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Analysis of 30 Biallelic INDEL Markers Using the Investigator DIPplex(®) Kit

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
Fulltext Analysis of Antarctic proteobacteria by PCR fingerprinting and screening for antimicrobial secondary metabolites

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*
Allele frequency distribution for 9 STR loci in the Tamil population of Malaysia

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
Allele frequency distribution for 10 STR loci in the Malay population of Malaysia

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
Allele frequencies for the PowerPlex 16 STR loci in Javanese population in Malaysia

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
Box-Behnken design optimisation of a green novel nanobio-based reagent for rapid visualisation of latent fingerprints on wet, non-porous substrates

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*
Construction of 13-locus X-STR multiplex PCR system that reinforces Argus X-12 kit discrimination capacity: Application to the Malay population

Minaguchi K, Samejima M, Nambiar P, Kaneko Y, Ochiai E, Kakimoto Y, et al.

Leg Med (Tokyo), 2024 Sep;70:102463.
PMID: 38823287 DOI: 10.1016/j.legalmed.2024.102463

Closely linked groups of markers on the X chromosome are very useful for testing complex kinship relationships involving X-STR transmission. The Argus X-12 kit, a unique commercially available kit, can obtain haplotypes of 4 linkage groups (LGs) consisting of 3 markers. Although many population data have been reported for forensic purposes, differences in discrimination ability exist between LG1 and LG2, 3, and 4 in East Asian populations, and the data of this kit would become more useful if the discrimination ability of the latter groups were increased. Therefore, for matches found using this kit for some linkage group data, then to increase the identification ability, we additionally introduced 13 X-STR loci and established a method allowing comparison using data from 25 loci. The 13X-STRs add two locus data to each of LG2, 3, and 4, and also add two closely linked group (CLG) data between LG2 and 3 and LG3 and 4 in one multiplex PCR. Assessment of this method for a Malay population for which data by Argus X-12 had already been reported showed that the frequencies of distinct haplotypes in LG2, 3, and 4 were increased by 33.0-42.6 %, and frequencies of unique haplotypes increased by 45.4-59.2 %. The respective haplotype diversity values of the additional 3-locus and 4-locus CLGs were 0.9838 and 0.9939, which helps to improve discriminatory power and to predict recombination locations on the X chromosome. Although we have been testing these loci with Japanese subjects, this system would also be useful for the Malay population.

Matched MeSH terms: DNA Fingerprinting/methods
STR data for the 13 CODIS loci in Singapore Malays

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
Polymorphism of 9 STRs in ethnic Chinese population of Malaysia

Panneerchelvam S, Kumara KT, KokFai L, Saravanakumar M, Sumathy V, Yuvaneswari KC, et al.

J Forensic Sci, 2004 Sep;49(5):1132-3.
PMID: 15461127
Matched MeSH terms: DNA Fingerprinting/methods
Fulltext Agro-ecological variations of sheath rot disease of rice caused by Sarocladium oryzae and DNA fingerprinting of the pathogen's population structure

Tajul Islam Chowdhury M, Salim Mian M, Taher Mia MA, Rafii MY, Latif MA

Genet. Mol. Res., 2015 Dec 28;14(4):18140-52.
PMID: 26782461 DOI: 10.4238/2015.December.23.1

To examine the impact of regional and seasonal variations on the incidence and severity of sheath rot, a major seed-borne disease of rice caused by Sarocladium oryzae, data on incidence and severity were collected from 27 selected fields in the Gazipur, Rangpur, Bogra, Chittagong, Comilla, Gopalgonj, Jessore, Manikgonj, and Bhola districts of Bangladesh in rain-fed and irrigated conditions. Cultural variability of 29 pathogen isolates obtained from 8 different locations was studied on potato dextrose agar (PDA) and genetic variability was determined by DNA fingerprinting using variable number tandem repeat-polymerase chain reaction markers. Overall, disease incidence and severity were higher in irrigated rice. Disease incidence and severity were highest in the Bhola district in rain-fed rice and lowest in irrigated rice. Mycelial growth of 29 representative isolates was found to vary on PDA and the isolates were divided into 6 groups. The range of the overall size of conidia of the selected isolates was 2.40-7.20 x 1.20-2.40 μm. Analysis of the DNA fingerprint types of the 29 isolates of S. oryzae, obtained from the amplification reactions, revealed 10 fingerprinting types (FPTs) that were 80% similar. FPT-1 was the largest group and included 13 isolates (44.8%), while FPT-2 was the third largest group and included 3 isolates. Each of FPT-3, 4, 5, and 6 included only 1 isolate. We observed no relationship between cultural and genetic groupings.

