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Fulltext α-Thalassemia with Haemoglobin Adana mutation: prenatal diagnosis

Zainal NZ, Alauddin H, Ahmad S, Hussin NH

Malays J Pathol, 2014 Dec;36(3):207-11.
PMID: 25500521

Thalassaemia carriers are common in the Asian region including Malaysia. Asymptomatic patients can be undiagnosed until they present for their antenatal visits. Devastating obstetric outcome may further complicate the pregnancy if both parents are thalassaemia carriers leading to hydrophic fetus due to haemoglobin Bart's disease. However in certain cases where unexplained hydrops fetalis occur in parents with heterozygous thalassaemia carrier,mutated α genes should be suspected. We report a twenty-nine year old woman in her third pregnancy with two previous pregnancies complicated by early neonatal death at 21 and 28 weeks of gestation due to hydrops fetalis. DNA analysis revealed the patient to have heterozygous (--SEA) α-gene deletion, while her husband has a compound heterozygosity for α(3.7) deletion and codon 59 (GGC → GAC) mutation of the α-gene. This mutation, also known as hemoglobin Adana, can explain hydrops fetalis resulting from two alpha gene deletions from the patient (mother) and a single alpha gene deletion with mutation from the father. The third pregnancy resulted in a grossly normal baby boy with 3 α-gene deletions (HbH disease). We postulate that, in view of heterogenisity of the α-thalassaemia in this patient with severely unstable haemoglobin Adana chains from her husband, there will be a 25% possibility of fetal hydrops in every pregnancy.

Matched MeSH terms: Genetic Testing/methods*
Fulltext Recommendations for HLA-B*15:02 and HLA-A*31:01 genetic testing to reduce the risk of carbamazepine-induced hypersensitivity reactions

Amstutz U, Shear NH, Rieder MJ, Hwang S, Fung V, Nakamura H, et al.

Epilepsia, 2014 Apr;55(4):496-506.
PMID: 24597466 DOI: 10.1111/epi.12564

To systematically review evidence on genetic risk factors for carbamazepine (CBZ)-induced hypersensitivity reactions (HSRs) and provide practice recommendations addressing the key questions: (1) Should genetic testing for HLA-B*15:02 and HLA-A*31:01 be performed in patients with an indication for CBZ therapy to reduce the occurrence of CBZ-induced HSRs? (2) Are there subgroups of patients who may benefit more from genetic testing for HLA-B*15:02 or HLA-A*31:01 compared to others? (3) How should patients with an indication for CBZ therapy be managed based on their genetic test results?

Matched MeSH terms: Genetic Testing/methods*
Fulltext Molecular genetic analysis of a supratentorial haemangioblastoma in a non-Von Hippel Lindau patient

Zamzuri I, Ghazali MM, Zainuddin N, Sulong S, Samarendra SM, Yusoff AAM, et al.

Med J Malaysia, 2005 Aug;60(3):360-3.
PMID: 16379193

We describe a rare tumor site in a 46 year old man who presented with a two week history of headache. Physical examination revealed bilateral papilloedema with no other localizing signs. Computed Tomographic Scan as well as Magnetic Resonance Imaging of the brain revealed a lesion with a dura tail located adjacent to the falx cerebri of the right frontal lobe. This lesion was not invading the inner table of the skull base. A tumor blush was seen on angiogram. There were no abnormalities on CT scan of the abdomen and fundoscopy was normal. Intraoperatively a vascular tumor not attached to the dura was noted and removed totally. Histopathological examination was typical of a hemangioblastoma. Analysis revealed no mutations of the VHL gene in 5 regions, exon 5-8 of the p53 gene, exon 1-2 of the p16 gene and exon 5,6 and 8 of the PTEN gene. This is the first case report of a supratentorial hemangioblastoma in a non-Von Hippel Lindau patient with genetic evidence.

