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ABSTRACT: Naming mtDNA sequences by listing only those sites that differ from a reference sequence is the standard practice for describing the observed variations. Consistency in nomenclature is desirable so that all sequences in a database that are concordant with an evidentiary sequence will be found for estimating the rarity of that profile. The operational alignment and nomenclature rules, i.e., “Wilson Rules,” suggested for this purpose do not always guarantee a single consistent sequence description for all observed polymorphisms. In this work, the operational alignment/nomenclature rules were reconfigured to better reflect traditional user preferences. The rules for selecting alignments are described. In addition, to avoid human error and to more efficiently name mtDNA sequence variants, a computer-facilitated method of aligning mtDNA sample sequences with a reference sequence was developed. There were 33 differences between these hierarchical rules and the data in SWGDAM, which translates into a 99.92% consistency between the new rules and the manual historical nomenclature approach. The data support the reliability of the current SWGDAM database. As the few discrepancies were changed in favor of the new hierarchical rules, the quality of the SWGDAM database is further improved.
Journal of Forensic Sciences 08/2010; 55(5):1190 - 1195. · 1.23 Impact Factor
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ABSTRACT: A consistent nomenclature scheme is necessary to characterize a forensic mitochondrial DNA (mtDNA) haplotype. A standard nomenclature, called the Mitotyper Rules™, has been developed that applies typing rules in a hierarchical manner reflecting the forensic practitioner’s nomenclature preferences. In this work, an empirical comparison between the revised hierarchical nomenclature rules and the phylogenetic approach to mtDNA type description has been conducted on 5173 samples from the phylogenetically typed European Mitochondrial DNA Population database (EMPOP) to identify the degree and significance of any differences. The comparison of the original EMPOP types and the results of retyping these sequences using the Mitotyper Rules demonstrates a high degree of concordance between the two alignment schemes. Differences in types resulted mainly because the Mitotyper Rules selected an alignment with the fewest number of differences compared with the rCRS. In addition, several identical regions were described in more than one way in the EMPOP dataset, demonstrating a limitation of a solely phylogenetic approach in that it may not consistently type nonhaplogroup-specific sites. Using a rule-based approach, commonly occurring as well as private variants are subjected to the same rules for naming, which is particularly advantageous when typing partial sequence data.
Journal of Forensic Sciences 08/2010; 55(5):1184 - 1189. · 1.23 Impact Factor
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Journal of Forensic Sciences 01/2010; 55(1):269 - 272. · 1.23 Impact Factor
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ABSTRACT: Three sampled populations of unrelated males—African American, Caucasian, and Hispanic, all from Texas—were typed for 16 Y short tandem repeat (STR) markers using the AmpFlSTR® YfilerTM kit. These samples also were typed previously for the 13 core CODIS autosomal STR loci. Most of the 16 marker haplotypes (2478 out of 2551 distinct haplotypes) were observed only once in the data sets. Haplotype diversities were 99.88%, 99.89%, and 99.87% for the African American, Caucasian, and Hispanic sample populations, respectively. FST values were very small when a haplotype comprised 10–16 markers. This suggests that inclusion of substructure correction is not required. However, haplotypes consisting of fewer loci may require the inclusion of FST corrections. The testing of independence of autosomal and Y STRs supports the proposition that the frequencies of autosomal and Y STR profiles can be combined using the product rule.