Matched MeSH terms: DNA Fingerprinting/methods
Genotypic characterization of Salmonella typhi by amplified fragment length polymorphism fingerprinting provides increased discrimination as compared to pulsed-field gel electrophoresis and ribotyping

Nair S, Schreiber E, Thong KL, Pang T, Altwegg M

J Microbiol Methods, 2000 Jun;41(1):35-43.
PMID: 10856775

Amplified fragment length polymorphism (AFLP) is a recently developed, PCR-based high resolution fingerprinting method that is able to generate complex banding patterns which can be used to delineate intraspecific genetic relationships among bacteria. In the present study, AFLP was evaluated for its usefulness in the molecular typing of Salmonella typhi in comparison to ribotyping and pulsed-field gel electrophoresis (PFGE). Six S. typhi isolates from diverse geographic areas (Malaysia, Indonesia, India, Chile, Papua New Guinea and Switzerland) gave unique, heterogeneous profiles when typed by AFLP, a result which was consistent with ribotyping and PFGE analysis. In a further study of selected S. typhi isolates from Papua New Guinea which caused fatal and non-fatal disease previously shown to be clonally related by PFGE, AFLP discriminated between these isolates but did not indicate a linkage between genotype with virulence. We conclude that AFLP (discriminatory index=0.88) has a higher discriminatory power for strain differentiation among S. typhi than ribotyping (DI=0.63) and PFGE (DI=0.74).

Matched MeSH terms: DNA Fingerprinting/methods*
STR Data for the AmpFlSTR Identifiler loci in three ethnic groups (Malay, Chinese, Indian) of the Malaysian population

Seah LH, Jeevan NH, Othman MI, Jaya P, Ooi YS, Wong PC, et al.

Forensic Sci Int, 2003 Dec 17;138(1-3):134-7.
PMID: 14642733

Allele frequencies for the 15 STR loci in the AmpFlSTR Identifiler kit were determined and compared for the three main ethnic groups of the Malaysian population comprising 210 Malays, 219 Chinese and 209 Indians. Blood was placed on FTA paper and DNA was purified in-situ.

Matched MeSH terms: DNA Fingerprinting/methods
Pangolin Indexing System: implications in forensic surveillance of large seizures

Singh A, Priyambada P, Jabin G, Singh SK, Joshi BD, Venkatraman C, et al.

Int J Legal Med, 2020 Sep;134(5):1613-1618.
PMID: 32621146 DOI: 10.1007/s00414-020-02362-5

Demand for pangolin scales in East Asia has increased dramatically in the past two decades, raising concern to the pangolin survival and bringing them to the brink of local extinction. Enumerating the number of individuals from the seized pangolin scales primarily goes undocumented, mostly due to the unavailability of the appropriate methods. In this study, we developed a Pangolin Indexing System, a multi-locus STR panel of eight dinucleotide microsatellites that showed promising results in individualization and assignment of scales into Chinese and Indian pangolins. The combined power of exclusion was 0.83 and 0.99 for Chinese and Indian pangolin. The select panel of eight polymorphic STRs exhibited the cumulative probability of identity 3.7 × 10-9 for Indian pangolin and 3.6 × 10-7 for Chinese pangolin and identified 51 unique genotypes from the 74 scales selected from the four pangolin seizures. The study demonstrated the first report of cross-species validation of STRs developed from Malayan pangolin to Indian pangolin and showed the potential application of Pangolin Indexing System in screening of large seizures through DNA profiling from the scales of Indian and Chinese pangolin.

Matched MeSH terms: DNA Fingerprinting/methods*
Evaluation of Y chromosomal SNP haplogrouping in the HID-Ion AmpliSeq™ Identity Panel

Ochiai E, Minaguchi K, Nambiar P, Kakimoto Y, Satoh F, Nakatome M, et al.

