The Precision Medicine Approach in Oncology
David E. Thurston, Ilona Pysz in Chemistry and Pharmacology of Anticancer Drugs, 2021
Although full genome sequencing can provide the basic nucleotide sequence of an organism’s DNA (Figure 11.5), further analysis is required to interpret the biological or clinical meaning of the sequence. Computational methods for analyzing sequencing data are still being developed and refined within the field of Bioinformatics. As sequencing generates an immense amount of data (for example, there are approximately six billion base pairs in each human diploid genome), the output has to be stored electronically and requires a large amount of computing power and storage capacity. A number of public and private companies are still competing to develop full genome sequencing platforms that are sufficiently robust and reliable to commercialize for both research and clinical use (e.g., Illumina, GE Global Research (General Electric), Affymetrix, and IBM, although there are many others). A commonly referred to commercial target for the cost of sequencing is the “$1,000 genome”. As of 2015, the cost of obtaining a whole-genome sequence was around $1,500. More recently, in 2019, one company (Veritas Inc) claimed to be able to provide a full genome sequence for $600, and predicted that they could reduce the cost to the $100–$200 range by 2021.
ChIP-seq analysis
Altuna Akalin in Computational Genomics with R, 2020
Peak calling can falsely identify enriched regions if the input sample is not sequenced to the proper depth. Because the input samples correspond to de facto whole genome sequencing, and the ChIP procedure enriches for a subset of the genome, it can often happen that many regions in the genome are not sufficiently covered by the Input sample. Such variability in the signal profile of Input samples can cause a region to be defined as a peak, enriched in the ChIP sample, while in reality it is depleted in the Input, due to under-sampling. For example, the figure in the previous chapter, showing an enriched region H3K36me3 over a gene body, shows a large depletion in the Input sample over the same region. Such depletion should be a concern and merit further investigation.
Precision medicine in oncology: An overview
Debmalya Barh in Precision Medicine in Cancers and Non-Communicable Diseases, 2018
Currently, most developments in personalized medicine are related to whole genome sequencing. At the beginning, a whole genome sequence cost about $2.7 billion (Weinberg, 2014). Today, whole genome/exome sequencing is easily achievable with next generation sequencing (NGS), within hours for approximately $1000. It provides high-throughput and totally personalized data in a short time with a lower price. Nevertheless, merely knowing the patients’ whole sequence cannot be considered as having entire knowledge about the patient. To have precise information extracted from the sequencing for treatment purposes, the data first should be analyzed. During the analysis, other factors such as epigenetic and environmental factors such as exposomics (exposure of infections, toxic agents) should be evaluated with the obtained data.
Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria
Published in Gut Microbes, 2019
Tamaki Ito, Tsuyoshi Sekizuka, Norimi Kishi, Akifumi Yamashita, Makoto Kuroda
Novel bacterial strains were cultured with GAM broth, and the cell pellet was mechanically homogenized with ZR BashingBead Lysis tubes (Zymo Research, Irvine, CA, USA) in 500 µl Tris-HCl (pH 8.0), 50 µl 1% sodium dodecyl sulfate (SDS), and 500 µl phenol-chloroform-isoamyl alcohol (25:24:1). The upper phase was purified by using the Qiagen MinElute PCR Purification Kit. Whole genome sequencing (WGS) was performed as follows. For short-read sequencing, a DNA-Seq library was prepared by using the Nextera XT DNA Sample Preparation Kit (Illumina), followed by sequencing using the Illumina MiSeq and NextSeq 500 systems according to the manufacturer’s instructions. For long-read sequencing by the PacBio RSII system (Pacific Biosciences; Menlo Park, CA, USA), SMRTbell library preparation was performed as previously described.28 The DNA sequencing was carried out with P6-C4 chemistry, and the movie length was 360 min. De novo assembly was conducted by using HGAP3 (SMRT Analysis version 2.2.0), further error correction with the Illumina short reads was performed by Pilon. 29 Genome annotation was performed by PROKKA version 1.11 30
Respiratory syncytial virus infection: why does disease severity vary among individuals?
Published in Expert Review of Respiratory Medicine, 2020
Alireza Tahamtan, Saeed Samadizadeh, Mostafa Rastegar, Britt Nakstad, Vahid Salimi
The possibility of different RSV strains having distinct infective properties is an attractive explanation for the diverse severity of RSV disease which merits further study. Different RSV strains may have divergent infective properties which primarily determine RSV virulence alongside other virus-related factors such as viral load and co-infection. Further research and in-depth knowledge on RSV subtypes and genotypes, and how they modulate immune responses, could help to predict the risk and avoid hospitalization and severe disease in both healthy and individuals with co-morbidities. Whole-genome sequencing perhaps provides the best future opportunity to further our understanding. Moreover, finding a relationship between viral factors and clinical consequence of RSV infection may be important to include the more virulent strains in future vaccines and treatments.
Playing the genome card
Published in Journal of Neurogenetics, 2020
But the direct medical use of genome sequencing for common and debilitating disorders seems to be perennially just around the corner, never quite here (Abul-Husn & Kenny, 2019; Doble et al., 2017; Horton & Lucassen, 2019; Joyner & Paneth, 2019; Lu et al., 2018). Thus, Shendure et al. suggested that “genome sequencing may only have marginal benefits for many if not most patients” (Shendure et al., 2019). Joyner and Paneth summarized, “we find no impact of the human genome project on the population’s life expectancy or any other public health measure, notwithstanding the vast resources that have been directed at genomics. Exaggerated expectations of how large an impact on disease would be found for genes have been paralleled by unrealistic timelines for success, yet the promotion of precision medicine continues unabated” (Joyner & Paneth, 2019).
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