Mark Wilson

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David Seamon

Kansas State University

José Francisco Pessanha

UERJ - Universidade do Estado do Rio de Janeiro / Rio de Janeiro State University

JAYARAM KOTTAPALLI

Agricultural Research Organization of Israel

Syed Fida Hussain Shah

COMSATS Institute of Information Technology,Abbottabad,Pakistan

Rosa Fregel

Universidad de La Laguna

Muhammad Imran Rasheed

COMSATS Institute of Information Technology

paolo mazzarello

University of Pavia

Alex Dommann

University of Bern

Mohammed Mahmood Mohammed

University of Baghdad

Füsun Akgül

Mehmet Akif Ersoy University

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Papers by Mark Wilson

Successful nuclear DNA profiling of rootless hair shafts: a novel approach

International journal of legal medicine, Jan 9, 2017

Historically, rootless hair shaft samples submitted to a forensic laboratory for DNA analysis are... more Historically, rootless hair shaft samples submitted to a forensic laboratory for DNA analysis are reserved for mitochondrial DNA (mtDNA) analysis due to the presence of highly degraded as well as insufficient amounts of nuclear DNA. Although mtDNA has been very successful in obtaining results from rootless hair, this system has its limitations, namely, it is a lineage marker that cannot differentiate between maternally related genotypes. Given the high incidence of hairs as forensic evidence, there is a need for the use of a nuclear DNA test system capable of producing reliable results for hair shaft forensic evidence. This study reports the utilization of an enhanced DNA extraction methodology for hairs, in combination with a recently developed novel, nuclear DNA typing assay, InnoTyper® 21, to improve the success rate for obtaining informative results from highly compromised, degraded, and trace forensic samples such as rootless hair shafts. The InnoTyper 21 kit is a small amplico...

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Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation

Proceedings of the National Academy of Sciences of the United States of America, Jan 22, 2011

Before the anthrax letter attacks of 2001, the developing field of microbial forensics relied on ... more Before the anthrax letter attacks of 2001, the developing field of microbial forensics relied on microbial genotyping schemes based on a small portion of a genome sequence. Amerithrax, the investigation into the anthrax letter attacks, applied high-resolution whole-genome sequencing and comparative genomics to identify key genetic features of the letters' Bacillus anthracis Ames strain. During systematic microbiological analysis of the spore material from the letters, we identified a number of morphological variants based on phenotypic characteristics and the ability to sporulate. The genomes of these morphological variants were sequenced and compared with that of the B. anthracis Ames ancestor, the progenitor of all B. anthracis Ames strains. Through comparative genomics, we identified four distinct loci with verifiable genetic mutations. Three of the four mutations could be directly linked to sporulation pathways in B. anthracis and more specifically to the regulation of the ...

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Sequential multiplex amplification (SMA) of genetic loci: A method for recovering template DNA for subsequent analyses of additional loci

International Journal of Legal Medicine, 1994

A method called Sequential Multiplex Amplification (SMA) has been developed whereby a limited amo... more A method called Sequential Multiplex Amplification (SMA) has been developed whereby a limited amount of DNA extracted from a sample can be reutilized for several single polymerase chain reaction (PCR) amplifications. The method involves recovery of genomic template DNA by microfiltration of PCR-amplified samples. Up to 5 different loci have been typed, each in a single system PCR-based assay, beginning with a test quantity of 5 ng template DNA. Genotypes of the DNA donors were compared with those obtained from individual amplifications and shown to be identical. This could be a useful technique for typing a number of loci from a limited amount of DNa and to recover template DNA from samples previously subjected to PCR. Obviously, when small quantities of template DNA are available, this technique can prove quite useful.

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Validation of mitochondrial DNA sequencing for forensic casework analysis

International Journal of Legal Medicine, 1995

Two sets of studies were performed to evaluate the forensic utility of sequencing human mitochond... more Two sets of studies were performed to evaluate the forensic utility of sequencing human mitochondrial DNA (mtDNA) derived from various tissues and amplified by the polymerase chain reaction (PCR). Sequencing was performed on a Perkin-Elmer/Applied Biosystems Division (PE/ABD) automated DNA sequencer (model 373A). The first set of experiments included typical validation studies that had previously been conducted on forensic DNA markers, such as: chemical contaminant effects on DNA from blood and semen and the effect of typing DNA extracted from body fluid samples deposited on various substrates. A second set of experiments was performed strictly on human hair shafts. These studies included typing mtDNA from hairs that were: (1) from different body areas, (2) chemically treated, (3) from deceased individuals, and (4) deliberately contaminated with various body fluids. The data confirm that PCR-based mtDNA typing by direct automated sequencing is a valid and reliable means of forensic identification.

