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bioRxiv · 10.1101/148718

A plausible explanation for in silico reporting of erroneous MET gene expression in tumor-educated platelets (TEP) intended for "liquid biopsy" of non-small cell lung carcinoma still refutes the TEP-study

Chakraborty, S.
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Abstract

Final amendment noteThis paper had proposed a plausible way for detecting large quantities of MET, which the authors have clarified was not done :the possible explanation proposed for this erroneous MET gene expression does bypass the filtering step we perform in the data processing pipeline, i.e. selection of intron-spanning reads, as can be read in the main text\" comments in http://www.biorxiv.org/content/early/2017/07/02/146134, where a continuing critique of the TEP study continues. Please consider this pre-print closed.\n\nOriginal abstractThe reported over-expression of MET genes in non-small cell lung carcinoma (NSCLC) from an analysis of the RNA-seq data from tumor-educated platelets (TEP), intended to supplement existing liquid biopsy techniques [1], has been refuted recently (http://biorxiv.org/content/early/2017/06/05/146134, not peer-reviewed). The MET proto-oncogene (Accid:NG 008996.1, RefSeqGene LRG 662 on chromosome 7, METwithintrons) encodes 21 exons resulting in a 6710 bps MET gene (Accid: NM 001127500.2, METonlyexons). METwithintrons has multiple matches in the RNA-seq derived reads of lung cancer samples (for example: SRR1982756.11853382). Unfortunately, these are non-specific sequences in the intronic regions, matching to multiple genes on different chromosomes with 100% identity (KIF6 on chr6, COL6A6 on chr3, MYO16 on chr13, etc. for SRR1982756.11853382). In contrast, METonlyexons has few matches in the reads, if at all [2]. However, even RNA-seq from healthy donors have similar matches for METwithintrons so the computation behind the over-expression statistic remains obscure, even if METwithintrons was used as the search gene. In summary, this work re-iterates the lack of reproducibility in the bioinformatic analysis that establishes TEP as a possible source for \"liquid biopsy\".

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Chakraborty, S.. 2017-06-11. A plausible explanation for in silico reporting of erroneous MET gene expression in tumor-educated platelets (TEP) intended for "liquid biopsy" of non-small cell lung carcinoma still refutes the TEP-study. https://doi.org/10.1101/148718

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