Journal of Forensic Sciences 08/2009; 54(5):1016 - 1021. · 1.23 Impact Factor
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Bruce Budowle Ph.D,
M.C.I.M. Anthony J. Onorato M.S.F.S,
Thomas F. Callaghan Ph.D,
Angelo Della Manna M.S,
Ann M. Gross M.S,
Richard A. Guerrieri M.S,
Jennifer C. Luttman M.F.S,
David Lee McClure B.S,
Bruce Budowle,
Anthony J. Onorato,
Thomas F. Callaghan,
Angelo Della Manna,
Ann M. Gross,
Richard A. Guerrieri,
Jennifer C. Luttman,
David Lee McClure
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ABSTRACT: Currently in the United States there is little direction for what constitutes sufficient guidelines for DNA mixture interpretation. While a standardized approach is not possible or desirable, more definition is necessary to ensure reliable interpretation of results is carried out. In addition, qualified DNA examiners should be able to review reports and understand the assumptions made by the analyst who performed the interpretation. Interpretation of DNA mixture profiles requires consideration of a number of aspects of a mixed profile, many of which need to be established by on-site, internal validation studies conducted by a laboratory’s technical staff, prior to performing casework analysis. The relevant features include: criteria for identification of mixed specimens, establishing detection and interpretation threshold values, defining allele peaks, defining nonallele peaks, identifying artifacts, consideration of tri-allelic patterns, estimating the minimum number of contributors, resolving components of a mixture, determining when a portion of the mixed profile can be treated as a single source profile, consideration of potential additive effects of allele sharing, impact of stutter peaks on interpretation in the presence of a minor contributor, comparison with reference specimens, and some issues related to the application of mixture calculation statistics. Equally important is using sensible judgment based on sound and documented principles of DNA analyses. Assumptions should be documented so that reliable descriptive information is conveyed adequately concerning that mixture and what were the bases for the interpretations that were carried out. Examples are provided to guide the community. Interpretation guidelines also should incorporate strategies to minimize potential bias that could occur by making inferences based on a reference sample. The intent of this paper is to promote more thought, provide assistance on many aspects for consideration, and to support that more formalized mixture interpretation guidelines are developed.
Journal of Forensic Sciences 06/2009; 54(4):810 - 821. · 1.23 Impact Factor
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Sree Kanthaswamy Ph.D,
Bradley K. Tom M.S,
Anna-Maria Mattila M.S,
Eric Johnston M.S,
Melody Dayton M.S,
Jennifer Kinaga B.S,
Bethany Joy-Alise Erickson B.S,
Joy Halverson D.V.M,
Dennis Fantin Ph.D,
Sue DeNise Ph.D,
Alexander Kou B.S,
Venkat Malladi B.S,
Jessica Satkoski Ph.D, Bruce Budowle Ph.D,
David Glenn Smith Ph.D,
Mikko T. Koskinen Ph.D
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ABSTRACT: Canine biological specimens are often part of the physical evidence from crime scenes. Until now, there have been no validated canine-specific forensic reagent kits available. A multiplex genotyping system, comprising 18 short tandem repeats (STRs) and a sex-linked zinc finger locus for gender determination, was developed for generating population genetic data assessing the weight of canine forensic DNA profiles. Allele frequencies were estimated for 236 pedigreed and 431 mixed breed dogs residing in the U.S. Average random match probability is 1 in 2 × 1033 using the regional database and 1 in 4 × 1039 using the breed dataset. Each pedigreed population was genetically distinct and could be differentiated from the mixed breed dog population but genetic variation was not significantly correlated with geographic transition. Results herein support the use of the allele frequency data with the canine STR multiplex for conveying the significance of identity testing for forensic casework, parentage testing, and breed assignments.
Journal of Forensic Sciences 05/2009; 54(4):829 - 840. · 1.23 Impact Factor
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ABSTRACT: Determining the gender of the source of forensic DNA evidence is based on the amelogenin test. However, at times the assay may not be indicative of gender assignment, because of deletions at the amelogenin site. Previously, we described successful coamplification of a marker residing within the SRY gene with the short tandem repeat markers from two commercially available human identification kits. The study herein addresses the validation of primers for the target SRY gene regarding specificity, sensitivity, and robustness. Among 115 unrelated male Slovenians no null allele was observed. Repeatable and reliable results were obtained from as little as 25 pg of template DNA, indicating a high sensitivity of detection for the assay. No polymerase chain reaction product was observed even at a concentration of 10 ng/μL of template female DNA. Additionally, the male specific marker could be detected in mixed male and female samples down to a ratio of 1:16.
Journal of Forensic Sciences 03/2009; 54(3):551 - 555. · 1.23 Impact Factor
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Esther Martinez-Espin M.S,
Luis J. Martínez-Gonzalez M.S,
Francisco Fernandez-Rosado M.S,
Carmen Entrala Ph.D,
J. Carlos Alvarez Ph.D,
Ph.D. Jose A. Lorente M.D, Bruce Budowle Ph.D,
Myriam Ovalle De Monroy M.A,
Esther Martinez‐Espin,
Luis J. Martínez‐Gonzalez,
Francisco Fernandez‐Rosado,
Carmen Entrala,
J. Carlos Alvarez,
Jose A. Lorente,
Bruce Budowle,
Myriam Ovalle De Monroy
Journal of Forensic Sciences 08/2006; 51(5):1216 - 1218. · 1.23 Impact Factor
