Gene Fusion Identification Using Anchor-Based Multiplex PCR and Next-Generation Sequencing

Cheng, Yu‐Wei; Meyer, Anders R.L.; Jakubowski, Maureen A.; Keenan, Sean; Brock, Jay E; Azzato, Elizabeth M.; Weindel, Michael; Farkas, Daniel H.; Rubin, Brian P.

doi:10.1093/jalm/jfaa230

Cited by 17 publications

(16 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Details of the Solid Tumor NGS fusion panel have been previously published 6–8 . Briefly, 5–10 unstained slides and one H&E‐stained slide from neutral buffered formalin‐fixed paraffin‐embedded tissue sectioned at 4 μm were obtained from each specimen.…”

Section: Methodsmentioning

confidence: 99%

“…N G S Details of the Solid Tumor NGS fusion panel have been previously published. [6][7][8] Briefly, 5-10 unstained slides and one H&E-stained slide from neutral buffered formalin-fixed paraffin-embedded tissue sectioned at 4 lm were obtained from each specimen. cDNA libraries were made by the use of an anchored multiplex polymerase chain reaction (Archer FusionPlex standard protocol and reagents; Archer DX, Boulder, CO, USA) and custom-designed gene-specific primer pools, targeting the 59 genes included in this panel that are involved in bone and soft tissue (BST) tumours.…”

Section: P a T I E N T C O H O R T A N D D A T A C O L L E C T I O Nmentioning

confidence: 99%

See 1 more Smart Citation

PRRX1–NCOA1‐rearranged fibroblastic tumour: a clinicopathological, immunohistochemical and molecular genetic study of six cases of a potentially under‐recognised, distinctive mesenchymal tumour

et al. 2021

Self Cite

View full text Add to dashboard Cite

Aims PRRX1–NCOA1‐rearranged fibroblastic tumour is a recently described, rare mesenchymal tumour. Only four cases have been previously reported. The aim of this article is to report six additional cases of this unusual mesenchymal neoplasm, with an emphasis on its differential diagnosis. Methods and results The six cases were from three females and three males (age, 20–49 years; median, 42 years). Three tumours were located on the abdominal wall; two from the shoulder/axillary areas, and one on the lateral hip. All presented as slow‐growing subcutaneous nodules, ranging from 26 to 55 mm (median, 40 mm). The tumours consisted of circumscribed, variably cellular nodules composed of relatively bland plump spindled to epithelioid cells arranged singly, in cords, and occasionally in nests, embedded in hyalinised and collagenous stroma. Small hypocellular myxoid zones with ropey collagen fibres were present, as were irregularly dilated, gaping, crescent‐shaped or staghorn‐like thin‐walled vessels, best appreciated at the periphery. Immunohistochemistry for CD34, S100, MUC4 and STAT6 was consistently negative. RNA‐sequencing revealed PRRX1–NCOA1 fusions in all cases. Of the four cases with limited follow‐up (1.5–4 months), none recurred following local surgical excision. Conclusions The morphological features of PRRX1–NCOA1‐rearranged fibroblastic tumour overlap with those of RB1‐deficient soft‐tissue tumours, solitary fibrous tumour, and low‐grade fibromyxoid sarcoma/sclerosing epithelioid fibrosarcoma. This differential diagnosis can be resolved with a combination of careful morphological study and the application of a panel of immunostains, although molecular genetic study is most definitive. The natural history of PRRX1–NCOA1‐rearranged fibroblastic tumour appears to be quite favourable, although longer‐term study of a larger number of cases is warranted.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: P a T I E N T C O H O R T A N D D A T A C O L L E C T I O Nmentioning

confidence: 99%

PRRX1–NCOA1‐rearranged fibroblastic tumour: a clinicopathological, immunohistochemical and molecular genetic study of six cases of a potentially under‐recognised, distinctive mesenchymal tumour

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…Several previous studies on genetic mutation detection, including fusion genes in sarcoma, have been reported by NGS analysis using various genetic mutation detection panel kits. 13,17,[36][37][38][39] These studies have mainly reported data on fusion genes, genetic mutations, and gene amplification. Our current study obtained similar results for fusion genes.…”

Section: Discussionmentioning

confidence: 99%

Identification of fusion transcripts in sarcoma from archival formalin‐fixed paraffin‐embedded tissues: A next‐generation sequencing approach

