Khalid Mahmood
A5073553657- Genetic factors in colorectal cancer
- Cancer Genomics and Diagnostics
- Liver Disease Diagnosis and Treatment
- Liver Disease and Transplantation
- Genomics and Rare Diseases
- DNA Repair Mechanisms
- Genetic Associations and Epidemiology
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Colorectal Cancer Screening and Detection
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Hepatitis C virus research
- Colorectal Cancer Treatments and Studies
- Genomic variations and chromosomal abnormalities
- Organ Transplantation Techniques and Outcomes
- Hepatitis B Virus Studies
- BRCA gene mutations in cancer
- Epigenetics and DNA Methylation
- Machine Learning in Bioinformatics
- Diabetes Management and Research
- Cell Adhesion Molecules Research
- RNA modifications and cancer
- Renal Diseases and Glomerulopathies
- Urological Disorders and Treatments
- Genomics and Chromatin Dynamics
The University of Melbourne
2016-2025
Melbourne Bioinformatics
2016-2025
Victorian Comprehensive Cancer Centre
2019-2025
Civil Hospital Karachi
2009-2024
Dow University of Health Sciences
2014-2024
Sutter Roseville Medical Center
2024
Nishtar Medical College and Hospital
2023
Lady Reading Hospital
2005-2022
Queens Hospital Center
2021
Icahn School of Medicine at Mount Sinai
2021
BackgroundThe lipoprotein(a) pathway is a causal factor in coronary heart disease. We used genetic approach to distinguish the relevance of two distinct components this pathway, apolipoprotein(a) isoform size and circulating concentration, disease.MethodsIn mendelian randomisation study, we measured concentration determined with method (kringle IV type 2 [KIV2] repeats LPA gene) serum-based electrophoretic assay patients controls (frequency matched for age sex) from Pakistan Risk Myocardial...
Abstract Background This study aimed to investigate clinicopathological and molecular tumour features associated with intratumoral pks + Escherichia coli ( E.coli ), - (non- bacteria harbouring the island), Enterotoxigenic Bacteroides fragilis (ETBF) Fusobacterium nucleatum F. ). Methods We screened 1697 tumour-derived DNA samples from Australasian Colorectal Cancer Family Registry, Melbourne Collaborative Cohort Study ANGELS using targeted PCR. Results Pks was male sex P < 0.01) APC...
Abstract Motivation: The caspase family of cysteine proteases play essential roles in key biological processes such as programmed cell death, differentiation, proliferation, necrosis and inflammation. complete repertoire substrates remains to be fully characterized. Accordingly, systematic computational screening studies substrate cleavage sites may provide insight into the specificity caspases further facilitating discovery putative novel substrates. Results: In this article we develop an...
Genetic variant effect prediction algorithms are used extensively in clinical genomics and research to determine the likely consequences of amino acid substitutions on protein function. It is vital that we better understand their accuracies limitations because published performance metrics confounded by serious problems circularity error propagation. Here, derive three independent, functionally determined human mutation datasets, UniFun, BRCA1-DMS TP53-TA, employ them, alongside previously...
We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. identified five individuals with MBD4 within four families and these had a personal and/or family history of adenomatous colorectal polyposis, acute myeloid leukemia, uveal melanoma. encodes glycosylase involved G:T mismatches resulting from deamination 5'-methylcytosine. The adenomas MBD4-deficient showed mutator...
Abstract Schizophrenia (SCZ) is a chronic mental illness and among the most debilitating conditions encountered in medical practice. A recent landmark SCZ study of protein-coding regions genome identified causal role for ten genes concentration rare variant signals evolutionarily constrained 1 . This study—and other large-scale human genetics studies—was mainly composed individuals European (EUR) ancestry, generalizability findings non-EUR populations remains unclear. To address this gap, we...
This study was designed to determine the comparative efficacy of different scoring system in assessing prognosis critically ill patients.This a retrospective conducted medical intensive care unit (MICU) and high dependency (HDU) Medical Unit III, Civil Hospital, from April 2012 August 2012. All patients over age 16 years old who have fulfilled criteria for MICU admission were included. Predictive mortality APACHE II, SAP II SOFA calculated. Calibration discrimination used validity each...
The Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) was established by the International Society for Gastrointestinal Tumours and Clinical Genome Resource, who set out to develop recommendations interpretation of germline APC variants underlying Familial Adenomatous Polyposis, most frequent hereditary polyposis syndrome.
