Mullerian agenesis or Mayer-Rokitansky-Kuster-Hauser Syndrome (MRKH) Type-II is a congenital defect in the Mullerian duct that results in the absence of a uterus in women. The aetiology of this syndrome is unknown and has been considered a sporadic genetic disease. MRKH, together with anorectal anomaly, is an extremely rare condition and has only been reported in a few cases without any information on genetic analysis. This study investigated the mutational profile of a girl diagnosed with MRKH and anorectal anomalies with rectovaginal fistula. The whole exome sequencing (WES) trio-genetic analysis of a 5-year-old Malaysian girl diagnosed with MRKH (having anorectal anomaly with rectovaginal fistula) was performed together with her normal parents, using the Ion AmpliSeq Exome RDY kit (ThermoFisher Scientific, USA). Data were analysed using Torrent Suite v.5.0.4 and annotated using ANNOVAR. Single nucleotide polymorphisms (SNPs) with an allele frequency >0.01 were excluded, and the remaining variants were filtered based on de novo mutations, autosomal recessive, and autosomal recessive genetic traits. Related genes were analysed by biological pathway analysis (g:Profiler) and protein-protein interaction (HIPPIE v.2.3, STRING v.11.5, dan GeneMANIA). A total of 36 mutations were identified, and two of them, the LHX5 (p.P358Q), inherited from the father, and CFTR (p.R1158X), inherited from the mother. There were 28 de-novo mutations from 28 genes. All genes were involved in 27 biological processes that connected with 23 interactions, and are likely to cause MRKH syndrome in this patient.

Mycobacterium tuberculosis is the causative agent of tuberculosis(TB),which is still the leading cause of mortality from a single infectious disease worldwide.The development of novel anti-TB drugs and vaccines is severely hampered by the complicated and time-consuming genetic manipulation techniques for M.tuberculosis.Here,we harnessed an endogenous type Ⅲ-A CRISPR/Cas10 system of M.tuberculosis for efficient gene editing and RNA interference(RNAi).This simple and easy method only needs to transform a single mini-CRISPR array plasmid,thus avoiding the introduction of exogenous protein and minimizing proteotoxicity.We demonstrated that M.tuberculosis genes can be efficiently and specifically knocked in/out by this system as con-firmed by DNA high-throughput sequencing.This system was further applied to single-and multiple-gene RNAi.Moreover,we successfully performed genome-wide RNAi screening to identify M.tuberculosis genes regulating in vitro and intracellular growth.This system can be extensively used for exploring the functional genomics of M.tuberculosis and facilitate the development of novel anti-TB drugs and vaccines.

Objective: In this present study, we aim to evaluate the accuracy of the HbA1c relative to fasting plasma glucose (FPG) in the diagnosis of diabetes and pre-diabetes among The Malaysian Cohort (TMC) participants. Methodology: FPG and HbA1c were taken from 40,667 eligible TMC participants that have no previous history of diabetes, aged between 35-70 years and were recruited from 2006 – 2012. Participants were classified as normal, diabetes and pre-diabetes based on the 2006 World Health Organization (WHO) criteria. Statistical analyses were performed using ANOVA and Chi-square test, while Pearson correlation and Cohen’s kappa were used to examine the concordance rate between FPG and HbA1c. Results: The study samples consisted of 16,224 men and 24,443 women. The prevalence of diabetes among the participants was 5.7% and 7.5% according to the FPG and HbA1c level, respectively. Based on FPG, 10.6% of the participants had pre-diabetes but this increased to 14.2% based on HbA1c (r=0.86; P<0.001). HbA1c had a sensitivity of 58.20 (95% CI: 56.43, 59.96) and a specificity of 98.59 (95% CI: 98.46, 98.70). Conclusion A higher prevalence of pre-diabetes and diabetes was observed when using HbA1c as a diagnosis tool, suggesting that it could possibly be more useful for early detection. However, given that HbA1c may also have lower sensitivity and higher false positive rate, several diagnostic criteria should be used to diagnose diabetes accurately.
Diabetes Mellitus, Type 2 ; Diagnosis

Background: Mutations in glucocerebrosidase (GBA) have been associated with the risk of developing Parkinson’s disease (PD) in different ethnic populations. The prevalence of GBA mutations among Malay PD patients is unknown. Thus, the aim of this study was to determine the frequency of GBA mutations among Malay PD patients, focusing on early (EOPD) and late-onset (LOPD) patients. Methods:EOPD (n = 50) and LOPD (n = 50) patients along with 50 ethnically and age-matched control wererecruited. The GBA exons of these patients were sequenced using the Ion Torrent PGMTM System. Results: Five heterozygous mutations exclusive to EOPD patients were identified; c.-203A>G,p.S146L, p.R159Q, p.L483P and p.L483R+c.-145G>A. In LOPD patients, c.543C>T(p.(F181=)), c.28-10C>A and p.R202Q were identified in which this p.R202Q was also present in a control subject. In addition, c.259C>A(p.(R87=)) and c.-145G>A were identified in two control subjects. In summary, we observed GBA mutations in 8% and 6% of Malay PD cases and control subject, respectively. The prevalence of GBA mutations was higher in EOPD (10%) than LOPD (6%). However, these differences were not statistically significant; [PD vs. controls: OR = 1.36, 95%CI 0.35-5.38, p = 0.752] and [EOPD vs. LOPD: OR = 1.74, 95%CI 0.39-7.71, p = 0.715]. Conclusion: We identified five exclusive heterozygous GBA mutations in EOPD patients which might predict the increase susceptibility of Malays to develop PD at young age. These findings could add knowledge into the existing evidences linking genetic alterations in GBA and PD.

