ORCID Profile
0000-0002-5445-6316
Current Organisations
Universities South Africa
,
San José State University
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Publisher: Cold Spring Harbor Laboratory
Date: 20-07-2016
DOI: 10.1101/060814
Abstract: Despite intensive research on genetics of the craniofacial morphology using animal models and human craniofacial syndromes, the genetic variation that underpins normal human facial appearance is still largely elusive. Recent development of novel digital methods for capturing the complexity of craniofacial morphology in conjunction with high-throughput genotyping methods, show great promise for unravelling the genetic basis of such a complex trait. As a part of our efforts on detecting genomic variants affecting normal craniofacial appearance, we have implemented a candidate gene approach by selecting 1,201 single nucleotide polymorphisms (SNPs) and 4,732 tag SNPs in over 170 candidate genes and intergenic regions. We used 3-dimentional (3D) facial scans and direct cranial measurements of 587 volunteers to calculate 104 craniofacial phenotypes. Following genotyping by massively parallel sequencing, genetic associations between 2,332 genetic markers and 104 craniofacial phenotypes were tested. An application of a Bonferroni–corrected genome–wide significance threshold produced significant associations between five craniofacial traits and six SNPs. Specifically, associations of nasal width with rs8035124 (15q26.1), cephalic index with rs16830498 (2q23.3), nasal index with rs37369 (5q13.2), transverse nasal prominence angle with rs59037879 (10p11.23) and rs10512572 (17q24.3), and principal component explaining 73.3% of all the craniofacial phenotypes, with rs37369 (5p13.2) and rs390345 (14q31.3) were observed. Due to over-conservative nature of the Bonferroni correction, we also report all the associations that reached the traditional genome-wide p-value threshold ( .00E-08) as suggestive. Based on the genome-wide threshold, 8 craniofacial phenotypes demonstrated significant associations with 34 intergenic and extragenic SNPs. The majority of associations are novel, except PAX3 and COL11A1 genes, which were previously reported to affect normal craniofacial variation. This study identified the largest number of genetic variants associated with normal variation of craniofacial morphology to date by using a candidate gene approach, including confirmation of the two previously reported genes. These results enhance our understanding of the genetics that determines normal variation in craniofacial morphology and will be of particular value in medical and forensic fields. There is a remarkable variety of human facial appearances, almost exclusively the result of genetic differences, as exemplified by the striking resemblance of identical twins. However, the genes and specific genetic variants that affect the size and shape of the cranium and the soft facial tissue features are largely unknown. Numerous studies on animal models and human craniofacial disorders have identified a large number of genes, which may regulate normal craniofacial embryonic development. In this study we implemented a targeted candidate gene approach to select more than 1,200 polymorphisms in over 170 genes that are likely to be involved in craniofacial development and morphology. These markers were genotyped in 587 DNA s les using massively parallel sequencing and analysed for association with 104 traits generated from 3-dimensional facial images and direct craniofacial measurements. Genetic associations (p-values .00E-08) were observed between 8 craniofacial traits and 34 single nucleotide polymorphisms (SNPs), including two previously described genes and 26 novel candidate genes and intergenic regions. This comprehensive candidate gene study has uncovered the largest number of novel genetic variants affecting normal facial appearance to date. These results will appreciably extend our understanding of the normal and abnormal embryonic development and impact our ability to predict the appearance of an in idual from a DNA s le in forensic criminal investigations and missing person cases.
Publisher: Academy of Science of South Africa
Date: 03-05-2021
Abstract: The POPIA Code of Conduct for Research, as it is currently being considered, pertains to research conducted in South Africa, which, as part of the research process, uses personal information as defined under POPIA. This Discussion Document outlines the main areas relating to the processing of personal information for research purposes which the proposed Code will address, including what consent models would be permissible under POPIA the issues in relation to genetic research and the processing of personal information contained in inherited characteristics the use of information matching programmes by researchers and the use of personal information obtained from social media platforms for research. With ongoing and wide consultation with the scientific community in South Africa and all relevant stakeholders, it is hoped that the Code will provide guidance in supporting the lawful and responsible use of personal information while conducting scientific research in South Africa. The purpose and scope of the Code of Conduct for Research are set out in the accompanying Commentary available at 0.17159/sajs.2021/10935
Publisher: Elsevier BV
Date: 07-2019
Publisher: Springer Science and Business Media LLC
Date: 12-06-2018
DOI: 10.1007/S00414-017-1617-3
Abstract: The aim of this work was to investigate the possibility of secondary and tertiary DNA transfer during laundry. The modes of transfer tested were mixed and separate laundry of worn and unworn garments in household and public washing machines. In addition, the possibility of a background DNA carry-over from a washing machine's drum was investigated. In the mixed (worn and unworn garments washed together) laundry experiment, 22% of s les from new unworn socks with no traceable DNA prior to experiment produced DNA profiles post-laundry. In the tertiary DNA transfer experiment performed in a public washing machine (unworn garments only), no detectable DNA profiles were observed. S les collected from the internal drum of 25 washing and drying machines did not produce detectable STR profiles. The implications of these results are discussed in the context of forensic DNA casework analysis. Graphical Abstract ᅟA real-life scenario of secondary DNA transfer between worn and unworn garments during machine washing has been evaluated. Experiments demonstrated this scenario is possible (22% of s les) and may in fact result in high quality DNA profiles. On the contrary, testing washing machine's interior for deposition of biological material between separate washing cycles to serve as a mediator of tertiary DNA transfer resulted in no DNA profiles.