Objective Germline pathogenic variants (PVs) in the DNA mismatch repair (MMR) genes and base excision gene MUTYH underlie hereditary colorectal cancer (CRC) polyposis syndromes. We evaluated robustness discriminatory potential of tumour mutational signatures CRCs for identifying germline PV carriers. Design Whole-exome sequencing formalin-fixed paraffin-embedded (FFPE) CRC tissue was performed on 33 MMR carriers, 12 biallelic 25 sporadic MLH1 methylated MMR-deficient (MMRd controls) 160...
Abstract Carriers of germline biallelic pathogenic variants in the MUTYH gene have a high risk colorectal cancer. We test 5649 cancers to evaluate discriminatory potential tumor mutational signature specific for identifying carriers and classifying uncertain clinical significance (VUS). Using matched targeted multi-gene panel approach, our classifier identifies all known non-carriers an independent set 3019 (accuracy = 100% (95% confidence interval 99.87–100%)). All monoallelic are...
Residue depth (RD) is a solvent exposure measure that complements the information provided by conventional accessible surface area (ASA) and describes to what extent residue buried in protein structure space. Previous studies have established RD correlated with several properties, such as stability, conservation amino acid types. Accurate prediction of has many potentially important applications field structural bioinformatics, for example, facilitating identification functionally residues,...
Broadly, computational approaches for ortholog assignment is a three steps process: (i) identify all putative homologs between the genomes, (ii) gene anchors and (iii) link to best matches given their order context. In this article, we engineer two methods improve important aspects of pipeline [specifically (iii)]. First, computing sequence similarity data [step (i)] computationally intensive task large sets, creating bottleneck in pipeline. We have designed fast highly scalable sort-join...
We studied a consanguineous Palestinian Arab family segregating an autosomal recessive progressive myoclonus epilepsy (PME) with early ataxia. PME is rare, often fatal syndrome, initially responsive to antiepileptic drugs which over time becomes refractory and can be associated cognitive decline. Linkage analysis was performed the disease locus narrowed chromosome 19p13.3. Fourteen candidate genes were screened by conventional Sanger sequencing in one, LMNB2, novel homozygous missense...
Abstract Routine screening of tumors for DNA mismatch repair (MMR) deficiency (dMMR) in colorectal (CRC), endometrial (EC) and sebaceous skin (SST) leads to a significant proportion unresolved cases classified as suspected Lynch syndrome (SLS). SLS (n = 135) were recruited from Family Cancer Clinics across Australia New Zealand. Targeted panel sequencing was performed on tumor 137; 80×CRCs, 33×ECs 24xSSTs) matched blood-derived assess microsatellite instability status, mutation burden,...
We investigated aberrant DNA methylation (DNAm) changes and the contribution of ageing-associated methylomic drift age acceleration to early-onset colorectal cancer (EOCRC) carcinogenesis. Genome-wide DNAm profiling using Infinium HM450K on 97 EOCRC tumour 54 normal colonic mucosa samples was compared with: (1) intermediate-onset CRC (IOCRC; diagnosed between 50-70 years; 343 35 normal); (2) late-onset (LOCRC; >70 318 40 normal). CpGs associated with age-related were identified a public...
Background: Lateral sphincterotomy is now the standard surgical treatment for chronic anal fissure. Aims and Objectives: To determine outcome of closed lateral in fissures. Materials Methods: This was a prospective cross-sectional study conducted Department Surgery, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh during period from September 2009 to June 2010 with view For this purpose, 50 patients fissures were enrolled after inclusion exclusion criteria. Results: The age...
Background & Objective: Pediatric acute leukemias can present with aberrant immunophenotypes characterized by a different pattern of antigen expression on malignant cells, unlike the process usual hematopoietic maturation. The objective this study was to determine immunophenotype expressions in newly diagnosed pediatric lymphoblastic and myeloid leukemias. Methods: This cross-sectional carried out at University Child Health Sciences, Children’s Hospital, Lahore, from October 2022...
The adverse gut microbiome may underlie the variability in risks of colorectal cancer (CRC) and metachronous CRC people with Lynch syndrome (LS). role pks+/-Escherichia coli (pks+/-E. coli), Enterotoxigenic Bacteroides fragilis (ETBF), Fusobacterium nucleatum (Fn) CRCs adenomas LS is unknown. A total 358 cases, including 386 CRCs, 90 adenomas, 195 normal colonic mucosa DNA from Australasian Colon Cancer Family Registry were tested using multiplex TaqMan qPCR. Logistic regression was used to...