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Journal articles on the topic 'Exon-spanning reads'

Author: Grafiati

Published: 14 March 2023

Last updated: 31 July 2025

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1

Hwangbo, Suhyun, Sungyoung Lee, Sheehyun Kim, and Hongseok Yun. "Abstract 6542: Detection of androgen receptor splice variants from clinical sequencing." Cancer Research 83, no. 7_Supplement (2023): 6542. http://dx.doi.org/10.1158/1538-7445.am2023-6542.

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Abstract Androgen receptor (AR) splice variants (AR-Vs) have been widely studied on its important role in prostate cancer (PC) progression. In particular, AR-Vs lacking ligand binding domains, such as AR splice variant 7 (AR-v7) that links exon 3 and cryptic exon 3 or AR variant that losses exons 5 to 7 (ARv567es), have been demonstrated as one of the resistant mechanisms to androgen deprivation therapy in PC. Despite its clinical importance, the current algorithms to detect fusions such as TopHat-Fusion have limitation to detect intra-chromosomal rearrangements including AR-Vs. In this respec

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2

Calvo-Roitberg, Ezequiel, Rachel F. Daniels, and Athma A. Pai. "Challenges in identifying mRNA transcript starts and ends from long-read sequencing data." Genome Research 34, no. 11 (2024): 1719–34. http://dx.doi.org/10.1101/gr.279559.124.

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Long-read sequencing (LRS) technologies have the potential to revolutionize scientific discoveries in RNA biology through the comprehensive identification and quantification of full-length mRNA isoforms. Despite great promise, challenges remain in the widespread implementation of LRS technologies for RNA-based applications, including concerns about low coverage, high sequencing error, and robust computational pipelines. Although much focus has been placed on defining mRNA exon composition and structure with LRS data, less careful characterization has been done of the ability to assess the term

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3

Anderson, Peter Meade, Luisa-Marie Manning, Brian Rubin, et al. "Nested set information derived from fusion genes in Ewing sarcoma and other cancers." Journal of Clinical Oncology 40, no. 16_suppl (2022): e23521-e23521. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e23521.

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e23521 Background: Ewing family tumors including Ewing sarcoma (ES) and desmoplastic small round cell tumor (DSRCT) are characterized by EWSR1 and ETS fusion partners including EWS-FLI1, EWS-ERG, EWS-WT1, and others. Since 2019 our Next Generation Sequencing (NGS) sarcoma panel (N = 338) identified both fusion partners and exons containing the EWS breakpoint in ES and DSRCT. Hence, it should be possible to learn more about the exact breakpoints of EWS fusion genes. The molecular diversity and functionality of these fusion transcripts, especially the exact sequence, which could be identical, si

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4

Maity, Ranjan, Paola E. Neri, Ines Tagoug, et al. "Cereblon (CRBN) Splice Isoform Lacking Exon 10 Attenuates Lenalidomide-Mediated Degradation of Aiolos and Is Upregulated in Immunomodulatory Drugs (IMiDs) Resistant Myeloma (MM) Patients." Blood 124, no. 21 (2014): 639. http://dx.doi.org/10.1182/blood.v124.21.639.639.

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Abstract Background: IMiDs cytotoxicity in MM cells is mediated through their binding to CRBN within the cullin ring (CRL4) ligase. This binding triggers the ubiquitylation and proteasomal degradation of IKZF1/3. CRBN thalidmomide binding domain (TBD) was mapped to its C-terminus and the crystal structure of the CRBN-IMiDs bound complex identified several aa within exons 10 and 11 as essential for the IMiDs glutarimide ring binding to CRBN. Several groups including ours have reported that loss of CRBN is associated with resistance to IMiDs, however this does not appear to be the sole mechanism

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5

Grossmann, Vera, Christiane Eder, Sonja Schindela, et al. "A Comprehensive Deep-Sequencing Study of Blast Crisis Chronic Myeloid Leukemia (CML) Reveals New Insights Into Molecular Heterogeneity and Detects Mutations In 12 Different Genes In 82.5% of Cases." Blood 116, no. 21 (2010): 884. http://dx.doi.org/10.1182/blood.v116.21.884.884.

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Abstract Abstract 884 Blast crisis is the terminal phase of chronic myeloid leukemia (CML) with a short median survival of approximately six months. At present, little is known about molecular mechanisms underlying disease progression. We hypothesized that mutations occurring in other myeloid and lymphatic malignancies are acquired during disease progression from chronic phase to blast crisis. Here, in total 40 blast crisis CML cases (n=25 myeloid, n=10 lymphoid, n=5 not specified) were analyzed, all diagnosed between 9/2005 and 7/2009. First, all cases were investigated for IKZF1 deletions by

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6

Mobegi, Fredrick M., Samuel Bruce, Naser El-Lagta, et al. "Characterisation of the ABO Blood Group Phenotypes Using Third-Generation Sequencing." International Journal of Molecular Sciences 26, no. 12 (2025): 5443. https://doi.org/10.3390/ijms26125443.