Leg Med (Tokyo), 2016 Sep;22:58-61.
PMID: 27591541 DOI: 10.1016/j.legalmed.2016.08.001

The Y chromosomal haplogroup determined from single nucleotide polymorphism (SNP) combinations is a valuable genetic marker to study ancestral male lineage and ethical distribution. Next-generation sequencing has been developed for widely diverse genetics fields. For this study, we demonstrate 34 Y-SNP typing employing the Ion PGM™ system to perform haplogrouping. DNA libraries were constructed using the HID-Ion AmpliSeq™ Identity Panel. Emulsion PCR was performed, then DNA sequences were analyzed on the Ion 314 and 316 Chip Kit v2. Some difficulties became apparent during the analytic processes. No-call was reported at rs2032599 and M479 in six samples, in which the least coverage was observed at M479. A minor misreading occurred at rs2032631 and M479. A real time PCR experiment using other pairs of oligonucleotide primers showed that these events might result from the flanking sequence. Finally, Y haplogroup was determined completely for 81 unrelated males including Japanese (n=59) and Malay (n=22) subjects. The allelic divergence differed between the two populations. In comparison with the conventional Sanger method, next-generation sequencing provides a comprehensive SNP analysis with convenient procedures, but further system improvement is necessary.

Matched MeSH terms: DNA Fingerprinting/methods
Fulltext DNA fingerprinting of methicillin-resistant Staphylococcus aureus by pulsed-field gel electrophoresis (PFGE): comparison of strains from 2 Malaysian hospitals

Norazah A, Liew SM, Kamel AG, Koh YT, Lim VK

Singapore Med J, 2001 Jan;42(1):15-9.
PMID: 11361232

To determine and compare the pulsed-field gel electrophoresis (PFGE) patterns of endemic MRSA strains in 2 major Malaysian hospitals and to compare the PFGE patterns with antibiotypes of the strains studied.

Matched MeSH terms: DNA Fingerprinting/methods*
Genetic diversity and forensic statistical support for the 12 X-STR markers in the Malaysian Indian population using Qiagen Investigator® Argus X-12 QS kit

Alwi AR, Mahat NA, Mohd Salleh F, Ishar SM, Kamaluddin MR, A Rashid MR, et al.

Leg Med (Tokyo), 2024 May;68:102416.
PMID: 38325234 DOI: 10.1016/j.legalmed.2024.102416

X-chromosome short tandem repeats (X-STRs) are useful for human identification, especially in complex kinship scenarios. Since forensic statistical parameters vary among populations and the X-STRs population data for the diverse population of Peninsular Malaysia's are unavailable, this attempt for Indians (n = 201) appears forensically relevant to support the 12 X-STRs markers' evidential value for human identification in Malaysia. The Qiagen Investigator® Argus X-12 QS kit showed that DXS10135 was the most polymorphic locus with high genetic diversity, polymorphism information richness, heterozygosity, and exclusion power. Based on allele frequencies, the strength of discrimination and mean exclusion chance (MECKrüger, MECKishida, MECDesmarais, and MECDesmaraisDuo) values for the Malaysian Indians were ≥0.999997790686228. As for haplotype frequencies, the overall discrimination power and mean exclusion probability (MECKrüger, MECKishida, MECDesmarais, and MECDesmaraisDuo) were ≥0.9999984801951. The genetic distance, neighbor-joining phylogenetic tree, and principal component analysis also supported the evidential value of the 12 X-STRs markers for forensic practical caseworks in Malaysia.

