Journal articles: 'Genomic techniques'

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Ramzan, Fahad, Adnan Younis, and Ki-Byung Lim. "Application of Genomic In Situ Hybridization in Horticultural Science." International Journal of Genomics 2017 (2017): 1–12. http://dx.doi.org/10.1155/2017/7561909.

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Molecular cytogenetic techniques, such as in situ hybridization methods, are admirable tools to analyze the genomic structure and function, chromosome constituents, recombination patterns, alien gene introgression, genome evolution, aneuploidy, and polyploidy and also genome constitution visualization and chromosome discrimination from different genomes in allopolyploids of various horticultural crops. Using GISH advancement as multicolor detection is a significant approach to analyze the small and numerous chromosomes in fruit species, for example,Diospyroshybrids. This analytical technique has proved to be the most exact and effective way for hybrid status confirmation and helps remarkably to distinguish donor parental genomes in hybrids such asClivia,Rhododendron, andLycorisornamental hybrids. The genome characterization facilitates in hybrid selection having potential desirable characteristics during the early hybridization breeding, as this technique expedites to detect introgressed sequence chromosomes. This review study epitomizes applications and advancements of genomic in situ hybridization (GISH) techniques in horticultural plants.

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Xin-Yun Zhang, Fei Chen, Yuan-Ting Zhang, S. C. Agner, M. Akay, Zu-Hong Lu, M. M. Y. Waye, and S. K. W. Tsui. "Signal processing techniques in genomic engineering." Proceedings of the IEEE 90, no. 12 (December 2002): 1822–33. http://dx.doi.org/10.1109/jproc.2002.805308.

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Damaj, Mona B., Phillip D. Beremand, Marco T. Buenrostro-Nava, John Ivy, Siva P. Kumpatla, John Jifon, Getu Beyene, Qingyi Yu, Terry L. Thomas, and T. Erik Mirkov. "Isolating promoters of multigene family members from the polyploid sugarcane genome by PCR-based walking in BAC DNA." Genome 53, no. 10 (October 2010): 840–47. http://dx.doi.org/10.1139/g10-064.

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The availability of a wider range of promoters for regulated expression in valuable transgenic crops would benefit functional genomics studies and current biotechnology programs aimed at improved productivity. Polymerase chain reaction (PCR)-based genome walking techniques are commonly used to isolate promoters or 5′ flanking genomic regions adjacent to known cDNA sequences in genomes that are not yet completely sequenced. However, these techniques are problematic when applied directly to DNA isolated from crops with highly complex and large genomes. An adaptor ligation-mediated PCR-based BAC genome walking method is described here for the efficient isolation of promoters of multigene family members, such as the putative defense and fiber biosynthesis DIRIGENT genes that are abundant in the stem of sugarcane, a species with a highly polyploid genome. The advantage of this method is the efficient and specific amplification of the target promoter using BAC genomic DNA as template for the adaptor ligation-mediated PCR walking.

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Morrison, Carl. "Fluorescent In Situ Hybridization and Array Comparative Genomic Hybridization: Complementary Techniques for Genomic Evaluation." Archives of Pathology & Laboratory Medicine 130, no. 7 (July 1, 2006): 967–74. http://dx.doi.org/10.5858/2006-130-967-fishaa.

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Abstract During the past few years a new high-throughput molecular technology, array comparative genomic hybridization, has received a great deal of attention. As a DNA-based tool, this technique is presumably more reproducible than expression arrays. In this review, I discuss how array comparative genomic hybridization is remarkably similar with regard to genome analysis to fluorescent in situ hybridization, a technique that is generally regarded as one of the more accurate and reproducible molecular techniques in diagnostic surgical pathology. A thorough understanding of this technology will be useful for all surgical pathologists in the near future, as this technology will no doubt have some influence on our daily practice.

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van Oppen, Madeleine J. H., and Melinda A. Coleman. "Advancing the protection of marine life through genomics." PLOS Biology 20, no. 10 (October 17, 2022): e3001801. http://dx.doi.org/10.1371/journal.pbio.3001801.

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The rapid growth in genomic techniques provides the potential to transform how we protect, manage, and conserve marine life. Further, solutions to boost the resilience of marine species to climate change and other disturbances that characterize the Anthropocene require transformative approaches, made more effective if guided by genomic data. Although genetic techniques have been employed in marine conservation for decades and the availability of genomic data is rapidly expanding, widespread application still lags behind other data types. This Essay reviews how genetics and genomics have been utilized in management initiatives for ocean conservation and restoration, highlights success stories, and presents a pathway forward to enhance the uptake of genomic data for protecting our oceans.

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Upadhyay, Tejal, and Samir Patel. "Identifying Subtypes of Cancer Using Genomic Data by Applying Data Mining Techniques." International Journal of Natural Computing Research 8, no. 3 (July 2019): 55–64. http://dx.doi.org/10.4018/ijncr.2019070104.

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This article is about the study of genomics structures and identifying cancer types from it. It divides into six parts. The first part is about the introduction of cancer, types of cancers, how cancer arises, etc. The second part is about the genomic study and how cancer is related to that, which features are used for the study. The third part is about the software which the authors have used to study these genomic structures, which data sets are used, and what is the final output for this study. The fourth part shows the proposed algorithm for the study. The fifth part shows the data preprocessing and clustering. Different preprocessing and clustering algorithms are used. The sixth part shows the results and conclusion with a future scope. The genomics data which is used by this article is taken from the Cancer Genome Atlas data portal which is freely available. Some applied imputation techniques fill up for the missing values and important features are extracted. Different clustering algorithms are applied on genome dataset and results are generated.