Matched MeSH terms: Genetic Testing*
Fulltext Thalassaemia in Malaysia: a strategy for prevention

Ainoon O, Cheong SK

Malays J Pathol, 1994 Jun;16(1):23-7.
PMID: 16329572

In Malaysia, alpha-thalassaemia, beta-thalassaemia, haemoglobin (Hb) E, deltabeta-thalassaemia and Hb Constant Spring are prevalent. It has been estimated that 1 in 4 persons carries one of the above genetic abnormalities. In clinical practice, the major problems are: Hb Bart's hydrops fetalis (homozygous alpha(o)thalassaemia), homozygous 3(o)-thalassaemia, E-alpha thalassaemia and HbH disease. The laboratory procedures for diagnosis are standardised and the molecular basis of most of these genetic abnormalities are characterised. Thus it is possible to formulate a strategy for the detection and prevention of these disorders. The steps include the setting-up of population screening and genetic counselling service for the affected individuals, Society of Thalassaemias for public education and group support, and prenatal diagnosis with selective abortion of affected pregnancies. We embarked on such a programme between 1988 and 1992 in Kuala Lumpur General Hospital and hope to kindle similar effort in other state hospitals.

Matched MeSH terms: Genetic Testing*
Fulltext Genetic analysis of the M2/ANXA5 haplotype as recurrent pregnancy loss predisposition in the Malay population

Ang KC, Kathirgamanathan S, Ch'ng ES, Lee YY, Roslani AL, Naidu B, et al.

J Assist Reprod Genet, 2017 Apr;34(4):517-524.
PMID: 28108842 DOI: 10.1007/s10815-017-0871-0

PURPOSE: The aim of this study was to evaluate a new predisposition factor, M2/ANXA5 (RPRGL3), in recurrent pregnancy loss (RPL) patients of Malay origin, since it was previously known that the prevalence of this condition is relatively high among the Malay population of Malaysia, where conventional hereditary thrombophilia factors have been generally ruled out.
METHODS: A total of 232 women who had experienced ≥2 unexplained RPL and 141 available male partners were recruited, with 360 healthy Malay and 166 parous female controls. Prevalence of M2 carriage and RPL odds ratios were calculated in (a) control and patient groups; (b) clinically defined subgroups in categories of pregnancy loss, primary, secondary, and tertiary; and (c) timing of pregnancy loss in early, ≤15th gestation week and "late" fetal losses, and >15th gestation week subgroups.
RESULTS: Both male and female subjects had similar M2/ANXA5 allele frequencies. The carrier rate of M2/ANXA5 for the general Malay population was 42.2 and 34.9% for parous controls. These carrier rates compared to Malay RPL subjects (52% M2 carriers) resulted in elevated odds ratios (95% confidence interval) of 1.53 (1.1 to 2.1) and 1.97 (1.3 to 3.1) accordingly for early fetal losses. Moreover, exceeding copy numbers of M2/ANXA5 alleles seemed to afflict a greater chance of RPL in couples, especially when both partners were M2 carriers.
CONCLUSION: This study confirmed the proposed role of M2/ANXA5 as embryonic, genetically associated thrombophilia predisposition factor for early RPL among ethnic Malay of Malaysia.

Matched MeSH terms: Genetic Testing*
Fulltext Diagnostic Accuracy of FOBT and Colorectal Cancer Genetic Testing: A Systematic Review & Meta-Analysis

Ramdzan AR, Abd Rahim MA, Mohamad Zaki A, Zaidun Z, Mohammed Nawi A

Ann Glob Health, 2019 05 15;85(1).
PMID: 31099505 DOI: 10.5334/aogh.2466

INTRODUCTION: Colorectal cancer (CRC) is the second leading cause of cancer related death in the world after lung cancer. Early detection of CRC leads to improvement in cancer survival rate. In recent years, efforts have been made to discover a non-invasive screening marker of higher sensitivity and specificity. Fecal occult blood testing (FOBT) and genetic testing become alternative modalities to screen CRC in the population other than colonoscopy. The aim of this systematic review and meta-analysis is to determine the diagnostic accuracy, sensitivity and specificity of FOBT and genetic testing as screening tools in colorectal cancer.
METHODS: A literature search of PubMed, ScienceDirect, and Scopus was carried out. The search strategy was restricted to human subjects and studies are published in English. Data on sensitivity and specificity were extracted and pooled. Heterogeneity was assumed at significance level of p < 0.10 and was tested by chi squared. Degree of heterogeneity was quantified using the I2 statistic, and values of less than 25% is considered as homogenous. All analyses were performed using the software Meta-Disc.
RESULTS: A total of eleven studies were suitable for data synthesis and analysis. Five studies were analyzed for the accuracy of genetic testing, the pooled estimate for sensitivity and specificity were 71% (95% CI: 66, 75%) and 95% (95% CI: 93, 97%) respectively. Another group of studies which had been evaluated for the accuracy of FOBT, the pooled sensitivity was 31% (95% CI: 25, 38%) while the pooled specificity was 87% (95% CI: 86, 89%).
CONCLUSIONS: FOBTs is recommended to use as population-based screening tools for colorectal cancer while genetic testing should be focusing on patients with moderate and high risk individuals.