Matched MeSH terms: DNA Fingerprinting/methods
DNA fingerprinting of septicemic and localized Burkholderia pseudomallei isolates from Malaysian patients

Azura MN, Norazah A, Kamel AG, Zorin SA

Southeast Asian J Trop Med Public Health, 2011 Jan;42(1):114-21.
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
Fulltext Molecular characterization of Streptococcus agalactiae strains isolated from fishes in Malaysia

Amal MN, Zamri-Saad M, Siti-Zahrah A, Zulkafli AR, Nur-Nazifah M

J Appl Microbiol, 2013 Jul;115(1):20-9.
PMID: 23557382 DOI: 10.1111/jam.12210

AIMS: The aim of this study was to characterize Streptococcus agalactiae strains that were isolated from fishes in Malaysia using random amplified polymorphic DNA (RAPD) and repetitive extragenic palindromic PCR (REP-PCR) techniques.
METHODS AND RESULTS: A total of 181 strains of Strep. agalactiae isolated from red hybrid tilapia (Oreochromis sp.) and golden pompano (Trachinotus blochii) were characterized using RAPD and REP-PCR techniques. Both the fingerprinting techniques generated reproducible band patterns, differing in the number and molecular mass amplicons. The RAPD technique displayed greater discriminatory power by its production of more complex binding pattern and divided all the strains into 13 groups, compared to 9 by REP-PCR technique. Both techniques showed the availability to differentiate the genetic profiles of the strains according to their geographical location of origin. Three strains of Strep. agalactiae that were recovered from golden pompano showed a genetic dissimilarity from the strains isolated from red hybrid tilapia, while the strain of ATCC 27956 that recovered from bovine displayed a unique profile for both methods.
CONCLUSIONS: Both techniques possess excellent discriminative capabilities and can be used as a rapid means of comparing Strep. agalactiae strains for future epidemiological investigation.
SIGNIFICANCE AND IMPACT OF THE STUDY: Framework as the guideline in traceability of this disease and in the search for potential local vaccine candidates for streptococcosis in this country.

Matched MeSH terms: DNA Fingerprinting/methods
Microsatellite and minisatellite markers based DNA fingerprinting and genetic diversity of blast and ufra resistant genotypes

Latif MA, Rafii Yusop M, Motiur Rahman M, Bashar Talukdar MR

C. R. Biol., 2011 Apr;334(4):282-9.
PMID: 21513897 DOI: 10.1016/j.crvi.2011.02.003

A total of 78 alleles and 29 loci were detected from nine microsatellite and three minisatellite markers, respectively across 26 blast and ufra disease resistant genotypes. For blast resistant genotypes, the Polymorphic Information Content (PIC) values ranged from 0.280 to 0.726 and RM21 was considered as the best marker. PIC values ranged from 0.5953 to 0.8296 for ufra resistant genotypes and RM23 was the best marker for characterization of ufra resistant genotypes. The genetic similarity analysis using UPGMA clustering generated nine clusters with coefficient of 0.66 for blast resistant genotypes while five genetic clusters with similarity coefficient of 0.42 for ufra resistant genotypes. In order to develop resistant varieties of two major diseases of rice, hybridisation should be made using the parents, BR29 and NJ70507, BR36 and NJ70507 for blast, while BR11 and Aokazi, BR3 and Aokazi, Rayda and BR3 and Rayda and BR11 for ufra.

Matched MeSH terms: DNA Fingerprinting/methods*
Higher failures of amelogenin sex test in an Indian population group

Chang YM, Burgoyne LA, Both K

J Forensic Sci, 2003 Nov;48(6):1309-13.
PMID: 14640276

The human sex test in forensic multiplexes is based on the amelogenin gene on both the X and Y chromosomes commonly used in sex genotyping. In this study of 338 male individuals in a Malaysian population comprising Malays, Chinese and Indians, using the AmpFlSTR Profiler Plus kit, the amelogenin test gave a significant proportion of null alleles in the Indian ethnic group (3.6% frequency) and 0.88% frequency in the Malay ethnic group due to a deletion of the gene on the Y chromosome. This sex test also failed in a forensic casework sample. Failure of the amelogenin test highlights the need for more reliable sex determination than is offered by the amelogenin locus in the Malay and Indian populations. The gender of the Indian-Malay amelogenin nulls was confirmed by the presence of three Y-STR alleles (DYS438, DYS390 and DYS439). For the Indian ethnic group, one of the Y-STR forms a stable haplotype with the amelogenin null. The amelogenin-deletion individuals also showed a null with a male-specific minisatellite MSY1, indicating that a very large deletion was involved that included the amelogenin and the MSY1 loci on the short arm of the Y chromosomes (Yp).

Matched MeSH terms: DNA Fingerprinting/methods*

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