Background & Objective: Circulating microRNAs (miRNAs) expressions have been suggested as potential biomarkers for Parkinson’s Disease (PD). Identification of early biomarkers for PD is important and crucial as PD symptoms occur at a late stage. Hence, these biomarkers could be used in molecular diagnosis for early detection. We therefore examined and compared the expression of circulating miRNAs between PD patients and controls. We also compared the miRNAs expression between early-onset PD (EOPD) and late-onset PD (LOPD). Methods: RNA was extracted from the plasma of EOPD (onset age <50 years; n=14), LOPD (onset age < 60 years; n=14) and healthy controls (n=11). The miRNAs expression was determined using the Affymetrix GeneChip microarray. Differential analysis was performed using the R software. Significantly differentiated miRNAs were subsequently analyzed for functional enrichment and biological pathway using the FunRich v1.3 software based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The Omics.net was used to determine the predicted target mRNAs of these miRNAs, and their interactions, based on the five most differentially expressed miRNAs. Results: In total, 273 miRNAs were upregulated in PD patients compared to controls. The most significant miRNAs were hsa-miR-301a-3p, 100-5p, 140-5p, 486-3p, 143-3p (fold change ranging from 11.2 – 32.0). A total of 140 circulating miRNAs were differentially expressed in EOPD compared to LOPD. Five of these miRNAs (one upregulated miRNA (hsa-miR-29b-3p) and four downregulated miRNAs (hsa-miR-297, 4462, 1909-5p and 346) belonged exclusively to the EOPD patients. The predicted gene targets of these miRNAs involved in dopaminergic synapse regulation, crucial to the pathogenesis of PD. Conclusion: Circulating miRNAs differ between PD patients and controls, and between EOPD and LOPD patients. A validation study with a larger and more diverse multi-ethnic population should be conducted to confirm our results.

Background: The HLA-B*15:02 polymorphism in epileptic patients is known to be associated with carbamazepine-induced Stevens-Johnson syndrome (SJS). The prevalence of HLA-B*15:02 polymorphism seemed to be ethnic-specific with a higher frequency of HLA-B*15:02 in Asian compared to the Europeans. This study was performed to determine the frequency of the HLA-B*15:02 polymorphism in epileptic patients at the Chancellor Tuanku Muhriz Hospital-UKM Medical Centre (HCTM-UKMMC) using high resolution melting-real time PCR (HRM-QPCR) method. Methods: We performed a fast and effective in-house high resolution melting-real time polymerase chain reaction method and compared it with the conventional multiplex-PCR method. The specificity and sensitivity of each test were also determined using DNA from saliva. Results: Using the conventional multiplex-PCR approach for screening, 25 out of 64 (39.1%) epileptic patients were positive for HLA-B*15:02. However, using the HRM-QPCR technique, 24/64 (37.5%) of the patients were positive. The one patient who tested positive by the multiplex-PCR but negative using the HRM-QPCR turned out to be negative by DNA sequencing. The HRM-QPCR and DNA sequencing showed 100% sensitivity and specificity. The multiplex-PCR showed 100% sensitivity and 98.4% specificity compared to both HRM-QPCR and DNA sequencing. The HRM-QPCR is also more cost-effective (<$16.40 USD/test) and less time-consuming when compared to the multiplex-PCR ($25.15 USD/test).Conclusion: Our result suggested that multiplex PCR, HRM-QPCR and Sanger sequencing can be used for detection of HLA-B*15:02. However, a qualitative method such as multiplex PCR should be confirmed with other quantitative methods such as HRM-QPCR and Sanger sequencing.

Objective To report presence of Leishmania major in Khyber Pakhtunkhwa of Pakistan, where cutaneous leishmaniasis (CL) is endemic and was thought to be caused by Leishmania tropica only. Methods Biopsy samples from 432 CL suspected patients were collected from 3 southern districts of Khyber Pakhtunkhwa during years 2011–2016. Microscopy on Giemsa stained slides were done followed by amplification of the ribosomal internal transcribed spacer 1 gene. Results Leishmania amastigotes were detected by microscopy in 308 of 432 samples (71.3%) while 374 out of 432 samples (86.6%) were positive by ribosomal internal transcribed spacer 1 PCR. Subsequent restriction fragment length polymorphism confirmed L. tropica in 351 and L. major in 6 biopsy samples. Conclusions This study is the first molecular characterization of Leishmania species in southern Khyber Pakhtunkhwa. It confirmed the previous assumptions that anthroponotic CL is the major CL form present in Khyber Pakhtunkhwa province. Furthermore, this is the first report of L. major from a classical anthroponotic CL endemic focus identified in rural areas of Kohat district in southern Khyber Pakhtunkhwa.