Matched MeSH terms: Genetic Testing*
Advancing Global Precision Medicine: An Overview of Genomic Testing and Counseling Services in Malaysia

Balasopoulou A, Mooy FM, Baker DJ, Mitropoulou C, Skoufas E, Bulgiba A, et al.

OMICS, 2017 12;21(12):733-740.
PMID: 29173101 DOI: 10.1089/omi.2017.0136

Precision medicine, genomic and diagnostic services are no longer limited to developed countries. This broadening in geography of biomarker applications and omics diagnostics also demands empirical study of implementation, diagnostic testing, and counseling practices in the field. For example, the Malaysian population has large ethnic diversity and high prevalence of genetic disorders such as hemoglobinopathies and metabolic disorders. Increased morbidity and mortality from such diseases have a direct impact on society and health system sustainability and for this, decision-making becomes of outmost importance. We report here on our findings on the landscape of genomic testing and genetic counseling services in Malaysia. We first defined the framework of all Malaysian stakeholders that offer genomics services and next, we identified the related information gaps, as depicted through the service providers' online websites. Our research framework revealed that there is a very diverse spectrum of genomics services in Malaysia, in which wet- and dry-laboratory services integrate. Moreover, we identify the current gaps and possible remedies to improve the quality of genomic and predictive analytics, not to mention considerations to ensure robust ethics and responsible innovation. To our knowledge, this is the first such study to be performed for a Southeast Asian country. Our genomics and precision medicine services mapping strategy presented in this study may serve as a model for field assessment at regional, national, and international levels as precision medicine is expanding globally and new governance challenges and opportunities continue to emerge for smart implementation science.

Matched MeSH terms: Genetic Testing/statistics & numerical data
Fulltext Permissibility of prenatal diagnosis and abortion for fetuses with severe genetic disorder: type 1 spinal muscular atrophy

Sasongko TH, Salmi AR, Zilfalil BA, Albar MA, Mohd Hussin ZA

Ann Saudi Med, 2010 Nov-Dec;30(6):427-31.
PMID: 21060155 DOI: 10.4103/0256-4947.72259

Abortion has been largely avoided in Muslim communities. However, Islamic jurists have established rigorous parameters enabling abortion of fetuses with severe congenital abnormalities. This decision-making process has been hindered by an inability to predict the severity of such prenatally-diagnosed conditions, especially in genetic disorders with clinical heterogeneity, such as spinal muscular atrophy (SMA). Heterogeneous phenotypes of SMA range from extremely severe type 1 to very mild type 4. Advances in molecular genetics have made it possible to perform prenatal diagnosis and to predict the types of SMA with its potential subsequent severity. Such techniques will make it possible for clinicians working in predominantly Muslim countries to counsel their patients accurately and in harmony with their religious beliefs. In this paper, we discuss and postulate that with our current knowledge of determining SMA types and severity with great accuracy, abortion is legally applicable for type 1 SMA.

