Publications by authors named "Hashom Mohd Hakim"

8 Publications

  • Page 1 of 1

Population data and genetic characteristics of 12 X-STR loci using the Investigator® Argus X-12 Quality Sensor kit for the Kedayan population of Borneo in Malaysia.

Int J Legal Med 2021 Jul 30;135(4):1433-1435. Epub 2021 Mar 30.

Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.

DNA profiling of X-chromosomal short tandem repeats (X-STR) has exceptional value in criminal investigations, especially for complex kinship and incest cases. In this study, Investigator® Argus X-12 Quality Sensor (QS) kits were successfully used to characterize 12 X-STR loci in 199 unrelated healthy Kedayan individuals living in Sabah and Sarawak, Malaysia. The LG1 haplogroup (DXS8378 - DXS10135 - DXS10148) has the largest HD (0.9799) as compared with all other closely linked haplotype groups examined (LG2; DXS7132-DXS10074-DXS10079, LG3; DXS10103-DXS10101-HPRTB and LG4; DXS10134-DXS7423-DXS10146). Data from statistical analysis showed that high combined of PD, PD, MEC_, MEC_, MEC_, and MEC_ values (0.999999994405922, 0.99999999999999, 0.999990463834938, 0.999999975914808, 0.999999975985006, and 0.999996491927194, respectively) in the Kedayan. In a two-dimensional scaling (MDS) plot and dendrogram constructed using allele frequencies at the 12 X-STR loci, Kedayan appear to be most closely related to their other Austronesian populations including the Malays and Filipinos as compared with other reference population groups. Findings from the present study thus demonstrate high genetic variability across the 12 tested X-STR loci and can be used for population studies and forensic applications.
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http://dx.doi.org/10.1007/s00414-021-02577-0DOI Listing
July 2021

Autosomal STR Profiling and Databanking in Malaysia: Current Status and Future Prospects.

Genes (Basel) 2020 09 23;11(10). Epub 2020 Sep 23.

Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, Kuala Nerus 21030, Terengganu, Malaysia.

Science and technology are extensively used in criminal investigation. From the mid- to late-1980s, one of the scientific discoveries that has had a particularly remarkable impact on this field has been the use of highly variable DNA sequence regions (minisatellites) in the human genome for individual identification. The technique was initially referred to as DNA fingerprinting, but is now more widely referred to as DNA profiling. Since then, many new developments have occurred within this area of science. These include the introduction of new genetic markers (microsatellites also known as short tandem repeats/STRs), the use of the polymerase chain reaction for target amplification, the development of DNA databases (databanking), and the advancement and/or improvement of genotyping protocols and technologies. In 2019, we described the progress of DNA profiling and DNA databanking in Malaysia for the first time. This report included information on DNA analysis regulations and legislation, STR genotyping protocols, database management, and accreditation status. Here, we provide an update on the performance of our DNA databank (numbers of DNA profiles and hits) plus the technical issues associated with correctly assigning the weight of evidence for DNA profiles in an ethnically diverse population, and the potential application of rapid DNA testing in the country. A total of 116,534 DNA profiles were obtained and stored in the Forensic DNA Databank of Malaysia (FDDM) by 2019, having increased from 70,570 in 2017. The number of hits increased by more than three-fold in just two years, where 17 and 69 hits between the DNA profiles stored in the FDDM and those from crime scenes, suspects, detainees, drug users, convicts, missing persons, or volunteers were recorded in 2017 and 2019, respectively. Forensic DNA analysis and databanking are thus progressing well in Malaysia and have already contributed to many criminal investigations. However, several other issues are discussed here, including the need for STR population data for uncharacterized population groups, and pilot trials for adopting rapid DNA profiling technology. These aspects should be considered by policy makers and law enforcement agencies in order to increase the reliability and efficiency of DNA profiling in criminal cases and in kinship analysis in Malaysia.
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http://dx.doi.org/10.3390/genes11101112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7597947PMC
September 2020

Dataset on 21 autosomal and two sex determining short tandem repeat loci in the Kedayan population in Borneo, Malaysia.

Data Brief 2020 Aug 21;31:105909. Epub 2020 Jun 21.

Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia.

This data article provides population frequencies for 21 autosomal and two sex determining short tandem repeat (STR) loci in unrelated Kedayan individuals. This article is related to the research paper entitled "Forensic parameters and ancestral fraction in the Kedayan population inferred using 21 autosomal STR loci" [1] where these same data were subjected to ancestry and forensic analyses. We have collected 200 blood samples consisting of 128 male and 72 female volunteer representatives from Kedayan people residing in various parts of Borneo. All 23 STR loci were simultaneously amplified using Globalfiler™ Express PCR and amplicons were separated using an ABI 3500xl Genetic Analyzer. The STR allele calls at each locus were called using GeneMapper ID-X Software v1.4, while several algorithms in Arlequin software version 3.5 were used to estimate Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) between pairs of STR loci.
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http://dx.doi.org/10.1016/j.dib.2020.105909DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334294PMC
August 2020

Population dataset for 21 simple tandem repeat loci in the Akan population of Ghana.

Data Brief 2020 Aug 22;31:105746. Epub 2020 May 22.

School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia.

