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“Omics”
Published in Kirk A. Phillips, Dirk P. Yamamoto, LeeAnn Racz, Total Exposure Health, 2020
A mosaic of several individuals is represented in the Genome Reference Consortium’s (GRC) human reference genome version GRCh38. Several large genome sequencing projects have captured a large amount of the variability, and GRCH38 has 261 alternate scaffolds to account for the “benign” variability in ethnically diverse populations. It is estimated that unrelated individuals would differ at ~15 million positions and carry as many as 2,000 structural variations like copy number variations (duplications and deletions) and genome rearrangements like inversions and translocations. Based on a genome size of 3.2 billion nucleotides, it can be expected that each human may have ~3 million nucleotide differences from the reference genome (1 every 300 base pair (bp)). Thus, variants (alleles) have to be contextualized and could be benign or associated with a phenotype or disease or yet to be determined significance (Jackson et al. 2018). Allelic variants are referred as single nucleotide variants (SNVs), and when present in >1% of the population are called polymorphisms (SNP). About 11 million SNPs in the human genome have been cataloged with any one individual carrying about 3 million of them (Chong et al. 2015). Currently, about 4,100 mutations linked to a phenotype have been documented; their current count and statistical breakdown of the spectrum of phenotypes associated with the genes can be found at (https://www.omim.org/statistics/geneMap).
Cell Line Development
Published in Wei-Shou Hu, Cell Culture Bioprocess Engineering, 2020
Aneuploid cells have abnormal chromosomal counts, and many of their chromosomes have macroscopic structural aberrations. Such chromosomal alterations accumulate over time, generating a heterogeneous cell population created by different cells carrying different sets of chromosomes with different structural abnormalities. Some cell lines are highly heterogenous, with a wide range of chromosome abnormality and numbers. For example, some CHO cell lines have a wide range of structural variation.4,15 Others, such as Vero cells,16 have a relatively low level of heterogeneity, with a narrow distribution of chromosome numbers and variations of karyotypes. At a detailed molecular level, base-pair mutations, varying lengths of segmental DNA duplications, deletions, inversions, and translocations frequently occur in aneuploid cells. These structural variations occur during DNA replication at the single-cell level. Some genomic structural variants may carry phenotypic or physiological variations as well. Cells with some types of genome or karyotype variations may grow to become a noticeable subpopulation. The population of an aneuploid cell line is thus heterogeneous in genomic variants.
Air pollution and molecular changes in age-related diseases
Published in International Journal of Environmental Health Research, 2022
B. Hermanova, P. Riedlova, A. Dalecka, V. Jirik, V. Janout, R. J. Sram
Copy number variation (CNV) is a state where parts of the genome are repeated. This is a type of genomic structural variation, involving both deletion (loss of part of the genome) or duplication (the duplication of part of the genome) (Freeman 2006). The deletion and duplication of chromosomal segments are the main source of variation among individual people and are also a basic factor in human evolution and many diseases (mental, development, cancer). CNV occur faster than other types of mutation, owing to specific mechanisms. There are two theories concerning the contemporary molecular mechanisms that probably relate to these variations. CNV are produced by homologous recombination between repeated sequences or by non-homologous recombination mechanisms occurring in the whole genome (non-repeating CNV) (Freeman 2006; Montavon et al. 2012).