Matched MeSH terms: Genetic Testing/methods*
Religious scholars' attitudes and views on ethical issues pertaining to pre-implantation genetic diagnosis (PGD) in Malaysia

Olesen A, Nor SN, Amin L

J Bioeth Inq, 2016 Sep;13(3):419-29.
PMID: 27365102 DOI: 10.1007/s11673-016-9724-2

Pre-Implantation Genetic Diagnosis (PGD) represents the first fusion of genomics and assisted reproduction and the first reproductive technology that allows prospective parents to screen and select the genetic characteristics of their potential offspring. However, for some, the idea that we can intervene in the mechanisms of human existence at such a fundamental level can be, at a minimum, worrying and, at most, repugnant. Religious doctrines particularly are likely to collide with the rapidly advancing capability for science to make such interventions. This paper focuses on opinions and arguments of selected religious scholars regarding ethical issues pertaining to PGD. In-depth interviews were conducted with religious scholars from three different religious organizations in the Klang Valley, Malaysia. Findings showed that Christian scholars are very sceptical of the long-term use of PGD because of its possible effect on the value of humanity and the parent-children relationship. This differs from Islamic scholars, who view PGD as God-given knowledge in medical science to further help humans understand medical genetics. For Buddhist scholars, PGD is considered to be new medical technology that can be used to save lives, avoid suffering, and bring happiness to those who need it. Our results suggest that it is important to include the opinions and views of religious scholars when it comes to new medical technologies such as PGD, as their opinions will have a significant impact on people from various faiths, particularly in a multi-religious country like Malaysia where society places high value on marital relationships and on the traditional concepts of family.

Matched MeSH terms: Genetic Testing/ethics*
Fulltext Metabolic and genetic screening of electromagnetic hypersensitive subjects as a feasible tool for diagnostics and intervention

De Luca C, Thai JC, Raskovic D, Cesareo E, Caccamo D, Trukhanov A, et al.

Mediators Inflamm, 2014;2014:924184.
PMID: 24812443 DOI: 10.1155/2014/924184

Growing numbers of "electromagnetic hypersensitive" (EHS) people worldwide self-report severely disabling, multiorgan, non-specific symptoms when exposed to low-dose electromagnetic radiations, often associated with symptoms of multiple chemical sensitivity (MCS) and/or other environmental "sensitivity-related illnesses" (SRI). This cluster of chronic inflammatory disorders still lacks validated pathogenetic mechanism, diagnostic biomarkers, and management guidelines. We hypothesized that SRI, not being merely psychogenic, may share organic determinants of impaired detoxification of common physic-chemical stressors. Based on our previous MCS studies, we tested a panel of 12 metabolic blood redox-related parameters and of selected drug-metabolizing-enzyme gene polymorphisms, on 153 EHS, 147 MCS, and 132 control Italians, confirming MCS altered (P < 0.05-0.0001) glutathione-(GSH), GSH-peroxidase/S-transferase, and catalase erythrocyte activities. We first described comparable-though milder-metabolic pro-oxidant/proinflammatory alterations in EHS with distinctively increased plasma coenzyme-Q10 oxidation ratio. Severe depletion of erythrocyte membrane polyunsaturated fatty acids with increased ω 6/ ω 3 ratio was confirmed in MCS, but not in EHS. We also identified significantly (P = 0.003) altered distribution-versus-control of the CYP2C19∗1/∗2 SNP variants in EHS, and a 9.7-fold increased risk (OR: 95% C.I. = 1.3-74.5) of developing EHS for the haplotype (null)GSTT1 + (null)GSTM1 variants. Altogether, results on MCS and EHS strengthen our proposal to adopt this blood metabolic/genetic biomarkers' panel as suitable diagnostic tool for SRI.

Matched MeSH terms: Genetic Testing/methods*
Fulltext Genetic analyses favour an ancient and natural origin of elephants on Borneo

Sharma R, Goossens B, Heller R, Rasteiro R, Othman N, Bruford MW, et al.

Sci Rep, 2018 01 17;8(1):880.
PMID: 29343863 DOI: 10.1038/s41598-017-17042-5

The origin of the elephant on the island of Borneo remains elusive. Research has suggested two alternative hypotheses: the Bornean elephant stems either from a recent introduction in the 17th century or from an ancient colonization several hundreds of thousands years ago. Lack of elephant fossils has been interpreted as evidence for a very recent introduction, whereas mtDNA divergence from other Asian elephants has been argued to favor an ancient colonization. We investigated the demographic history of Bornean elephants using full-likelihood and approximate Bayesian computation analyses. Our results are at odds with both the recent and ancient colonization hypotheses, and favour a third intermediate scenario. We find that genetic data favour a scenario in which Bornean elephants experienced a bottleneck during the last glacial period, possibly as a consequence of the colonization of Borneo, and from which it has slowly recovered since. Altogether the data support a natural colonization of Bornean elephants at a time when large terrestrial mammals could colonise from the Sunda shelf when sea levels were much lower. Our results are important not only in understanding the unique history of the colonization of Borneo by elephants, but also for their long-term conservation.

