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Hypertrophic Cardiomyopathy
Published in Andreas P. Kalogeropoulos, Hal A. Skopicki, Javed Butler, Heart Failure, 2023
Ahmad Masri, Stephen B. Heitner
Cascade screening of relatives of patients with HCM is essential. First-degree relatives of the proband should undergo serial intermittent EKG and echocardiography in the absence of a known disease-causing genetic mutation.30 Phenotypic screening frequency depends on the age of the relative, with children aged 7–18 years old requiring screening every 12–18 months, with relatives >18 years old tested only every 3–5 years. Genetic analysis is useful to confirm the genetic etiology and to differentiate isolated HCM from other syndromic conditions associated with it (such as Danon disease, Fabry disease, amyloidosis, and mitochondrial cardiomyopathy). A significant portion of HCM can also be attributed to de novo variants, compound variants, or pathogenic variants in multiple genes; each of these scenarios conveys a different risk to a proband's relatives.40 Whereas genotyping is a useful tool for familial risk stratification, there are serious pitfalls and implications, especially on young individuals, that mandate thorough professional genetic counseling and understanding of the limitations of the technique.
Carrier Screening For Inherited Genetic Conditions
Published in Vincenzo Berghella, Obstetric Evidence Based Guidelines, 2022
Whitney Bender, Lorraine Dugoff
Testing: Carrier testing can be performed using DNA-based testing and hexosaminidase enzymatic activity testing [37]. Labs that use a sequencing approach may detect 99% of carriers regardless of ethnicity [36]. Historically, genotyping was used to determine carrier status in individuals of Ashkenazi Jewish descent and enzyme testing was used to evaluate individuals of non- Ashkenazi Jewish descent, as the enzyme assay detects all carriers, regardless of ethnicity [30]. Enzyme testing in pregnant women and women taking oral contraceptives should be performed using leukocyte testing, as serum testing is associated with an increased false-positive rate in these populations.
Using Genotyping and Molecular Surveillance to Investigate Tuberculosis Transmission
Published in Lloyd N. Friedman, Martin Dedicoat, Peter D. O. Davies, Clinical Tuberculosis, 2020
Sarah Talarico, Laura F. Anderson, Benjamin J. Silk
Genotyping methods for M. tuberculosis can be divided into two main categories: (1) conventional genotyping methods that examine variation affecting a small portion of the M. tuberculosis genome and (2) whole-genome sequencing (WGS), which examines most of the M. tuberculosis genome at the nucleotide level. The three most commonly used conventional genotyping methods are restriction fragment length polymorphism (RFLP), spacer oligonucleotide typing (spoligotyping), and mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR). These methods are all based on repetitive DNA sequences found either interspersed throughout the bacterial genome (insertion sequences) or at specific loci. Changes in these repetitive DNA sequences serve as a proxy for genetic diversification that is occurring throughout the entire genome. However, as DNA sequencing technologies have advanced, WGS is replacing the use of conventional genotyping methods for public health purposes to provide direct analysis of phylogenetic relationships at the nucleotide level.
Association of miRNA-146a Gene Polymorphism Rs2910164 with Behcet’s Disease: A Meta-analysis
Published in Ocular Immunology and Inflammation, 2022
Jiankang Shan, Pengyi Zhou, Zhenzhen Liu, Kaifeng Zheng, Xuemin Jin, Liping Du
Database search yielded 37 studies from PubMed and Embase databases (PubMed: 13, Embase: 24). The literature selection process was shown in Figure 1. Finally, 32 articles were excluded, of which 13 were duplicate ones, 17 with no relation to this topic, one without detailed genotype data and one meta-analysis. Five eligible case-control studies (1167 BD cases and 1662 controls)21–25 were ultimately included in the present meta-analysis. The characteristics of each study were shown in Table 1. The subjects recruited in the four included studies22–25 were Caucasian and the subjects in the last study were Asian.21 Different genotyping methods were utilized, including polymerase-chain reaction-restriction fragment length polymorphism (PCR-RFLP) and TaqMan. The genotype distribution was not in agreement with Hardy–Weinberg equilibrium (HWE) in all three studies.22–24
High dose methotrexate in adult Egyptian patients with hematological malignancies: impact of ABCB1 3435C > T rs1045642 and MTHFR 677C > T rs1801133 polymorphisms on toxicities and delayed elimination
Published in Journal of Chemotherapy, 2022
Abdel-Hameed I. M. Ebid, Ahmed Hossam, Mosaad M. El Gammal, Sameh Soror, Nadia O.M Mangoud, Mohamed Adel Mahmoud
The extraction of DNA was done using GeneJet Whole Blood Genomic DNA purification Mini Kit (Thermo Fisher Scientific, USA). The DNA samples were stored at −80 0C until genotyping. Assessment for purity and concentration of the extracted DNA samples were done using ‘Quawell Q5000 nanodrop’ (Quawell Technology, Inc., San Jose, CA). DNA purity of A260/280 ranged from 1.7 to 1.9 was considered pure for genotyping. The genotyping was done by the TaqMan SNP Genotyping Assay (Applied Biosystems, Foster City, CA) for our selected SNP assays: rs1801133 (assay ID = C___1202883_20, assay type = functionally tested) and rs1045642 (assay ID = C___7586657_20, assay type = drug-metabolizing enzyme) together with TaqMan Genotyping Master Mix (Applied Biosystems, Foster City, CA) on the Rotor-Gene Q real-time thermocycler instrument (Qiagen, Hilden, Germany). The reaction mixture composed of 10 μL of master mix, one μL of DNA sample, 0.5 μL SNP assay, and finally DNase Free water to a total volume of 20 μL. Some samples were selected randomly to assess the accuracy of the genotyping process. Rates of concordance were 100% for the tested samples.
CDH1 Gene rs1801552 C/T Polymorphism Increases Susceptibility to Esophageal Squamous Cell Carcinoma but Not to Gastric Cardiac Adenocarcinoma
Published in Cancer Investigation, 2021
Xi Huang, Yan Li, Rong-Miao Zhou, Sai-Jin Cui, Shi-Ru Cao, Xiang-Ran Huo, Na Wang
Genotyping was determined by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Accordingly, a 356 base pair (bp) PCR amplification fragment was generated using the primers: forward, 5′-ACCAGAATAAAGACCAAGTGACCAC-3′ and reverse, 5′-GGCCTTCCCATCTTAGACCATTTAC-3′. The PCR product was subjected to digestion overnight in a 10 ul reaction volume containing restriction enzyme MspI. For the rs1801552 C/T polymorphism, the homozygous C/C genotype was represented by DNA bands of 61 and 295 bp, however, the T/T genotype was not cleaved at the mutated site and revealed a fragment of 356 bp, whereas the heterozygous C/T exhibited a combination of all the above bands (61, 295 and 356 bp). For a negative control, distilled water was used instead of DNA in the reaction system for each PCR run. The PCR of 15% of the samples were run in duplicate for quality control, with a reproducibility of 100%.