Modern Genomic Implications

2021 ◽  
pp. 148-173
Author(s):  
Maryam Javed ◽  
Asif Nadeem ◽  
Faiz-ul Hassan
Keyword(s):  
Modern Genomic

The Roles of Twin Studies and Modern Genomic Technologies in Integrative Health Science

2018 ◽  
pp. 34-46
Author(s):  
Robert F. Krueger ◽  
Susan C. South
Keyword(s):  
Allostatic Load ◽  
Twin Studies ◽  
Transcriptional Response ◽  
The United States ◽  
Health Science ◽  
Research Strategies ◽  
Integrative Health ◽  
Genomic Technologies ◽  
Health And Illness ◽  
Modern Genomic

This chapter focuses on genetically informative research design and strategy in integrative health science (IHS). A feature of IHS is studying individual differences in health outcomes together and in a multidisciplinary manner. The chapter focuses on the advantages of using genetically informative research strategies for IHS. Genetically informative strategies are tools to enrich inferences within the IHS paradigm. They help parse the meaning of observed associations between exposures and outcomes. Two strategies are considered for the Midlife in the United States study : (1) Gene × Environment interactions and (2) correlations between education and allostatic load. A strategy likely to be employed in IHS research involves using segments of RNA to understand mechanisms underlying health and illness, focusing on the conserved transcriptional response to adversity (CTRA). The conclusion is that IHS and genetically informative research strategies are natural allies in understanding origins of health and illness in the population at large.

scholarly journals Role of Legal Principles in Eliminating and Minimizing the Risks of Genomic Technologies

Lex Russica ◽  
2019 ◽  
pp. 121-128 ◽  
Author(s):  
M. N. Maleina
Keyword(s):  
Genetic Information ◽  
Personal Data ◽  
Negative Consequences ◽  
Genetic Characteristics ◽  
Legal Principles ◽  
Genomic Technologies ◽  
Preventive Actions ◽  
The Individual ◽  
Modern Genomic

The use of modern genomic technologies, along with the benefits to the man and society, can lead to negative consequences. Such risks exist both in the process and after the production, isolation, modification, storage of DNA. Prior to detailed legislative regulation of relations regarding the use of genomic technologies for medicinal purposes and not for medical reasons, legal principles become vital.The paper formulates the following basic legal principles of genomic technologies application: the principle of preventive actions of the state to protect citizens from the risks of using genomic technologies; the principle of preserving the human genome as a special species; the principle of guaranteeing the inviolability of the individual of every citizen when using genomic technologies; the principle of priority of life and health of citizens over the interests of science and society; the principle of equality of citizens regardless of genetic characteristics; the principle of protection of genetic information of every citizen as part of personal data; the principle of guaranteeing access to the citizen’s own genetic information. Legal principles can be used to resolve a dispute by analogy of law.

scholarly journals Experience of using modern genomic technologies to study microorganisms and their communities

2021 ◽  
pp. 159-167
Author(s):  
E. V. Voropaev ◽  
I. O. Stoma ◽  
D. V. Tapalski
Keyword(s):  
Risk Groups ◽  
Metagenomic Analysis ◽  
Minimal Amount ◽  
Genomic Technologies ◽  
Bacterial Microbiome ◽  
Genomic Studies ◽  
H Pylori ◽  
Sequencing Platforms ◽  
Modern Genomic ◽  
Medical University

Objective. The aim of this work was to review the main results of genomic studies of microorganisms and their communities performed on the base of the Research Laboratory of Gomel State Medical University.Materials and methods. Genomic, transcriptomic and metagenomic analysis of the microorganisms of the stomach and respiratory tract.Results. The capabilities of modern next-generation sequencing platforms have been analyzed, and the authors` own results of the use of genomic, transcriptomic and metagenomic analysis of the microbiota in patients with various gastric and respiratory pathologies have been described.Conclusion. The analysis of the obtained data has revealed peculiarities of the structure of the microbial communities of the stomach of the patients infected with H. pylori with different gastric pathology: the proportion participation of H. pylori in the metagenome of the samples with different forms of gastric cancer did not exceed 25 %, of gastritis — 6 %, of peptic ulcer — 1 %. At the same time, the minimal amount of H. pylori in all the cases could reach 0.1 %. A signifcant degree of CagA and CagY loci variability of H. pylori was detected. Streptoccocus genus bacteria dominated (36 %) in the bacterial microbiome of a patient diagnosed with the coronavirus disease, and in the viral microbiome, SARS-CoV-2 constituted 59 % of the total number of viruses in the material. The analysis of 13 strains of Klebsiella pneumoniae with multiple and extreme resistance to antibiotics has found that the studied strains belong to fve MLST-types, three of which are classifed as high epidemic risk groups.

scholarly journals Analysis of Wheat Bread-Making Gene (wbm) Evolution and Occurrence in Triticale Collection Reveal Origin via Interspecific Introgression into Chromosome 7AL

