Displaying publications 1 - 20 of 112 in total

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  1. Bashir M, Hassan NH
    Methods Mol Biol, 2016;1420:135-42.
    PMID: 27259737 DOI: 10.1007/978-1-4939-3597-0_11
    Insertion/deletion polymorphisms (INDELs) are a relatively new class of a DNA marker to be used in forensic casework; used most commonly as a supplementary method to STR-based typing. INDELs, like SNPs, are particularly useful for the analysis of highly degraded DNA as the amplicon sizes are typically below 160 bp; they can also be valuable as an additional tool to help resolve kinship cases, with the advantage over STRs that they do not have high mutation rates. INDELs have an advantage over SNPs in that they are length polymorphisms and so can be analyzed by simply measuring the length of the allele(s). The Qiagen Investigator(®) DIPplex Kit is currently only one of two commercially available kits for the amplification of INDEL polymorphisms; it amplifies 30 biallelic INDEL loci and the amelogenin locus. The primers used are fluorescence labeled with 6-FAM, BTG, BTY, and BTR. This technique is robust, relatively simple, and the results are analyzed using the same capillary electrophoresis equipment and software as used for STR typing.
    Matched MeSH terms: DNA Fingerprinting/methods
  2. Lee LH, Cheah YK, Nurul Syakima AM, Shiran MS, Tang YL, Lin HP, et al.
    Genet. Mol. Res., 2012;11(2):1627-41.
    PMID: 22782582 DOI: 10.4238/2012.June.15.12
    Fifty-seven proteobacterium species were successfully isolated from soils of Barrientos Island of the Antarctic using 11 different isolation media. Analysis of 16S rDNA sequencing of these isolates showed that they belonged to eight different genera, namely Bradyrhizobium, Sphingomonas, Methylobacterium, Caulobacter, Paracoccus, Ralstonia, Rhizobium, and Staphylococcus. All isolates were studied for capability of producing antimicrobial and antifungal secondary metabolites using high-throughput screening models. Approximately 23 (13/57) and 2% (1/57) of isolates inhibited growth of Candida albicans ATCC 10231(T) and Staphylococcus aureus ATCC 51650(T), respectively. These results indicated that proteobacterium species isolates from Antarctic could serve as potential source of useful bioactive metabolites. Enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting produced nine clusters and 13 single isolates, with a high D value of 0.9248. RAPD fingerprinting produced six clusters and 13 single isolates, with a relatively low D value of 0.7776. ERIC-PCR analysis proved to have better discrimination capability than RAPD analysis and generated better clustering for all proteobacterium species isolates. We conclude that ERIC-PCR is a robust, reliable and rapid molecular typing method for discriminating different genera of proteobacteria.
    Matched MeSH terms: DNA Fingerprinting/methods*
  3. Panneerchelvam S, Thevan KK, KokFai L, Saravanakumar M, Sumathy V, Yuvaneswari KC, et al.
    J Forensic Sci, 2004 Jul;49(4):863-4.
    PMID: 15317219
    Matched MeSH terms: DNA Fingerprinting/methods
  4. Panneerchelvam S, Haslindawaty N, Ravichandran M, Norazmi MN, Zainuddin ZF
    J Forensic Sci, 2003 Mar;48(2):451-2.
    PMID: 12665016
    Matched MeSH terms: DNA Fingerprinting/methods
  5. Alfizah H, Norazah A, Nordiah AJ, Lim VKE
    Med J Malaysia, 2002 Sep;57(3):319-28.
    PMID: 12440272 MyJurnal
    Methicillin-resistant Staphylococcus aureus (MRSA) has been prevalent in our hospital over the last three years. Differentiation among MRSA strains by DNA typing in addition to antibiotic resistance pattern surveillance is crucial in order to implement infection control measures. The aim of this study was to characterize MRSA isolates from patients admitted to Hospital Universiti Kebangsaan Malaysia (HUKM) by phenotypic (analyses of antibiotic susceptibility pattern) and genotypic (PFGE) techniques to determine the genetic relatedness of the MRSA involved and to identify endemic clonal profiles of MRSA circulating in HUKM. Seventy one MRSA strains collected between January to March 2000 from patients from various wards in HUKM were tested for antimicrobial resistance and typed by pulsed-field gel electrophoresis (PFGE). Four major types of PFGE patterns were identified (A, B, C and D) among MRSA strains. Two predominant PFGE types were recognised, Type A (59.2%) and Type B (33.8%). Most of these strains were isolated from ICU, Surgical wards and Medical wards. MRSA strains with different PFGE patterns appeared to be widespread among wards. Strains with the same antibiotype could be of different PFGE types. Most of isolates were resistant to ciprofloxacin, erythromycin, gentamicin and penicillin. One isolate with a unique PFGE pattern Type D and susceptible to gentamicin was identified as a different clone. Some isolates obtained from the same patient showed different PFGE subtypes suggesting that these patients were infected/colonized with multiple MRSA strains. PFGE analysis suggests that MRSA strains with different PFGE types was propagated within our hospital. The relationship between antibiotic susceptibility and PFGE patterns was independent. The ability of PFGE technique in differentiating our MRSA strains make it a method of choice for investigating the source, transmission and spread of nosocomial MRSA infection, and thus an appropriate control programme can be implemented to prevent the spread of MRSA infection.