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Kyselová, Jitka, Ladislav Tichý, and Kateřina Jochová. "The role of molecular genetics in animal breeding: A minireview." Czech Journal of Animal Science 66, No. 4 (March 26, 2021): 107–11. http://dx.doi.org/10.17221/251/2020-cjas.

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Current animal breeding approaches are strongly associated with the development of sophisticated molecular genetics methods and techniques. Worldwide expansion of genomic selection can be achieved by the identification of genetic DNA markers and implementation of the microarray (“chip”) technology. Further advancement was associated with next-generation sequencing methods, high-throughput genotyping platforms, targeted genome editing techniques, and studies of epigenetic mechanisms. The remarkable development of “omics” technologies, such as genomics, epigenomics, transcriptomics, proteomics and metabolomics, has enabled individual genomic prediction of animal performance, identification of disease-causing genes and biomarkers for the prevention and treatment and overall qualitative progress in animal production.

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Tramontano, Anna. "Comparative Modelling Techniques: Where are we?" Comparative and Functional Genomics 4, no. 4 (2003): 402–5. http://dx.doi.org/10.1002/cfg.306.

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The enormous increase in data availability brought about by genomic projects is paralleled by an equally unprecedented increase in the expectations for new medical, pharmacological, environmental and biotechnological discoveries. Whether or not we will be able to meet (at least partially) these expectations will depend on how well we will be able to interpret the data and translate the mono-dimensional information encrypted in genomes into a detailed understanding of its biological meaning at the phenotypic level. The process is far from being trivial, and the obstacles along the road are formidable: even the problem of identifying coding regions in eukaryotic genomes is not completely solved. Far more complex is identification of the function of the encoded proteins, and this will probably represent the most challenging problem for the next generations of scientists.

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Aziz, Md Momin Al, Md Nazmus Sadat, Dima Alhadidi, Shuang Wang, Xiaoqian Jiang, Cheryl L. Brown, and Noman Mohammed. "Privacy-preserving techniques of genomic data—a survey." Briefings in Bioinformatics 20, no. 3 (November 7, 2017): 887–95. http://dx.doi.org/10.1093/bib/bbx139.

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Nusrat, S., T. Harbig, and N. Gehlenborg. "Tasks, Techniques, and Tools for Genomic Data Visualization." Computer Graphics Forum 38, no. 3 (June 2019): 781–805. http://dx.doi.org/10.1111/cgf.13727.

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Pérez-Ortín, José E., Daniel A. Medina, and Antonio Jordán-Pla. "Genomic Insights into the Different Layers of Gene Regulation in Yeast." Genetics Research International 2011 (November 22, 2011): 1–12. http://dx.doi.org/10.4061/2011/989303.

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The model organism Saccharomyces cerevisiae has allowed the development of new functional genomics techniques devoted to the study of transcription in all its stages. With these techniques, it has been possible to find interesting new mechanisms to control gene expression that act at different levels and for different gene sets apart from the known cis-trans regulation in the transcription initiation step. Here we discuss a method developed in our laboratory, Genomic Run-On, and other new methods that have recently appeared with distinct technical features. A comparison between the datasets generated by them provides interesting genomic insights into the different layers of gene regulation in eukaryotes.

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Swales, A. K. E., and N. Spears. "Genomic imprinting and reproduction." Reproduction 130, no. 4 (October 2005): 389–99. http://dx.doi.org/10.1530/rep.1.00395.

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Genomic imprinting is the parent-of-origin specific gene expression which is a vital mechanism through both development and adult life. One of the key elements of the imprinting mechanism is DNA methylation, controlled by DNA methyltransferase enzymes. Germ cells undergo reprogramming to ensure that sex-specific genomic imprinting is initiated, thus allowing normal embryo development to progress after fertilisation. In some cases, errors in genomic imprinting are embryo lethal while in others they lead to developmental disorders and disease. Recent studies have suggested a link between the use of assisted reproductive techniques and an increase in normally rare imprinting disorders. A greater understanding of the mechanisms of genomic imprinting and the factors that influence them are important in assessing the safety of these techniques.

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Sabatello, Maya, and Paul S. Appelbaum. "Raising Genomic Citizens: Adolescents and the Return of Secondary Genomic Findings." Journal of Law, Medicine & Ethics 44, no. 2 (2016): 292–308. http://dx.doi.org/10.1177/1073110516654123.

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Whole genome and exome sequencing (WGS/WES) techniques raise hope for a new scale of diagnosis, prevention, and prediction of genetic conditions, and improved care for children. For these hopes to materialize, extensive genomic research with children will be needed. However, the use of WGS/WES in pediatric research settings raises considerable challenges for families, researchers, and policy development. In particular, the possibility that these techniques will generate genetic findings unrelated to the primary goal of sequencing has stirred intense debate about whether, which, how, and when these secondary or incidental findings (SFs) should be returned to parents and minors. The debate is even more pronounced when the subjects are adolescents, for whom decisions about return of SFs may have particular implications. In this paper, we consider the rise of “genomic citizenship” and the main challenges that arise for these stakeholders: adolescents' involvement in decisions relating to return of genomic SFs, the types of SFs that should be offered, privacy protections, and communication between researchers and adolescents about SFs. We argue that adolescents' involvement in genomic SF-related decisions acknowledges their status as valuable stakeholders without detracting from broader familial interests, and promotes more informed genomic citizens.

