kinship searches, and for international data sharing. Informativeness (for example, match probability, average kinship index (AKI)) and mutation rates of each locus were some of the criteria to consider for loci selection. However, the primary factor was performance with challenged forensic samples.The current battery of loci provided in already validated commercial kits meet the needs for single-source profile comparisons and international data sharing, even with relatively large databases. However, the 13 CODIS core loci are not sufficiently powerful for kinship analyses and searching potential contributors of mixtures in larger databases; 19 or more autosomal STR loci perform better. Y-chromosome STR (Y-STR) loci are very useful to trace paternal lineage, deconvolve female and male mixtures, and resolve inconsistencies with Amelogenin typing. The DYS391 locus is of little theoretical or practical use. Combining five or six Y-chromosome STR loci with existing autosomal STR loci can produce better performance than the same number of autosomal loci for kinship analysis and still yield a sufficiently low match probability for single-source profile comparisons.A more comprehensive study should be performed to provide the necessary information to decision makers and stakeholders about the construction of a new set of core loci for CODIS. Finally, selection of loci should be driven by the concept that the needs of casework should be supported by the processes of CODIS (or for that matter any forensic DNA database).DNA database searching is now a fundamental tool for developing investigative leads. The purpose of a DNA database is to collect and store DNA profiles (for example, from crime scenes, offenders, or missing-persons cases) and enable com
Welcome to Investigative Genetics
Manfred Kayser, Bruce Budowle, Antti Sajantila
Investigative Genetics , 2010, DOI: 10.1186/2041-2223-1-1
Abstract: Investigative Genetics provides an open access, online-only highly visible venue for novel cutting-edge research and technological developments, which through the application of molecular genetics and genomics, answer questions about past and present life, enhance life quality, and provide a safer living environment. The journal aims to reflect the breadth of molecular genetic and genomic research, its development and validation, and its application to a greater understanding, improvement in quality of life, and enhanced safety in our society. It bridges the gap between different areas of science that similarly exploit molecular genetics and genomics, allowing findings and developments to be disseminated efficiently and effectively across disciplines. Articles published in this journal will be hypothesis-driven and will apply, if appropriate, statistical principles (purely descriptive studies will be of limited interest to the journal). The main areas of interest include forensic genetics, biosafety and biosecurity, synthetic biology, legal medicine, genetic epidemiology, identity and lineage testing, personalized genetics and genomics, population genetics and genomics, evolutionary genetics and genomics, mechanisms of inheritance, ancient bio-materials, anthropological genetics and genomics, and archaeogenetics and archaeogenomics. In addition, the journal will publish articles addressing the important issues of statistics, validity, reliability, and ethics related to the use and understanding of genetics and genomics. We are also pleased to announce a special contribution in the form of a regular commentary from Professor Mark Jobling [1]. His insight and depth of knowledge will make for interesting and exciting thought-provoking discussion in many of the areas covered by Investigative Genetics.Investigative Genetics is considering for fast and thorough peer-review two types of original research papers that will form its major content. Research Reports: full-lengt
The demise of the United Kingdom's Forensic Science Service (FSS): loss of world-leading engine of innovation and development in the forensic sciences
Bruce Budowle, Manfred Kayser, Antti Sajantila
Investigative Genetics , 2011, DOI: 10.1186/2041-2223-2-4
Abstract: For the past quarter century, the forensic sciences have seen substantial advancements and improvements promulgated in part by the advent of the field of forensic DNA analysis. The FSS was the initial player in bringing DNA technology to forensic analysis. In 1985, its scientists had the foresight to partner with Sir Alec Jeffreys to solve the murder of two teenage girls using multilocus restriction fragment length polymorphism technology, marking the beginning of the application of DNA analysis for human identification in criminal investigations. The FSS then continued as one of the few leading institutions worldwide on applying DNA technology to forensic applications, by developing, validating and implementing improved and better capabilities. The technology and the field have evolved and increased substantially since those early days in 1985, and along the way the FSS continued its role as a major contributor to the burgeoning discipline of forensic genetics, by its investigators' publishing the results of their efforts in peer-reviewed journals, making the FSS's knowledge available to the worldwide forensic community. Clearly, the global success story of short tandem repeat profiling in forensic analysis would not have been possible without the leading contributions of the FSS. Various forensic institutions around the world emulated the FSS model, and many forensic scientists worldwide owe their scientific and everyday practice heritage to the FSS.Thus, we were dismayed to read that the UK government has decided to dismantle the FSS. No longer will there be this organization, that has contributed to the foundations of forensic genetics and other forensic science disciplines. Indeed, we cannot think of any other forensic institution worldwide that has contributed more to the advancement of the forensic sciences than the FSS. It is a tragic state of affairs indeed that the UK government is willing to dismiss its own forensic treasure with negative consequences wel
Response to: DNA identification by pedigree likelihood ratio accommodating population substructure and mutations- authors' reply
Ranajit Chakraborty, Jianye Ge, Bruce Budowle
Investigative Genetics , 2011, DOI: 10.1186/2041-2223-2-8