Agronomy ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 854 ◽  
Author(s):  
Ilya Kirov ◽  
Andrey Pirsikov ◽  
Natalia Milyukova ◽  
Maxim Dudnikov ◽  
Maxim Kolenkov ◽  
...  
Keyword(s):  
Orthologous Gene ◽  
Wheat Breeding ◽  
Wheat Bread ◽  
Bread Making ◽  
Pcr Screening ◽  
Interspecific Introgression ◽  
Unknown Species ◽  
Long Interspersed Nuclear Elements ◽  
Modern Genomic ◽  
Gene Information

Bread-making quality is a crucial trait for wheat and triticale breeding. Several genes significantly influence these characteristics, including glutenin genes and the wheat bread-making (wbm) gene. World wheat collection screening showed that only a few percent of cultivars carry the valuable wbm variant, providing a useful source for wheat breeding. In contrast, no such analysis has been performed for triticale (wheat (AABB genome) × rye (RR) amphidiploid) collections. Despite the importance of the wbm gene, information about its origin and genomic organization is lacking. Here, using modern genomic resources available for wheat and its relatives, as well as PCR screening, we aimed to examine the evolution of the wbm gene and its appearance in the triticale genotype collection. Bioinformatics analysis revealed that the wheat Chinese Spring genome does not have the wbm gene but instead possesses the orthologous gene, called wbm-like located on chromosome 7A. The analysis of upstream and downstream regions revealed the insertion of LINE1 (Long Interspersed Nuclear Elements) retrotransposons and Mutator DNA transposon in close vicinity to wbm-like. Comparative analysis of the wbm-like region in wheat genotypes and closely related species showed low similarity between the wbm locus and other sequences, suggesting that wbm originated via introgression from unknown species. PCR markers were developed to distinguish wbm and wbm-like sequences, and triticale collection was screened resulting in the detection of three genotypes carrying wbm-specific introgression, providing a useful source for triticale breeding programs.

scholarly journals Modern Genomic Tools for Pigeonpea Improvement: Status and Prospects

2017 ◽  
pp. 41-54 ◽  
Author(s):  
Abhishek Bohra ◽  
Shalini Pareek ◽  
Rintu Jha ◽  
Rachit K. Saxena ◽  
Indra P. Singh ◽  
...  
Keyword(s):  
Genomic Tools ◽  
Modern Genomic

scholarly journals Bi-allelic GAD1 variants cause a neonatal onset syndromic developmental and epileptic encephalopathy

Brain ◽  
2020 ◽  
Vol 143 (5) ◽  
pp. 1447-1461 ◽  
Author(s):  
Nicolas Chatron ◽  
Felicitas Becker ◽  
Heba Morsy ◽  
Miriam Schmidts ◽  
Katia Hardies ◽  
...  
Keyword(s):  
Cleft Palate ◽  
Epileptic Encephalopathy ◽  
Allelic Loss ◽  
Loss Of Function ◽  
Seizure Onset ◽  
Joint Contractures ◽  
Epileptic Encephalopathies ◽  
Genomic Technologies ◽  
Pes Equinovarus ◽  
Modern Genomic

Abstract Developmental and epileptic encephalopathies are a heterogeneous group of early-onset epilepsy syndromes dramatically impairing neurodevelopment. Modern genomic technologies have revealed a number of monogenic origins and opened the door to therapeutic hopes. Here we describe a new syndromic developmental and epileptic encephalopathy caused by bi-allelic loss-of-function variants in GAD1, as presented by 11 patients from six independent consanguineous families. Seizure onset occurred in the first 2 months of life in all patients. All 10 patients, from whom early disease history was available, presented with seizure onset in the first month of life, mainly consisting of epileptic spasms or myoclonic seizures. Early EEG showed suppression-burst or pattern of burst attenuation or hypsarrhythmia if only recorded in the post-neonatal period. Eight patients had joint contractures and/or pes equinovarus. Seven patients presented a cleft palate and two also had an omphalocele, reproducing the phenotype of the knockout Gad1−/− mouse model. Four patients died before 4 years of age. GAD1 encodes the glutamate decarboxylase enzyme GAD67, a critical actor of the γ-aminobutyric acid (GABA) metabolism as it catalyses the decarboxylation of glutamic acid to form GABA. Our findings evoke a novel syndrome related to GAD67 deficiency, characterized by the unique association of developmental and epileptic encephalopathies, cleft palate, joint contractures and/or omphalocele.

scholarly journals T-cell acute lymphoblastic leukemia

Hematology ◽  
2016 ◽  
Vol 2016 (1) ◽  
pp. 580-588 ◽  
Author(s):  
Elizabeth A. Raetz ◽  
David T. Teachey
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
T Cell ◽  
De Novo ◽  
Residual Disease ◽  
Lymphoblastic Leukemia ◽  
Survival Rates ◽  
Disease Response ◽  
Cell Acute Lymphoblastic Leukemia ◽  
Relapsed Disease ◽  
Modern Genomic