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Chu, Philomena, and Sarah Zanon Agapito-Tenfen. "Unintended Genomic Outcomes in Current and Next Generation GM Techniques: A Systematic Review." Plants 11, no. 21 (November 7, 2022): 2997. http://dx.doi.org/10.3390/plants11212997.

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Classical genetic engineering and new genome editing techniques, especially the CRISPR/Cas technology, increase the possibilities for modifying the genetic material in organisms. These technologies have the potential to provide novel agricultural traits, including modified microorganisms and environmental applications. However, legitimate safety concerns arise from the unintended genetic modifications (GM) that have been reported as side-effects of such techniques. Here, we systematically review the scientific literature for studies that have investigated unintended genomic alterations in plants modified by the following GM techniques: Agrobacterium tumefaciens-mediated gene transfer, biolistic bombardment, and CRISPR-Cas9 delivered via Agrobacterium-mediated gene transfer (DNA-based), biolistic bombardment (DNA-based) and as ribonucleoprotein complexes (RNPs). The results of our literature review show that the impact of such techniques in host genomes varies from small nucleotide polymorphisms to large genomic variation, such as segmental duplication, chromosome truncation, trisomy, chromothripsis, breakage fusion bridge, including large rearrangements of DNA vector-backbone sequences. We have also reviewed the type of analytical method applied to investigate the genomic alterations and found that only five articles used whole genome sequencing in their analysis methods. In addition, larger structural variations detected in some studies would not be possible without long-read sequencing strategies, which shows a potential underestimation of such effects in the literature. As new technologies are constantly evolving, a more thorough examination of prospective analytical methods should be conducted in the future. This will provide regulators working in the field of genetically modified and gene-edited organisms with valuable information on the ability to detect and identify genomic interventions.

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Makarova, Т. О. "The use of molecular cytogenetic methods in the investigation of distant potato hybrids." Plant Biotechnology and Breeding 3, no. 2 (December 29, 2020): 30–38. http://dx.doi.org/10.30901/2658-6266-2020-2-o4.

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This paper reviews the results of studies of interspecies hybridization, polyploidization, as well as phylogenetic relationships of Solanum species and members of closely related taxa by such molecular cytogenetic techniques as genomic (GISH) and fluorescent (FISH) DNA-DNA in situ hybridization. The latter was used to determine the genomic composition and origin of wild species of the Petota section, while the FISH technique was used for detecting intergenomic collinearity. The combination of these two types of research made possible a comparative analysis of karyotypes and genomes, thus allowing a better understanding of the meiotic interchromosomal interactions in hybrids. This review primarily focuses on the studies of wild allopolyploid potato species and artificially created intergeneric and interspecific hybrids of the genus Solanum and their offspring.

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Monaco, Alfonso, Ester Pantaleo, Nicola Amoroso, Antonio Lacalamita, Claudio Lo Giudice, Adriano Fonzino, Bruno Fosso, et al. "A primer on machine learning techniques for genomic applications." Computational and Structural Biotechnology Journal 19 (2021): 4345–59. http://dx.doi.org/10.1016/j.csbj.2021.07.021.

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Ceciliani, F., P. Roccabianca, C. Giudice, and C. Lecchi. "Application of post-genomic techniques in dog cancer research." Molecular BioSystems 12, no. 9 (2016): 2665–79. http://dx.doi.org/10.1039/c6mb00227g.

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We present in this review the most recent achievement in the application of transcriptomics, proteomics and metabolomics to canine cancer research. The protocols to recover material suitable for omics analyses from formalin-fixed, paraffin-embedded tissues are highlighted, together with the potential of omics in veterinary cancer diagnostics.

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Torres-Corral, Yolanda, and Ysabel Santos. "Identification and typing ofVagococcus salmoninarumusing genomic and proteomic techniques." Journal of Fish Diseases 42, no. 4 (February 11, 2019): 597–612. http://dx.doi.org/10.1111/jfd.12967.

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Moldovan, Valeriu, and Elena Moldovan. "Multiplex ligation-dependent probe amplification – a short overview." Revista Romana de Medicina de Laborator 28, no. 2 (April 1, 2020): 123–31. http://dx.doi.org/10.2478/rrlm-2020-0016.

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AbstractMultiplex Ligation-dependent Probe Amplification is a technique proposed for the detection of deletions or duplications that may lead to copy number variations in genomic DNA, mainly due to its higher resolution, and shorter overall diagnosis time, when compared with techniques traditionally used, namely karyotyping, fluorescence in situ hybridization, and array comparative genomic hybridization. Multiplex Ligation-dependent Probe Amplification is a fast (about 2 days), useful and cost-effective technique, being suitable for the diagnosis of hereditary conditions caused by complete or partial gene deletions or duplications, as these conditions are either more difficult or impossible to be diagnosed by other techniques, such as PCR, Real-Time PCR, or sequencing (Sanger or Next Generation). Due to its numerous advantages over conventional cytogenetic analysis techniques, Multiplex Ligation-dependent Probe Amplification could be used in the near future as the main technique for the molecular investigation of genetic conditions caused by copy number variations, in both rare and complex genetic disorders.

