scholarly journals Publisher Correction: Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yosuke Ito ◽  
Yasuhisa Terao ◽  
Shohei Noma ◽  
Michihira Tagami ◽  
Emiko Yoshida ◽  
...  
Keyword(s):  
Nanopore Sequencing ◽  
Intronic Promoter

scholarly journals Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yosuke Ito ◽  
Yasuhisa Terao ◽  
Shohei Noma ◽  
Michihira Tagami ◽  
Emiko Yoshida ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Primary Lesion ◽  
Computational Error ◽  
Nanopore Sequencing ◽  
High Confidence ◽  
Normal Endometrium ◽  
Node Metastasis ◽  
Endometrial Cancers ◽  
Long Range Pcr ◽  
Intronic Promoter

AbstractGene expression is controlled at the transcriptional and post-transcriptional levels. The TACC2 gene was known to be associated with tumors but the control of its expression is unclear. We have reported that activity of the intronic promoter p10 of TACC2 in primary lesion of endometrial cancer is indicative of lymph node metastasis among a low-risk patient group. Here, we analyze the intronic promoter derived isoforms in JHUEM-1 endometrial cancer cells, and primary tissues of endometrial cancers and normal endometrium. Full-length cDNA amplicons are produced by long-range PCR and subjected to nanopore sequencing followed by computational error correction. We identify 16 stable, 4 variable, and 9 rare exons including 3 novel exons validated independently. All variable and rare exons reside N-terminally of the TACC domain and contribute to isoform variety. We found 240 isoforms as high-confidence, supported by more than 20 reads. The large number of isoforms produced from one minor promoter indicates the post-transcriptional complexity coupled with transcription at the TACC2 locus in cancer and normal cells.

Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing

2021 ◽  
Author(s):  
Oguzhan Begik ◽  
Morghan C. Lucas ◽  
Leszek P. Pryszcz ◽  
Jose Miguel Ramirez ◽  
Rebeca Medina ◽  
...  
Keyword(s):  
Nanopore Sequencing ◽  
Quantitative Profiling

scholarly journals Pan-genomic Matching Statistics for Targeted Nanopore Sequencing

iScience ◽  
2021 ◽  
pp. 102696
Author(s):  
Omar Ahmed ◽  
Massimiliano Rossi ◽  
Sam Kovaka ◽  
Michael C. Schatz ◽  
Travis Gagie ◽  
...  
Keyword(s):  
Nanopore Sequencing

scholarly journals Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing

2021 ◽  
Author(s):  
Alan Tourancheau ◽  
Edward A. Mead ◽  
Xue-Song Zhang ◽  
Gang Fang
Keyword(s):  
Dna Methylation ◽  
Nanopore Sequencing

scholarly journals MBRS-47. RAPID MOLECULAR SUBGROUPING OF MEDULLOBLASTOMA BASED ON DNA METHYLATION BY NANOPORE SEQUENCING

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii406-iii406
Author(s):  
Julien Masliah-Planchon ◽  
Elodie Girard ◽  
Philipp Euskirchen ◽  
Christine Bourneix ◽  
Delphine Lequin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Single Molecule ◽  
Nanopore Sequencing ◽  
Molecular Subgroup ◽  
Group Assignment ◽  
Group 4 ◽  
Methylation Assay ◽  
Tumor Group ◽  
Long Read ◽  
Group 3

