Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data

Abstract Background Accurate fusion transcript detection is essential for comprehensive characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools have been developed to predict fusions from RNA-seq, based on either read mapping or de novo fusion transcript assembly. Results We benchmark 23 different methods including applications we develop, STAR-Fusion and TrinityFusion, leveraging both simulated and real RNA-seq. Overall, STAR-Fusion, Arriba, and STAR-SEQR are the most accurate and fastest for fusion detection on cancer transcriptomes. Conclusion The lower accuracy of de novo assembly-based methods notwithstanding, they are useful for reconstructing fusion isoforms and tumor viruses, both of which are important in cancer research.

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Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq

Nature Biotechnology ◽

10.1038/s41587-021-00965-w ◽

2021 ◽

Author(s):

Martin Philpott ◽

Jonathan Watson ◽

Anjan Thakurta ◽

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.

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Overexpression of UBE2C in Esophageal Squamous Cell Carcinoma Tissues and Molecular Analysis

10.21203/rs.3.rs-405953/v1 ◽

2021 ◽

Author(s):

Rong Li ◽

xingfeng pang ◽

Zhiguang Huang ◽

Lihua Yang ◽

Zhigang Peng ◽

...

Keyword(s):

Esophageal Cancer ◽

Survival Analysis ◽

Survival Rate ◽

Comprehensive Evaluation ◽

Synergistic Effects ◽

Comprehensive Treatment ◽

Rna Seq ◽

Mrna Expression Data ◽

Risk Of Recurrence ◽

Lower Survival Rate

Abstract Background: The treatment of esophageal cancer is mainly based on a combination of traditional surgery and radiotherapy/chemotherapy. Some new progress has been made in multidisciplinary comprehensive treatment and imaging diagnosis in recent years, but the 5-year survival rate for esophageal cancer is much lower than 30% due to its invasiveness and pronounced metastasis ability, as well as the difficulty in early diagnosis. This study aimed to elucidate the molecular mechanism of UBE2C in ESCC.Methods: In this study, we conducted a comprehensive evaluation of the UBE2C expression in ESCC by collecting the protein and mRNA expression data (including in house RNA- seq, in hosue IHC, TCGA-GTEx RNA-seq and tissue microarray) to calculate a combined SMD and sROC. K-M method was used for survival analysis. We also explored the mechanism of UBE2C in ESCC by combing the DEGs of ESCC, related-genes of UBE2C in ESCC and the putative miRNAs and lncRNAs which may regulate UBE2C.Results: UBE2C protein and mRNA were highly expressed in ESCC tissues. The pooled SMD of UBE2C expression values was 1.98 (95% CI: 1.51–2.45, P < 0.001), and the the AUC of the sROC was 0.93 (95% CI: 0.90–0.95). The results of survival analysis suggested an association between high expression of UBE2C and a poor prognosis and a higher risk of recurrence. Pathways anaylsis showed that UBE2C mainly influenced the biological function of esophageal cancer by synergistic effects with CDK1, PTTG1 and SKP2. We also constructed a potential UBE2C-related ceRNA network for ESCC (HCP5/hsa-mir-139-5p/UBE2C).Conclusion: UBE2C mRNA and protein level were highly expressed in ESCC and a higher UBE2C expression generally predicts a lower survival rate and a higher risk of recurrence.

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Immunophenotype-Genotype Correlations in Clear Cell Sarcoma of Kidney—An Evaluation of Diagnostic Ancillary Studies

Pediatric and Developmental Pathology ◽

10.1177/1093526620910658 ◽

2020 ◽

Vol 23 (5) ◽

pp. 345-351

Author(s):

Colin Kenny ◽

David Grehan ◽

Mevlut Ulas ◽

Gloria Badi Banga ◽

Aurore Coulomb ◽

...

Keyword(s):

Triple Negative ◽

Clear Cell ◽

Comprehensive Evaluation ◽

Single Case ◽

Fusion Transcript ◽

Clear Cell Sarcoma ◽

Cell Sarcoma ◽

Genotypic Analysis ◽

Synovial Sarcomas ◽

Rhabdoid Tumors

Introduction The purpose of this study was to establish a reliable panel of antibodies for immunohistochemical corroboration of a diagnosis of clear cell sarcoma of kidney (CCSK), taking into consideration the various genotypic subsets of CCSK. Methods We conducted full genotypic analysis for evidence of YWHAE-NUTM2, BCOR internal tandem duplication (ITD), and BCOR-CCNB3 in 68 archival cases of CCSK and then immunostained all cases for CCND1, TLE1, and BCOR along with 63 control samples representing tumor types that may enter into the differential diagnosis of CCSK, including 7 congenital mesoblastic nephromas, 2 desmoplastic small round cell tumors, 13 malignant rhabdoid tumors, 9 Ewing sarcomas/primitive neuroectodermal tumor, 5 synovial sarcomas, and 27 Wilms' tumors. Results Molecular assays showed that 54 CCSKs harbored a BCOR-ITD, 1 case expressed a YWHAE-NUTM2 fusion transcript while none expressed the BCOR-CCNB3 fusion. The remaining 13 CCSKs were designated “triple-negative” based on the molecular findings. CCND1 showed positive immunoreactivity across all subgroups. TLE1 was positive in 94% of cases, including 1 YWHAE-NUTM2 fusion-positive case. Three BCOR-ITD-positive tumors were TLE1-negative. BCOR immunostaining was most variable among subgroups, with triple-negative tumors showing the weakest staining. In all, 10/68 (15%) tumors did not stain for BCOR, of which 4 were triple-negative (4/13 = 31%) and 6 were BCOR-ITD-positive (6/54 = 11%). The single YWHAE-NUTM2-positive tumor showed strong staining for all 3 markers. No single case was negative for all 3 stains; however, 3 cases showed no reactivity for either BCOR or TLE1 of which 1 was triple-negative and 2 BCOR-ITD-positive. Conclusion Having completed the first comprehensive evaluation of immunostaining of 68 fully genotyped CCSK tumors, we show herein that there is a rationale for the use of a small panel of antibodies to assist in the diagnosis of CCSK regardless of genotype, and we demonstrate that in combination CCND1, TLE1, and BCOR are compelling markers in aiding CCSK diagnosis.

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