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Curren, Liam, Jane Kaye, Paula Boddington, Karen Melham, Naomi Hawkins, Heather Gowans, and Nadja Kanellopoulou. "Identifiability, Genomics and UK Data Protection Law." European Journal of Health Law 17, no. 4 (2010): 329–44. http://dx.doi.org/10.1163/157180910x516943.

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AbstractAnalyses of individuals’ genomes — their entire DNA sequence — have increased knowledge about the links between genetics and disease. Anticipated advances in ‘next generation’ DNA-sequencing techniques will see the routine research use of whole genomes, rather than distinct parts, within the next few years. The scientific benefits of genomic research are, however, accompanied by legal and ethical concerns. Despite the assumption that genetic research data can and will be rendered anonymous, participants’ identities can sometimes be elucidated, which could cause data protection legislation to apply. We undertake a timely reappraisal of these laws — particularly new penalties — and identifiability in genomic research.

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Miedaner, Thomas, Ana Luisa Galiano-Carneiro Boeven, David Sewodor Gaikpa, Maria Belén Kistner, and Cathérine Pauline Grote. "Genomics-Assisted Breeding for Quantitative Disease Resistances in Small-Grain Cereals and Maize." International Journal of Molecular Sciences 21, no. 24 (December 19, 2020): 9717. http://dx.doi.org/10.3390/ijms21249717.

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Generating genomics-driven knowledge opens a way to accelerate the resistance breeding process by family or population mapping and genomic selection. Important prerequisites are large populations that are genomically analyzed by medium- to high-density marker arrays and extensive phenotyping across locations and years of the same populations. The latter is important to train a genomic model that is used to predict genomic estimated breeding values of phenotypically untested genotypes. After reviewing the specific features of quantitative resistances and the basic genomic techniques, the possibilities for genomics-assisted breeding are evaluated for six pathosystems with hemi-biotrophic fungi: Small-grain cereals/Fusarium head blight (FHB), wheat/Septoria tritici blotch (STB) and Septoria nodorum blotch (SNB), maize/Gibberella ear rot (GER) and Fusarium ear rot (FER), maize/Northern corn leaf blight (NCLB). Typically, all quantitative disease resistances are caused by hundreds of QTL scattered across the whole genome, but often available in hotspots as exemplified for NCLB resistance in maize. Because all crops are suffering from many diseases, multi-disease resistance (MDR) is an attractive aim that can be selected by specific MDR QTL. Finally, the integration of genomic data in the breeding process for introgression of genetic resources and for the improvement within elite materials is discussed.

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Marçais, Guillaume, Brad Solomon, Rob Patro, and Carl Kingsford. "Sketching and Sublinear Data Structures in Genomics." Annual Review of Biomedical Data Science 2, no. 1 (July 20, 2019): 93–118. http://dx.doi.org/10.1146/annurev-biodatasci-072018-021156.

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Large-scale genomics demands computational methods that scale sublinearly with the growth of data. We review several data structures and sketching techniques that have been used in genomic analysis methods. Specifically, we focus on four key ideas that take different approaches to achieve sublinear space usage and processing time: compressed full-text indices, approximate membership query data structures, locality-sensitive hashing, and minimizers schemes. We describe these techniques at a high level and give several representative applications of each.

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Sulaiman, Irshad M., Lihua Xiao, and Altaf A. Lal. "Evaluation of Cryptosporidium parvumGenotyping Techniques." Applied and Environmental Microbiology 65, no. 10 (October 1, 1999): 4431–35. http://dx.doi.org/10.1128/aem.65.10.4431-4435.1999.

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ABSTRACT We evaluated the specificity and sensitivity of 11 previously described species differentiation and genotyping PCR protocols for detection of Cryptosporidium parasites. Genomic DNA from three species of Cryptosporidium parasites (genotype 1 and genotype 2 of C. parvum, C. muris, and C. serpentis), two Eimeria species (E. neischulzi and E. papillata), and Giardia duodenalis were used to evaluate the specificity of primers. Furthermore, the sensitivity of the genotyping primers was tested by using genomic DNA isolated from known numbers of oocysts obtained from a genotype 2 C. parvum isolate. PCR amplification was repeated at least three times with all of the primer pairs. Of the 11 protocols studied, 10 amplified C. parvum genotypes 1 and 2, and the expected fragment sizes were obtained. Our results indicate that two species-differentiating protocols are notCryptosporidium specific, as the primers used in these protocols also amplified the DNA of Eimeria species. The sensitivity studies revealed that two nested PCR-restriction fragment length polymorphism (RFLP) protocols based on the small-subunit rRNA and dihydrofolate reductase genes are more sensitive than single-round PCR or PCR-RFLP protocols.

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Beyer, Wolfgang, Adam M. Novak, Glenn Hickey, Jeffrey Chan, Vanessa Tan, Benedict Paten, and Daniel R. Zerbino. "Sequence tube maps: making graph genomes intuitive to commuters." Bioinformatics 35, no. 24 (August 1, 2019): 5318–20. http://dx.doi.org/10.1093/bioinformatics/btz597.

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Abstract Motivation Compared to traditional haploid reference genomes, graph genomes are an efficient and compact data structure for storing multiple genomic sequences, for storing polymorphisms or for mapping sequencing reads with greater sensitivity. Further, graphs are well-studied computer science objects that can be efficiently analyzed. However, their adoption in genomic research is slow, in part because of the cognitive difficulty in interpreting graphs. Results We present an intuitive graphical representation for graph genomes that re-uses well-honed techniques developed to display public transport networks, and demonstrate it as a web tool. Availability and implementation Code: https://github.com/vgteam/sequenceTubeMap. Demonstration https://vgteam.github.io/sequenceTubeMap/. Supplementary information Supplementary data are available at Bioinformatics online.