    Matched MeSH terms: DNA Fingerprinting*
  6. Othman MI, Seah LH, Panneerchelvam S, Nor NM
    J Forensic Sci, 2004 Jan;49(1):190-1.
    PMID: 14979376
    Matched MeSH terms: DNA Fingerprinting/methods
  7. Azman AR, Mahat NA, Wahab RA, Ahmad WA, Puspanadan JK, Huri MAM, et al.
    Biotechnol Lett, 2021 Apr;43(4):881-898.
    PMID: 33389272 DOI: 10.1007/s10529-020-03052-3
    OBJECTIVE: Optimisation of the green novel nanobio-based reagent (NBR) for rapid visualisation of groomed fingerprints on wet non-porous substrates using response surface methodology and assessment of its stability and sensitivity were attempted for forensic applications.

    RESULTS: Scanning electron microscopy images demonstrated successful attachments of NBR onto the constituents of fingerprints on the substrates. The highest average quality of visualised fingerprints was attained at the optimum condition (100 mg of CRL; 75 mg of acid-functionalised multi-walled carbon nanotubes; 5 h of immobilisation). The NBR produced comparable average quality of fingerprints with the commercially available small particle reagent, even after 4 weeks of storage (without any preservatives) in both chilled and sultry conditions. The NBR was sensitive enough to visualise the increasingly weaker fingerprints, particularly on glass slides.

    CONCLUSION: The optimised novel NBR could be the relatively greener option for visualising latent fingerprints on wet, non-porous substrates for forensic applications.

    Matched MeSH terms: DNA Fingerprinting/methods*
  8. Chan Mun Wei J, Zhao Z, Li SC, Ng YK
    Comput Biol Chem, 2018 Jun;74:428-433.
    PMID: 29625871 DOI: 10.1016/j.compbiolchem.2018.03.010
    DNA fingerprinting, also known as DNA profiling, serves as a standard procedure in forensics to identify a person by the short tandem repeat (STR) loci in their DNA. By comparing the STR loci between DNA samples, practitioners can calculate a probability of match to identity the contributors of a DNA mixture. Most existing methods are based on 13 core STR loci which were identified by the Federal Bureau of Investigation (FBI). Analyses based on these loci of DNA mixture for forensic purposes are highly variable in procedures, and suffer from subjectivity as well as bias in complex mixture interpretation. With the emergence of next-generation sequencing (NGS) technologies, the sequencing of billions of DNA molecules can be parallelized, thus greatly increasing throughput and reducing the associated costs. This allows the creation of new techniques that incorporate more loci to enable complex mixture interpretation. In this paper, we propose a computation for likelihood ratio that uses NGS (next generation sequencing) data for DNA testing on mixed samples. We have applied the method to 4480 simulated DNA mixtures, which consist of various mixture proportions of 8 unrelated whole-genome sequencing data. The results confirm the feasibility of utilizing NGS data in DNA mixture interpretations. We observed an average likelihood ratio as high as 285,978 for two-person mixtures. Using our method, all 224 identity tests for two-person mixtures and three-person mixtures were correctly identified.
