Bruce Budowle

Elsevier B.V., Filadelfia, Pennsylvania, United States

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Publications (461)1145.35 Total impact

  • Sarah Schemedes · jonathan King · bruce budowle
    Frontiers in Bioengineering and Biotechnology 08/2015;
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    ABSTRACT: Mitochondrial DNA is a useful marker for population studies, human identification, and forensic analysis. Commonly used hypervariable regions I and II (HVI/HVII) were reported to contain as little as 25 % of mitochondrial DNA variants and therefore the majority of power of discrimination of mitochondrial DNA resides in the coding region. Massively parallel sequencing technology enables entire mitochondrial genome sequencing. In this study, buccal swabs were collected from 114 unrelated Estonians and whole mitochondrial genome sequences were generated using the Illumina MiSeq system. The results are concordant with previous mtDNA control region reports of high haplogroup HV and U frequencies (47.4 and 23.7 % in this study, respectively) in the Estonian population. One sample with the Northern Asian haplogroup D was detected. The genetic diversity of the Estonian population sample was estimated to be 99.67 and 95.85 %, for mtGenome and HVI/HVII data, respectively. The random match probability for mtGenome data was 1.20 versus 4.99 % for HVI/HVII. The nucleotide mean pairwise difference was 27 ± 11 for mtGenome and 7 ± 3 for HVI/HVII data. These data describe the genetic diversity of the Estonian population sample and emphasize the power of discrimination of the entire mitochondrial genome over the hypervariable regions.
    Deutsche Zeitschrift für die Gesamte Gerichtliche Medizin 08/2015; DOI:10.1007/s00414-015-1249-4 · 2.60 Impact Factor
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    ABSTRACT: Capillary electrophoresis (CE) and multiplex amplification with fluorescent tagging have been routinely used for STR typing in forensic genetics. However, CE-based methods restrict the number of markers that can be multiplexed simultaneously and cannot detect any intra-repeat variations within STRs. Several studies already have indicated that massively parallel sequencing (MPS) may be another potential technology for STR typing. In this study, the prototype PowerSeq™ Auto System (Promega) containing the 23 STR loci and amelogenin was evaluated using Illumina MiSeq. Results showed that single source complete profiles could be obtained using as little as 62pg of input DNA. The reproducibility study showed that the profiles generated were consistent among multiple typing experiments for a given individual. The mixture study indicated that partial STR profiles of the minor contributor could be detected up to 19:1 mixture. The mock forensic casework study showed that full or partial profiles could be obtained from different types of single source and mixture samples. These studies indicate that the PowerSeq Auto System and the Illumina MiSeq can generate concordant results with current CE-based methods. In addition, MPS-based systems can facilitate mixture deconvolution with the detection of intra-repeat variations within length-based STR alleles. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
    07/2015; 19. DOI:10.1016/j.fsigen.2015.07.015
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    ABSTRACT: Human physical performance is a complex multifactorial trait. Historically, environmental factors (e.g., diet, training) alone have been unable to explain the basis of all prominent phenotypes for physical performance. Therefore, there has been an interest in the study of the contribution of genetic factors to the development of these phenotypes. Support for a genetic component is found with studies that shown that monozygotic twins were more similar than were dizygotic twins for many physiological traits. The evolution of molecular techniques and the ability to scan the entire human genome enabled association of several genetic polymorphisms with performance. However, some biases related to the selection of cohorts and inadequate definition of the study variables have complicated the already difficult task of studying such a large and polymorphic genome, often resulting in inconsistent results about the influence of candidate genes. This review aims to provide a critical overview of heritable genetic aspects. Novel molecular technologies, such as next-generation sequencing, are discussed and how they can contribute to improving understanding of the molecular basis for athletic performance. It is important to ensure that the large amount of data that can be generated using these tools will be used effectively by ensuring well-designed studies. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
    Scandinavian Journal of Medicine and Science in Sports 07/2015; DOI:10.1111/sms.12503 · 3.17 Impact Factor
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    ABSTRACT: To perform a blind study to assess the capability of the Ion Personal Genome Machine® (PGM™) system to sequence forensically relevant genetic marker panels and to characterize unknown individuals for ancestry and possible relatedness. Twelve genomic samples were provided by a third party for blinded genetic analysis. For these 12 samples, the mitochondrial genome and three PGM™ panels containing human identity single nucleotide polymorphisms (SNPs), ancestry informative SNPs, and short tandem repeats (STRs) were sequenced on the PGM™ system and analyzed. All four genetic systems were run and analyzed on the PGM™ system in a reasonably quick time frame. Completeness of genetic profiles, depth of coverage, strand balance, and allele balance were informative metrics that illustrated the quality and reliability of the data produced. SNP genotypes allowed for identification of sex, paternal lineage, and population ancestry. STR genotypes were shown to be in complete concordance with genotypes generated by standard capillary electrophoresis-based technologies. Variants in the mitochondrial genome data provided information on population background and maternal relationships. All results from analysis of the 12 genomic samples were consistent with sample information provided by the sample providers at the end of the blinded study. The relatively easy identification of intra-STR allele SNPs offered the potential for increased discrimination power. The promising nature of these results warrants full validation studies of this massively parallel sequencing technology and its further development for forensic data analysis.