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Cristea, Ileana M., Simon J. Gaskell, and Anthony D. Whetton. "Proteomics techniques and their application to hematology." Blood 103, no. 10 (May 15, 2004): 3624–34. http://dx.doi.org/10.1182/blood-2003-09-3295.

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Abstract The recent sequencing of a number of genomes has raised the level of opportunities for studies on proteins. This area of research has been described with the all-embracing term, proteomics. In proteomics, the use of mass spectrometric techniques enables genomic databases to be used to establish the identity of proteins with relatively little data, compared to the era before genome sequencing. The use of related analytical techniques also offers the opportunity to gain information on regulation, via posttranslational modification, and potential new diagnostic and prognostic indicators. Relative quantification of proteins and peptides in cellular and extracellular material remains a challenge for proteomics and mass spectrometry. This review presents an analysis of the present and future impact of these proteomic technologies with emphasis on relative quantification for hematologic research giving an appraisal of their potential benefits.

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Cao, Mingshu, David A. Sleper, Fenggao Dong, and Jiming Jiang. "Genomic in situ hybridization (GISH) reveals high chromosome pairing affinity between Lolium perenne and Festuca mairei." Genome 43, no. 2 (March 15, 2000): 398–403. http://dx.doi.org/10.1139/g99-129.

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Intergeneric hybridizations have been made between species of Lolium and Festuca. It has been demonstrated, largely through conventional cytogenetic analysis, that the genomes of the two genera are related, however, much information is lacking on exactly how closely related the genomes are between the two species. We applied genomic in situ hybridization (GISH) techniques to the F1 hybrids of tetraploid Festuca mairei with a genomic constitution of M1M1M2M2 and diploid Lolium perenne with a genomic constitution of LL. It was shown in the triploid hybrids (LM1M2) that the chromosomes of M1 and M2 from F. mairei could pair with each other, and it was further discovered that L chromosomes of L. perenne paired with M1 and M2 chromosomes. Our results showed that meiocytes of Lolium-Festuca are amenable to GISH analysis, and provided direct evidence for the hypothesis that the chromosomes of Lolium and Festuca may be genetically equivalent and that reciprocal mixing of the genomes may be possible. Key words: Lolium, Festuca, in situ hybridization, meiosis.

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Waldispuhl, Jerome, and Mathieu Blanchette. "Phylo and Open-Phylo: A Human-Computing Platform for Comparative Genomics." Proceedings of the AAAI Conference on Human Computation and Crowdsourcing 2 (September 5, 2014): 73–74. http://dx.doi.org/10.1609/hcomp.v2i1.13137.

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Comparative genomics is a field of research that aims to provide us accurate mappings between the genetic material of multiple species. These techniques are useful for biomedical research and evolutionary studies. We present Phylo and Open-Phylo, an open citizen science platform and human computing-game for comparative genomic studies that reached more than 300,000 users.

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Gilbertson, Marie L. J., Nicholas M. Fountain-Jones, and Meggan E. Craft. "Incorporating genomic methods into contact networks to reveal new insights into animal behaviour and infectious disease dynamics." Behaviour 155, no. 7-9 (2018): 759–91. http://dx.doi.org/10.1163/1568539x-00003471.

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Abstract Utilization of contact networks has provided opportunities for assessing the dynamic interplay between pathogen transmission and host behaviour. Genomic techniques have, in their own right, provided new insight into complex questions in disease ecology, and the increasing accessibility of genomic approaches means more researchers may seek out these tools. The integration of network and genomic approaches provides opportunities to examine the interaction between behaviour and pathogen transmission in new ways and with greater resolution. While a number of studies have begun to incorporate both contact network and genomic approaches, a great deal of work has yet to be done to better integrate these techniques. In this review, we give a broad overview of how network and genomic approaches have each been used to address questions regarding the interaction of social behaviour and infectious disease, and then discuss current work and future horizons for the merging of these techniques.

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Ahmar, Sunny, Paulina Ballesta, Mohsin Ali, and Freddy Mora-Poblete. "Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing." International Journal of Molecular Sciences 22, no. 19 (September 30, 2021): 10583. http://dx.doi.org/10.3390/ijms221910583.

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Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.

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Turzynski, Victoria, Indra Monsees, Cristina Moraru, and Alexander J. Probst. "Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples." Viruses 13, no. 11 (October 21, 2021): 2126. http://dx.doi.org/10.3390/v13112126.

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Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses—bacteriophages and archaeal viruses—influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage–host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth’s ecosystems.

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TSAI, Huai-Jen, Mao-Shen YEH, and Yen-Ling SONG. "Characterization of Vibrio species by using genomic DNA fingerprinting techniques." Fish Pathology 25, no. 4 (1990): 201–6. http://dx.doi.org/10.3147/jsfp.25.201.

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Zeng, Huawei. "Genomic and Proteomic Techniques and their Application in Selenium Research." Current Pharmacogenomics 1, no. 1 (March 1, 2003): 59–65. http://dx.doi.org/10.2174/1570160033378367.

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B., Abinaya, and Santhi S. "A survey on genomic data by privacy-preserving techniques perspective." Computational Biology and Chemistry 93 (August 2021): 107538. http://dx.doi.org/10.1016/j.compbiolchem.2021.107538.

