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Reliable Biomedical Applications Using AI Models
Published in Punit Gupta, Dinesh Kumar Saini, Rohit Verma, Healthcare Solutions Using Machine Learning and Informatics, 2023
Shambhavi Mishra, Tanveer Ahmed, Vipul Mishra
This application is used in various fields of biology such as medical diagnosis, virology, biological research, medical diagnosis and biological systematics. Genomic sequencing is one of the basic processes that determine the exact order of nucleotides in the DNA molecule.
Genomic Informatics in the Healthcare System
Published in Salvatore Volpe, Health Informatics, 2022
DNA is the code of all biological life on earth. Humans have sought to unravel its mysteries so that the origins of life itself may be revealed. The first sequencing methodology, known as Sanger sequencing, uses specifically manipulated nucleotides to read through a DNA template during DNA synthesis. This sequencing technology requires a specific primer to start the read at a specific location along the DNA template and record the different labels for each nucleotide within the sequence up to 1000–1200 base pairs (bps). Subsequently, an approach called shotgun sequencing was developed for longer read of sequences. In this approach, genomic DNA is enzymatically or mechanically broken down into smaller fragments and cloned into sequencing vectors in which cloned DNA fragments can be sequenced individually. The complete sequence of a long DNA fragment can be eventually generated by these methods by alignment and reassembly of sequence fragments based on partial sequence overlaps.
Methods in molecular exercise physiology
Published in Adam P. Sharples, James P. Morton, Henning Wackerhage, Molecular Exercise Physiology, 2022
Adam P. Sharples, Daniel C. Turner, Stephen Roth, Robert A. Seaborne, Brendan Egan, Mark Viggars, Jonathan C. Jarvis, Daniel J. Owens, Jatin G. Burniston, Piotr P. Gorski, Claire E. Stewart
RNA-sequencing, typically referred to as ‘RNA-seq’, is a thorough method for analysing all RNAs simultaneously. Unlike microarrays, RNA-seq does not require prior knowledge of the RNA sequence that is explored and, therefore, has the capacity to detect single nucleotide variants, alternate splicing, post-transcriptional modifications and silencing RNAs (also called micro-RNAs/miRNA), non-coding RNA (ncRNA), exon-intron boundaries and pre-mRNA via NGS technology. The present section will focus on the use of RNA-seq for quantifying gene expression, as this is the analysis that is becoming more frequently used in molecular exercise physiology. To undertake RNA-seq, sequencing ‘libraries’ are first created using the isolated RNA. As with RT-qPCR and microarrays, RNA is first isolated, and reverse transcribed to cDNA. The cDNA is then fragmented into small consistent sizes and sequencing ‘adaptors’ are added or ‘ligated’ to the ends of the cDNA fragments. These adaptors contain constant sequences that enable the sequencers to recognise where to start sequencing. NGS is then performed similar to that explained in the above sections. Prior to these crucial steps, the total RNA obtained from the muscle biopsy may be first treated to remove ribosomal RNA that makes up the majority (~90%) of extracted RNA. Therefore, if left untreated, sequencing data would be representative of predominantly rRNA rather than other RNAs of interest (e.g. pre-mRNA, mRNA, miRNA and ncRNA).
QPCTL regulates macrophage and monocyte abundance and inflammatory signatures in the tumor microenvironment
Published in OncoImmunology, 2022
Kaspar Bresser, Meike E. W. Logtenberg, Mireille Toebes, Natalie Proost, Justin Sprengers, Bjorn Siteur, Manon Boeije, Lona J. Kroese, Ton N. Schumacher
RNA sequencing. RNA was extracted from the indicated frozen tissues using the RNeasy Mini Kit (Qiagen). Cell populations isolated by FACS were washed once in PBS, and subsequently lysed in RLT buffer (Qiagen). Whole-transcriptome sequencing samples were prepared with the TruSeq Stranded mRNA Kit (Illumina). Paired-end 50 bp sequencing was performed on a NovaSeq 6000 system (S1 flowcell, Illumina), obtaining an average of 18 × 106 reads per sample. Reads were aligned to the pre-built GRCm38 genome_snp_tran reference using HISAT2,50 and transcript counts were obtained using an in-house generated pipeline (GenSum, https://github.com/NKI-GCF/gensum). Differential gene expression analysis was performed using the edgeR package.51 Network analysis was performed using the stringDB database, applying the igraph package for visualization.
Genomic landscape of treatment refractory metastatic colorectal cancer
Published in Acta Oncologica, 2021
R. L. Eefsen, K. S. Simonsen, P. Grundtvig, L. Klarskov, I. M. Chen, D. Høgdall, B. V. Jensen, T. Lorentzen, T. S. Poulsen, S. Theile, D. Nielsen, E. Høgdall
Promising targets for mCRC are the kinase fusions NTRK-, ALK-, and ROS fusions, however, these alterations are only observed in 0.5–2.0% of the mCRC patients [42,43]. No NTRK fusions were observed in our patient population during this period. ERBB2 amplification and HER2 overexpression are observed in ∼2% of the CRC patients and are described in the Heracles trials and MyPathway trial as a possible druggable target for CRC [44–49]. Furthermore, KRASG12C inhibition has been investigated in a phase 1 trial, where a response rate of 7.1%, was described for heavily pretreated mCRC and NSCLC patients [50,51]. Homologous recombinant DNA damage repair (HR-DDR) deficiencies are identified in mCRC, but no HR-DRR directed therapies have yet been approved for mCRC [52]. Genomic sequencing is a need for the development, understanding, and improvement of personalized medicine. In Denmark, a national trial of targeted therapy, the ProTarget trial (EudraCT 2019-004771-40, NCT04341181), has been initiated to enable targeted therapies to cancer patients with specific drugable genomic variants. The trial is inspired by the Dutch DRUP trial, EudraCT 2015-004398-33, and the TAPUR trial, NCT0263535 [53].
Premature ovarian insufficiency – the need for a genomic map
Published in Climacteric, 2021
Until recently, linkage analysis and candidate gene approaches have been the mainstay methodology for gene identification, either through genes identified in mouse models or selection from manually mined genes involved in ovarian development, function and atresia. Single nucleotide polymorphism array analysis studies in POI have been performed. Genome-wide association studies have revealed loci-associated correlations [12,13], but such studies require larger cohorts in multiple populations to generate replicative results. More recently, emerging data from using newer techniques such as whole-exome sequencing and whole-genome sequencing have highlighted the role of several genes behind the pathophysiology of POI [14–20]. Whole-genome sequencing techniques can map an entire human genome. These sequences can be compared to references, allowing identification of variations in DNA. Genome sequencing therefore has the capability of transforming the landscape for POI genomics.