Publisher: Informa UK Limited
Date: 14-02-2019
Publisher: Elsevier BV
Date: 06-2011
Publisher: Springer Science and Business Media LLC
Date: 30-04-2019
DOI: 10.1007/S00414-019-02069-2
Abstract: When fingermarks are left on a surface, bacteria originating from the donor's skin are also deposited. The skin microbiome is believed to be extremely erse between in iduals, allowing for potential matching between the bacterial communities and touched objects, known as "bacterial profiling". This study stepped further and investigated how the bacterial profile could be used as an indicator of donor characteristics of potential forensic intelligence interest. Forty-five participants were asked to touch DNA-free playing cards with their dominant and non-dominant hands. Cards were swabbed and bacterial communities determined through 16S rRNA sequencing. Diversity and abundance of bacteria were compared to donor characteristics of gender, age, ethnicity, handedness, home location, s le location, occupation, diet type, use of moisturisers, use of hand sanitisers and use of public transport. Correlations between the bacterial profile with gender, ethnicity, diet type and hand sanitiser use were found. Specifically, the absence of Lactococcus indicated a primarily Chinese diet, while the absence of Alloiococcus indicated female gender, Asian ethnicity and hand sanitiser use. Testing of the prediction models demonstrated highest accuracy for gender estimation, while the prediction of other characteristics showed lower success. This study showed a correlation between the presence of certain bacterial species on donor's hands and personal characteristics of potential forensic relevance, thus demonstrating a novel application of microbiome genotyping in forensic science.
Publisher: Informa UK Limited
Date: 21-07-2021
Publisher: Frontiers Media SA
Date: 06-08-2020
Publisher: Springer Science and Business Media LLC
Date: 07-09-2017
Publisher: Wiley
Date: 25-03-2010
DOI: 10.1111/J.1556-4029.2010.01416.X
Abstract: The selection of the appropriate method of collection of biological material from crime scene items can be crucial to obtaining a DNA profile. The three techniques commonly used for s ling items are: cutting, swabbing, and taping. The tape s ling technique offers an advantage, in that it enables the collection of a potentially highly informative source of DNA, shed epithelial cells, from selected areas on crime scene items (the inside fingers of a glove, for instance). Furthermore, surface collection of biological material by taping reduces co-s ling of known PCR inhibitors such as clothing dyes. The correct choice of tape for crime scene item s ling is important. Not all tapes are suitable for biological trace evidence collection as well as DNA extraction. We report on one tape that met both these criteria. Three different cases are presented which demonstrate the usefulness of adhesive tape s ling of crime items. Finally, the advantages of the tape collection technique are discussed and guidelines for preferred areas of tape s ling on various casework items are presented.
Publisher: MDPI AG
Date: 10-06-2021
DOI: 10.3390/FORENSICSCI1010006
Abstract: Continuous probabilistic genotyping (PG) systems are becoming the default method for calculating likelihood ratios (LRs) for competing propositions about DNA mixtures. Calculation of the LR relies on numerical methods and simultaneous probabilistic simulations of multiple variables rather than on analytical solutions alone. Some also require modelling of in idual laboratory processes that give rise to electropherogram artefacts and peak height variance. For these reasons, it has been argued that any LR produced by continuous PG is unique and cannot be compared with another. We challenge this assumption and demonstrate that there are a set of conditions defining specific DNA mixtures which can produce an aspirational LR and thereby provide a measure of reproducibility for DNA profiling systems incorporating PG. Such DNA mixtures could serve as the basis for inter-laboratory comparisons, even when different STR lification kits are employed. We propose a procedure for an inter-laboratory comparison consistent with these conditions.
Publisher: Wiley
Date: 05-03-2012
DOI: 10.1111/J.1556-4029.2012.02095.X
Abstract: A sexual assault case resulted in a pregnancy, which was subsequently aborted. The alleged father of the fetus was unknown. Maternal and fetal types were obtained using the 11-locus AmpFℓSTR(®) SGM Plus(®) kit. The national DNA database was searched for the paternal obligatory alleles and detected two suspects who could not be excluded as father of the male fetus. Additional typing using the AmpFℓSTR(®) Minifiler(™) kit, containing three additional autosomal loci, was not sufficient to exclude either suspect. Subsequent typing using the PowerPlex(®) 16, containing four additional loci, and Y-Filer(™) kits resulted in excluding one suspect. Searching a database for paternal obligatory alleles can be fruitful, but is fraught with possible false positive results so that finding a match must be taken as only preliminary evidence.
