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Abstract

Objective: Information that is present in our DNA is transferred to RNA, which is in turn transcribed into proteins. This is a central principle of molecular biology. Over the years, there have been many attempts to document the thousands of places where transcribed RNA does not match the DNA template it was created from. This behavior is called RNA Editing, and is generally thought to be mainly an A->I change, that is, adenosine to inosine (read as guanine by DNA sequencers), with occasional cytosine to uracil changes as well. Cancer, with its volatility due to DNA base changes, gets more complex with the occurrences of RNA editing. To ensure a fair ground to study RNA editing, we have considered exome and RNASeq library pairs from the cancer-affected ovarian, lymph node and peritoneum tissues in three individual. This data set will help identify RNA editing locations in these tissues, and the role it plays in metastasis. Methods: The exome libraries were prepared using Illumina Paired End Sample Preparation kit and Agilent SureSelect Target Enrichment System kit. RNASeq libraries were prepared using Illumina paired-end protocol. Both the libraries were sequenced using the Illumina NextGen Sequencing platform. Exome libraries were aligned using bowtie2 and RNASeq using tophat2. SNPs were called using samtools. The RNAEditing database from Ensemble was used to filter out known editing sites. With the remaining editing locations, a blat was run against the surrounding sequence to check for similarity to other parts of the genome, to rule out editing sites being called as a result of incorrect alignment scoring. Results: From our preliminary analysis, we see that a majority of the RNA Editing positions represent A->I changes, with a few C->U changes as well. Some of these positional changes are seen across all tissues in an individual. There are few RNA edited sites that are mainly seen only in the metastatic locations, and not seen in the primary. Conclusions: By analyzing the initial results, we can identify the mutations and RNA edited sites that originate from the primary tumor tissue, and those that are acquired in the metastatic tissues.

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/content/papers/10.5339/qfarc.2014.HBPP0225
2014-11-18
2020-06-05
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http://instance.metastore.ingenta.com/content/papers/10.5339/qfarc.2014.HBPP0225
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