Childhood obesity is a global epidemic, which leads to the increasing number of studies on genetic locations associated with obesity-related traits. Polymorphisms of insulin (INS) gene have been shown to be associated with obesity-related phenotypes in Europeans; while insulin receptor (INSR) gene has been associated with energy regulation. Therefore, this study was conducted to investigate the association between the INS (rs689) and INSR (rs3745551) gene polymorphisms with childhood obesity risk in a Malay childhood population. Normal weight (538) and overweight or obese (557) children aged 6-12 years old were genotyped using semi-automated Sequenom iPLEX® Gold. Body mass index (BMI) was calculated from measured body weight and height. The rs689 (T/T: 0.006, A/T: 0.159 and A/A: 0.835) and rs3745551 (G/G: 0.054, A/G: 0.378 and A/A: 0.568) genotype distributions were consistent with Hardy Weinberg equilibrium. The T-minor allele frequency for rs689 was 8.6% and G-minor allele frequency for rs3745551 was 24.3%. Minor allele of INS gene polymorphisms significantly increased risk of obesity among Malay children (sex- and age-adjusted OR=1.580; 95%CI: 1.134-2.201). However, INSR gene polymorphisms were not significantly associated with childhood obesity. In conclusion, the polymorphisms of INS gene, rather than INSR gene, were associated with childhood obesity in the Malay population.
Pediatric Obesity ; Receptor, Insulin

Aims: VraSR and GraSR were shown to be important in conferring intermediate vancomycin resistance in VISA. Nevertheless, the exact mechanism modulated by these systems leading to the development of VISA remains unclear. We employed a proteomic approach to determine the VraS and GraR regulons and subsequently derive the possible vancomycin resistance regulatory pathway(s) in the Mu50 lineage of Staphylococcus aureus. Methodology and results: Staphylococcus aureus strains Mu50Ω, Mu50Ω-vraSm and Mu50Ω-vraSm-graRm are isogenic strains with ascending levels of vancomycin resistance. Total proteins were extracted from the 3 strains and trypsin digested prior to protein isolation and identification by LC-ESI MS/MS and PLGS 2.4. Expression profiles of resulting proteins were analyzed using Progenesis LC/MS software. Differential expression profiles revealed 3 regulons, each controlled by VraS (Mu50Ω-vraSm vs Mu50Ω), GraR (Mu50Ω-vraSm-graRm vs Mu50Ω-vraSm) and VraS-GraR (Mu50Ω-vraSm-graRm vs Mu50Ω), respectively. The regulon down-regulated by VraS in Mu50Ω-vraSm were proteins associated with virulence (MgrA, Rot, and SarA), while GraR up-regulated resistance-associated proteins (TpiA, ArcB and IsaA) in Mu50Ω-vraSm-graRm. The VraS-GraR regulon mediated both up-regulation of resistance-associated proteins (ArgF, ArcB, VraR and SerS) and down-regulation of virulence-associated protein GapB. Conclusion, significance and impact of study: Down-regulation of virulence- in concert with up-regulation of resistance-associated proteins appears to be integral for development of intermediate-vancomycin resistance in the Mu50 lineage of S. aureus.
Staphylococcus aureus

Validation of instruments is essential when assessing physical activity (PA). The aim of this study was to validate a Malay language version of the International Physical Activity Questionnaire (IPAQ-M) against Actical accelerometer and to determine its reliability and validity. A total of 90 Malay adults aged 35-65 years old participating in The Malaysian Cohort project were recruited for this study. The IPAQ-M is comprised of 12 items, covering vigorous, moderate, walking, sitting and sleeping activities, and was administered on two occasions (Day 1 and Day 9) by interviewing the participants. Participants wore the Actical accelerometer for seven consecutive days between the two interview sessions. Validity tests showed that time spent in moderate-vigorous physical activity (MVPA) (min wk-1) from IPAQ-M was significantly correlated with MVPA from accelerometer (ρ=0.32, p<0.01). Time spent in vigorous activity (ρ=0.44) and total activity (ρ=0.36) from IPAQ-M were significantly correlated (p<0.01) with that measured by accelerometer, but no correlation was observed for sedentary behaviour. Reliability tests revealed significant correlations between the two interview sessions for all intensities of PA (=ρ0.55 to 0.71, p<0.01). Bland-Altman plots showed that time spent in MVPA for IPAQ-M was significantly different from that measured by accelerometer (mean difference: 98.02 min wk-1; 95% limits of agreement: -785.33 to 1317.83 min wk-1; p<0.01). When classifying people into meeting PA recommendation, the agreement between the two instruments was fair (κ=0.22). The IPAQ-M has acceptable validity for MVPA, vigorous and total physical activity, and was reliable for assessing the physical activity of Malay adults.​