Fujii

Takeda

Uchiyama

et al. 2022

Pathology International

View full text Add to dashboard Cite

Most sarcomas are highly aggressive, and cause necrosis and hemorrhage. The diagnosis of sarcoma is challenging because of the lack of specificity of immunohistochemical staining; however, molecular biological approaches, such as genetic mutation, chromosomal translocation, and gene amplification, are promising. In this study, we extracted RNA from formalin‐fixed paraffin‐embedded (FFPE) tissue derived from surgically resected specimens of sarcoma stored for various periods and performed next‐generation sequencing (NGS) analysis by MiniSeq using the Archer Fusion‐Plex Sarcoma Panel. RNA was extracted from 63 FFPE tissue samples, and the degree of RNA degradation was assessed. The number of reads and fragment lengths were evaluated by NGS analysis. RNA extraction and cDNA synthesis were successful in 56 cases and library preparation was possible. Fusion genes were detected in 16 of 63 archived FFPE tissue samples in this study. However, in 18 cases, fragmentation was strong, and high‐quality libraries could not be obtained. Nevertheless, comprehensive analysis of fusion genes with high sequence specificity by NGS can be a powerful alternative to reverse transcription‐polymerase chain reaction and fluorescence in situ hybridization methods.

show abstract

“…Details of the solid tumour NGS fusion panel were previously published 13 . Briefly, five to 10 unstained slides and one haematoxylin and eosin (H&E)‐stained slide from neutral buffered formalin‐fixed paraffin‐embedded (FFPE) tissue sectioned at 4 μm were obtained from each specimen.…”

Section: Methodsmentioning

confidence: 99%

“…Details of the solid tumour NGS fusion panel were previously published. 13 Briefly, five to 10 unstained slides and one haematoxylin and eosin (H&E)-stained slide from neutral buffered formalin-fixed paraffinembedded (FFPE) tissue sectioned at 4 lm were obtained from each specimen. Slides were macrodissected and total nucleic acid (TNA) was extracted using the Maxwell â RSC RNA FFPE Kit (Promega, Madison, WI, USA, cat.…”

Section: M M U N O H I S T O C H E M I C a L S T A I N I N Gmentioning

confidence: 99%

YAP1–TFE3 gene fusion variant in clear cell stromal tumour of lung: report of two cases in support of a distinct entity

et al. 2021

View full text Add to dashboard Cite

YAP1-TFE3 gene fusion variant in clear cell stromal tumour of lung: report of two cases in support of a distinct entity Aims: Clear cell (haemangioblastoma-like) stromal tumour of the lung is a newly described, rare pulmonary neoplasm. Recurrent YAP1-TFE3 gene fusions have recently been reported in three cases. We describe two additional cases and confirm the characteristic YAP1-TFE3 gene fusion. Methods and results: Two mesenchymal tumours of lung were identified from our soft tissue pathology consultation services and RNA sequencing was performed. Both cases were in male patients, aged 35 and 77 years. Both presented as solitary lung nodules measuring 3.9 and 7.5 cm in greatest dimension. Histopathologically, the tumours were composed of epithelioid to plump spindle cells arranged in packets and solid sheets. The cells showed fusiform to ovoid nuclei with open chromatin, variably prominent nucleoli and scant to moderate, clear to eosinophilic cytoplasm. Cytological atypia and significant mitotic activity were minimal. None of the tumours expressed lineage-specific immunophenotypical markers. Both cases were diffusely positive for nuclear TFE3. Unlike YAP1-TFE3-fused epithelioid haemangioendothelioma, for which the fusion breakpoint occurs in YAP1 exon 1 and TFE3 exons 4 or 6, the fusion breakpoints of these tumours were located in YAP1 exon 4 and TFE3 exon 7. Following complete surgical resection, neither of the tumours has recurred or metastasised (follow-up period 6-7 months). Conclusions: We validate the presence of YAP1-TFE3 gene fusion in a unique primary mesenchymal tumour of lung, adding additional support for clear cell stromal tumour of the lung as a distinct entity.

show abstract

Gene Fusion Identification Using Anchor-Based Multiplex PCR and Next-Generation Sequencing

Cited by 17 publications

References 27 publications

PRRX1–NCOA1‐rearranged fibroblastic tumour: a clinicopathological, immunohistochemical and molecular genetic study of six cases of a potentially under‐recognised, distinctive mesenchymal tumour

PRRX1–NCOA1‐rearranged fibroblastic tumour: a clinicopathological, immunohistochemical and molecular genetic study of six cases of a potentially under‐recognised, distinctive mesenchymal tumour

Identification of fusion transcripts in sarcoma from archival formalin‐fixed paraffin‐embedded tissues: A next‐generation sequencing approach

YAP1–TFE3 gene fusion variant in clear cell stromal tumour of lung: report of two cases in support of a distinct entity

Contact Info

Product

Resources

About