Genetics and exercise: an introduction
Adam P. Sharples, James P. Morton, Henning Wackerhage in Molecular Exercise Physiology, 2022
We have already mentioned that DNA sequence variants influence body height, strength, VO2max trainability or disease risk. We will now discuss how variations in the DNA sequence occur, the different types of DNA variants and their frequency in human populations. But first we need to explain the vocabulary used to define DNA variants. A mutation is an event that changes a DNA sequence. The consequence of a mutation is a DNA variant. For example, a mutation may change a “…CTGT…” to a “…CTAT…” sequence resulting in a G/A DNA variant. Alleles are DNA variants of a given sequence. For example, assume that 20% of a population have a “CTGT” and 80% a “CTAT” DNA sequence in the myostatin gene (important in muscle mass regulation, covered in Chapter 4 and 8); the CTGT variant would be the minor (frequency) allele, whereas the CTAT variant would be the major (frequency) allele. Alleles with a frequency of less than 1% are referred to as rare alleles, whilst those in the range of 1–5% are known as low frequency alleles. DNA variants with a minor allele carried by 5% and more of the population are labelled as common alleles. If a one-base substitution occurs in at least 1% of a population, then it is termed a single-nucleotide polymorphism and is abbreviated as SNP. SNPs are the most studied DNA variants.
Genomics and Hearing Loss: Toward a New Standard of Care?
Stavros Hatzopoulos, Andrea Ciorba, Mark Krumm in Advances in Audiology and Hearing Science, 2020
The genotype of an individual is determined by alleles (variant form of a gene) that are received from the individual’s parents. The alleles contribute to the organism’s phenotype, which is the combination of an individual’s observable characteristics or traits, such as its morphology, development, physiological properties, and behavior. The phenotype is the result of the expression of an individual’s genotype, but also of the influence of environmental factors and the interactions between the two. The alleles of an individual control if a trait is dominant or recessive. Traits are dominant if only one copy of the allele is required for expression of the trait. Traits are recessive if two copies of an allele are required for expression of the trait. X-linked traits are those controlled by an allele that is carried on the X chromosome, while autosomal characteristics are controlled by alleles located on any “nonsexual” chromosome, that is, excluding the chromosomes X or Y. For any given phenotypical characteristic, an individual inherits one gene from each parent so that the individual has a pairing of two genes. If the two alleles that form the pair for a trait are identical, then the individual is said to be homozygous for that characteristic and if not, the individual is then heterozygous.
Major histocompatibility complex
Gabriel Virella in Medical Immunology, 2019
An astonishing number of alleles have been identified at several HLA loci. Alleles are designated by a number that follows the relevant locus (e.g., HLA-A1, HLA-B8, or HLA-DR17). In fact, these are the most polymorphic structural gene loci in the entire human genome. Alleles may differ from each other by a single nucleotide or multiple nucleotides. Nucleotide substitutions may be either synchronous (no change to the amino acid in the encoded protein) or nonsynchronous (a different amino acid in the encoded protein). Many nonsynchronous substitutions are clustered in particular stretches of nucleotides in the gene sequence. This suggests that these differences did not arise by chance but rather were the result of natural selection. As of December 2017, 4,081 HLA-A, 4,950 HLA-B, and 3,685 HLA-C alleles have been identified. Many class II loci are also polymorphic, with 4,802 alleles currently identified. The IPD-IMGT/HLA Database is the repository for HLA DNA sequences and approved alleles and is located at https://www.ebi.ac.uk/ipd/imgt/hla/.