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Blandino, G., M. Fanciulli, M. Levrero, and G. Piaggio. "The post-genomic era: workshop on chromatin immunoprecipitation-related techniques." Cell Death & Differentiation 14, no. 7 (May 18, 2007): 1390–91. http://dx.doi.org/10.1038/sj.cdd.4402164.

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Pipis, Menelaos, Henry Houlden, and Mary M. Reilly. "Advancing Charcot-Marie-Tooth disease diagnostics, through the UK 100,000 Genomes Project." Medizinische Genetik 32, no. 3 (September 1, 2020): 227–31. http://dx.doi.org/10.1515/medgen-2020-2037.

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Abstract Whole genome sequencing (WGS) is regarded by many as the pinnacle of contemporary molecular genetic testing, and has only been possible because of the rapid development and roll-out of next-generation sequencing technologies. It provides a phenotype-agnostic analysis of the genome and has important advantages compared to other techniques including a consistent coverage across the coding and non-coding genome, the application of high resolution homozygosity mapping and the ability to detect and highlight structural variation. Realising this potential and with a bid to sequence 100,000 genomes, the UK rolled out the 100,000 Genomes Project as a proof of concept of integrating genomics in the national health service. Participants with cancer and rare diseases enrolled in the project whose infrastructure comprises of a central national biorepository and 13 regional genomic medicine centres where clinicians, geneticists and other scientists work as part of a multidisciplinary team. Amongst participants are also patients with genetically unclassified Charcot-Marie-Tooth disease who have benefited substantially from improved diagnostic rates and many more stand to benefit as the analysis of genomic data is ongoing. WGS is an important tool as we head towards more personalised medicine and in our quest to improve public health and treat and where possible prevent disease.

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Pascoal, Túlio, Jérémie Decouchant, Antoine Boutet, and Marcus Völp. "I-GWAS: Privacy-Preserving Interdependent Genome-Wide Association Studies." Proceedings on Privacy Enhancing Technologies 2023, no. 1 (January 2023): 437–54. http://dx.doi.org/10.56553/popets-2023-0026.

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Genome-wide Association Studies (GWASes) identify genomic variations that are statistically associated with a trait, such as a disease, in a group of individuals. Unfortunately, careless sharing of GWAS statistics might give rise to privacy attacks. Several works attempted to reconcile secure processing with privacy-preserving releases of GWASes. However, we highlight that these approaches remain vulnerable if GWASes utilize overlapping sets of individuals and genomic variations. In such conditions, we show that even when relying on state-of-the-art techniques for protecting releases, an adversary could reconstruct the genomic variations of up to 28.6% of participants, and that the released statistics of up to 92.3% of the genomic variations would enable membership inference attacks. We introduce I-GWAS, a novel framework that securely computes and releases the results of multiple possibly interdependent GWASes. I-GWAS continuously releases privacy-preserving and noise-free GWAS results as new genomes become available.

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Calia, Kerstin E., Matthew K. Waldor, and Stephen B. Calderwood. "Use of Representational Difference Analysis To Identify Genomic Differences between Pathogenic Strains of Vibrio cholerae." Infection and Immunity 66, no. 2 (February 1, 1998): 849–52. http://dx.doi.org/10.1128/iai.66.2.849-852.1998.

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ABSTRACT Representational difference analysis (RDA) is a recently developed technique used for amplifying genetic differences between two closely related genomes. We compared RDA and a modified version of RDA to examine genomic differences between the two Vibrio choleraeserogroups that cause epidemic cholera, O1 and O139, and between the two biotypes of the O1 serogroup. With both techniques, we recovered several sequences known to be found only in V. choleraeO139 but absent in its presumed progenitor, V. cholerae O1 El Tor. A greater number of unique fragments were generated in comparing the two V. cholerae O1 biotypes, consistent with the probable greater genetic differences between the two biotypes.

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Dunn, Scott, Sarah M. Rudman, and Jonathan S. Marchant. "Teaching genetics: A genomic science bootcamp." Biochemist 29, no. 6 (December 1, 2007): 36–37. http://dx.doi.org/10.1042/bio02906036.

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How can school teachers get hands-on training in using DNA-based methods? Here, we highlight the availability of a free course, supported by the Goldsmiths' Company, which provides the opportunity for educators to get back into the laboratory and gain confidence with molecular genetic techniques.

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Saylor, Brent, Tyler A. Elliott, Stefan Linquist, Stefan C. Kremer, T. Ryan Gregory, and Karl Cottenie. "A novel application of ecological analyses to assess transposable element distributions in the genome of the domestic cow, Bos taurus." Genome 56, no. 9 (September 2013): 521–33. http://dx.doi.org/10.1139/gen-2012-0162.

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Transposable elements (TEs) are among the most abundant components of many eukaryotic genomes. Efforts to explain TE abundance, as well as TE diversity among genomes, have led some researchers to draw an analogy between genomic and ecological processes. Adopting this perspective, we conducted an analysis of the cow (Bos taurus) genome using techniques developed by community ecologists to determine whether environmental factors influence community composition. Specifically, each chromosome within the Bos taurus genome was treated as a “linear transect”, and a multivariate redundancy analysis (RDA) was used to identify large-scale spatial patterns in TE communities associated with 10 TE families. The position of each TE community on the chromosome accounted for ∼50% of the variation along the chromosome “transect”. Multivariate analysis further revealed an effect of gene density on TE communities that is influenced by several other factors in the (genomic) environment, including chromosome length and TE density. The results of this analysis demonstrate that ecological methods can be applied successfully to help answer genomic questions.