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Third-generation sequencing (TGS), also known as long-read sequencing, has become a promising tool in clinical and research laboratories because it delivers high-resolution results with unmatched throughput. Specialised immunohematology laboratories currently employ sequencing-based methods to characterise rare ABO blood group phenotypes that cannot be identified through serology and genotyping methods. However, routine clinical application of these methods remains elusive due to the absence of validated laboratory protocols and bioinformatics tools. In this study, we have developed and valida

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7

Wille, Sandra, Vera Grossmann, Tamara Alpermann, et al. "Landscape of TET2 Mutations In Acute Myeloid Leukemia (AML): A Next-Generation Sequencing Study Investigating 76 Cases Comprehensively Characterized for Cytogenetics and Other Molecular Markers." Blood 116, no. 21 (2010): 1035. http://dx.doi.org/10.1182/blood.v116.21.1035.1035.

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Abstract Abstract 1035 Mutations of the ten eleven translocation (TET2) gene have been reported to be frequent in hematological malignancies. However, data are preliminary and investigation is challenging and labor-intensive with standard sequencing techniques. Here, we used massively parallel Titanium amplicon next-generation sequencing (NGS) technology (454 Life Sciences, Branford, CT) and investigated 76 patients with acute myeloid leukemia (AML), including 66 de novo AML, 6 s-AML and 4 t-AML cases, respectively, diagnosed between 8/2005 and 5/2010. The median age of the cohort was 64.7 yea

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8

Ghetti, Martina, Antonella Padella, Eugenio Fonzi, et al. "Abstract 1555: circPVT1 and linear PVT1 isoforms regulate cell growth, metabolic and DNA damage response related gene signatures in acute myeloid leukemia." Cancer Research 82, no. 12_Supplement (2022): 1555. http://dx.doi.org/10.1158/1538-7445.am2022-1555.

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Abstract Non-coding (nc)RNAs, including circular (circ)RNAs, contribute to tumor development and progression. Several ncRNAs were shown to affect the onset, prognosis, and treatment of acute myeloid leukemia (AML) in the past years. The human Plasmacytoma Variant Translocation 1 (PVT1) gene maps on the long arm of chromosome 8 (8q24), in the same genomic region hosting MYC and encoding for 83 linear (PVT1, lncipedia.org) and 26 high-confidence circular isoforms (circPVT1, www.circbase.org). The most common isoform of circPVT1 is a product of back-splicing of 410 nt and contains the whole exon

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9

Velusamy, Thirunavukkarasu, Mark J. Kiel, Anagh A. Sahasrabuddhe, et al. "Novel Gene Translocations Involving TYK2 in Cutaneous CD30-Positive Lymphoproliferative Disorders." Blood 124, no. 21 (2014): 3032. http://dx.doi.org/10.1182/blood.v124.21.3032.3032.

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Abstract Introduction: The CD30-positive cutaneous T-cell lymphoproliferative disorders (CD30-positive LPD) include lymphomatoid papulosis (LYP) and primary cutaneous anaplastic large cell lymphoma (ALCL). Recurrent chromosomal translocations frequently underlie the pathogenesis of several hematologic malignancies and often define molecular subtypes with distinct biological behavior. The genetic events that contribute to the pathogenesis of CD30-positive LPD are largely unknown. Goal: The goal of our study was to identify chromosomal translocations that result in the generation of oncogenic ch

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10

Chandrasekhar, Shwetha, Siying Lin, Neringa Jurkute, et al. "Investigating Splice Defects in USH2A Using Targeted Long-Read Sequencing." Cells 13, no. 15 (2024): 1261. http://dx.doi.org/10.3390/cells13151261.

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Biallelic variants in USH2A are associated with retinitis pigmentosa (RP) and Type 2 Usher Syndrome (USH2), leading to impaired vision and, additionally, hearing loss in the latter. Although the introduction of next-generation sequencing into clinical diagnostics has led to a significant uplift in molecular diagnostic rates, many patients remain molecularly unsolved. It is thought that non-coding variants or variants of uncertain significance contribute significantly to this diagnostic gap. This study aims to demonstrate the clinical utility of the reverse transcription–polymerase chain reacti

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11

Escherich, Gabriele, Udo zur Stadt, Malik Alawi, and Martin A. Horstmann. "Rapid Capture Targeted Next Generation Sequencing (NGS) for Detection of Genomic Kinase- and Cytokine-Receptor Rearrangements in B-Precursor Acute Lymphoblastic Leukemia." Blood 126, no. 23 (2015): 2609. http://dx.doi.org/10.1182/blood.v126.23.2609.2609.