Abstract Medulloblastoma (MB) can be classified into four molecular subgroups (WNT group, SHH group, group 3, and group 4). The gold standard of assignment of molecular subgroup through DNA methylation profiling uses Illumina EPIC array. However, this tool has some limitation in terms of cost and timing, in order to get the results soon enough for clinical use. We present an alternative DNA methylation assay based on nanopore sequencing efficient for rapid, cheaper, and reliable subgrouping of clinical MB samples. Low-depth whole genome with long-read single-molecule nanopore sequencing was used to simultaneously assess copy number profile and MB subgrouping based on DNA methylation. The DNA methylation data generated by Nanopore sequencing were compared to a publicly available reference cohort comprising over 2,800 brain tumors including the four subgroups of MB (Capper et al. Nature; 2018) to generate a score that estimates a confidence with a tumor group assignment. Among the 24 MB analyzed with nanopore sequencing (six WNT, nine SHH, five group 3, and four group 4), all of them were classified in the appropriate subgroup established by expression-based Nanostring subgrouping. In addition to the subgrouping, we also examine the genomic profile. Furthermore, all previously identified clinically relevant genomic rearrangements (mostly MYC and MYCN amplifications) were also detected with our assay. In conclusion, we are confirming the full reliability of nanopore sequencing as a novel rapid and cheap assay for methylation-based MB subgrouping. We now plan to implement this technology to other embryonal tumors of the central nervous system.

scholarly journals Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq

2021 ◽  
Author(s):  
Martin Philpott ◽  
Jonathan Watson ◽  
Anjan Thakurta ◽  
Tom Brown ◽  
Tom Brown ◽  
...  
Keyword(s):  
Single Cell ◽  
Error Detection ◽  
Single Cells ◽  
Fusion Transcript ◽  
Building Blocks ◽  
Myeloma Cell ◽  
Nanopore Sequencing ◽  
Long Read ◽  
Unique Molecular Identifier ◽  
Transcript Detection

AbstractHere we describe single-cell corrected long-read sequencing (scCOLOR-seq), which enables error correction of barcode and unique molecular identifier oligonucleotide sequences and permits standalone cDNA nanopore sequencing of single cells. Barcodes and unique molecular identifiers are synthesized using dimeric nucleotide building blocks that allow error detection. We illustrate the use of the method for evaluating barcode assignment accuracy, differential isoform usage in myeloma cell lines, and fusion transcript detection in a sarcoma cell line.

Nanopore Sequencing Accurately Identifies the Cisplatin Adduct on DNA

ACS Sensors ◽  
2021 ◽  
Author(s):  
Fubo Ma ◽  
Shuanghong Yan ◽  
Jinyue Zhang ◽  
Yu Wang ◽  
Liying Wang ◽  
...  
Keyword(s):  
Nanopore Sequencing

scholarly journals Differential Expression of BARD1 Isoforms in Melanoma

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 320
Author(s):  
Lorissa I. McDougall ◽  
Ryan M. Powell ◽  
Magdalena Ratajska ◽  
Chi F. Lynch-Sutherland ◽  
Sultana Mehbuba Hossain ◽  
...  
Keyword(s):  
Long Range ◽  
Patient Outcomes ◽  
Splice Variants ◽  
Significant Proportion ◽  
Nanopore Sequencing ◽  
Rna Seq ◽  
Splice Isoforms ◽  
Tissue Samples ◽  
Multiple Transcripts ◽  
Mrna Variants

Melanoma comprises <5% of cutaneous malignancies, yet it causes a significant proportion of skin cancer-related deaths worldwide. While new therapies for melanoma have been developed, not all patients respond well. Thus, further research is required to better predict patient outcomes. Using long-range nanopore sequencing, RT-qPCR, and RNA sequencing analyses, we examined the transcription of BARD1 splice isoforms in melanoma cell lines and patient tissue samples. Seventy-six BARD1 mRNA variants were identified in total, with several previously characterised isoforms (γ, φ, δ, ε, and η) contributing to a large proportion of the expressed transcripts. In addition, we identified four novel splice events, namely, Δ(E3_E9), ▼(i8), IVS10+131▼46, and IVS10▼176, occurring in various combinations in multiple transcripts. We found that short-read RNA-Seq analyses were limited in their ability to predict isoforms containing multiple non-contiguous splicing events, as compared to long-range nanopore sequencing. These studies suggest that further investigations into the functional significance of the identified BARD1 splice variants in melanoma are warranted.

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