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Ahmad, S. Rehan. "Artificial Intelligence: Use in Clinical and Genomic Diagnostics." Emerging Trends in Nutraceuticals 1, no. 2 (August 28, 2022): 42–50. http://dx.doi.org/10.18782/2583-4606.111.

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The development of computer systems that are capable of carrying out tasks that typically require human intelligence is known as artificial intelligence (AI). Recent and quickly rising interest in medical AI applications is a result of AI software and technology improvements, especially deep learning algorithms and the graphics processing units (GPUs) that enable their training. While other AI subtypes have started to show similar promise in different diagnostic modalities, AI-based computer vision methods are poised to change image-based diagnostics in clinical diagnostics. Large and complicated genomic datasets are processed using a particular form of AI algorithm known as deep learning in various fields, such as clinical genomics. In this review, we first provide an overview of the primary categories of issues that AI systems are best adapted to address, followed by a description of the clinical diagnostic tasks that are aided by these solutions. Then, we concentrate on recently developed techniques for certain clinical genomics applications, such as variant calling, genome annotation and variant categorization, and phenotype-to-genotype correlation. We conclude by talking about the future potential of AI in individualized medicine applications, particularly for risk prediction in common complex diseases, as well as the issues, constraints, and biases that must be carefully addressed for the successful deployment of AI in medical applications, particularly those using data from genomics and human genetics.

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Gurling, H. M. D. "Testing the Retrovirus Hypothesis of Manic Depression and Schizophrenia with Molecular Genetic Techniques." Journal of the Royal Society of Medicine 81, no. 6 (June 1988): 332–34. http://dx.doi.org/10.1177/014107688808100610.

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Crow's viral hypothesis of schizophrenia proposes that psychosis may be the result of mutagenesis caused by viral integration or transposition in human genomic DNA. Molecular genetic techniques can be used to systematically investigate this hypothesis. In a study of genomic lymphocyte DNA unexpected DNA polymorphisms which were probably insertions and deletions were found in specific human genomic retroviral (proviral) related sequences. However these changes were found exclusively in normal Icelandic individuals and are probably of evolutionary origin. The extent to which human retroviral insertion and deletion has taken place and the mobility of such sequences will help in understanding their evolutionary origin and might provide a source of polymorphic marker sequences that could be used in genetic linkage studies of disease.

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Rasool, Rabia, Inam Ullah, Bismillah Mubeen, Sultan Alshehri, Syed Sarim Imam, Mohammed M. Ghoneim, Sami I. Alzarea, et al. "Theranostic Interpolation of Genomic Instability in Breast Cancer." International Journal of Molecular Sciences 23, no. 3 (February 7, 2022): 1861. http://dx.doi.org/10.3390/ijms23031861.

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Breast cancer is a diverse disease caused by mutations in multiple genes accompanying epigenetic aberrations of hazardous genes and protein pathways, which distress tumor-suppressor genes and the expression of oncogenes. Alteration in any of the several physiological mechanisms such as cell cycle checkpoints, DNA repair machinery, mitotic checkpoints, and telomere maintenance results in genomic instability. Theranostic has the potential to foretell and estimate therapy response, contributing a valuable opportunity to modify the ongoing treatments and has developed new treatment strategies in a personalized manner. “Omics” technologies play a key role while studying genomic instability in breast cancer, and broadly include various aspects of proteomics, genomics, metabolomics, and tumor grading. Certain computational techniques have been designed to facilitate the early diagnosis of cancer and predict disease-specific therapies, which can produce many effective results. Several diverse tools are used to investigate genomic instability and underlying mechanisms. The current review aimed to explore the genomic landscape, tumor heterogeneity, and possible mechanisms of genomic instability involved in initiating breast cancer. We also discuss the implications of computational biology regarding mutational and pathway analyses, identification of prognostic markers, and the development of strategies for precision medicine. We also review different technologies required for the investigation of genomic instability in breast cancer cells, including recent therapeutic and preventive advances in breast cancer.

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Hattinger, Claudia M., Gemma Reverter-Branchat, Daniel Remondini, Gastone C. Castellani, Stefania Benini, Michela Pasello, Maria C. Manara, Katia Scotlandi, Piero Picci, and Massimo Serra. "Genomic imbalances associated with methotrexate resistance in human osteosarcoma cell lines detected by comparative genomic hybridization-based techniques." European Journal of Cell Biology 82, no. 9 (September 2003): 483–93. http://dx.doi.org/10.1078/0171-9335-00336.

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Mustafa, Sarbast Ihsan, Trude Schwarzacher, and John S. Heslop-Harrison. "The Nature and Chromosomal Landscape of Endogenous Retroviruses (ERVs) Integrated in the Sheep Nuclear Genome." DNA 2, no. 1 (March 16, 2022): 86–103. http://dx.doi.org/10.3390/dna2010007.

