Abstract

   In recent years, lots of studies have reported the relationship between
   genetic variation or expression and cancer prognosis with
   radiotherapy-based treatment. However, due to limitation in available
   journals or literature database, inconsistent nomenclature system of
   genetic variation and cancer and time-consuming investigation on
   literature searching and reading, considerable researches could hardly
   get found and cited. In this study, we constructed the Radiotherapy
   Prognosis Database (RTPDB), which contains a comprehensive resource
   about genes and related cancer prognosis. It included 775 studies,
   which consist of 275 Single Nucleotide Polymorphism (SNP) studies with
   59 765 patients, 261 genes, 708 SNPs, 16 tumors and 16 treatment types,
   and 500 expression studies with 55 751 patients, 264 genes, 27 tumors
   and 15 treatment types. The names of genes and their variants were
   converted and displayed in the form of the official symbol. The
   detailed information of the tumor, treatment and prognosis were
   classified. We hope RTPDB will be a useful resource with great
   potential for researches on genes, variants and cancer prognosis.

Introduction

   Radiotherapy is a common treatment for cancer today, alone or in
   combination with other treatments. According to the American Society of
   Radiation Oncology, >60% of cancer patients will receive
   radiotherapy—radiotherapy using high-energy radiation to shrink tumors
   and kill cancer cells—contributing to 40% of curative treatment for
   cancer ([38]1). When the DNA of a cancer cell is damaged by radiation,
   it will stop dividing or it will die, and then it will be eliminated by
   the immune system. As surgery will inevitably remove normal tissues,
   chemotherapy has its drawbacks in unavoidably killing normal cells.
   Radiotherapy not only kills cancer cells but also affects normal cells
   around the cancer cells, and further leads to side effects. Based on
   the time of occurrence, it can be divided into acute and late side
   effects. Various cancer patients have different sensitivity to
   radiotherapy. In general, high sensitivity to radiotherapy and mild
   side effects are important for long-term survival ([39]2).

   Analogous to pharmacogenomics, the term radiogenomics is used to
   explain the differences in radiotherapy response between individuals.
   In 2009, a Radiogenomics Consortium was established to facilitate and
   promote multi-center collaboration of researchers linking genetic
   variation with response to radiotherapy ([40]3). It might lead to
   improved decision making, and as a result, improved patient outcomes
   ([41]4). During the past years, thousands of researches have studied
   the relationship between genetic variation or expression and patient
   prognosis who received radiotherapy-based treatment. Most of them focus
   on genes which take part in cell growth, differentiation,
   proliferation, and apoptosis, such as XRCC1 ([42]5) and TP53 ([43]6).
   Unlike pharmacogenomics, radiogenomics studies now lack a database
   similar to PharmGKB, which is responsible for the aggregation,
   curation, integration and dissemination of knowledge regarding the
   impact of human genetic variation on drug response ([44]7). Due to the
   relatively small number of radiogenomic studies compared to the
   pharmacogenomics and the dispersion of the literature, the advances in
   radiogenomics have been hindered. Most of the researches could hardly
   get found and cited. Therefore, a high-quality resource platform with
   unlimited use, standard nomenclature and convenient searching process
   is believed to be of great value in the understanding of gene variants
   or expression and cancer prognosis under radiotherapy.

   In this paper, we describe the Radiotherapy Prognosis Database (RTPDB),
   a comprehensive online database established to collect the associations
   between genetic variants or expression and cancer prognosis of patients
   who received radiotherapy-based treatment and were documented in
   biomedical literature. It is the first database for genes and related
   cancer radiotherapy prognosis. The database offers exciting
   opportunities for scientists and clinicians to better explore the
   overview of the relationship between genes and related cancer
   radiotherapy prognosis. In addition, it will be helpful for researchers
   to understand the mechanism of cancer prognosis with radiation
   treatment. The RTPDB can be publicly accessed from
   [45]http://www.rtpdb.com/.

Materials and methods

Software design and implementation

   In RTPDB database, all data sets were organized in our web server using
   the client–server model based on Python, Django, JavaScript and
   PostgreSQL. The database is available at [46]http://www.rtpdb.com/.
   RTPDB contains pages for searching, browsing and downloading.

Literature searching and inclusion

   In addition to the common database such as China Knowledge
   Infrastructure, PubMed, Web of Science, EMBASE and Google Scholar, we
   also conducted a detailed manual review for the references of the