scholarly journals Ultrasensitive gene fusion detection reveals fusion variant associated tumor heterogeneity

2020 ◽  
Author(s):  
Baifeng Zhang ◽  
Zhengbo Song ◽  
Chloe Yufan Bao ◽  
Chunwei Xu ◽  
Wenxian Wang ◽  
...  
Keyword(s):  
Tumor Heterogeneity ◽  
Intratumor Heterogeneity ◽  
Cryptic Splice Site ◽  
Functional Prediction ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Novel Method ◽  
Sensitivity Specificity ◽  
Fusion Detection ◽  
Formalin Fixed

Abstract Gene fusions are common drivers and therapeutic targets in cancers, but clinical-grade bioinformatics callers are lacking. Here we introduce a novel method SplitFusion, which is fast by leveraging BWA-MEM split alignments, can detect cryptic splice site fusions, and can infer frame-ness and exon-boundary alignments for functional prediction and minimizing false-positives. SplitFusion demonstrates superior sensitivity, specificity, accuracy and consumes minimal computing resources. In our study of 1,076 formalin-fixed paraffin-embedded lung cancer samples, SplitFusion detected not only common fusions (EML4 4.7%, ROS1 2.0% and RET 1.1%) with various partners, but also rare (KLC1-ALK, CD74-NRG1, and TPR-NTRK1) and novel (FGFR3-JAKMP1, CLIP2-BRAF, and ITPR2-ETV6) fusions. In 35 glioblastoma samples, SplitFusion-Target detected six (17%) EGFR vIII (exons 2-7 deletion) cases. Furthermore, we find that the EML4-ALK variant 3 is significantly associated with occurrence of multiple breakpoint-defined subclones, namely high intratumor heterogeneity. In conclusion, SplitFusion is well-suited for clinical use and for studying fusion-defined tumor heterogeneity.

KRAS mutation analysis in genomic DNA isolated from formalin-fixed paraffin-embedded ovarian tissue: evaluation of a strip-based reverse-hybridisation assay

2011 ◽  
Vol 64 (3) ◽  
pp. 252-256 ◽  
Author(s):  
Gernot Kriegshäuser ◽  
Veronika Auner ◽  
Eva Schuster ◽  
Barbara Holzer ◽  
Christian Oberkanins ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Ovarian Tissue ◽  
Analytical Sensitivity ◽  
Tissue Samples ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
Sensitivity Specificity ◽  
Formalin Fixed ◽  
Reverse Hybridisation Assay

AimsTo evaluate a reverse-hybridisation assay (strip assay) designed for the sensitive detection of 10 mutations in codons 12 and 13 of the KRAS gene. The strip assay relies on mutant-enriched PCR followed by reverse-hybridisation of biotinylated amplification products to oligonucleotide probes immobilised as an array of parallel lines on nitrocellulose test strips.MethodsThe strip assay was used to analyse genomic DNA isolated from 120 formalin-fixed paraffin-embedded (FFPE) ovarian tissue samples. The samples were analysed in parallel using a biochip-based protocol (biochip assay) covering the same mutation spectrum, and results were compared with respect to sensitivity, specificity and operational input.ResultsThe strip assay identified 19 (16%) of 120 FFPE samples to carry a KRAS mutation; results were in agreement with those obtained by biochip hybridisation. Both assays had an analytical sensitivity of 1% when performed on FFPE-extracted DNA with approximately the same operational input needed for post-PCR processing. In contrast to the biochip assay, strip assay hybridisation may be automated to a large extent.ConclusionsThe strip assay is an accurate and sensitive tool for the low to medium throughput detection of KRAS mutation in genomic DNA isolated from FFPE tissue.