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Endogenous retroviruses (ERVs) represent genomic components of retroviral origin that are found integrated in the genomes of various species of vertebrates. These genomic elements have been widely characterized in model organisms and humans. However, composition and abundances of ERVs have not been categorized fully in all domestic animals. The advent of next generation sequencing technologies, development of bioinformatics tools, availability of genomic databases, and molecular cytogenetic techniques have revolutionized the exploration of the genome structure. Here, we investigated the nature, abundance, organization and assembly of ERVs and complete genomes of Jaagsiekte sheep retrovirus (JSRV) from high-throughput sequencing (HTS) data from two Iraqi domestic sheep breeds. We used graph-based read clustering (RepeatExplorer), frequency analysis of short motifs (k-mers), alignment to reference genome assemblies and fluorescent in situ hybridization (FISH). Three classes of ERVs were identified with the total genomic proportions of 0.55% from all analyzed whole genome sequencing raw reads, while FISH to ovine metaphase chromosomes exhibited abundant centromeric to dispersed distribution of these ERVs. Furthermore, the complete genomes of JSRV of two Iraqi sheep breeds were assembled and phylogenetically clustered with the known enJSRV proviruses in sheep worldwide. Characterization of partial and complete sequences of mammalian ERVs is valuable in providing insights into the genome landscape, to help with future genome assemblies, and to identify potential sources of disease when ERVs become active.

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Klinger and Richardson. "Small Genomes and Big Data: Adaptation of Plastid Genomics to the High-Throughput Era." Biomolecules 9, no. 8 (July 24, 2019): 299. http://dx.doi.org/10.3390/biom9080299.

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Plastid genome sequences are becoming more readily available with the increase in high-throughput sequencing, and whole-organelle genetic data is available for algae and plants from across the diversity of photosynthetic eukaryotes. This has provided incredible opportunities for studying species which may not be amenable to in vivo study or genetic manipulation or may not yet have been cultured. Research into plastid genomes has pushed the limits of what can be deduced from genomic information, and in particular genomic information obtained from public databases. In this Review, we discuss how research into plastid genomes has benefitted enormously from the explosion of publicly available genome sequence. We describe two case studies in how using publicly available gene data has supported previously held hypotheses about plastid traits from lineage-restricted experiments across algal and plant diversity. We propose how this approach could be used across disciplines for inferring functional and biological characteristics from genomic approaches, including integration of new computational and bioinformatic approaches such as machine learning. We argue that the techniques developed to gain the maximum possible insight from plastid genomes can be applied across the eukaryotic tree of life.

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SCHELTEMA, RICHARD A., SASKIA DECUYPERE, RUBEN T'KINDT, JEAN-CLAUDE DUJARDIN, GRAHAM H. COOMBS, and RAINER BREITLING. "The potential of metabolomics for Leishmania research in the post-genomics era." Parasitology 137, no. 9 (January 29, 2010): 1291–302. http://dx.doi.org/10.1017/s0031182009992022.

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SUMMARYThe post-genomics era has provided researchers with access to a new generation of tools for the global characterization and understanding of pathogen diversity. This review provides a critical summary of published Leishmania post-genomic research efforts to date, and discusses the potential impact of the addition of metabolomics to the post-genomic toolbox. Metabolomics aims at understanding biology by comprehensive metabolite profiling. We present an overview of the design and interpretation of metabolomics experiments in the context of Leishmania research. Sample preparation, measurement techniques, and bioinformatics analysis of the generated complex datasets are discussed in detail. To illustrate the concepts and the expected results of metabolomics analyses, we also present an overview of comparative metabolic profiles of drug-sensitive and drug-resistant Leishmania donovani clinical isolates.

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López, Alicia, Aveliano Fernández, and Lidia Poggio. "Genomic affinities in Turnera (subseries Turnera, Turneraceae) inferred by in situ hybridization techniques." Genome 53, no. 8 (August 2010): 594–98. http://dx.doi.org/10.1139/g10-037.

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Subseries Turnera comprises a polyploid complex with ploidy levels ranging from diploid (2n = 2x = 10) to octoploid (2n = 8x = 40). The use of fluorescent in situ hybridization greatly improved the knowledge of the karyotypes of Turnera species by detecting and mapping rDNA sites. Interspecific variability in the number of sites was detected, but not in correlation with the ploidy level. A chromosome pair with a strong hybridization signal was always visible and this signal corresponded to the secondary constriction detectable by conventional techniques. Genomic in situ hybridization experiments combined with information on meiotic pairing in species and interspecific hybrids revealed that homologies detected by molecular analysis are greater than those detected by chromosome pairing. This suggests that the formation of the allopolyploids could involve species more closely related than previously assumed. Despite the molecular affinity among the genomes, the meiotic pairing is probably controlled by specific genes that restrict homeologous pairing in polyploids.

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Li, Nan. "Multi-classification and Variable Selection Techniques in Cancer Genomic Data Research." American Journal of Biomedical Science & Research 12, no. 2 (March 3, 2021): 114–16. http://dx.doi.org/10.34297/ajbsr.2021.12.001725.

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CHAI, Jing, GuoLiang LIN, Feng HUANG, and W. Murphy ROBERT. "Genomic evolution in polyploid vertebrates: Models and progress in research techniques." SCIENTIA SINICA Vitae 49, no. 4 (April 1, 2019): 484–97. http://dx.doi.org/10.1360/n052018-00210.

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Bazilchuk, Nancy. "Sequencing the Ocean. Genomic techniques revolutionize our view of marine biodiversity." Conservation in Practice 6, no. 4 (October 2005): 35–37. http://dx.doi.org/10.1111/j.1526-4629.2005.tb00133.x.

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Journal articles on the topic 'Genomic techniques'

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