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Genetics of endurance
Published in Adam P. Sharples, James P. Morton, Henning Wackerhage, Molecular Exercise Physiology, 2022
Stephen M. Roth, Henning Wackerhage
A different model is inbred mice. In this case, the genetic variations are fixed in a species by interbreeding family members for at least 20 consecutive generations. Via this procedure, the animals become genetically more or less identical and have similar phenotypes and thus retain exercise-related traits such as muscularity or fibre-type percentages. Such inbred mice strains are a powerful tool for molecular sport and exercise geneticists because the DNA of many of these inbred mouse strains have now been sequenced across the genome. Researchers can thus measure the phenotype or QTs such as voluntary running, muscle size, number of muscle fibres for a given muscle or fibre-type proportions. Then, by using linkage analysis, they can identify the regions that harbour variations in the DNA sequence or quantitative trait loci (QTLs) that are responsible for the variation of QTs in between inbred strains. New DNA-sequencing technologies can then be used to directly sequence those regions and identify the specific DNA sequence variants underlying the traits.
Preimplantation Genetic Testing for Polygenic Disorders
Published in Carlos Simón, Carmen Rubio, Handbook of Genetic Diagnostic Technologies in Reproductive Medicine, 2022
Nathan R. Treff, Diego Marin, Laurent C. A. M. Tellier
Many common human diseases are polygenic in nature, including several among the top ten leading causes of death (1). Recent development of population level genome-wide DNA sequence and medical record repositories have made it possible to develop genomic predictors of polygenic disease (2–10). Typically, DNA sequence data (genotypes) from a set of cases and controls are used as a “training set.” The training set often involves a vast number of datapoints (i.e., 500,000 genomes x 800,000 genotypes = 400 trillion datapoints). The analysis of the training set requires the use of machine learning (computational analysis). The computer is supplied an algorithm to produce a DNA sequence-based predictor. The machine learning algorithm may give varying weight to different positions in the genome in order to maximize the predictor's ability to separate cases and controls. The algorithm may also incorporate methods such as LASSO to account for sparsity of data (i.e., 800,000 genotype positions/3 billion human genome positions = 0.03%). The predictor is then applied to a new “test” set of cases and controls in order to determine its validity and establish its performance characteristics (5,11,12) (Figure 17.1).
Basic genetics and patterns of inheritance
Published in Hung N. Winn, Frank A. Chervenak, Roberto Romero, Clinical Maternal-Fetal Medicine Online, 2021
The human genome contains three billion base pairs of DNA, packaged into units known as chromosomes and encoding an estimated 20,000 to 25,000 genes (1,2). At the present time, over 12,000 human genes have been mapped and almost 3000 single-gene disorders have been described for which the molecular genetic basis is known (3). The Human Genome Project, begun in the late 1980s and completed in 2003, produced a haploid human genome sequence, which was a composite of the DNA sequence of several individuals. As a result, new genes and new information about the genetic basis for many disorders have been discovered. This has already begun to have a huge impact on the practice of medical genetics and medicine in general.
Plasma insulin-like growth factor binding protein 1 in pulmonary arterial hypertension
Published in Scandinavian Cardiovascular Journal, 2021
Habib Bouzina, Roger Hesselstrand, Göran Rådegran
Proseek multiplex cardiovascular II and III, as well as oncology II, 96-plex immunoassays (Olink Proteomics, Uppsala, Sweden) were used to analyse the present biomarkers. From these panels, biomarkers related to tumour biology were chosen for analysis; including cancer antigen 125 (CA-125), carbonic anhydrase 9 (CA-IX), carcinoembryonic antigen-related cell adhesion molecule (CEACAM)-1 and -5, cornulin, cyclin-dependent kinase inhibitor 1 (p21), folate receptor α (FR-α), human epididymis protein 4 (HE4), IGF-1 receptor, IGFBP-1, -2 and -7, kallikrein-6, -8, -11, -13 and -14, mesothelin, protein S100-A4 (S100A4) and -A11 (S100A11) and vimentin. These biomarkers, as well as N-terminal prohormone of brain natriuretic peptide (NT-proBNP), were assessed using proximity extension assays, as previously described [18,19]. In brief, oligonucleotide-labelled antibody pairs are used to detect targeted biomarkers, in order to avoid unspecific antibody binding and potential cross-reactivity events. As two related probes are brought in close proximity the oligonucleotides hybridise in a pair-wise manner. DNA polymerase addition results in a proximity-dependent DNA polymerisation event, creating a unique PCR target sequence. The DNA sequence is then detected and quantified using a microfluidic real-time PCR instrument (Biomark HD; Fluidigm, San Francisco, CA, USA). Data quality control and normalization is performed utilizing an internal extension control and an inter-plate control, in order to adjust for intra- and inter-run variation. Assay validation data and panel information are available at www.olink.com.
Isolation and cultivation of candidate phyla radiation Saccharibacteria (TM7) bacteria in coculture with bacterial hosts
Published in Journal of Oral Microbiology, 2020
Pallavi P. Murugkar, Andrew J. Collins, Tsute Chen, Floyd E. Dewhirst
All Saccharibacteria isolates were initially identified and fingerprinted by sequencing the rRNA operon from a 9–27 forward 16S rRNA primer to the third tRNA (usually tRNA Val) located between 16S and 23S rRNA genes (Table 2, primers 5–14). Specific primer pairs were designed to differentiate strains of species whose sequences differed by less than two bases over the 16S rRNA – tRNA region (Table 2, primers 15–24). Upon complete genome sequencing, the genomes were aligned, and regions of DNA sequence difference were identified. Two primer pairs about 500 bases apart in the mutual alignment were selected where each of the 4 primers was specific to its target. Alternately, a single primer pair identical for both strains, but flanking a region of 7–10 base differences between strains over a span of 500 bases was identified. Fingerprinting primers for host bacterial strains of each species were also designed from comparison of their whole genome sequences as described for Saccharibacteria.
Diagnostic markers for glaucoma: a patent and literature review (2013-2019)
Published in Expert Opinion on Therapeutic Patents, 2019
In 2001, Craig J. E. et al. formulated another method for the detection of mutation p. Q368X in the myocilin gene which analyzes single-stranded DNA conformational polymorphisms (SSCP) [65,66]. SSCP analysis detects sequence variations (single-point mutations and other small-scale changes) through electrophoretic mobility differences. DNA with a sequence mutation shows a significant mobility difference compared to wild type DNA when it is subjected to nondenaturing (or partially denaturing) conditions [65,66]. The method consists of 5 steps, where DNA extraction is the critical, first step. The overall quality, accuracy, and length of the read DNA sequence can be significantly affected by the characteristics of the sample itself, and the method chosen for nucleic acid extraction. The choice of the DNA extraction method depends on the source or tissue type, and on how it was obtained, handled or stored prior to extraction [66].