    Croatian Medical Journal 06/2015; 56(3):218-29. DOI:10.3325/cmj.2015.56.218 · 1.37 Impact Factor
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    DESCRIPTION: National Institute of Justice report (January 2015), Office of Investigative and Forensic Sciences; in collaboration with the Forensic Technology Center of Excellence (FTCOE)
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    ABSTRACT: STR typing in forensic genetics has been performed traditionally using capillary electrophoresis (CE). However, CE-based method has some limitations: a small number of STR loci can be used; stutter products, dye artifacts and low level alleles. Massively parallel sequencing (MPS) has been considered a viable technology in recent years allowing high-throughput coverage at a relatively-affordable price. Some of the CE-based limitations may be overcome with the application of MPS. In this study, a prototype multiplex STR System (Promega) was amplified and prepared using the TruSeq DNA LT Sample Preparation Kit (Illumina) in 24 samples. Results showed that the MinElute PCR Purification Kit (Qiagen) was a better size selection method compared with recommended diluted bead mixtures. The library input sensitivity study showed that a wide range of amplicon product (6–200 ng) could be used for library preparation without apparent differences in the STR profile. PCR sensitivity study indicated that 62 pg may be minimum input amount for generating complete profiles. Reliability study results on 24 different individuals showed that high depth of coverage (DoC) and balanced heterozygote allele coverage ratios (ACRs) could be obtained with 250 pg of input DNA, and 62 pg could generate complete or nearly complete profiles. These studies indicate that this STR multiplex system and the Illumina MiSeq can generate reliable STR profiles at a sensitivity level that competes with current widely used CE-based method.
    Forensic Science International: Genetics 05/2015; 16. DOI:10.1016/j.fsigen.2014.11.022 · 3.20 Impact Factor
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    ABSTRACT: The majority of STR loci are not ideal for the analysis of forensic samples with degraded and/or low template DNA. One alternative to overcome these limitations is the use of bi-allelic markers, which have low mutation rates and shorter amplicons. Human identification (HID) InDel marker panels have been described in several countries, including Brazil. The commercial kit available is, however, mostly suitable for Europeans, with lower discrimination power for other population groups. Recently a combination of 49 InDel markers used in four different ethnic groups in the United States has been shown to be more informative than another panel from Portugal, already tested in a Rio de Janeiro sample. However, these 49 InDels have yet to be applied to other admixed or isolated populations. We assessed the efficiency of this panel in two urban admixed populations (Rio de Janeiro, Brazil; Tripoli, Libya), and one isolated Native Brazilian community. All markers are in Hardy-Weinberg equilibrium (HWE) after the Bonferroni correction, and no Linkage disequilibrium was detected. Assuming loci independence and no substructure effect, cumulative RMP were 2.7x10- 18, 1.5x10-20, and 4.5x10-20 for Native Brazilian, Rio de Janeiro, and Tripoli populations, respectively. The overall Fst value was 0.05512. Rio de Janeiro and Tripoli showed similar admixture levels, however for Native Brazilians one parental cluster represented over 60% of the total parental population. We conclude that this panel is suitable for HID on these urban populations, but is less efficient for the isolated group.