    Matched MeSH terms: DNA Fingerprinting
  9. Yeasmin L, Ali MN, Gantait S, Chakraborty S
    3 Biotech, 2015 Feb;5(1):1-11.
    PMID: 28324361 DOI: 10.1007/s13205-014-0201-5
    Genetic diversity represents the heritable variation both within and among populations of organisms, and in the context of this paper, among bamboo species. Bamboo is an economically important member of the grass family Poaceae, under the subfamily Bambusoideae. India has the second largest bamboo reserve in Asia after China. It is commonly known as "poor man's timber", keeping in mind the variety of its end use from cradle to coffin. There is a wide genetic diversity of bamboo around the globe and this pool of genetic variation serves as the base for selection as well as for plant improvement. Thus, the identification, characterization and documentation of genetic diversity of bamboo are essential for this purpose. During recent years, multiple endeavors have been undertaken for characterization of bamboo species with the aid of molecular markers for sustainable utilization of genetic diversity, its conservation and future studies. Genetic diversity assessments among the identified bamboo species, carried out based on the DNA fingerprinting profiles, either independently or in combination with morphological traits by several researchers, are documented in the present review. This review will pave the way to prepare the database of prevalent bamboo species based on their molecular characterization.
    Matched MeSH terms: DNA Fingerprinting
  10. Panneerchelvam S, Norazmi MN
    Malays J Med Sci, 2003 Jul;10(2):20-6.
    PMID: 23386793 MyJurnal
    The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection.
    Matched MeSH terms: DNA Fingerprinting
  11. Maruyama S, Minaguchi K, Takezaki N, Nambiar P
    Leg Med (Tokyo), 2008 May;10(3):160-2.
    PMID: 18180191 DOI: 10.1016/j.legalmed.2007.11.002
    Allele frequencies for 15 short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA (AmpF/STR Identifiler PCR Amplification kit, PE Applied Biosystems) were obtained from a sample of 110 unrelated individuals from the Malay population living in and around Kuala Lumpur, Malaysia, and the characteristics of the population was compared with other East Asian populations.
    Matched MeSH terms: DNA Fingerprinting
  12. Pern YC, Lee SY, Ng WL, Mohamed R
    3 Biotech, 2020 Mar;10(3):103.
    PMID: 32099744 DOI: 10.1007/s13205-020-2072-2
    Tree species in the Aquilarieae tribe of the Thymelaeaceae family produce agarwood, a natural product highly valued for its fragrance, but the species are under threat due to indiscriminate harvesting. For conservation of these species, molecular techniques such as DNA profiling have been used. In this study, we assessed cross-amplification of microsatellite markers, initially developed for three Aquilaria species (A.crassna, A.malaccensis, and A.sinensis), on ten other agarwood-producing species, including members of Aquilaria (A.beccariana, A.hirta, A.microcarpa, A.rostrata, A.rugosa, A.subintegra, and A.yunnanensis) and Gyrinops (G.caudata, G.versteegii, and G.walla), both from the Aquilarieae tribe. Primers for 18 out of the 30 microsatellite markers successfully amplified bands of expected sizes in 1 sample each of at least 10 species. These were further used to genotype 74 individuals representing all the 13 studied species, yielding 13 cross-amplifiable markers, of which only 1 being polymorphic across all species. At each locus, the number of alleles ranged from 7 to 23, indicating a rather high variability. Four markers had relatively high species discrimination power. Our results demonstrated that genetic fingerprinting can be an effective tool in helping to manage agarwood genetic resources by potentially supporting the chain-of-custody of agarwood and its products in the market.
    Matched MeSH terms: DNA Fingerprinting
  13. Bilung, Lesley Maurice, Yong, Sy Fuh, Linang, Velnetti, Benjamin, Adam, Vincent, Micky, Apun, Kasing, et al.
    MyJurnal
    Thirty one Vibrio cholera isolates recovered from cholera outbreak in Bintulu, Sarawak (Malaysia) were detected with the presence of ctx gene by using specific PCR. These isolates were further characterized and differentiated by using the Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR) and BOX-PCR to determine their genomic fingerprints. The specific PCR result confirmed the identities of 27 isolates out of 31 as pathogenic V. cholerae. The ERIC-PCR generated several genetic profiles consisting of 4-6 bands with sizes in the range of 100 to 600 bp, while the BOX-PCR produced profiles numbering 2-7 bands in the sizes between 200 to 1000 bp. Based on the dendrogram generated from the DNA fingerprinting profiles (ERIC-PCR and BOX-PCR), all of the isolates can be divided into 2 main clusters that is further divided into 2 sub-clusters. The low genetic diversity of the isolates indicated the outbreak of V. cholerae in the study area was due to the contamination from a single or few sources of V. cholerae.