Publisher: Elsevier BV
Date: 03-2011
DOI: 10.1016/J.SCIJUS.2010.09.001
Abstract: Sexual assault or rape cases occasionally result in unwanted pregnancies. In almost all such cases the foetus is aborted. A forensic laboratory may receive the foetus, the placenta, or paraffin embedded abortion material for paternity testing. Obtaining a foetal profile DNA from a foetus or placenta may not be successful due to the age or condition of the tissue. Moreover, maternal contamination of placental material will invariably result in a mixed DNA profile. However, the use of properly screened abortion material from paraffin blocks will almost always result in obtaining a foetal DNA profile. Furthermore, foetal tissue fixed in paraffin blocks does not require special conditions for submission and storage as required to preserve fresh foetal or placental tissue. As hospitals routinely prepare foetal tissue in paraffin blocks, which should be readily obtainable by forensic laboratories, these s les would appear to be the preferred choice for paternity testing.
Publisher: Academy of Science of South Africa
Date: 06-05-2021
DOI: 10.17159/SAJS.2021/10933C
Abstract: Jerome Amir Singh's affiliation was erroneously given as: Centre for Medical Ethics and Law, Stellenbosch University, Stellenbosch, South Africa. Thecorrect affiliation is: School of Law, Howard College, University of KwaZulu-Natal, Durban, South Africa. The error appears in the Discussion Document by Adams et al. [0.17159/sajs.2021/10933] on Page 1 under Affiliations (no. 22) and on Page 11 in the table under Authors' information, as well as in the accompanying Commentary by Adams et al. [0.17159/sajs.2021/10935] in Table 1 on Page 3.
Publisher: Elsevier BV
Date: 12-2020
Publisher: Elsevier BV
Date: 09-2018
Publisher: Elsevier BV
Date: 06-2002
DOI: 10.1016/S0378-1119(02)00703-5
Abstract: A novel human transcript, C9orf19, mapped to the genomic region involved in hereditary inclusion body myopathy (IBM2) at chromosome 9p12-p13, has been cloned and characterized. A single cDNA clone consisting of the full-length 1.9 kb transcript has been isolated from a human placenta cDNA library and further analyzed. Genomic characterization of the C9orf19 gene identified five exons extending over 27.2 kb of genomic DNA, located 12 kb centromeric to the tumor suppressor RECK gene. C9orf19 mRNA is expressed in a wide range of adult tissues as a single transcript, most abundantly in lung and peripheral blood leukocytes. The predicted protein contains the SCP-like extracellular protein signature classified to IPR001283, a family of evolutionary related proteins with extracellular domains, which includes the human glioma pathogenesis-related protein (GliPR), the human testis specific glycoprotein (TPX-1), and several other extracellular proteins from rodents (SCP), insects venom allergens (Ag5, Ag3), plants pathogenesis proteins (PR-1) and yeast hypothetical proteins. Homology searches with the deduced 154 amino acid protein sequence of C9orf19 revealed highly similar proteins in mouse, drosophila, nematode and yeast. Mutation analysis of C9orf19 in IBM2 patients excluded it as the disease causing gene and revealed four single nucleotide polymorphisms within and in the vicinity of the gene, which will certainly be useful tools to study its potential role in several human diseases mapped to chromosome 9p12-p13. Parallel to this study, the gene termed GNE, approximately 50 kb centromeric to C9orf19, was shown to be the disease causing gene in IBM2.
Publisher: Avens Publishing Group
Date: 2013
Publisher: Wiley
Date: 30-01-2018
Abstract: The Early Access AmpliSeq™ Mitochondrial Panel lifies whole mitochondrial genomes for phylogenetic and kinship identifications, using Ion Torrent™ technology. There is currently limited information on its performance with degraded DNA, a common occurrence in forensic s les. This study evaluated the performance of the Panel with DNA s les degraded in vitro, to mimic conditions commonly found in forensic investigations. Purified DNA from five in iduals was heat‐treated at five time points each (125°C for 0, 30, 60, 120, and 240 min total n = 25). The quality of DNA was assessed via a real‐time DNA assay of genomic DNA and prepared for massively parallel sequencing on the Ion Torrent™ platform. Mitochondrial sequences were obtained for all s les and had an licon coverage averaging between 66X to 2803X. Most licons (157/162) displayed high coverages (452 ± 333X), while reads with less than 100X coverage were recorded in five licons only (90 ± 5X). Amplicon coverage was decreased with prolonged heating. At 72% strand balance, reads were well balanced between forward and reverse strands. Using a coverage threshold of ten reads per SNP, complete sequences were recovered in all s les and resolved kinship and, haplogroup relations. Additionally, the HV1 and HV2 regions of the reference and 240‐min heat‐treated s les ( n = 10) were Sanger‐sequenced for concordance. Overall, this study demonstrates the efficacy of a novel forensic Panel that recovers high quality mitochondrial sequences from degraded DNA s les.
Publisher: Springer Science and Business Media LLC
Date: 27-08-2001
DOI: 10.1038/NG718
Location: United States of America
Location: United States of America
Start Date: 2017
End Date: 2018
Funder: University of Technology Sydney
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