Matched MeSH terms: Genetic Testing/methods
Fulltext Genetic analysis and selection of Bambara groundnut (Vigna subterranea [L.] Verdc.) landraces for high yield revealed by qualitative and quantitative traits

Khan MMH, Rafii MY, Ramlee SI, Jusoh M, Al Mamun M

Sci Rep, 2021 Apr 07;11(1):7597.
PMID: 33828137 DOI: 10.1038/s41598-021-87039-8

As a crop for the new millennium Bambara groundnut (Vigna subterranea [L.] Verdc.) considered as leading legumes in the tropical regions due to its versatile advantages. The main intent of this study was to find out the high yielding potential genotypes and considering these genotypes to develop pure lines for commercial cultivation in Malaysia. Considering the 14 qualitative and 27 quantitative traits of fifteen landraces the variation and genetic parameters namely, variability, heritability, genetic advance, characters association, and cluster matrix were determined. ANOVA revealed significant variation for all the agronomic traits (except plant height). Among the accessions, highly significant differences (P ≤ 0.01) were found for almost all the traits excluding fifty percent flowering date, seed length, seed width. The 16 traits out of the 27 quantitative traits had a coefficient of variation (CV) ≥ 20%. A positive and intermediate to perfect highly significant association (r = 0.23 to 1.00; P

Matched MeSH terms: Genetic Testing/methods
Analysis of dynein intermediate chains, light intermediate chains and light chains in a cohort of hereditary peripheral neuropathies

Tey S, Ahmad-Annuar A, Drew AP, Shahrizaila N, Nicholson GA, Kennerson ML

Neurogenetics, 2014 Oct;15(4):229-35.
PMID: 25028179 DOI: 10.1007/s10048-014-0414-0

The cytoplasmic dynein heavy chain (DYNC1H1) gene has been increasingly associated with neurodegenerative disorders including axonal Charcot-Marie-Tooth disease (CMT2), intellectual disability and malformations of cortical development. In addition, evidence from mouse models (Loa, catabolite repressor-activator (Cra) and Sprawling (Swl)) has shown that mutations in Dync1h1 cause a range of neurodegenerative phenotypes with motor and sensory neuron involvement. In this current study, we examined the possible contribution of other cytoplasmic dynein subunits that bind to DYNC1H1 as a cause of inherited peripheral neuropathy. We focused on screening the cytoplasmic dynein intermediate, light intermediate and light chain genes in a cohort of families with inherited peripheral neuropathies. Nine genes were screened and ten variants were detected, but none was identified as pathogenic, indicating that cytoplasmic dynein intermediate, light intermediate and light chains are not a cause of neuropathy in our cohort.

Matched MeSH terms: Genetic Testing
Fulltext Partial deletion 9p syndrome in Malaysian children

Chew HB, Thong MK

Med J Malaysia, 2010 Sep;65(3):215-7.
PMID: 21939171 MyJurnal

We report the first two Malaysian children with partial deletion 9p syndrome, a well delineated but rare clinical entity. Both patients had trigonocephaly, arching eyebrows, anteverted nares, long philtrum, abnormal ear lobules, congenital heart lesions and digital anomalies. In addition, the first patient had underdeveloped female genitalia and anterior anus. The second patient had hypocalcaemia and high arched palate and was initially diagnosed with DiGeorge syndrome. Chromosomal analysis revealed a partial deletion at the short arm of chromosome 9. Karyotyping should be performed in patients with craniostenosis and multiple abnormalities as an early syndromic diagnosis confers prognostic, counselling and management implications.