Abstract T-cell acute lymphoblastic leukemia (T-ALL) is biologically distinct from its B lymphoblastic (B-ALL) counterpart and shows different kinetic patterns of disease response. Although very similar regimens are used to treat T-ALL and B-ALL, distinctions in response to different elements of therapy have been observed. Similar to B-ALL, the key prognostic determinant in T-ALL is minimal residual disease (MRD) response. Unlike B-ALL, other factors including age, white blood cell count at diagnosis, and genetics of the ALL blasts are not independently prognostic when MRD response is included. Recent insights into T-ALL biology, using modern genomic techniques, have identified a number of recurrent lesions that can be grouped into several targetable pathways, including Notch, Jak/Stat, PI3K/Akt/mTOR, and MAPK. With contemporary chemotherapy, outcomes for de novo T-ALL have steadily improved and now approach those observed in B-ALL, with approximately 85% 5-year event-free survival. Unfortunately, salvage has remained poor, with less than 25% event-free and overall survival rates for relapsed disease. Thus, current efforts are focused on preventing relapse by augmenting therapy for high-risk patients, sparing toxicity in favorable subsets and developing new approaches for the treatment of recurrent disease.

scholarly journals Puffaligner : A Fast, Efficient, and Accurate Aligner Based on the Pufferfish Index

2021 ◽  
Author(s):  
Fatemeh Almodaresi ◽  
Mohsen Zakeri ◽  
Rob Patro
Keyword(s):  
Open Source Software ◽  
Transcript Abundance ◽  
Supplementary Information ◽  
Abundance Estimation ◽  
Time Space ◽  
Highly Sensitive ◽  
Genomic Analyses ◽  
Variant Detection ◽  
Reference Sequences ◽  
Modern Genomic

Abstract Motivation Sequence alignment is one of the first steps in many modern genomic analyses, such as variant detection, transcript abundance estimation and metagenomic profiling. Unfortunately, it is often a computationally expensive procedure. As the quantity of data and wealth of different assays and applications continue to grow, the need for accurate and fast alignment tools that scale to large collections of reference sequences persists. Results In this paper, we introduce PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish index. PuffAligner is able to produce highly-sensitive alignments, similar to those of Bowtie2, but much more quickly. While exhibiting similar speed to the ultrafast STAR aligner, PuffAligner requires considerably less memory to construct its index and align reads. PuffAligner strikes a desirable balance with respect to the time, space, and accuracy tradeoffs made by different alignment tools, and provides a promising foundation on which to test new alignment ideas over large collections of sequences. Availability PuffAligner is a free and open-source software. It is implemented in C ++14 and can be obtained from https://github.com/COMBINE-lab/pufferfish/tree/cigar-strings Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals GWAS of a soybean breeding collection from South East and South Kazakhstan for resistance to fungal diseases

2018 ◽  
Vol 22 (5) ◽  
pp. 536-543 ◽  
Author(s):  
A. Zatybekov ◽  
S. Abugalieva ◽  
S. Didorenko ◽  
A. Rsaliyev ◽  
Y. Turuspekov
Keyword(s):  
Genome Wide Association Study ◽  
Field Evaluation ◽  
Fungal Diseases ◽  
Brown Spot ◽  
The South ◽  
Genome Wide ◽  
Genomic Studies ◽  
Local Breeding ◽  
Efficient Breeding ◽  
Modern Genomic

Soybean (Glycine max(L.) Merr) is an essential food, feed, and technical culture. In Kazakhstan the area under soybean is increasing every year, helping to solve the problem of protein deficiency in human nutrition and animal feeding. One of the main problems of soybean production is fungal diseases causing yields losses of up to 30 %. Modern genomic studies can be applied to facilitate efficient breeding research for improvement of soybean fungal disease tolerance. Therefore, the objective of this genome-wide association study (GWAS) was analysis of a soybean collection consisting of 182 accessions in relation to fungal diseases in the conditions of South East and South Kazakh­stan. Field evaluation of the soybean collection suggested thatFusariumspp. andCercospora sojinaaffected plants in the South region (RIBSP), andSeptoria glycines– in the South East region (KRIAPP). The major objective of the study was identification of QTL associated with resistance to fusarium root rot (FUS), frogeye leaf spot (FLS), and brown spot (BS). GWAS using 4 442 SNP (single nucleotide polymorphism) markers of Illumina iSelect array allowed for identification of fifteen marker trait associations (MTA) resistant to the three diseases at two different stages of growth. Two QTL both for FUS (chromosomes 13 and 17) and BS (chromosomes 14 and 17) were genetically mapped, including one presumably novel QTL for BS (chromo­some 17). Also, five presumably novel QTL for FLS were genetically mapped on chromosomes 2, 7, and 15. The results can be used for improvement of the local breeding projects based on marker-assisted selection approach.          

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