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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
Widespread adoption of NIPT is likely to continue, leading to a dramatic reduction in invasive sampling for prenatal genetic diagnostic tests. From a technical point of view, non-invasive deep sequencing of the fetal genome may serve as a universal screening or even diagnostic test to detect genetic diseases in a fetus (1). However, whether it should be routinely offered to pregnant women without a known risk is a complex issue requiring ethical and socio-economical discussions. Regardless, genome-wide profiling will improve overall pregnancy management. A workflow for the follow-up of NIPT results is proposed in Figure 26.4 (47). Despite technological advances in NIPT for monogenic diseases, widespread clinical uptake will remain hindered by the rarity of individual genetic diseases and the subsequent need for individual, customized development.
Liquid Biopsies for Pancreatic Cancer: A Step Towards Early Detection
Published in Surinder K. Batra, Moorthy P. Ponnusamy, Gene Regulation and Therapeutics for Cancer, 2021
Joseph Carmicheal, Rahat Jahan, Koelina Ganguly, Ashu Shah, Sukhwinder Kaur
Other targeted approaches are being developed based on Deep sequencing/Next Generation Sequencing (NGS) using site-specific primers to amplify a particular genomic region. Some examples of these regions include “Safe-SeqS”, Tagged Amplicon Sequencing (TAm-Seq), AmpliSeq and Personalized Analysis of Rearranged Ends (PARE). Though they require further standardization and experimental study, these are some of the advanced technologies that will prove invaluable in the identification of specific hotspot mutations found in ctDNA [15, 16].
Drug-Resistant Tuberculosis
Published in Lloyd N. Friedman, Martin Dedicoat, Peter D. O. Davies, Clinical Tuberculosis, 2020
Keertan Dheda, Aliasgar Esmail, Anzaan Dippenaar, Robin Warren, Jennifer Furin, Christoph Lange
An alternative to WGS is targeted next-generation deep sequencing.110,111 This method allows variants to be detected in minor M. tuberculosis populations, termed heteroresistance. This has allowed researchers to find resistance at a frequency below the classical 1% proportion method. It is envisaged that targeted deep sequencing may be a replacement for culture-based DST. It also has the potential to identify resistance earlier, thereby allowing researchers to get a greater understanding of the biology of the evolution of drug resistance. An added advantage is the potential for clinical decisions to be made earlier and for treatment regimens to be individualized based on the comprehensive drug resistance profile of the M. tuberculosis isolate infecting the patient, but exactly how this should be implemented remains unclear.110,112 However, the limited number of genetic targets being evaluated currently precludes targeted deep sequencing as a method to study the epidemiology of DR-TB.
Analysis of RBP expression and binding sites identifies PTBP1 as a regulator of CD19 expression in B-ALL
Published in OncoImmunology, 2023
Nicole Ziegler, Mariela Cortés-López, Francesca Alt, Maximilian Sprang, Arsenij Ustjanzew, Nadine Lehmann, Khalifa El Malki, Arthur Wingerter, Alexandra Russo, Olaf Beck, Sebastian Attig, Lea Roth, Julian König, Claudia Paret, Jörg Faber
Our in vitro studies revealed that PTBP1 mediates CD19 protein abundance by controlling exon 2 splicing as simultaneously suggested by another study.18 This mechanism aligns with patient data showing that decreased PTBP1 expression in patients at diagnosis compared to controls goes along with an increase in intron 2 retention. Significance was not reached in our cohort due to limitations in sample size, but could be shown in the TARGET cohort.18 Moreover, intron 2 retention was shown to increase in samples at relapse under CAR T cell therapy.18, Unfortunately, in our study, the same patients could not be screened by deep sequencing, so that we cannot evaluate the potential impact of CD19 mutations on these correlations. Future studies, however, will address this issue in more detail.
Unpacking the genetic etiology of uveal melanoma
Published in Expert Review of Ophthalmology, 2020
Sophie Thornton, Helen Kalirai, Karen Aughton, Sarah E. Coupland
After the successes of the TCGA and 100,000 Genome studies in the USA and UK, respectively, deep sequencing of clinical samples is transforming the way cancer patients are being managed, enabling them to receive personalized treatments. The genomics industry is growing exponentially worldwide, and the combination of sequencing data with patient’s medical records provides an invaluable resource for clinicians and researchers alike. In cancer alone, it is estimated that around half of all malignancies have the potential for a therapy or a clinical trial. Whilst the genetic etiology of UM enables clinicians to tailor surveillance programs to a patient’s individual metastatic risk, at present no targeted treatments exist, and little is known about how UM progresses from primary to metastatic disease.
Genetic and epigenetic regulation of natural resistance to HIV-1 infection: new approaches to unveil the HESN secret
Published in Expert Review of Clinical Immunology, 2020
Claudio Fenizia, Irma Saulle, Mario Clerici, Mara Biasin
GWAS (genome-wide association studies), which investigate common gene variant’s role in HIV infection, explain approximately 20% of viral load variation and disease progression, suggesting that other still unknown factors are involved in the control of this disease. Notably, innovative technologies in genome sequencing allow the identification of uncommon variants as well, both by sequencing of the entire exome (2% of the genome), or through the deep sequencing of the complete genome or transcriptome (RNA-seq). In 2018, a study published by Nissen et al. on whole exome sequencing (WES) on 7 LTNPs and 4 ECs led to the identification of 24 relevant variants localized in 20 different genes, mainly encoding innate immune sensors (LRRIF1P, IRAK2, TAB2, NOD2, SLX4) and proteins involved in HIV uptake and intracellular trafficking (FN1, FRK, PIK3C2B, PIK3R5, MAP1A, PIK3R6) [185]. However, no single unifying mechanism common to both ECs and LTNPs was identified, suggesting that slow disease progression in these two different phenotypes may depend on a diverse genetic background.