DNA repair in lung cancer: a large-scale quantitative analysis for polymorphisms in DNA repairing pathway genes and lung cancer susceptibility
Published in Expert Review of Respiratory Medicine, 2022
Zexi Liao, Minhan Yi, Jiaxin Li, Yuan Zhang
We thoroughly investigated the relationship between the risk of LC and the SNPs of the key players in the DNA repair pathway. Four SNPs (p53 rs1042522, XRCC1 rs3213245, ERCC1 rs11615, and XPD/ERCC2 rs238406) appear to lower the risk of LC in the analysis of the whole population, but five additional SNPs (APEX1 rs1760944, CCND1 rs9344, XPD/ERCC2 rs13181, XRCC1 rs1001581, and XRCC1 rs915927) increased the risk of LC. Risky SNPs were also somewhat variable between ethnographies and LC subtypes. Additionally, there were a variety of ways that diverse genotypes contributed to risk alleles. Although there are additional meta-analysis publications evaluating the association between LC risk and gene variations in DNA repair pathways, the majority of them simply describe or examine variations within a single pathway [27–31]. With subgroup analysis by ethnicity and subtypes within LC, our meta-analysis provides by far one of the most comprehensive summaries of the cell cycle control system and six DNA mending pathways (including BER, NER, HRR, NHEJ, MMR, and DNA direct repair).
Association between Psoriasis Disease and IFN-λ Gene Polymorphisms
Published in Immunological Investigations, 2022
Büşra Yilmaz, Güneş Çakmak Genç, Sevim Karakaş Çelik, Nilgün Solak Tekin, Murat Can, Ahmet Dursun
Statistical analysis was performed using SPSS (version. 19.0; SPSS Inc., Chicago, IL, USA). A post-hoc power calculation was performed using the G-Power software to determine the sample size. A case-control study was conducted. The allelic and genotypic frequencies of the polymorphisms were calculated for both for cases and for controls. Analyses were performed using dominant, additive, and recessive models. Dominance was defined in terms of allele 2 (minor allele) effects. In the dominant allele 2 models, homozygous individuals for allele 1 were compared with carriers of allele 2. In the recessive allele 2 models, homozygous individuals for allele 2 were compared with carriers of allele 1. The χ2 test was used to compare the genotype and allele frequencies of each gene polymorphism in psoriasis patients and controls. The odds ratio (OR) and 95% confidence interval (CI) were calculated to compare psoriasis risk for the alleles and genotypes. The Hardy–Weinberg equilibrium (HWE) test was conducted using Excel (Microsoft Office Excel, Microsoft Corp., Redmond, WA). Data distribution was determined with the Shapiro–Wilk test. Continuous variables were expressed as mean ± standard deviation or median (minimum-maximum). The categorical variables were frequency and percent. Continuous variables were compared using the independent-sample t-test or the Mann–Whitney U-test. P values < .05 were considered statistically significant.
Mutational analysis of 16 STR markers in the Slovak population
Published in Annals of Human Biology, 2022
Zdenko Červenák, Filip Červenák, Marian Baldovič, Andrea Patlevičová, Soňa Masnicová
Moreover, several studies revealed that the mutation rate of a particular marker, as well as its individual alleles, varies from population to population (Sun et al. 2014; Shao et al. 2016). Therefore, we compared the mutation rates present in our study with mutation rates from seven other populations (Henke and Henke 2006; Hohoff et al. 2006; Martinez et al. 2017; Wang et al. 2017; Droździok et al. 2018; Qu et al. 2019; Xu et al. 2019). As a result, three significant differences were identified, two in comparison with Upper Silesia (vWA and D8S1179), and one in comparison with the Guangdong Han population (D8S1179). These differences are most likely due to different overall numbers of meiotic transfers collected, however different allelic structures of the markers may also play a role as the vWA STR marker encompasses alleles with identical physical length, but with a different number of the longest run of perfect repeats (LRPRs) (STRbase database, https://strbase.nist.gov). Therefore, it might be possible that different variants of the same allele are presented in geographically distant regions, thus leading to the different mutational rates of the same marker.
Related Knowledge Centers
- DNA
- Multicellular Organism
- Nucleotide
- Phenotypic Trait
- Locus
- DNA
- Single-Nucleotide Polymorphism
- Base Pair
- Pea
- Chromosome
- Biological Life Cycle