Matched MeSH terms: Genetic Testing
Fulltext The history of introduction of the African baobab (Adansonia digitata, Malvaceae: Bombacoideae) in the Indian subcontinent

Bell KL, Rangan H, Kull CA, Murphy DJ

R Soc Open Sci, 2015 Sep;2(9):150370.
PMID: 26473060 DOI: 10.1098/rsos.150370

To investigate the pathways of introduction of the African baobab, Adansonia digitata, to the Indian subcontinent, we examined 10 microsatellite loci in individuals from Africa, India, the Mascarenes and Malaysia, and matched this with historical evidence of human interactions between source and destination regions. Genetic analysis showed broad congruence of African clusters with biogeographic regions except along the Zambezi (Mozambique) and Kilwa (Tanzania), where populations included a mixture of individuals assigned to at least two different clusters. Individuals from West Africa, the Mascarenes, southeast India and Malaysia shared a cluster. Baobabs from western and central India clustered separately from Africa. Genetic diversity was lower in populations from the Indian subcontinent than in African populations, but the former contained private alleles. Phylogenetic analysis showed Indian populations were closest to those from the Mombasa-Dar es Salaam coast. The genetic results provide evidence of multiple introductions of African baobabs to the Indian subcontinent over a longer time period than previously assumed. Individuals belonging to different genetic clusters in Zambezi and Kilwa may reflect the history of trafficking captives from inland areas to supply the slave trade between the fifteenth and nineteenth centuries. Baobabs in the Mascarenes, southeast India and Malaysia indicate introduction from West Africa through eighteenth and nineteenth century European colonial networks.

Matched MeSH terms: Genetic Testing
Fulltext The whole genome sequence data analyses of a Mycobacterium tuberculosis strain SBH321 isolated in Sabah, Malaysia, belongs to Ural family of Lineage 4

Jani J, Mustapha ZA, Ling CK, Hui ASM, Teo R, Ahmed K

Data Brief, 2020 Dec;33:106388.
PMID: 33102655 DOI: 10.1016/j.dib.2020.106388

In 2019, 10 million new cases of tuberculosis have been reported worldwide. Our data reports genetic analyses of a Mycobacterium tuberculosis strain SBH321 isolated from a 31-year-old female with pulmonary tuberculosis. The genomic DNA of the strain was extracted from pure culture and subjected to sequencing using Illumina platform. M. tuberculosis strain SBH321 consists of 4,374,895 bp with G+C content of 65.59%. The comparative analysis by SNP-based phylogenetic analysis using maximum-likelihood method showed that our strain belonging to sublineage of the Ural family of Europe-America-Africa lineage (Lineage 4) and clustered with M. tuberculosis strain OFXR-4 from Taiwan. The whole genome sequence is deposited at DDBJ/ENA/GenBank under the accession WCJH00000000 (SRR10230353).

Matched MeSH terms: Genetic Testing
Fulltext Blau Syndrome Associated with Nucleotide-binding Oligomerization Domain Containing 2 Mutation in a Baby from Malaysia

Leong KF, Sato R, Oh GGK, Surana U, Pramono ZAD

Indian J Dermatol, 2019 9 24;64(5):400-403.
PMID: 31543536 DOI: 10.4103/ijd.IJD_44_18

Blau syndrome (BS) is a very rare autosomal dominant juvenile inflammatory disorder caused by mutation in nucleotide-binding oligomerization domain containing 2 (NOD2). Usually, dermatitis is the first symptom that appears in the 1st year of life. About 220 BS cases with confirmed NOD2 mutation have been reported. However, the rarity and lack of awareness of the disease, especially in the regions where genetic tests are very limited, often result in late diagnosis and misdiagnosis. Here, we report a de novo BS case from Malaysia, which may be the first report from southeast Asia. PCR and DNA sequencing of peripheral blood mononuclear cells were performed to screen the entire coding region of NOD2 gene. A heterozygous c.1000C>T transition in exon 4, p. R334W, of the NOD2 gene was identified in the patient. This report further reaffirms the ubiquitousness of the disease and recurrency of p. R334W mutation.

Matched MeSH terms: Genetic Testing
Fulltext The CHEK2 Variant C.349A>G Is Associated with Prostate Cancer Risk and Carriers Share a Common Ancestor

Brandão A, Paulo P, Maia S, Pinheiro M, Peixoto A, Cardoso M, et al.