A family exhibiting heteroplasmy in the human mitochondrial DNA control region reveals both somatic mosaicism and pronounced segregation of mitotypes

Human Genetics, 1997

A family exhibiting heteroplasmy at position 16355 in hypervariable region I of the human mtDNA c... more A family exhibiting heteroplasmy at position 16355 in hypervariable region I of the human mtDNA control region has been identified. This family consists of a mother, daughter, and son. DNA samples extracted from blood stains, buccal swabs, and hairs from these individuals were amplified by PCR and sequenced utilizing fluoresence-labeled dye terminator chemistry in an automated DNA sequencer. In both the daughter and mother, heteroplasmy was observed in DNA extracted from blood stains, buccal swabs, and hairs. In the blood stains, the proportion of cytosine was greater than thymine in both individuals. Buccal swab extracts showed a more balanced contribution from the two nucleotides. Telogenic hair root and hair shaft samples exhibited a wide range of nucleotide contributions at this position, from predominately cytosine in some samples to predominately thymine in others. The apparent stochastic segregation of mitotypes in hair samples is discussed from a forensic viewpoint, and the mechanism of mtDNA heteroplasmy is considered.

Characterization of human control region sequences of the African American SWGDAM forensic mtDNA data set

Forensic Science International, 2005

The scientific working group on DNA analysis Methods (SWGDAM) mitochondrial DNA (mtDNA) populatio... more The scientific working group on DNA analysis Methods (SWGDAM) mitochondrial DNA (mtDNA) population data set is used to infer the relative rarity of control region mtDNA profiles obtained from evidence samples and of profiles used for identification of missing persons. In this study, the African American haplogroup patterns in the SWGDAM data were analyzed in a phylogenetic context to determine relevant single nucleotide polymorphisms (SNPs) and to describe haplogroup distributions for Africans observed in these data sets. Over 200 SNPs (n ¼ 217) were observed in the African American data set (n ¼ 1148). These SNPs ranged from having 1-39 changes in the phylogenetic tree, with sites 152 and 16519 being the most variable. On average there were 5.8 changes for a character on the tree. The most variable sites (with 19 or more changes each)

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Spanish population data on seven loci: D1S80, D17S5, HUMTH01, HUMVWA, ACTBP2, D21S11 and HLA-DQA1

Forensic Science International, 1997

Blood samples from 120 Spanish Caucasian individuals were amplified and typed by electrophoresis ... more Blood samples from 120 Spanish Caucasian individuals were amplified and typed by electrophoresis at six loci, and by reverse dot-blot hybridization at one locus. Results demonstrate the assumption of independence within and between the seven loci analyzed. Therefore, a Spanish population database has been established and statistical analysis shows that a high degree of discrimination can be obtained when all seven (or fewer) loci are used to characterize forensic biological evidence.

Analysis of short tandem repeat (STR) HUMVWA in the Spanish population

Forensic Science International, 1994

Amplification by polymerase chain reaction (PCR) of variable number of tandem repeat (VNTR) loci ... more Amplification by polymerase chain reaction (PCR) of variable number of tandem repeat (VNTR) loci and subsequent typing by electrophoresis and silver staining has become a useful tool for identity testing. One viable group of genetic markers amenable to amplification by PCR is the short tandem repeat (STR) loci. A horizontal discontinuous polyacrylamide gel electrophoresis (PAGE) method was used to type the amplified products of the STR HUMVWA. Typing for 'VWA of 120 unrelated Spanish Caucasians was done. Six alleles were observed with frequencies in the range 0.096-0.242. The genotype distribution meets Hardy-Weinberg expectations (0.25 < P < 0.50). The heterozygosity was 73.3% and the discrimination power (DP) 0.94. Simultaneously, in a small sample of families (n = 24) no new mutations could be bound.

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Critique of interpretation of high levels of heteroplasmy in the human mitochondrial DNA hypervariable region I from hair