    International Journal of Legal Medicine 03/2015; 129(2). DOI:10.1007/s00414-014-1137-3 · 2.69 Impact Factor
  • Forensic Science International: Genetics 01/2015; 16C:203-204. DOI:10.1016/j.fsigen.2015.01.007 · 3.20 Impact Factor
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    ABSTRACT: Background Massively parallel sequencing (MPS) technologies have the capacity to sequence targeted regions or whole genomes of multiple nucleic acid samples with high coverage by sequencing millions of DNA fragments simultaneously. Compared with Sanger sequencing, MPS also can reduce labor and cost on a per nucleotide basis and indeed on a per sample basis. In this study, whole genomes of human mitochondria (mtGenome) were sequenced on the Personal Genome Machine (PGMTM) (Life Technologies, San Francisco, CA), the out data were assessed, and the results were compared with data previously generated on the MiSeqTM (Illumina, San Diego, CA). The objectives of this paper were to determine the feasibility, accuracy, and reliability of sequence data obtained from the PGM. Results 24 samples were multiplexed (in groups of six) and sequenced on the at least 10 megabase throughput 314 chip. The depth of coverage pattern was similar among all 24 samples; however the coverage across the genome varied. For strand bias, the average ratio of coverage between the forward and reverse strands at each nucleotide position indicated that two-thirds of the positions of the genome had ratios that were greater than 0.5. A few sites had more extreme strand bias. Another observation was that 156 positions had a false deletion rate greater than 0.15 in one or more individuals. There were 31-98 (SNP) mtGenome variants observed per sample for the 24 samples analyzed. The total 1237 (SNP) variants were concordant between the results from the PGM and MiSeq. The quality scores for haplogroup assignment for all 24 samples ranged between 88.8%-100%. Conclusions In this study, mtDNA sequence data generated from the PGM were analyzed and the output evaluated. Depth of coverage variation and strand bias were identified but generally were infrequent and did not impact reliability of variant calls. Multiplexing of samples was demonstrated which can improve throughput and reduce cost per sample analyzed. Overall, the results of this study, based on orthogonal concordance testing and phylogenetic scrutiny, supported that whole mtGenome sequence data with high accuracy can be obtained using the PGM platform.
    BMC Genomics 01/2015; 16(1). DOI:10.1186/1471-2164-16-S1-S4 · 4.04 Impact Factor
  • Antti Sajantila · Bruce Budowle
    European journal of human genetics: EJHG 12/2014; DOI:10.1038/ejhg.2014.247 · 4.23 Impact Factor
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    ABSTRACT: The TruSeq™ Forensic Amplicon library preparation protocol, originally designed to attach sequencing adapters to chromatin-bound DNA for chromatin immunoprecipitation sequencing (TruSeq™ ChIP-Seq), was used here to attach adapters directly to amplicons containing markers of forensic interest. In this study, the TruSeq™ Forensic Amplicon library preparation protocol was used to detect 160 single nucleotide polymorphisms (SNPs), including human identification SNPs (iSNPs), ancestry, and phenotypic SNPs (apSNPs) in 12 reference samples. Results were compared with those generated by a second laboratory using the same technique, as well as to those generated by whole genome sequencing (WGS). The genotype calls made using the TruSeq™ Forensic Amplicon library preparation protocol were highly concordant. The protocol described herein represents an effective and relatively sensitive means of preparing amplified nuclear DNA for massively parallel sequencing (MPS).
    Deutsche Zeitschrift für die Gesamte Gerichtliche Medizin 11/2014; 129(1):1-6. DOI:10.1007/s00414-014-1108-8 · 2.60 Impact Factor
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    ABSTRACT: Mitochondrial DNA testing is a useful tool in the analysis of forensic biological evidence. In cases where nuclear DNA is damaged or limited in quantity, the higher copy number of mitochondrial genomes available in a sample can provide information about the source of a sample. Currently, Sanger-type sequencing (STS) is the primary method to develop mitochondrial DNA profiles. This method is laborious and time consuming. Massively parallel sequencing (MPS) can increase the amount of information obtained from mitochondrial DNA samples while improving turnaround time by decreasing the numbers of manipulations and more so by exploiting high throughput analyses to obtain interpretable results. In this study 18 buccal swabs, three different tissue samples from five individuals, and four bones samples from casework were sequenced at hypervariable regions I and II using STS and MPS. Sample enrichment for STS and MPS was PCR-based. Library preparation for MPS was performed using Nextera® XT DNA Sample Preparation Kit and sequencing was performed on the MiSeq™ (Illumina, Inc.). MPS yielded full concordance of base calls with STS results, and the newer methodology was able to resolve length heteroplasmy in homopolymeric regions. This study demonstrates short amplicon MPS of mitochondrial DNA is feasible, can provide information not possible with STS, and lays the groundwork for development of a whole genome sequencing strategy for degraded samples.
