Tuberculosis and associated factors among type 2 diabetic patients in Perak: a case control study

This is a case-control study conducted with diabetic patients in Kinta, Kampar and Larut-Matang-Selama districts of Perak, Malaysia. We intended to determine the factors contributing to the development of active tuberculosis among diabetes patients. Cases were culture-proven and registered in the Malaysian National Tuberculosis Surveillance Registry (MyTB) from 2012 to 2018. Controls were diabetes patients identified from the National Diabetes Registry and were matched with cases based on the clinic in which they were registered at a ratio of 1:1. 119 cases and 119 controls were included in this study. Multivariate analysis was used to identify clinical factors associated with tuberculosis. Patient had increased odds of having tuberculosis if they had higher glycaemic (HbA1c) levels (OR=1.41, 95% CI 0.22-0.96, p<0.001) or nephropathy (OR=8.91, 95% CI 2.31-34.05, p<0.001). The odds ratio was lower if they have diabetes for at or more than 5 years (OR=0.46, 95% CI 0.22-0.96, p=0.04) and older (OR=0.96, CI 0.92-0.99, p=0.02). In conclusion, this study suggests that routine screening for tuberculosis in patients with diabetes should consider the diabetic duration, glycemic control, presence of nephropathy, and age of the patient

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Perioperative outcomes of laparoscopic and open distal pancreatectomy: Our institution’s 5-year experience

Application of minimally invasive techniques in the surgical management of distal pancreatic lesions is increasing. Despite this, numbers of laparoscopic distal pancreatectomy remain low and limited to treatment of benign and premalignant lesions. Retrospective analysis of 31 patients who underwent distal pancreatectomy from 2005 to 2010. Patients were grouped according to mode of surgical access: open (ODP) or laparoscopic (LDP). Perioperative parameters were compared. Twenty-one (67.7%) patients underwent ODP and 10 (32.3%) LDP (median age 61, 80.0% females in LDP group, p = 0.030). Postoperative morbidity rate were comparable between the two groups. In the LDP group, there were significantly lower estimated blood loss (p < 0.001) and amount of blood transfusion (p = 0.001), smaller tumor size (p = 0.010) and fewer lymph nodes harvested (p = 0.020), shorter postoperative length of stay (p = 0.020), and shorter length of stay in surgical high dependency (p = 0.001). LDP is a safe, efficient technique for resection of benign and premalignant pancreatic lesions. Indices reflecting perioperative outcomes in this study are highly competitive with those in other major centers

Perioperative outcomes of laparoscopic and open distal pancreatectomy: Our institution’s 5-year experience

Background: Application of minimally invasive techniques in the surgical management of distal pancreatic lesions is increasing. Despite this, numbers of laparoscopic distal pancreatectomy remain low and limited to treatment of benign and premalignant lesions. Methods: Retrospective analysis of 31 patients who underwent distal pancreatectomy from 2005 to 2010. Patients were grouped according to mode of surgical access: open (ODP) or laparoscopic (LDP). Perioperative parameters were compared. Results: Twenty-one (67.7%) patients underwent ODP and 10 (32.3%) LDP (median age 61; 80.0% females in LDP group, p = 0.030). Postoperative morbidity rate were comparable between the two groups. In the LDP group, there were significantly lower estimated blood loss (p < 0.001) and amount of blood transfusion (p = 0.001), smaller tumor size (p = 0.010) and fewer lymph nodes harvested (p = 0.020), shorter postoperative length of stay (p = 0.020), and shorter length of stay in surgical high dependency (p = 0.001). Conclusion: LDP is a safe, efficient technique for resection of benign and premalignant pancreatic lesions. Indices reflecting perioperative outcomes in this study are highly competitive with those in other major centers

Video directly observed therapy for tuberculosis in Malaysia: Early insights from a multicentre proof-of-concept initiative

Conventional in-person DOTS is often inconvenient, while virtual directlyobserved therapy improves adherence and bacteriological resolution. 1,2 • Virtual DOTS can be synchronous or asynchronous – of the two, asynchronous V-DOTS (AVDOTS) is believed to be more convenient due to flexibility in timing (daily video submission and review can occur at different times in a day). • The Angsana AVDOTS platform (i) outsources DOTS to independent observers, reducing burden on government facilities, and (ii) is available daily, including weekends and public holidays • The objectives of this proof-of-concept initiative were: • Primary: assess technical and patient-related barriers to AVDOTS • Secondary: assess treatment adherence & completion rates under AVDOT

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

: The impact of somatic structural variants (SVs) on gene expression in cancer is largely unknown. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing data and RNA sequencing from a common set of 1220 cancer cases, we report hundreds of genes for which the presence within 100 kb of an SV breakpoint associates with altered expression. For the majority of these genes, expression increases rather than decreases with corresponding breakpoint events. Up-regulated cancer-associated genes impacted by this phenomenon include TERT, MDM2, CDK4, ERBB2, CD274, PDCD1LG2, and IGF2. TERT-associated breakpoints involve ~3% of cases, most frequently in liver biliary, melanoma, sarcoma, stomach, and kidney cancers. SVs associated with up-regulation of PD1 and PDL1 genes involve ~1% of non-amplified cases. For many genes, SVs are significantly associated with increased numbers or greater proximity of enhancer regulatory elements near the gene. DNA methylation near the promoter is often increased with nearby SV breakpoint, which may involve inactivation of repressor elements

Author Correction: The landscape of viral associations in human cancers

author correctio