Forensic Science International, 2002

The phenomenon known as heteroplasmy can be operationally observed in some human mitochondrial DN... more The phenomenon known as heteroplasmy can be operationally observed in some human mitochondrial DNA (mtDNA) samples. Typically, heteroplasmy manifests itself in an individual presenting two mtDNA species that differ at a single base. Heteroplasmy at two, and even possibly three sites, also may occur, but at very low rates. A recent report (Grzybowski, 2000, see ref. [13]) suggests that much higher levels of mtDNA (point substitution) heteroplasmy can occur in hair. This observation is contrary to the experience of the forensic mtDNA community. There are several explanations for the unusual ®ndings of high levels of heteroplasmy. First, the template quantities of DNA are approximately three orders of magnitude higher than required for mtDNA sequencing, and an excessive number of ampli®cation cycles were used. Thus, the protocol used did not follow routine practices by the forensic community. Second, there are misidenti®cations and tabular errors that call into question the reliability of the ®ndings. Third, by comparing the natural human mtDNA variation with a reference sample population with that observed in the heteroplasmy in hair study, the data are inconsistent with population genetic expectations. The observation of high levels of heteroplasmy may be due to contamination of the samples and/or possibly the ampli®cation of nuclear pseudogenes. The results observed in the heteroplasmy in hair study do not apply to other methods of mtDNA analysis and cannot be used to question the reliability of the current forensic mtDNA practices.

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DNA Commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs

Forensic Science International, 2001

During the past few years the DNA commission of the International Society of Forensic Genetics ha... more During the past few years the DNA commission of the International Society of Forensic Genetics has published a series of documents providing guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. This latest report addresses a relatively new area, namely Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). This report addresses nomenclature, use of allelic ladders, population genetics and reporting methods.

Mitochondrial DNA regions HVI and HVII population data

Forensic Science International, 1999

Data from 1393 unrelated individuals have been compiled from eight population groups: African Ame... more Data from 1393 unrelated individuals have been compiled from eight population groups: African Americans, Africans (Sierra Leone), U.S. Caucasians, Austrians, French, Hispanics, Japanese, and Asian Americans. The majority of the mtDNA sequences were observed only once within each population group (i.e., ranging from a low of 60.3% (35/58) of the Asian American sequences to a high of 85.3% (93/109) of the French sequences). Genetic diversity ranged from 0.990 in the African sample to 0.998 in African Americans. Random match probability ranged from 2.50% in the Asian American sample to 0.52% in U.S. Caucasians. The average number of nucleotide differences between individuals in a database is greatest for the African American and African samples (14.1 and 13.1, respectively), and the least variable are the Caucasians (ranging from 7.2 to 8.4). Substitutions are the predominate polymorphism, and at least 92% of the substitutions are transitions. The most prevalent transversions are As substituted for Cs and Cs substituted for As. For most population groups these transversions occurred predominately in the HVI region; however, the African, African American, and Hispanic samples also demonstrated a large portion of their C to A and A to C transversions in the HVII region (at sites 186 and/or 189). Most insertions occur in the HVII region at sites 309.1 and 315.1, within a stretch of C&amp;amp;#39;s. Insertions of an additional C are common in all population groups. The sequence data were converted to SSO mtDNA types and compared with population data on Caucasians, Africans, Asians, Japanese, and Mexicans described by Stoneking et al. [M. Stoneking, D. Hedgecock, R.G. Higuchi, L. Vigilant, H.A. Erlich, Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes, Am. J. Hum. Genet. 48 (1991) 370-382] using an R x C contingency table test. Differences between major population groups (i.e., between African, Caucasian, and Asian) are quite evident, and similar ethnic population groups carried similar SSO polymorphism frequencies. There were only a few SSO types that showed significant differences between subpopulation groups. The SSO data alone can not be used to describe the population genetics with complete sequence data. However, the results of the SSO comparisons are similar to other analyses, and differences in sequence data in regions HVI and HVII are greater between major population groups than between subgroups.

Interpretation guidelines for mitochondrial DNA sequencing

Proceedings of the Tenth International …, 1999

... sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticit... more

Recommendations for consistent treatment of length variants in the human mitochondrial DNA control region

Forensic Science International, 2002

Human mitochondrial DNA (mtDNA) analysis is a valuable forensic tool, useful in cases where the a... more Human mitochondrial DNA (mtDNA) analysis is a valuable forensic tool, useful in cases where the amount of extracted DNA is low or highly degraded. Population databases are used to determine the relative rarity of a particular profile obtained in a forensic case. Rather than full DNA sequence information, sequence profiles are compared to a reference sequence, and the differences from the reference are recorded in forensic databases. A standard method is proposed for characterizing length variants, and examples are described using actual human control region mtDNA profiles. Consistency in alignment and nomenclature avoids inadvertently describing two sequences as different when in fact they are the same.

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Successful nuclear DNA profiling of rootless hair shafts: a novel approach

International journal of legal medicine, Jan 9, 2017

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Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation

Proceedings of the National Academy of Sciences of the United States of America, Jan 22, 2011

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Sequential multiplex amplification (SMA) of genetic loci: A method for recovering template DNA for subsequent analyses of additional loci

International Journal of Legal Medicine, 1994

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Validation of mitochondrial DNA sequencing for forensic casework analysis

International Journal of Legal Medicine, 1995