Cancers (Basel), 2020 Nov 04;12(11).
PMID: 33158149 DOI: 10.3390/cancers12113254

The identification of recurrent founder variants in cancer predisposing genes may have important implications for implementing cost-effective targeted genetic screening strategies. In this study, we evaluated the prevalence and relative risk of the CHEK2 recurrent variant c.349A>G in a series of 462 Portuguese patients with early-onset and/or familial/hereditary prostate cancer (PrCa), as well as in the large multicentre PRACTICAL case-control study comprising 55,162 prostate cancer cases and 36,147 controls. Additionally, we investigated the potential shared ancestry of the carriers by performing identity-by-descent, haplotype and age estimation analyses using high-density SNP data from 70 variant carriers belonging to 11 different populations included in the PRACTICAL consortium. The CHEK2 missense variant c.349A>G was found significantly associated with an increased risk for PrCa (OR 1.9; 95% CI: 1.1-3.2). A shared haplotype flanking the variant in all carriers was identified, strongly suggesting a common founder of European origin. Additionally, using two independent statistical algorithms, implemented by DMLE+2.3 and ESTIAGE, we were able to estimate the age of the variant between 2300 and 3125 years. By extending the haplotype analysis to 14 additional carrier families, a shared core haplotype was revealed among all carriers matching the conserved region previously identified in the high-density SNP analysis. These findings are consistent with CHEK2 c.349A>G being a founder variant associated with increased PrCa risk, suggesting its potential usefulness for cost-effective targeted genetic screening in PrCa families.

Matched MeSH terms: Genetic Testing
Fulltext Dataset on 21 autosomal and two sex determining short tandem repeat loci in the Kedayan population in Borneo, Malaysia

Hakim HM, Khan HO, Ismail SA, Lalung J, Kofi AE, Abdullah MT, et al.

Data Brief, 2020 Aug;31:105909.
PMID: 32642519 DOI: 10.1016/j.dib.2020.105909

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.

Matched MeSH terms: Genetic Testing
Fulltext Non-tenera Contamination and the Economic Impact of SHELL Genetic Testing in the Malaysian Independent Oil Palm Industry

Ooi LC, Low ET, Abdullah MO, Nookiah R, Ting NC, Nagappan J, et al.

Front Plant Sci, 2016;7:771.
PMID: 27446094 DOI: 10.3389/fpls.2016.00771

Oil palm (Elaeis guineensis) is the most productive oil bearing crop worldwide. It has three fruit forms, namely dura (thick-shelled), pisifera (shell-less) and tenera (thin-shelled), which are controlled by the SHELL gene. The fruit forms exhibit monogenic co-dominant inheritance, where tenera is a hybrid obtained by crossing maternal dura and paternal pisifera palms. Commercial palm oil production is based on planting thin-shelled tenera palms, which typically yield 30% more oil than dura palms, while pisifera palms are female-sterile and have little to no palm oil yield. It is clear that tenera hybrids produce more oil than either parent due to single gene heterosis. The unintentional planting of dura or pisifera palms reduces overall yield and impacts land utilization that would otherwise be devoted to more productive tenera palms. Here, we identify three additional novel mutant alleles of the SHELL gene, which encode a type II MADS-box transcription factor, and determine oil yield via control of shell fruit form phenotype in a manner similar to two previously identified mutant SHELL alleles. Assays encompassing all five mutations account for all dura and pisifera palms analyzed. By assaying for these variants in 10,224 mature palms or seedlings, we report the first large scale accurate genotype-based determination of the fruit forms in independent oil palm planting sites and in the nurseries that supply them throughout Malaysia. The measured non-tenera contamination rate (10.9% overall on a weighted average basis) underscores the importance of SHELL genetic testing of seedlings prior to planting in production fields. By eliminating non-tenera contamination, comprehensive SHELL genetic testing can improve sustainability by increasing yield on existing planted lands. In addition, economic modeling demonstrates that SHELL gene testing will confer substantial annual economic gains to the oil palm industry, to Malaysian gross national income and to Malaysian government tax receipts.

Matched MeSH terms: Genetic Testing

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