Abstract: In their letter to the editor, Egeland et al. [1] criticize the mutation model used in our paper [2], and propose that our comments about the mutation model used by Dawid et al. [3] are not convincing, because we do not provide any data in support of our assertions. Their criticisms are primarily based on three premises: 1) that our mutation model, presented on page 5 of our paper [2], is mathematically incorrect, because our equation 8 does not define a proper probability distribution (that is, the probabilities do not add to 1); 2) that our mutation model allows for production of alleles of zero or negative repeat sizes, which are not meaningful; and 3) that the model used in the paper by Dawid et al [3] uses the relationship between mutational transition probabilities and allele frequency on the basis that allele frequencies are representative of the stationary distribution of a mutation process, and hence, in the absence of natural selection, is presumably applicable to the sequence tagged repeat (STR) loci used in DNA forensics. Each of these issues needs further discussion, and we thank the authors for giving us an opportunity to explain them further.First, the mutation model, explained by equation 8 of page 5 of our paper [2], clearly states that the geometric distribution for Pr (X = x) applies to 'alleles to change by adding or subtracting an absolute number of x repeat units'. Hence, by definition x > 0, and as noted just after equation 8 'equal probabilities for gaining or losing repeats are assumed', it is incorrect to multiply the geometric terms by a factor of 2, as Egeland et al. have done [1]. Following this logic, our equation 8 mathematically represents a valid probability distribution, because the total probability of mutation (that is, X ≠ 0) becomes μ, by summing the individual terms over all non-zero positive integer values of X. In addition, we are not the first to use such formulations of a mutation model. Estoup et al. [4] used exactly the s
DNA identification by pedigree likelihood ratio accommodating population substructure and mutations
Jianye Ge, Bruce Budowle, Ranajit Chakraborty
Investigative Genetics , 2010, DOI: 10.1186/2041-2223-1-8
Abstract: Over the past two decades, forensic DNA typing has become widely accepted as a powerful tool in criminal and civil investigations. This technology has become invaluable in many missing-person identifications. There are a number of scenarios in which person identification is required: these include cases of war victims found in mass graves, missing soldiers or military personnel from past wars, people missing due to dynamic social reasons (for example, murder), remains from mass disasters due to natural catastrophes or terrorism attacks (for example, airplane crashes, the World Trade Center tragedy and the southeast Asia tsunami) and basic paternity testing. In attempts to identify these individuals, DNA profiles from unidentified people may be compared with direct reference samples of the missing person (antemortem samples), such as buccal swabs collected before their disappearance, or items they have used, such as toothbrushes, hairbrushes or preserved dental casts. In some cases, direct comparisons are not possible because an antemortem sample is not available, or the chain of custody may not be established reliably, reducing the confidence in an association. Alternatively, a missing person may be identified by kinship analysis using family reference samples (biological relatives such as parents, offspring, siblings or cousins) of the person to be identified.Traditionally, statistical inference was based on pairwise comparison of the DNA profiles of the unknown sample and a single family reference sample, and then ranking the likelihood ratios (LRs) for specified biological relationships. Numerous statistical methods are available for evaluation of kinship between individuals. Li and Sacks [1] first provided a general method to obtain the conditional probability for any pair of relatives. Jacquard [2] described the most general method for a pairwise relationship using nine condensed identity states. Thompson [3] pioneered the maximum likelihood method by summarizi
Biocrimes, Microbial Forensics, and the Physician
Steven E Schutzer ,Bruce Budowle,Ronald M Atlas
PLOS Medicine , 2005, DOI: 10.1371/journal.pmed.0020337
Abstract:
Response to: Use of prior odds for missing persons identifications - authors' reply
Bruce Budowle, Jianye Ge, Ranajit Chakraborty, Harrell Gill-King
Investigative Genetics , 2012, DOI: 10.1186/2041-2223-3-3
Abstract: We are concerned that statisticians, such as Biedermann et al. [1], advocate the position that data may not be needed to support assumptions 'as long as probability is properly considered as an expression of personal belief'. At a time when the National Academy of Sciences [2] has urged the need for the forensic science community to provide reliable results based on 'objective' data, these authors' position cannot be reconciled. The Report noted (on its page 8), 'The simple reality is that the interpretation of forensic evidence is not always based on scientific studies to determine its validity ... A body of research is required to establish the limits and measures of performance and to address the impact of sources of variability and potential bias. Such research is sorely needed, but it seems to be lacking in most of the forensic disciplines that rely on subjective assessments of matching characteristics. These disciplines need to develop rigorous protocols to guide these subjective interpretations and pursue equally rigorous research and evaluation programs'. It is this approach that distinguishes science from other epistemologies. Then the Report called for research in its Recommendation 3 (page 23), 'Research is needed to address issues of accuracy, reliability, and validity in the forensic science disciplines ... [and in section c of Recommendation 3] the development of quantifiable measures of uncertainty in the conclusions of forensic analyses'.Foremost, none should abide the inclusion of overstated evidence in reports or legal proceedings as it can impinge on the presumption of innocence. The tenet of this presumption should be held dearly by all, and we as scientists should strive to reduce practices that cannot be supported. Biedermann et al. [1] appear to argue that, because there is 'subjectivity in science', one does not necessarily have to be held to a standard of justifying assumptions. It is well accepted that there is subjectivity in science. Inde
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