    10/2014; 17(2). DOI:10.1016/j.legalmed.2014.10.004
  • David H Warshauer · Jonathan L King · Bruce Budowle
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    ABSTRACT: STRait Razor (the STR Allele Identification Tool – Razor) was developed as a bioinformatic software tool to detect short tandem repeat (STR) alleles in massively parallel sequencing (MPS) raw data. The method of detection used by STRait Razor allows it to make reliable allele calls for all STR types in a manner that is similar to that of capillary electrophoresis. STRait Razor v2.0 incorporates several new features and improvements upon the original software, such as a larger default locus configuration file that increases the number of detectable loci (now including X-chromosome STRs and Amelogenin), an enhanced custom locus list generator, a novel output sorting method that highlights unique sequences for intra-repeat variation detection, and a genotyping tool that emulates traditional electropherogram data. Users also now have the option to choose whether the program detects autosomal, X-chromosome, Y-chromosome, or all STRs. Concordance testing was performed, and allele calls produced by STRait Razor v2.0 were completely consistent with those made by the original software.
    10/2014; 14. DOI:10.1016/j.fsigen.2014.10.011
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    ABSTRACT: Allele frequencies for 15 autosomal STR loci (N = 290) and haplotype data for 17 Y-STR loci (N = 157) were determined for an admixed population from Belize. There were no detectable departures from Hardy-Weinberg equilibrium expectations at any autosomal STR loci except for the D8S1179 locus (p = 0.002). The combined power of discrimination (PD) and combined power of exclusion (PE) were greater than 0.99999999 and 0.99999951, respectively. In addition, a total of 144 distinct Y-STR haplotypes were observed with 133 Y-STR haplotypes observed only once. The most common Y-STR haplotype was observed three times for two separate haplotypes. The various analyses of these forensically relevant STR loci showed that these markers are informative in the Belize population for forensic and parentage testing applications.
    International Journal of Legal Medicine 09/2014; DOI:10.1007/s00414-014-1082-1 · 2.69 Impact Factor
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    ABSTRACT: Mitochondrial DNA typing in forensic genetics has been performed traditionally using Sanger-type sequencing. Consequently sequencing of a relatively-large target such as the mitochondrial genome (mtGenome) is laborious and time consuming. Thus, sequencing typically focuses on the control region due to its high concentration of variation. Massively parallel sequencing (MPS) has become more accessible in recent years allowing for high-throughput processing of large target areas. In this study, Nextera® XT DNA Sample Preparation Kit and the Illumina MiSeq™ were utilized to generate quality whole genome mitochondrial haplotypes from 283 individuals in a both cost-effective and rapid manner. Results showed that haplotypes can be generated at a high depth of coverage with limited strand bias. The distribution of variants across the mitochondrial genome was described and demonstrated greater variation within the coding region than the non-coding region. Haplotype and haplogroup diversity were described with respect to whole mtGenome and HVI/HVII. An overall increase in haplotype or genetic diversity and random match probability, as well as better haplogroup assignment demonstrates that MPS of the mtGenome using the Illumina MiSeq system is a viable and reliable methodology.
    Forensic Science International: Genetics 09/2014; 12:128–135. DOI:10.1016/j.fsigen.2014.06.001 · 3.20 Impact Factor
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    Forensic Science International: Genetics 09/2014; 12. DOI:10.1016/j.fsigen.2014.05.008 · 3.20 Impact Factor
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    ABSTRACT: In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend towards smaller genetic distances resulting from larger numbers of markers became apparent.
