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Investigation of Sudden Cardiac Death
Published in Mary N. Sheppard, Practical Cardiovascular Pathology, 2022
In recent years, with rapid development in next generation sequencing technology, the frequent identification of rare variants in both healthy and affected individuals has been found and determining this variant pathogenicity is challenging. Other genes implicated in BrS include calcium handling genes and desmosomal gene PKP2 but are rare. Current guidelines recommend SCN5A testing which is useful for predictive testing of family members but does not affect clinical management. Compared with genotype negative individuals, pore region mutations in SCN5A are associated with increased risk of cardiac arrest. Given the relatively modest contribution of monogenic SCN5A towards BrS phenotype, polygenic inheritance with environmental and epigenetic factors are important.
“Omics” Technologies in Vaccine Research
Published in Mesut Karahan, Synthetic Peptide Vaccine Models, 2021
The genomic era is a revolution in vaccine development. It started with the shotgun sequencing technology producing the genome sequence of Haemophilus influenzae in 1995 by The Institute for Genomic Research (TIGR). Later, many technologies were developed for next-generation sequencing, such as massively parallel signature sequencing, polony sequencing, 454 pyrosequencing, reversible terminator sequencing, sequencing by oligonucleotide ligation detection (SOLiD), single-molecule real-time sequencing, ion torrent sequencing, or DNA nanoball sequencing (reviewed by Rajesh and Jaya 2017). Due to these advanced technologies, the number of published bacterial genomes increased considerably with 14,754 completed and 128,146 permanent draft genomes deposited in the Genomes Online Database (GOLD, https://gold.jgi.doe.gov) by June 2020. The organisms with completed genomes cover various bacterial pathogens, and they serve vaccine development to find out potential antigens (Serruto et al. 2009).
EML4-ALK Fusion Gene and Therapy with ALK-Targeted Agents in Non-Small Cell Lung Cancer
Published in Sherry X. Yang, Janet E. Dancey, Handbook of Therapeutic Biomarkers in Cancer, 2021
Francisco E. Vera-Badillo, Janet E. Dancey
As screening tool, RT-PCR allows identification of specific fusion partners and includes rapid turnaround time and limited tissue requirements. It has high sensitivity and specificity. However, results depend on the RNA quality, which can be degraded in formalin-fixed paraffin-embedded tissues. Next-generation sequencing has emerged as a powerful approach to look for genetic abnormalities. Whole-genome and whole-transcriptome sequencing has been used to identify ROS1 rearrangements [24]. Although NGS is a very attractive option, it is expensive and requires additional infrastructure and time for analysis [96]. Although they are rare mutations, current guidelines recommend to analyze for the presence of ALK and ROS1 in parallel [97, 98].
The angiotensin-converting enzyme gene insertion/deletion polymorphism interacts with fear of falling in relation to stepping speed in community-dwelling older adults
Published in Physiotherapy Theory and Practice, 2023
Allon Goldberg, Joseph F. Sucic, Susan Ann Talley
The advent of next-generation sequencing technologies (Petersen et al., 2017) is increasingly placing genetic information in the hands of clinicians (Brittain, Scott, and Thomas, 2017; Prokop et al., 2018), as genomic data are being linked and integrated with electronic medical records (Abul-Husn and Kenny, 2019; Dennis et al., 2021; Hartwell et al., 2021). Patients are also gaining access to their own genomic data (personal genomic testing [PGT]) (Moneer, Miller, Shah, and Ross, 2021) through direct-to-consumer (DTC) platforms (Gerdes et al., 2021; Moneer, Miller, Shah, and Ross, 2021). It is plausible that physical therapy clinicians in the not-too-distant future will be confronted by patients with questions about their genotypes obtained through the medical system (e.g., via whole genome and exome sequencing), as well as through DTC-PGT companies. Patients are likely to be interested in genetic variations found in genes, such as those related to physical performance (e.g., ACE and ACTN3) (Keogh, Palmer, Taylor, and Kilding, 2015; Ma et al., 2013; Yoshihara et al., 2009), or recovery after stroke or brain injury (e.g., brain-derived neurotrophic factor [BDNF]) (Gustafsson, Klang, Thams, and Rostami, 2021; Liu et al., 2021). Practicing in the “genomic era” (Collins, Green, Guttmacher, and Guyer, 2003) will require rehabilitation and other clinicians to increase their knowledge and competencies in the principles of genomics (Goldberg, 2005).
Disparities in Inherited Retinal Degenerations
Published in Seminars in Ophthalmology, 2023
Sarah Chorfi, Emily M. Place, Rachel M. Huckfeldt
While the cost of testing has significantly decreased in recent years due to the advent of next generation sequencing,44 cost may remain a barrier to diagnostic testing in some instances. In a recent multinational survey across Europe and Israel, Birgit et al. found that no coverage was available for the costs pertaining to genetic testing in 15% of centers (75% of which were in Spain).45 One can speculate that this number may be higher in some developing countries. In recent years, initiatives aiming at sponsoring genetic testing for patients with IRDs have been on the rise. One such example is the My Retina Tracker (MRT) genetic testing program by the Foundation Fighting Blindness,46 which offers fully subsidized testing and genetic counselling services to eligible patients living in the United States. Zhao et al. compared the rate of genetic testing obtention before and after the launch of this program among 369 patients at an academic referral eye center.47 They reported a nearly 30% increase in the testing rate following the advent of the MRT testing program.47 The advent of sponsored programs for IRDs has also facilitated ordering of genetic testing by community-based health care providers, and resulting availability of testing outside tertiary referral centers will allow more patients to pursue and obtain molecular diagnoses. However, more specialized expertise may still be required in response to results.
Testing differentially methylated regions through functional principal component analysis
Published in Journal of Applied Statistics, 2022
Mohamed Milad, Gayla R. Olbricht
The methodology proposed and illustrated here builds on the interpretation of next-generation sequencing data. The FPCA method can be applied in cancer research as well as in the pursuit of therapies to combat or prevent lupus, muscular dystrophy, and other diseases. In fact, because hypermethylation occurs early in colon cancer, detection of hypermethylation could be an important indicator of potential health problems, which might be detected using the FPCA method. In addition, future studies are needed to investigate the use of other functional data analysis techniques, such as functional linear regression or functional canonical correlation analysis, as well as incorporating smoothing penalties into the analysis. Although the FPCA framework was investigated using RRBS data, it should scale up well for utilization in whole genome bisulfite sequencing studies, but this should be investigated more fully. Finally, although the FPCA method exhibited robustness in detecting DMRs under low coverage and replications in two groups, it is of interest to extend the method to work for experiments that require testing for differences between more than two groups or that have covariate information.