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Advances in Non-Invasive Diagnosis of Single-Gene Disorders and Fetal Exome Sequencing
Published in Carlos Simón, Carmen Rubio, Handbook of Genetic Diagnostic Technologies in Reproductive Medicine, 2022
Liesbeth Vossaert, Roni Zemet, Ignatia B. Van den Veyver
Genome and exome sequencing are technologies that examine the genome at a nucleotide level. NGS is achieved by sequencing many distributed, overlapping sites throughout the genome in a massively parallel manner.56,57 Briefly, for NGS library preparation, genomic DNA is sheared into 50–400 nt fragments, ligated to adapters, and purified. For panel or exome sequencing, an enrichment step is included to capture regions of interest using “DNA baits.” Massively parallel sequencing of the NGS library then rapidly and accurately derives the nucleotide sequences of each fragment, which are then aligned to a reference genome to detect potential sequence variants56–58 (Figure 27.3). Two quality parameters for NGS accuracy are the sequencing depth, which refers to the number of overlapping reads for each base-pair, and the breadth of sequence coverage, which is the fraction of the reference sequence that is covered at sufficient depth. The American College of Medical Genetics and Genomics (ACMG) recommends an average depth of ≥ 100-fold with 90–95% of the sequence covered at least 10-fold for diagnostic exome sequencing (ES).59 With recent advances in NGS technology, clinical laboratories can offer increasingly better sequencing depth and shorter turnaround time (TAT) to results, which is crucial for fetal ES.60,61
Lung Cancer
Published in Pat Price, Karol Sikora, Treatment of Cancer, 2020
The 2015 WHO classification encourages diagnostic precision, made possible with the greater availability of immunohistochemistry and molecular techniques, and is at the forefront of the international effort to reduce NSCLC not-otherwise-specified diagnosis rates. There are now several driver mutations that have been identified in NSCLC, and those in adenocarcinoma and squamous cell carcinoma are specifically depicted in Table 7.1. Some of the commonest molecular techniques used to identify these are summarized in Table 7.2. The table shows the applications of each technique for the different types of aberrations that may be encountered in lung cancer. Targeted exome sequencing on tissue or blood is being increasingly utilized to sequence a focused panel of genes as costs and turnaround times have reduced. Polymerase chain reaction (PCR) technology can also be used to target more specific areas of the genome, identifying single gene mutations and their RNA counterparts in tissue or in circulating tumor cells in blood. Fluorescent in-situ hybridization (FISH) makes use of microscopy to identify fusion and amplification products of fluorescently labeled genes, and although it has been transformational for identifying common fusion/amplifications such as anaplastic lymphoma kinase (ALK), it is also labor-intensive. Immunohistochemistry can be a very cheap, widely performed assay, which can be highly sensitive and specific for identifying protein products of fusions/amplifications such as ALK.
Will Systems Biology Transform Clinical Decision Support?
Published in Paul Cerrato, John Halamka, Reinventing Clinical Decision Support, 2020
Studying network medicine’s essential components is also providing useful insights into the nature of asthma, as we discussed earlier. Oligonucleotide microarrays and sequencing are homing in on single-nucleotide polymorphisms (SNPs) that may be involved in the pathophysiology of asthma, for instance. Some of the strongest evidence comes from genome-wide association studies (GWAS) that focus on the 17q21 locus, referring to chromosome 17—the lower q section, position 21. Four genes in this section of the chromosome—ORMDL3, GSDMB, ZPBP2, and IKZF3—have been linked to inflammatory response, a major problem for patients with asthma. GWAS also suggest that specific gene variants in the FLG gene contribute to atopic dermatitis in Europeans and Asians. The mutations are not usually found in Africans, as demonstrated by whole exome sequencing. (The exome is that fraction of the genome that contains protein-encoding DNA.)18
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.
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].
Variants in RCBTB1 are Associated with Autosomal Recessive Retinitis Pigmentosa but Not Autosomal Dominant FEVR
Published in Current Eye Research, 2021
Junxing Yang, Xueshan Xiao, Wenmin Sun, Shiqiang Li, Xiaoyun Jia, Qingjiong Zhang
Exome sequencing data was obtained from a total of 6303 unrelated families with different eye conditions from our in-house data, including 5280 from WES data, and 1023 from TES data. In brief, exome was captured from genomic DNA from probands by the Agilent SureSelect Human All Exon Enrichment Kit (Agilent, Santa Clara, CA, USA). Enriched DNA fragments were then sequenced using the HiSeq platform (Illumina, San Diego, CA, USA) with an average depth of 125X. Variants were detected by aligning the sequencing reads with the hg19 reference genome using the Burrows-Wheeler Aligner (BWA, http://bio-bwa.sourceforge.net/). Variant calling, annotation, and functional prediction were performed by SAMTOOLS (http://samtools.sourceforge.net/), SnpEff (http://snpeff.sourceforge.net/), ANNOVAR (http://annovar.openbioinformatics.org/en/latest/), and dbNSFP (http://varianttools.sourceforge.net/Annotation/DbNSFP), respectively. Simultaneously, TES was performed in our laboratory on the Chinese population based on variant frequency, including RCBTB1 and other related genetic eye disease genes.