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Differential Genetic Diagnosis between Leiomyoma and Leiomyosarcoma
Published in Carlos Simón, Carmen Rubio, Handbook of Genetic Diagnostic Technologies in Reproductive Medicine, 2022
Alba Machado-Lopez, Aymara Mas
Next-generation sequencing (NGS) technologies have been applied across various scientific disciplines, from basic research to translational medicine. Specifically, The Cancer Genome Atlas (TCGA) is one of the most relevant projects, which aims to characterize the molecular signatures of human cancers. Accordingly, genetic risk assessment, prognostic information, identification of molecular subtypes, or development of therapeutic strategies are some of the possible approaches currently being applied to breast, ovarian, endometrial vulvar, and cervical cancers.
Whole exome and whole genome sequencing
Published in Moshe Hod, Vincenzo Berghella, Mary E. D'Alton, Gian Carlo Di Renzo, Eduard Gratacós, Vassilios Fanos, New Technologies and Perinatal Medicine, 2019
Historically, prenatal diagnosis has focused on detection of chromosomal abnormalities, particularly trisomy 21. Chromosomal microarray analysis (CMA) now provides higher-resolution scanning of the genome, such that more cytogenetic abnormalities can be detected (1). With advances in DNA technology, particularly since the completion of the human genome project, an increasing number of single gene disorders have become amenable to genetic diagnosis. Yet even with these available tests, for the majority of fetuses with sonographic abnormalities, the cause and potential associated abnormalities are not detected until after birth. Recently, next-generation sequencing (NGS) has been introduced and provides the ability to screen for a much larger number of conditions when a genetic diagnosis is suspected, but a precise disorder is not evident.
Companion Diagnostics for Oncogenic Fusion Proteins
Published in Il-Jin Kim, Companion Diagnostics (CDx) in Precision Medicine, 2019
Roman Groisberg, Vivek Subbiah
The use of IHC to detect fusions is becoming more difficult as the number of clinically relevant oncogenic fusions grows. Most fusions are rare events and some occur in a wide array of tumor types making individual staining less practical. More often than not, patients harboring an oncogenic fusion will be missed. Enter next generation sequencing (NGS), a high-throughput sequencing technology that is commercially available, accurate, and inexpensive. NGS is quickly replacing IHC as the preferred companion diagnostic for oncogenic fusions.
Associations of common genetic risk variants of the muscarinic acetylcholine receptor M2 with cardiac autonomic dysfunction in patients with schizophrenia
Published in The World Journal of Biological Psychiatry, 2023
Alexander Refisch, Shoko Komatsuzaki, Martin Ungelenk, Ha-Yeun Chung, Andy Schumann, Susann S. Schilling, Wibke Jantzen, Sabine Schröder, Thomas W. Mühleisen, Markus M. Nöthen, Christian A. Hübner, Karl-Jürgen Bär
An AmpliSeqTM Custom DNA Panel for Illumina® (Illumina Inc., San Diego, CA, USA) was developed to perform high-throughput sequencing containing the three CHMR2 SNPs (rs73158705 A>G, rs8191992 T>A and rs2350782 T>C) that we found in the literature to be associated with cardiac autonomic features (Hautala et al. 2009; den Hoed et al. 2013; Eppinga et al. 2016). Next-generation sequencing (NGS) was applied using the AmpliSeqTM for Illumina® workflow on 10 ng high-quality DNA from all participants according to the manufacturer’s instructions. In brief, participant DNA was fragmented by endonucleases and hybridised to biotinylated gene specific probes incorporating Illumina paired-end sequencing motifs and indexed primers. Hybridised molecules were captured by magnetic beads, PCR amplified, and sequenced with the MiSeq system (Illumina Inc., San Diego, CA, USA).
Diagnostic utility of rapid sequencing in critically ill infants: a systematic review and meta-analysis
Published in Expert Review of Molecular Diagnostics, 2022
Feifan Xiao, Kai Yan, Meiling Tang, Xiaoshan Ji, Liyuan Hu, Lin Yang, Wenhao Zhou
Since 2010, next-generation sequencing (NGS), which can simultaneously sequence thousands of genes, has been used to diagnose genetic disorders at a relatively low cost. A meta-analysis with 37 studies concluded that the diagnostic rate and clinical utility of whole-genome sequencing (WGS)/whole-exome sequencing (WES) was greater than for chromosomal microarray [4]. However, the turnaround time (TAT) of standard NGS may take two months or longer, which is not suitable for the genetic diagnosis of critically ill infants. In early 2012, Saunders et al. [5] diagnosed two neonates using WGS within 50 hours. Subsequently, Willing et al. [6] reported that 57% (20/35) of infants with suspected genetic causes in their study obtained genetic diagnoses using rapid WGS (rWGS). Additionally, Stark et al. [7] suggested that rapid WES (rWES) can be used as a first-tier sequencing test for infants suspected of having monogenic disorders. These studies indicated good performance of rapid genomic sequencing in critically ill infants.
Homeostasis and Defense at the Surface of the Eye. The Conjunctival Microbiota
Published in Current Eye Research, 2021
Arnulfo Garza, Giancarlo Diaz, Marah Hamdan, Akaanksh Shetty, Bo-Young Hong, Jorge Cervantes
The era of Next Generation Sequencing (NGS) opened the doors to better characterization of the microbiota composition, by DNA-based detection (i.e. the microbiome), surpassing the limitations of culturing techniques.6 The second decade of the 21st century contemplated new knowledge of the bacterial communities in the ocular surface, with description of a “core” of conjunctival microbiota (Table 1) composed of 12 genera: Pseudomonas, Propionibacterium, Bradyrhizobium, Corynebacterium, Acinetobacter, Brevundimonas, Staphylococci, Aquabacterium, Sphingomonas, Streptococcus, Streptophyta, and Methylobacterium.7 Later studies showed overlapping results for the composition of the core microbiome of the conjunctiva, which included genera: Corynebacterium, Pseudomonas, Staphylococcus, Acinetobacter, Streptococcus, Bacillus, Millisia, Anaerococcus, Finegoldia, Simonsiella, Ralstonia, and Veillonella.8 This core composition is not maintained temporally, with a limited number of species always present, which supports the notion that the ocular surface contains a low diversity of microorganisms.9