What is whole genome sequencing?5 answersWhole-genome sequencing (WGS) is a powerful technique that involves analyzing the complete genetic makeup of an organism. Initially, the Sanger Technique was used for sequencing, but it had limitations in terms of speed, cost, and inability to detect structural rearrangements. However, with the advent of Next-Generation Sequencing (NGS) technologies, WGS has become more efficient, allowing for rapid and accurate sequencing, making it invaluable in clinical diagnostics, outbreak monitoring, and drug development. In the context of food safety, WGS plays a crucial role in identifying foodborne pathogens, tracing contamination sources, and preventing outbreaks through precise characterization of pathogens. Despite challenges like cost and data governance, advancements in bioinformatics and collaboration are enhancing the adoption and effectiveness of WGS for various applications in public health and food safety.
Whole Genome Sequencing methods5 answersWhole genome sequencing methods have been developed to accurately determine the complete genetic makeup of organisms. Next-generation sequencing (NGS) techniques, such as PCR-NGS and RCA-NGS, have been optimized for high-throughput sequencing machines like MinION, enabling rapid and economical sequencing of RNA viral genomes with 100% accuracy. These methods eliminate the need for nucleic acid amplification with virus-specific primers, viral particle enrichment, and rapid amplification of cDNA ends (RACE). Whole-genome sequencing using NGS has played a crucial role in studying pathogens like SARS-CoV-2, providing comprehensive genetic information for the development of test kits, vaccines, and treatment regimens. Non-targeted whole genome sequencing is a powerful tool for identifying microbial communities without prior identification, allowing for the assessment of genetic aberrations and monitoring virus changes and evolution. These sequencing methods have revolutionized genetic research and have become routine in transcriptomic, ecological, and epidemiological studies.
Whole exome sequencing in Thalassemia5 answersWhole exome sequencing has been used in several studies to investigate the genetic factors associated with the clinical severity of thalassemia. In one study by Chattree et al., rare variants in protein-coding regions were analyzed in Thai patients with hemoglobin E/beta-thalassemia, and six genes (COL4A3, DLK1, FAM186A, PZP, THPO, and TRIM51) were found to be strongly associated with severity. Another study by Liang et al. evaluated the clinical utility of a long-read sequencing-based approach called comprehensive analysis of thalassemia alleles (CATSA) in prenatal diagnosis of thalassemia. CATSA was found to be more comprehensive and accurate compared to PCR-based methods, potentially enabling more informed genetic counseling and improved clinical outcomes. Basu et al. performed whole expanded exome sequencing in two families with E/beta thalassemia and identified KEGG pathways involved in each subject, suggesting the combined effect of mutation load in major pathways may be responsible for the severe phenotype. Jiang et al. used whole-genome sequencing with long reads to accurately detect thalassemia deletions, including rare deletions in the alpha-globin and beta-globin gene clusters.
What are the most common mutations found in patients with thalassemia in Turkey?4 answersThe most common mutations found in patients with thalassemia in Turkey include IVS-I-110 (G>A), IVS-I-6 (T>C), IVS-I-1 (G>A), and codon 39 (C>T). Other common mutations include IVS-II-1 (G>A), IVS-I-5 (G>C), codon 5 (-CT), codon 44 (-C) del, and IVS-II-745 (C>G). These mutations account for a significant percentage of all mutations in thalassemia patients in Turkey. Additionally, two new β thalassemia mutations, HBB:C*62 A>G (3'UTR+1536 A>G) and HBB:C*1 G>A (3'UTR+1475 G>A), were identified in the Mediterranean region of Turkey. The distribution of mutations in thalassemia patients in Turkey is similar throughout the country.
Whole genome sequencing breast cancer5 answersWhole-genome sequencing of breast cancer has provided valuable insights into the molecular characteristics of the disease and has led to advancements in personalized treatment options. Transcriptomic analysis and molecular subtyping have improved our understanding of breast cancer biology and enabled personalized treatment regimens. Whole-genome sequencing has also revealed the diversity of breast tumors and identified novel subgroups with distinct clinical outcomes. Additionally, whole-genome sequencing has been used to classify triple-negative breast cancers (TNBCs) and predict homologous-recombination-repair deficiency, providing independent prognostic information. Furthermore, deep whole-genome sequencing of breast cancer cell lines and patient-derived xenografts has identified novel genomic alterations and provided a comprehensive resource for studying these models. Overall, whole-genome sequencing has proven to be a valuable tool in understanding the genetic landscape of breast cancer and has the potential to improve clinical decision-making and treatment strategies.
Whole genome sequencing in human genetic disease5 answersWhole genome sequencing (WGS) has revolutionized the field of human genetic disease research. WGS utilizes massively-parallel short-read DNA sequencing and genome assembly methods to rapidly search and analyze genomes on a large scale. It has become increasingly prevalent in detecting disease genetics, studying causative relations with cancers, and reconstructing human population history. WGS has applications in both mendelian and complex diseases, providing valuable insights into disease mechanisms and potential therapeutic targets. It has also played a significant role in cancer studies, regulatory variant analysis, predictive medicine, and precision medicine. However, there are challenges associated with WGS, including data analysis and interpretation. Despite these challenges, WGS has the potential to become a common medical practice, aiding in the diagnosis and treatment of genetic diseases.