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Abstract Background: Next generation sequencing (NGS) applications have recently identified various recurrent kinase and cytokine receptor rearrangements in a subgroup of B-progenitor acute lymphoblastic leukemia (BPC-ALL) that is characterized by a Ph-like gene expression signature. Implementation of whole genome applications into diagnostics have so far been hampered by high costs and long turnover times. Therefore we developed a custom-made NGS based capture panel without the need for gene specific PCR amplification steps. With a rapid turnover time, pooling of multiple samples and standard

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12

Hardwick, Simon A., Wen Hu, Anoushka Joglekar, et al. "Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue." Nature Biotechnology, March 7, 2022. http://dx.doi.org/10.1038/s41587-022-01231-3.

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AbstractSingle-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder the study of isoforms. Here we present single-nuclei isoform RNA sequencing (SnISOr-Seq). Using microfluidics, PCR-based artifact removal, target enrichment and long-read sequencing, SnISOr-Seq increased barcoded, exon-spanning long reads 7.5-fold compared to naive long-read single-nuclei sequencing. We applied SnISOr-Seq to adult human frontal cortex and found that exons associated with autism exhib

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13

Fernández-Suárez, Elena, María González-del Pozo, Cristina Méndez-Vidal, et al. "Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene." Mobile DNA 15, no. 1 (2024). http://dx.doi.org/10.1186/s13100-024-00320-1.

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Abstract Background Biallelic variants in EYS are the major cause of autosomal recessive retinitis pigmentosa (arRP) in certain populations, a clinically and genetically heterogeneous disease that may lead to legal blindness. EYS is one of the largest genes (~ 2 Mb) expressed in the retina, in which structural variants (SVs) represent a common cause of disease. However, their identification using short-read sequencing (SRS) is not always feasible. Here, we conducted targeted long-read sequencing (T-LRS) using adaptive sampling of EYS on the MinION sequencing platform (Oxford Nanopore Technolog

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14

Li, Qianqian, Zhanni Chen, Hui Xiong, et al. "Novel Partial Exon 51 Deletion in the Duchenne Muscular Dystrophy Gene Identified via Whole Exome Sequencing and Long-Read Whole-Genome Sequencing." Frontiers in Genetics 12 (November 26, 2021). http://dx.doi.org/10.3389/fgene.2021.762987.

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Duchenne muscular dystrophy (DMD), one of the most common progressive and severely disabling neuromuscular diseases in children, can be largely attributed to the loss of function of the DMD gene on chromosome Xp21.2-p21.1. This paper describes the case of a 10-year-old boy diagnosed with DMD. Whole exome sequencing confirmed the hypothesized large partial exonic deletion of c.7310-11543_7359del (chrX:g.31792260_31803852del) spanning exon 51 and intron 50 in DMD. This large deletion was verified to be de novo by PCR, and the two breakpoints were further confirmed by Sanger sequencing and long-r

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15

Daida, Kensuke, Manabu Funayama, Kimberley J. Billingsley, et al. "Long‐Read Sequencing Resolves a Complex Structural Variant in PRKN Parkinson's Disease." Movement Disorders, November 5, 2023. http://dx.doi.org/10.1002/mds.29610.

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AbstractBackgroundParkin RBR E3 ubiquitin‐protein ligase (PRKN) mutations are the most common cause of young onset and autosomal recessive Parkinson's disease (PD). PRKN is located in FRA6E, which is one of the common fragile sites in the human genome, making this region prone to structural variants. However, complex structural variants such as inversions of PRKN are seldom reported, suggesting that there are potentially unrevealed complex pathogenic PRKN structural variants.ObjectivesTo identify complex structural variants in PRKN using long‐read sequencing.MethodsWe investigated the genetic

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16

Celemín, Enrique, Nikolai Gusev, Marisol Domínguez, et al. "Evolution and Organisation of MHC II Genes in Harbour Porpoises: Insights From Long‐Read Cetacean Genome Assemblies, Whole Genome Re‐Sequencing and Locus‐Specific Genotyping." Molecular Ecology, June 23, 2025. https://doi.org/10.1111/mec.70006.

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ABSTRACTThe Major Histocompatibility Complex (MHC) is a central element in the vertebrate immune system. While MHC genes are a common target of conservation genomic studies, it has been challenging to reliably amplify locus‐specific alleles, which is especially problematic when studying endangered lineages, like some harbour porpoise (Phocoena phocoena) populations and subspecies. Here, we manually annotated all MHC II genes in the harbour porpoise genome and genotyped every exon 2 in 47 individuals (94 individuals for DRB1 and DQB genes) spanning six geographical regions, including the endang

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