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Non-Invasive Prenatal Testing (NIPT)
Published in Carlos Simón, Carmen Rubio, Handbook of Genetic Diagnostic Technologies in Reproductive Medicine, 2022
Nuria Balaguer, Emilia Mateu-Brull, Miguel Milán
There are many approaches to prenatal cfDNA testing. The most commonly used are whole-genome sequencing (WGS), targeted genome sequencing, and single-nucleotide polymorphism (SNP)-based sequencing. These techniques can determine both the FF and the likelihood of aneuploidy. The fundamentals of each cfDNA testing platform are discussed below.
The Precision Medicine Approach in Oncology
Published in David E. Thurston, Ilona Pysz, 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.
Genetics
Published in Cathy Laver-Bradbury, Margaret J.J. Thompson, Christopher Gale, Christine M. Hooper, Child and Adolescent Mental Health, 2021
Exome sequencing studies have been used to identify individual genetic variants in the protein-coding regions of the genome (approximately 1%) in both case-control cohorts and in families (to identify de novo mutations). Whole-genome sequencing is more time-consuming and expensive than whole-exome sequencing since both the protein-coding and non-coding regions are sequenced. Work is currently underway through the Whole Genome Sequencing for Psychiatric Disorders Consortium to integrate sequencing data across disorders in large cohorts of patients and controls that should yield some interesting insights into biological mechanisms underlying cross-disorder risk (Sanders et al., 2017).
Genomic medicine in Africa: a need for molecular genetics and pharmacogenomics experts
Published in Current Medical Research and Opinion, 2023
Oluwafemi G. Oluwole, Marc Henry
Limited capacity is the forefront of the challenges facing the implementation of genomic medicine,5 because advanced genomic techniques are needed to implement genomic medicine. For example, it costs about $250 per sample for whole-exome sequencing of X50 coverage, and about $1800 for whole-genome sequencing. The issue regarding the storage systems and securing licenses for cloud computing also limit robust data analyses in genomic medicine. Beside, due to numerous identification of variants of unknown significance,6. more advanced knowledge and analyses are necessary to determine the relevance of these genetic variants to genomic medicine. The study aims to identify the gaps in knowledge and highlight the current state of genomic medicine in Africa to improve research interests in this area.
Neoantigen-based personalized cancer vaccines: the emergence of precision cancer immunotherapy
Published in Expert Review of Vaccines, 2022
Guilhem Richard, Michael F. Princiotta, Dominique Bridon, William D. Martin, Gary D. Steinberg, Anne S. De Groot
Nearly simultaneously with the development of CPI, ‘next generation sequencing’ (NGS) methods have led to significant reductions in the time and cost required to sequence tumor genomes. According to the National Human Genome Research Institute (NHGRI) Genome Sequencing Program (GSP), the cost of sequencing a genome (such as a cancer genome) dropped from more than $10 M to roughly $1,000 between 2008 and 2015 when most sequencing centers transitioned from Sanger-based sequencing to ‘next-generation’ DNA sequencing technologies (Figure 1) [15]. This fundamental shift has enabled consumers to obtain information about their ancestors and risks for certain diseases, while also placing revolutionary new cancer treatments within the reach of individuals seeking care in their local cancer centers, where NGS is becoming routine.
Beyond the Usual Suspects: Expanding on Mutations and Detection for Familial Hypercholesterolemia
Published in Expert Review of Molecular Diagnostics, 2021
Shirin Ibrahim, Joep C. Defesche, John J.P. Kastelein
NGS refers to a variety of methods that use massive parallel sequencing designs to amplify and examine multiple segments of DNA concurrently, offering the possibility of sequencing the whole human genome or exome in a relatively short time. Most of these methods contain three main components: 1) fragmentation of the DNA of the source into many small pieces, which are used to prepare sequencing libraries; 2) amplification and enrichment, expediting many simultaneous chemical reactions; and 3) detection of signals from this massive series of sequencing reactions [34]. Several NGS approaches exist to clinically diagnose a disorder where the causative genes are already known, as is the case with FH. These approaches include: 1) targeted selection of pre-specified genes; 2) whole exome sequencing (WES) in which all protein-coding parts of the DNA are sequenced; or 3) whole genome sequencing (WGS) in which the entire genome is sequenced. Since the vast majority of the WES and WGS data are irrelevant for focused diagnosis of a specific condition such as FH, a structured targeted sequencing panel can be used. These targeted NGS panels can be designed to screen for rare variants in coding regions as well as evaluating non-coding common single nucleotide polymorphisms (SNPs) as part of a polygenic risk score. The costs of targeted sequencing panels are decreasing steadily, and they are now considered as the current standard for clinical diagnosis for the genetic analysis of dyslipidaemias [45].