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Identifying Breast Cancer Treatment Biomarkers Using Transcriptomics
Published in Shazia Rashid, Ankur Saxena, Sabia Rashid, Latest Advances in Diagnosis and Treatment of Women-Associated Cancers, 2022
Genomic biomarkers like somatic structural variations (Tubio, 2015) can help in zooming in to the change-maker genes in cancer. Previously studies have shown that structural variations in circadian genes like Per3 can increase the risk of breast cancer (Zhu et al., 2005). Therefore, it’s worth looking at structural variations like insertions, deletions, copy number variations, and translocations in trying to understand the links between what is happening in the genome and how it is affecting the transcriptome.
STRIVE Principles
Published in James Crossley, Functional Exercise and Rehabilitation, 2021
Each and every person also varies. We are all built differently (structural variation), have different levels of fitness (physiological variation) and think and behave differently (behavioral variation). Some people are naturally more flexible, others have better endurance, some are stronger or faster (performance parameters). The ability to bend, reach and lift varies from person to person (functional capacity). Variation is extremely normal and healthy.
Genetics
Published in Cathy Laver-Bradbury, Margaret J.J. Thompson, Christopher Gale, Christine M. Hooper, Child and Adolescent Mental Health, 2021
In recent years there have been growing efforts to identify genetic variation and relate this variation to human disease and traits. There are many sources of genetic variation which occur at different rates in the population including variation in the total number of chromosomes (aneuploidy), structural variation of large DNA segments resulting in the deletion or duplication of DNA segments (copy number variation; CNVs) and variation of single nucleotides (single nucleotide polymorphisms; SNPS) that include common and intermediate frequency variants (>1% population frequency) and rare mutations (<1% population frequency). In each case, variation can be inherited or occur spontaneously (de novo), e.g. during gamete formation.
A patent review of MAT2a inhibitors (2018–2021)
Published in Expert Opinion on Therapeutic Patents, 2022
Stephen J. Atkinson, Laura Evans, James S. Scott
The third application contained 21 compounds of an alternate pyrimidine bicyclic core [26]. Banded MAT2a enzyme assay data, with two compounds binned as <200 nM potency, was presented. Example 1.001 (19) is representative of the equity described, and notably contains a meta-hydroxy (or carbonyl if drawn as the alternate tautomer) relative to a carbon-linked pendant phenyl group in contrast to other filings. Other functionality are described here instead of OH, but all appear (where tested) >500 nM. An unsubstituted phenyl ring was featured in most examples and chloro- was the most common lipophilic group on the bicyclic aryl ring, although bromo-, cyclopropyl, methyl and trifluoromethyl were also reported. The fourth application from Ideaya Biosciences contained 28 compounds of an alternate pyridone core, of which 26 were screened in a MAT2a phosphate sensor fluorescence assay [27]. 14 compounds exhibited potency of <200 nM with 1 compound (example 1.023, 20) <10 nM. 20 has a trifluoromethyl group on the bicyclic aryl, a methyl substituted pyridyl and a hydroxy group in the 3 position. Most of the exemplified groups in the lipophilic region (6 position) are the same as previous Ideaya applications (chloro-, bromo-, trifluoromethyl, cyclopropyl). Most of the structural variation claimed is in the 3 position. Examples include methoxy, methyl sulfone, dimethylamino and some bicyclic aryl groups such as benzothiazole, although OH is the most common.
Nitric oxide pathway as a plausible therapeutic target in autism spectrum disorders
Published in Expert Opinion on Therapeutic Targets, 2022
Rishab Mehta, Anurag Kuhad, Ranjana Bhandari
The structural variations in the DNA segments are known as copy number variations (CNVs). Structural variations can exist in the range of 50 base pairs to several megabases. Affected DNA segments should be larger than 1Kb to be classified as a copy number variant. Various mutations are responsible for the occurrence of CNVs such as deletion, duplication, insertion, inversion, or complex recombination [26,27]. The frequency of their occurrence is 6–10% in the ASD population. CNVs can occur de-novo or may be inherited depending on whether they are present spontaneously in germ cells of offspring or somatic cells or if they arise in parental germ cells. The degree of functional deficits during development in somatic cells depends on the occurrence of de-novo CNVs [28]. CNVs play an important part in the development of ASD and it depends on the location where they are present on the chromosomes, such as duplication at loci 15q13 or microdeletion at loci 16p11.2, 15q11-13, 22q11.2, and 1q21.1 [29,30].
Cytogenetic and molecular genetic methods for chromosomal translocations detection with reference to the KMT2A/MLL gene
Published in Critical Reviews in Clinical Laboratory Sciences, 2021
Nikolai Lomov, Elena Zerkalenkova, Svetlana Lebedeva, Vladimir Viushkov, Mikhail A. Rubtsov
Special programs have been created to detect structural variation, including translocations, based on sequencing data. Each program has been adapted to different input data, and existing programs are based on several strategies. In the de novo assembly approach, a genome is assembled from reads and aligned with a reference human genome. The presence of translocations is revealed on a pairwise alignment dot plot. In the short-read-based mapping algorithm, reads are mapped onto the genome, allowing the identification of split reads and discordant paired reads. Split reads are single reads that map to the genome discontinuously, in which one section of the read maps to one genomic region, whereas the remainder of the read maps to a separate genomic region. Discordant paired reads refer to those reads that do not map as expected [114]. Overviews of the different structural variation methodologies that are currently being used have been published previously [114–117].