How many reads were used to detect MET exon skipping?

the reads containing a jump of 4,429 bp from chr7:116398664, 3,226 bp from chr7:116411700, and 1,3666 bp from chr7:116422042 were counted to identify the candidate MET exon 10, 14, and 19 skipping events, respectively.

What was the default parameter used to detect gene fusion in RNA-seq data?

STAR-Fusion v1.2.0 (https://www.biorxiv.org/content/10.1101/120295v1) was used to detect gene fusion in RNA-seq data, with default parameters.(which was not certified by peer review) is the author/funder.

What is the MET alterations in sGBM?

(F) The comparison of frequencies of malignant cells form sGBM with or without ZM fusion in 4 clusters of single-cell transcriptional analysis.

How was the sensitivity of the PDCs determined?

10 μl of CCK-8 reagent was added to each well, and sample optical density at 450 nm and 630 nm was determined after 2 h incubation and 37°C in a humidified atmosphere of 5% CO2.

Who is the author/funder of this preprint?

(G) The proliferation rate of patient derived cells with or without MET alterations.(which was not certified by peer review) is the author/funder.

What primers were used to detect MET exon skipping?

The following primers were used to detect exon 14 skipping: forward: 5′-AATCTTTTATTAGTGGTGGGAGCACAAT-3′; and reverse: 5′-GAATTAGGAAACTGATCTTTAATTTGC-3′.

What was the p-value of the MET gene?

Differentially expressed genes were selected based on fold change and adjusted p-value, which was calculated by using DESeq2 [26].

What primers were used to detect MET exon 19 skipping?

The following primers were used to detect MET exon 19 skipping: forward: 5′-GATCAGTTTCCTAATTCATCTCAGAAC-3′; reverse: 5′- GCCAAAGGACCAATACAGTTTCTT-3′.

How was the sensitivity of the PDCs evaluated?

Cell drug sensitivity was evaluated by using the CCK-8 kit (Dojindo Laboratories, Kumamoto, Japan) according to the manufacturer’s protocol.

What is the enriched cancer hallmarks and KEGG pathways for applying the gene set?

(C) The most enriched cancer hallmarks and KEGG pathways for applying the gene set enrichment analysis (GSEA) in pLGG cases with MET alterations versus that without MET alterations.

What was the smrt function used to normalize the cell counts?

The matrix was then normalized such that the number of UMIs in each cell was equal to the median UMI count across the dataset and log-transformed.

What was the NES for the gene sets that were downloaded from MSigDB?

Normalized enrichment scores (NES) were calculated for gene sets that were downloaded from MSigDB database version 6.1(which was not certified by peer review) is the author/funder.

What is the MET status of sGBM?

(D) The most enriched cancer hallmarks and KEGG pathways for applying the gene set enrichment analysis (GSEA) in sGBM cases with MET alterations versus that without MET alterations.

Open AccessPosted Content10.1101/2020.11.02.364711

Extensive MET alterations confer clinical response to MET inhibitors in gliomas

Zheng Zhao, +22 more

- 03 Nov 2020

- bioRxiv

TL;DR: In vitro and clinical studies indicate cells and patients harboring MET alterations have better response to MET inhibitors, and data suggest that a subgroup of gliomas harboringMET alterations likely to have benefit from MET-targeted therapy.

Abstract: Activating alterations of the MET gene are well-characterized oncogenic drivers, and MET inhibitors could successfully treat several tumor types with MET alterations, including gliomas with PTPRZ1-MET fusion. However, the full diversity and prevalence of MET alterations in gliomas are still lacking to accurately identify a subset of patients likely to benefit from MET inhibitor treatment. Here, we interrogated genomic profiles of 1,351 gliomas, and further identify 60 cases harboring MET alterations, including MET fusions and various MET exon skipping events. MET RNA alterations, but not MET amplification, are highly enriched in the secondary glioblastomas (sGBM) with significantly worse prognosis. Further molecular analysis has shown that MET RNA alterations acting an additive effects of MET overexpression are induced in the course of glioma evolution. In vitro and clinical studies indicate cells and patients harboring MET alterations have better response to MET inhibitors. Collectively, these data suggest that a subgroup of gliomas harboring MET alterations likely to have benefit from MET-targeted therapy.

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Most frequently asked questions

1. What was used to amplify a 626-bp fragment?

In all reactions, DNA polymerase (GoTaq, Promega) was used to amplify a 626-bp fragment, with 30 cycles of 94°C, 30 s; 58°C, 30 s; 72°C, 60s; and a final extension at 72°C for 10 min.

2. What was used to identify somatic mutations?

SAVI2 was used to identify somatic mutations (including single-nucleotide variations and short insertion/deletions), as previously described [23, 24].

3. What was the coding function used to screen differentially expressed genes?

The differentially expressed genes between clusters were screened using the FindMarkers function and a comprehensive biological functional annotation of the gene list was performed in Metascape (https://metascape.org/).

4. How long did the sections remain in the buffer?

After incubation with ethanol containing 3% hydrogen peroxide for 10 min and washing with PBS buffer, the sections were incubated with the secondary antibodies (1:100, ZSGB-Bio, Beijing, China) at 25°C for 1 h.

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- 27 May 2022

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References

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David N. Louis, +9 more

- 09 May 2016

- Acta Neuropathologica

TL;DR: The 2016 World Health Organization Classification of Tumors of the Central Nervous System is both a conceptual and practical advance over its 2007 predecessor and is hoped that it will facilitate clinical, experimental and epidemiological studies that will lead to improvements in the lives of patients with brain tumors.

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- PLOS Computational Biology

TL;DR: A method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome, successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes.

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Extensive MET alterations confer clinical response to MET inhibitors in gliomas

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AI Agents for this Paper

Most frequently asked questions

1. What was used to amplify a 626-bp fragment?

2. What was used to identify somatic mutations?

3. What was the coding function used to screen differentially expressed genes?

4. How long did the sections remain in the buffer?

5. How many reads were used to detect MET exon skipping?

6. What was the default parameter used to detect gene fusion in RNA-seq data?

7. What is the MET alterations in sGBM?

8. How was the sensitivity of the PDCs determined?

9. Who is the author/funder of this preprint?

10. What primers were used to detect MET exon skipping?

11. What was the p-value of the MET gene?

12. What primers were used to detect MET exon 19 skipping?

13. How was the sensitivity of the PDCs evaluated?

14. What is the enriched cancer hallmarks and KEGG pathways for applying the gene set?

15. What was the smrt function used to normalize the cell counts?

16. What was the NES for the gene sets that were downloaded from MSigDB?

17. What is the MET status of sGBM?

Citations

Fusion genes as diagnostic and predictive biomarkers for tumor

References

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

The Sequence Alignment/Map format and SAMtools

Fast and accurate short read alignment with Burrows–Wheeler transform

The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary.

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

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