Integrative genomics

Part 1 book "Quantitative genetics, genomics and plant breeding" includes content: Quantitative genetics, genomics and the future of plant breeding; why quantitative geneticists should care about bioinformatics; QTL analysis - problems and (possible) solutions; association mapping in plant populations; integrating molecular techniques into quantitative genetics and plant breeding; use of molecular markers in plant breeding - drought tolerance improvement in tropical maize, explorations with barley genome maps;... and other contents.

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Paclitaxel is commonly used as a second-line therapy for advanced gastric cancer (AGC). The decision to proceed with second-line chemotherapy and select an appropriate regimen is critical for vulnerable patients with AGC progressing after first-line chemotherapy.

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Chemoradiotherapy is a critical treatment for patients with locally advanced and unresectable nonsmall cell lung cancer (NSCLC), and it is essential to identify high-risk patients as early as possible owing to the high incidence of radiation pneumonitis (RP). This study aimed to investigate the value of computed tomography (CT)-based radiomics combined with genomics in analyzing the risk of grade≥2 RP in unresectable stage III NSCLC.

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Although substantial efforts have been made to build molecular biomarkers to predict radiation sensitivity, the ability to accurately stratify the patients is still limited. In this study, we aim to leverage large-scale radiogenomics datasets to build genomic predictors of radiation response using the integral of the radiation dose–response curve.

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T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease with poor prognosis and inferior outcome. Although multiple studies have been perform on genomics of T-ALL, data from Indian sub-continent is scarce.

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Copy-number alterations (CNAs) are a hallmark of cancer and can regulate cancer cell states via altered gene expression values. Herein, we have developed a copy-number impact (CNI) analysis method that quantifies the degree to which a gene expression value is impacted by CNAs and leveraged this analysis at the pathway level.

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Ebook "Genome mapping and genomics in arthropods" provides comprehensive and up-to-date reviews on genomic research on a large variety of selected animal systems, contributed by leading scientists from around the world. Insects and other arthropods, the largest group of animals in number of species, have global impact on agriculture, industry, human health and environment. They are of particular economic importance for food production as pollinators, for natural products like silk and also as pests and parasites.

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In this study, the hn gene coding for the HN antigen of NDV genotype VIII was artificially synthesized, ligated into donor vector pFastBacHT A and integrated into the baculovirus genome for the purpose of HN expression in Spodoptera frugiperda 9 (Sf9) cells. The recombinant HN protein was successfully expressed in Sf9 cells in the SF900 III medium.

8p dianmotminh02 03-05-2024 1 1   Download

Ebook "Tomato yellow leaf curl virus disease: Management, molecular biology, breeding for resistance" will awaken the interest of breeders, phytopathologists, environmentalists, extension services, plant virologists, entomologists and molecular biologists. It deals both with the epidemiological aspects of the disease and with integrated pest management in the field. It discusses the efforts aimed at breeding tomato plants resistant to the virus (using classical breeding, marker-assisted breeding and genetic engineering).

437p ladongphongthanh1008 22-04-2024 2 2   Download

Accumulating evidence suggests alternative splicing (AS) is a co-transcriptional splicing process not only controlled by RNA-binding splicing factors, but also mediated by epigenetic regulators, such as chromatin structure, nucleosome density, and histone modification. Aberrant AS plays an important role in regulating various diseases, including cancers.

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Targeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients’ treatment options.

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Hepatocellular carcinoma (HCC) is the one of the most common cancers and lethal diseases in the world. DNA methylation alteration is frequently observed in HCC and may play important roles in carcinogenesis and diagnosis.

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Although large-scale, next-generation sequencing (NGS) studies of cancers hold promise for enabling precision oncology, challenges remain in integrating NGS with clinically validated biomarkers. To overcome such challenges, we utilized the Database of Evidence for Precision Oncology (DEPO) to link druggability to genomic, transcriptomic, and proteomic biomarkers.

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Genome–phenome studies have identified thousands of variants that are statistically associated with disease or traits; however, their functional roles are largely unclear. A comprehensive investigation of regulatory mechanisms and the gene regulatory networks between phenome-wide association study (PheWAS) and genomewide association study (GWAS) is needed to identify novel regulatory variants contributing to risk for human diseases.

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Cerebral amyloidosis, neuroinflammation, and tauopathy are key features of Alzheimer’s disease (AD), but interactions among these features remain poorly understood. Our previous multiscale molecular network models of AD revealed TYROBP as a key driver of an immune- and microglia-specific network that was robustly associated with AD pathophysiology.

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Exome sequencing is now being incorporated into clinical care for pediatric and adult populations, but its integration into prenatal diagnosis has been more limited. One reason for this is the paucity of information about the clinical utility of exome sequencing in the prenatal setting.

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Transcriptome analysis of breast cancer discovered distinct disease subtypes of clinical significance. However, it remains a challenge to define disease biology solely based on gene expression because tumor biology is often the result of protein function. Here, we measured global proteome and transcriptome expression in human breast tumors and adjacent non-cancerous tissue and performed an integrated proteotranscriptomic analysis.

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Only a small fraction of patients respond to the drug prescribed to treat their disease, which means that most are at risk of unnecessary exposure to side effects through ineffective drugs. This inter-individual variation in drug response is driven by differences in gene interactions caused by each patient’s genetic background, environmental exposures, and the proportions of specific cell types involved in disease.

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The extent to which changes in gene expression can influence cardiovascular disease risk across different tissue types has not yet been systematically explored. We have developed an analysis pipeline that integrates tissue-specific gene expression, Mendelian randomization and multiple-trait colocalization to develop functional mechanistic insight into the causal pathway from a genetic variant to a complex trait.

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Genomic medicine has considerable potential to provide novel diagnostic and therapeutic solutions for patients who have molecularly complex diseases and who are not responding to existing therapies. To bridge the gap between genomic medicine and clinical practice, integration of various data types, resources, and joint international initiatives will be required.

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