Immunohistochemistry of CA 125

1998 ◽  
Vol 13 (4) ◽  
pp. 210-215 ◽  
Author(s):  
M. Nap
Keyword(s):  
Unknown Origin ◽  
Daily Practice ◽  
Metastatic Carcinoma ◽  
Ca 125 ◽  
Gynecological Tumors ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Number Of Publications ◽  
Sensitivity Specificity ◽  
Formalin Fixed

CA 125 is known as the marker that is most strongly associated with epithelial gynecological tumors. Compared to the number of publications on its use in serum assays, the application in immunohistochemistry is still limited. The availability of many good antibodies that perform well in formalin-fixed paraffin-embedded tissue opens good possibilities for a wider use. Outside the gynecological tract several other structures may react positive for CA 125. Among these are the lung and breast but also the epithelial cells of the conjunctiva and to some extent prostate glandular epithelium. In the fetus reactions can be found in the serosal linings of body cavities but also in the esophagus and skin. In diagnostic pathology CA 125 plays a role in identifying the primary locations of metastatic carcinoma of unknown origin. It is recommended to use CA 125 antibodies not in a solitary setting but in combination with CEA, BRST-2 and Vimentin to discriminate best between the most frequent sites of origin of metastatic carcinoma. Regular analysis of sensitivity/specificity ratios in a balanced population, representing the composition of the patient population seen in daily practice, should be performed to evaluate the position of CA 125 in diagnostic immunohistochemistry.

scholarly journals Mutant Allele Frequency-Based Intra-Tumoral Genetic Heterogeneity Related to the Tumor Shrinkage Mode After Neoadjuvant Chemotherapy in Breast Cancer Patients

2021 ◽  
Vol 8 ◽  
Author(s):  
Chun-hui Zheng ◽  
Zhao-yun Liu ◽  
Chen-xi Yuan ◽  
Xiao-yun Dong ◽  
Hai-mei Li ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Neoadjuvant Chemotherapy ◽  
Mutant Allele ◽  
Tumor Heterogeneity ◽  
Tumor Tissue ◽  
Area Under The Curve ◽  
Formalin Fixed Paraffin ◽  
Before And After ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

The shrinkage mode of tumor extent after neoadjuvant chemotherapy (NAC) is an important index to evaluate the odds of breast-conserving surgery. However, there is no sufficient measurement to predict the shrinkage mode after NAC. In this study, we analyzed 24 patients' formalin-fixed, paraffin-embedded samples before and after treatment and analyzed 456 cancer-related genes panel by using target next-generation sequencing. Meanwhile, the pathological shrinkage mode was reconstructed in three dimensions after surgery, and the genetic heterogeneity level was estimated by mutant-allele tumor heterogeneity (MATH). We measured the genetic intra-tumor heterogeneity and explored its correlation with the shrinkage mode after NAC. A total of 17 matched pair samples of primary tumor tissue and residual tumor tissue were successfully accessed. It was found that the most common mutated genes were TP53 and PIK3CA in both samples before and after NAC, and no recurrent mutations were significantly associated with the shrinkage mode. Besides, the MATH value of formalin-fixed, paraffin-embedded samples before and after NAC was analyzed by the area under the curve of the receiver operating characteristic, and it is feasible to classify patients into concentric shrinkage mode and non-concentric shrinkage mode in NAC based on the MATH threshold of 58. Our findings indicate that the MATH value was associated with the shrinkage mode of breast cancer in a non-linear model. Patients with the MATH value below the threshold of 58 before and after NAC displayed a concentric shrinkage mode. The area under the curve was 0.89, with a sensitivity of 0.69 and specificity of 1. Our study might provide a promising application of intra-tumor heterogeneity that is measured by MATH to make a choice of surgery.

scholarly journals A novel method for analyzing formalin-fixed paraffin embedded (FFPE) tissue sections by mass spectrometry imaging

2007 ◽  
Vol 83 (7) ◽  
pp. 205-214 ◽  
Author(s):  
Yutaka AOKI ◽  
Atsuhiko TOYAMA ◽  
Takashi SHIMADA ◽  
Tetsuyoshi SUGITA ◽  
Chikage AOKI ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Imaging ◽  
Ffpe Tissue ◽  
Tissue Sections ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Novel Method ◽  
Formalin Fixed
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