    Matched MeSH terms: DNA Fingerprinting
  14. Vincent, M., Chan, C. S. W., Apun, K.
    MyJurnal
    The present study was conducted to assess the rapid molecular identification and characterization of 45 Vibrio parahaemolyticus isolates from 15 samples of 3 different types of fish (Kembung, Bawal and Sangeh) in the Kuching-Samarahan district. Polymerase chain reaction (PCR) based confirmation was done targeting the 450 bp fragment of the thermolabile (tl) gene, while DNA fingerprinting was performed using Randomly Amplified Polymorphic DNA (RAPD) PCR with the primer GEN15008. All the 45 V. parahaemolyticus isolates were positive for the tl gene, however, only 34 were typable via RAPD-PCR with bands sizes ranging from slightly over 250 bp to 2.5 kbp. The degree of diversity was then determined via the Simpson Index which showed a value of 0.891, indicating high diversity among the isolates. Data from the RAPD-PCR fingerprints were later used to construct a dendrogram for clustal analysis. From the dendrogram, the 34 isolates were grouped into 2 major clusters containing 26 and 8 isolates, respectively. Further analyses of the dendrogram also indicated that the 34 isolated were clustered according to the period of sampling. This is an interesting observation as it shows the high discriminatory capability of RAPD-PCR to be used as molecular epidemiological tool to study the temporal distribution of V. parahaemolyticus.
    Matched MeSH terms: DNA Fingerprinting
  15. Adzitey F, Ali GR, Huda N, Ahmad R
    3 Biotech, 2013 Dec;3(6):521-527.
    PMID: 28324423 DOI: 10.1007/s13205-013-0115-7
    Salmonella species are important foodborne pathogens that can cause illness and death in humans. The objective of this study was to determine the genetic relatedness of 115 Salmonella strains isolated from ducks and their environment using random amplified polymorphic deoxyribonucleic acid (RAPD). The analysis of Salmonella strains by RAPD produced DNA fingerprints of different sizes for differentiation purposes, and cluster analysis at a coefficient of 0.85 grouped the Salmonella strains into various clusters and singletons. S. Typhimurium were grouped into nine clusters and ten singletons, S. Hadar were grouped into seven clusters and nine singletons, S. Enteritidis were grouped into four clusters and five singletons, S. Braenderup were grouped into five clusters and four singletons, S. Albany were grouped into two clusters and seven singletons, and S. Derby were grouped into two clusters and four singletons at a coefficient of 0.85 with discriminatory index (D) ranging from 0.879 to 0.957. With the exception of S. Typhimurium strains which were grouped into three major groups (genotypes) by RAPD analysis, the rest were grouped into two major genotypes. RAPD was a useful genotyping tool for determining the genetic relatedness of the duck Salmonella strains. Comparison of the genetic relatedness among foodborne pathogens and their sources of isolation are important to trace their source and possibly the source of human infection.
    Matched MeSH terms: DNA Fingerprinting
  16. Nakamura Y, Samejima M, Minaguchi K, Nambiar P
    Bull. Tokyo Dent. Coll., 2016;57(4):233-239.
    PMID: 28049971 DOI: 10.2209/tdcpublication.2016-1400
    Short tandem repeat (STR) polymorphisms were investigated in 341 unrelated Malay individuals (218 males and 123 females) living in or around Kuala Lumpur by using a forensic analysts kit. The following STRs were targeted: D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA. The purpose of this study was to elucidate population genetics in Malaysia and calculate statistical parameters for forensic and anthropological research. Data on these STRs in the target population were obtained and subjected to statistical analysis. Accordance with the Hardy-Weinberg equilibrium was proven for all the loci targeted. The combined power of discrimination was greater than 0.9999999999, indicating that this multiplex system is an excellent tool for forensic casework. The allele frequency in the data were weighed against that in four other local populations (Chinese, Iranian, Belgian, and African). The average coefficient of correlation was strongest in the order of Africa (0.092522), Belgium (0.264822), Iran (0.404363), and China (0.706661). These results are consistent with what is known about the anthropological history of and prehistoric human migration in the Malay region. We believe that these data offer a valuable anthropological resource, being applicable to the statistical evaluation of DNA evidence in human identification, as well as the determination of ethnicity in healthy populations.
    Matched MeSH terms: DNA Fingerprinting
  17. Kofi AE, Agyemang DA, Ghansah A, Awandare GA, Hakim HM, Khan HO, et al.
    Biochem Genet, 2023 Oct;61(5):1850-1866.