    Forensic Science International: Genetics 09/2014; DOI:10.1016/j.fsigen.2014.04.008 · 3.20 Impact Factor
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    Bruce Budowle
    08/2014; 5(1):11. DOI:10.1186/2041-2223-5-11
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    ABSTRACT: Vuorio A, Laukkala T, Navathe P, Budowle B, Eyre A, Sajantila A. Aircraft-assisted pilot suicides: lessons to be learned. Aviat Space Environ Med 2014; 85:841–6. Aircraft assisted suicides were studied in the United States, United Kingdom, Germany, and Finland during 1956-2012 by means of literature search and accident case analysis. According to our study the frequency varied slightly between the studies. Overall, the new estimate of aircraft assisted suicides in the United States in a 20-yr period (1993-2012) is 0.33% (95% CI 0.21-0.49) (24/7244). In the detailed accident case analysis, it was found that in five out of the eight cases from the United States, someone knew of prior suicidal ideation before the aircraft assisted fatality. The caveats of standard medico-legal autopsy and accident investigation methods in investigation of suspected aircraft assisted suicides are discussed. It is suggested that a psychological autopsy should be performed in all such cases. Also the social context and possibilities of the prevention of aviation-related suicides were analyzed. In addition, some recent aircraft assisted suicides carried out using commercial aircraft during scheduled services and causing many casualties are discussed.
    Aviation Space and Environmental Medicine 08/2014; 85(8). DOI:10.3357/ASEM.4000.2014 · 0.78 Impact Factor

Publication Stats

9k Citations
1,145.35 Total Impact Points

Institutions

  • 2015
    • Elsevier B.V.
      Filadelfia, Pennsylvania, United States
  • 2013–2015
    • King Abdulaziz University
      Djidda, Makkah, Saudi Arabia
  • 2009–2015
    • University of North Texas HSC at Fort Worth
      • Department of Molecular and Medical Genetics
      Fort Worth, Texas, United States
    • Fort Worth Nature Center & Refuge
      Fort Worth, Texas, United States
    • University of California, Davis
      • Department of Anthropology
      Davis, CA, United States
  • 2014
    • University of Helsinki
      Helsinki, Uusimaa, Finland
  • 2009–2012
    • University of North Texas
      • • Department of Forensic and Investigative Genetics
      • • Health Science Center
      Denton, Texas, United States
  • 1991–2009
    • Federal Bureau of Investigation
      Washington, Washington, D.C., United States
    • National Public Health Institute
      Helsinki, Southern Finland Province, Finland
  • 2008
    • Centers for Disease Control and Prevention
      • National Center for Emerging and Zoonotic Infectious Diseases
      Атланта, Michigan, United States
  • 2005–2008
    • Rutgers New Jersey Medical School
      • • Department of Medicine (RWJ Medical School)
      • • Department of Medicine
      Newark, New Jersey, United States
    • William Penn University
      Worcester, Massachusetts, United States
    • Victor Babes University of Medicine and Pharmacy of Timisoara
      Freidorf, Timiş, Romania
  • 2007
    • Harvard Medical School
      • Department of Genetics
      Boston, Massachusetts, United States
  • 2000–2004
    • University of Zaragoza
      • Faculty of Medicine
      Zaragoza, Aragon, Spain
    • Ministrstvo za notranje zadeve
      Lubliano, Ljubljana, Slovenia
  • 2003
    • University of Cincinnati
      • Department of Environmental Health
      Cincinnati, Ohio, United States
  • 2001–2003
    • DNA Analysis, LLC
      Cincinnati, Ohio, United States
  • 1999–2003
    • University of Granada
      • Facultad de Medicina
      Granada, Andalusia, Spain
  • 2002
    • West Virginia University
      Morgantown, West Virginia, United States
  • 1999–2000
    • Universität Bern
      • Institute of Legal Medicine
      Bern, BE, Switzerland
  • 1998
    • University of Rome Tor Vergata
      Roma, Latium, Italy
    • University of Oslo
      • Institute of Medical Informatics (IMI)
      Kristiania (historical), Oslo County, Norway
  • 1997
    • University of Innsbruck
      Innsbruck, Tyrol, Austria
    • University of Münster
      • Institute of Legal Medicine
      Muenster, North Rhine-Westphalia, Germany
  • 1994
    • University of Texas Health Science Center at Houston
      • Human Genetics Center
      Houston, Texas, United States