Short tandem repeat (STR) loci are widely used as genetic marker for ancestral and forensic analyses. The latter application includes for paternity testing and DNA profiling of samples collected from scenes of crime and suspects. This survey provides the first dataset for 21 STR loci across the Akan population in Ghana by genotyping of 109 unrelated healthy individuals using Investigator 24plex kit. None of the STR loci screened deviated from Hardy-Weinberg equilibrium after applying Bonferroni correction. Overall, 224 unique alleles were observed with allele frequencies ranging from 0.005 to 0.518. The combined match probability, combined power of exclusion and combined power discrimination were 1 in 4.07 × 10, 0.999999999 and 1, respectively. Principal coordinate analysis carried out using 21 STR allele frequency data mapped the Akans with Nigerian subpopulation groups (Hausa, Igbo and Yoruba), but separated from Thais of Thailand, Chechen of Jordan and Tijuana of Mexico.
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http://dx.doi.org/10.1016/j.dib.2020.105746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7262416PMC
August 2020

Population data for 23 Y chromosome STR loci using the Powerplex® Y23 STR kit for the Kedayan population in Malaysia.

Int J Legal Med 2020 Jul 2;134(4):1335-1337. Epub 2020 Jan 2.

Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.

Genetic polymorphisms at 23 Y chromosome short tandem repeat (STRs) loci included in the Powerplex® Y23 PCR kit were successfully scored in 128 unrelated Kedayan individuals living in Sabah, East Malaysia. Complete haplotypes were recorded for all individuals and included 92 different types with 72 being unique to single male subjects. Three important forensic statistics were calculated from these data; haplotype diversity = 0.993, discriminating capacity = 0.719, and match probability = 0.015. The Kedayan appear to be most closely related to Malays and Filipinos in a multidimensional scaling plot and are separated from other mainland Asia populations including Thais and Hakka Han. These new data for Kedayan have been deposited in the YHRD database (accession number: YA004621). Our statistical analyses showed the reliability of Y-STR loci for geographically extended use in forensic casework and for studying human population history.
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http://dx.doi.org/10.1007/s00414-019-02237-4DOI Listing
July 2020

Violent crime datasets: Incidence and patterns in Malaysia from 2006 to 2017.

Data Brief 2019 Oct 3;26:104449. Epub 2019 Sep 3.

School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.

This article provides violent crime data in Malaysia from 2006 to 2017. The violent crimes include murder, rape, gang robbery, robbery and voluntarily causing hurt cases. A total of 330,395 violent crime cases were reported in this 12 year period and the data were tabulated state by state for all thirteen states of Malaysia, including two states in Borneo (Sabah and Sarawak) and one federal territory (Kuala Lumpur). In general, violent crimes show a decreasing trend from 2006 to 2017 in Malaysia. However, armed gang robbery and armed robbery show a fluctuating pattern from 2008 to 2011. A similar pattern was also recorded for unarmed gang robbery from 2008 to 2010. The violent crime data deposited here are available for further analysis, e.g., for identifying risk factors such as demography, lifestyle, socio-economic status, government policies etc. which may be associated with violent crime incidence and pattern across the country.
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http://dx.doi.org/10.1016/j.dib.2019.104449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6811922PMC
October 2019

Assessment of autosomal and male DNA extracted from casework samples using Casework Direct Kit, Custom and Maxwell 16 System DNA IQ Casework Pro Kit for autosomal-STR and Y-STR profiling.

Sci Rep 2019 10 10;9(1):14558. Epub 2019 Oct 10.

Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.

Short repetitive regions in autosomal and Y chromosomes known as short tandem repeats (STRs) are currently used for DNA profiling in crime investigations. However, DNA profiling requires a sufficient quality and quantity of DNA template, which is often not obtained from trace evidence or degraded biological samples collected at the scene of a crime. Here, we assessed autosomal and male DNA components extracted from crime scene and mock casework samples using the Casework Direct Kit, Custom and compared the results against those obtained by extraction of matching samples using well-established Maxwell 16 System DNA IQ Casework Pro Kit. The quantity and quality of extracted DNA obtained using both Casework Direct Kit, Custom and Maxwell 16 System DNA IQ Casework Pro Kit were analyzed using PowerQuant Systems followed by autosomal and Y-chromosome STR profiling using GlobalFiler Express PCR Amplification Kit and PowerPlex Y23 System, respectively. Our results showed that the Casework Direct Kit and Maxwell 16 DNA IQ Casework Pro Kit have more or less equal capacity to extract inhibitor free DNA, but that the latter produces slightly better quality and more DNA template and subsequently higher numbers of STR allele calls for autosomal and Y-STR analyses. Nonetheless, the Casework Direct Kit, Custom is the quicker and cheaper option for extraction of good, clean DNA from high content material and might best be used for extraction of reference samples. Such reference DNA samples typically come from buccal swabs or freshly drawn blood. So, in general, they can confidently be expected to have a high nucleic acid content and to be inhibitor-free.
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http://dx.doi.org/10.1038/s41598-019-51154-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6787247PMC
October 2019

Population data of 23 Y chromosome STR loci for the five major human subpopulations of Ghana.

Int J Legal Med 2020 Jul 1;134(4):1313-1315. Epub 2019 Jun 1.

School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.

In this study, 268 samples for unrelated males belonging to the five major human subpopulation groups in Ghana (Akan, Ewe, Mole-Dagbon, Ga-Dangme and Guang) were genetically characterised for 23 Y chromosome short tandem repeat (STR) loci using the Powerplex® Y23 STR kit. A total of 263 complete haplotypes were recorded of which 258 were unique. The haplotype diversity, discriminating capacity and match probability for the pooled population data were 0.9998, 0.9627 and 0.0039, respectively. The pairwise genetic distance (R) for the Ghanaian datasets and other reference populations deposited in the Y-STR Haplotype Reference Database (YHRD) were estimated and mapped using multidimensional scaling (MDS) plot. The Guang and Ewe were significantly different from the Akan, Mole-Dagbon and Ga-Dangme. However, the five Ghanaian datasets were all plotted close together with other African populations in the MDS data mapping.
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http://dx.doi.org/10.1007/s00414-019-02099-wDOI Listing
July 2020