    PMID: 36869999 DOI: 10.1007/s10528-023-10347-3
    Autosomal short tandem repeat (STR) population data collected from a well characterized population are needed to correctly assigning the weight of DNA profiles in the courtroom and widely used for ancestral analyses. In this study, allele frequencies for the 15 autosomal short tandem repeat (STR) loci included in the AmpFlSTR® Identifiler® plus kit (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA) were obtained by genotyping 332 unrelated individuals of Ghanaian origin. Statistical tests on STR genotype data showed no significant departure from Hardy-Weinberg equilibrium (HWE). The overall match probability, combined power of exclusion and combined power of discrimination for these loci were 1 in 3.85 × 1017, 0.99999893 and 0.99999998, respectively. Polymorphic information content (PIC) greater than 0.70 was observed for all loci except TH01 and D13S317. These statistical parameters confirm that this combination of loci is valuable for forensic identification and parentage analysis. Our results were also compared with those for 20 other human populations analyzed for the same set of markers. We observed that the Ghanaian population grouped with other African populations in two-dimensional principal coordinate (PCO) and a neighbor-joining (N-J) data mapping and placed closest to Nigerians. This observation reflects cultural similarities and geographical factors, coupled with the long history of migration and trading activities between Ghana and Nigeria. Our report provides what we believe to be the first published autosomal STR data for the general Ghanaian population using 15 loci genotyped using the AmpFlSTR® Identifiler® plus kit methodology. Our data show that the loci tested have sufficient power to be used reliably for DNA profiling in forensic casework and help to elucidate the genetic history of people living in the country.
    Matched MeSH terms: DNA Fingerprinting
  18. Javadi Nobandegani MB, Saud HM, Yun WM
    Biomed Res Int, 2014;2014:496562.
    PMID: 25580434 DOI: 10.1155/2014/496562
    Primers corresponding to conserved bacterial repetitive of BOX elements were used to show that BOX-DNA sequences are widely distributed in phosphate solubilizing Pseudomonas strains. Phosphate solubilizing Pseudomonas was isolated from oil palm fields (tropical soil) in Malaysia. BOX elements were used to generate genomic fingerprints of a variety of Pseudomonas isolates to identify strains that were not distinguishable by other classification methods. BOX-PCR, that derived genomic fingerprints, was generated from whole purified genomic DNA by liquid culture of phosphate solubilizing Pseudomonas. BOX-PCR generated the phosphate solubilizing Pseudomonas specific fingerprints to identify the relationship between these strains. This suggests that distribution of BOX elements' sequences in phosphate solubilizing Pseudomonas strains is the mirror image of their genomic structure. Therefore, this method appears to be a rapid, simple, and reproducible method to identify and classify phosphate solubilizing Pseudomonas strains and it may be useful tool for fast identification of potential biofertilizer strains.
    Matched MeSH terms: DNA Fingerprinting*
  19. Azura MN, Norazah A, Kamel AG, Zorin SA
    PMID: 21323173
    We have analysed DNA fingerprinting patterns by pulsed-field gel electrophoresis (PFGE) of 52 unrelated Burkholderia pseudomallei strains isolated from septicemic and localized infections from Malaysian subjects. A total of 38 PFGE types were observed among 36 septicemic and 16 localized strains with no predominant pattern. Type 25 was seen in 2 epidemiologically related strains, suggesting human to human transmission. Twelve PFGE types were shared among 26 strains (21 septicemic and 5 localized) showing close genetic relatedness with coefficient of similarity of 0.81 to 1.0. The other 26 strains (15 septicemic and 11 localized) were unrelated as shown by the similarity coefficient of < 0.8. This study showed that our B. pseudomallei strains in Malaysia were mainly heterogenous with no predominant type both in septicemic or localized strains.
    Matched MeSH terms: DNA Fingerprinting/methods
  20. Ang HC, Sornarajah R, Lim SE, Syn CK, Tan-Siew WF, Chow ST, et al.
    Forensic Sci Int, 2005 Mar 10;148(2-3):243-5.
    PMID: 15639622
    Allele frequencies for the 13 CODIS (Combined DNA Index System, USA) STR loci included in the AmpFISTR Profiler Plus and AmpFISTR Cofiler kits (Applied Biosystems, Foster City, USA) were determined in a sample of 197 unrelated Malays in Singapore.
    Matched MeSH terms: DNA Fingerprinting/methods
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