PanDrugs: a novel method to prioritize anticancer drug treatments according to individual genomic data

Precision oncology for gallbladder cancer: insights from genetic alterations and clinical practice

Background

Gallbladder cancer (GBC) is an uncommon but highly fatal malignancy, with limited adjuvant therapy. The present study aims to explore the actionable alterations and precision oncology for GBC patients.

Methods

Patients with pathologically confirmed GBC who progressed after first-line systemic treatment were enrolled. Genomic alterations were captured by ultra-deep targeted next-generation sequencing (tNGS). The actionabilities of alterations and the therapeutic regimens were evaluated by a multidisciplinary tumor board (MDTB).

Results

Sixty patients with GBC were enrolled and analyzed. tNGS was successfully achieved in all patients. The median tumor mutation burden for GBC patients was 5.4 (range: 0.8-36.74) mutations/Mb, and the most common mutations were in TP53 (73%), CDKN2A (25%) and PIK3CA (20%). The most frequently copy-number altered genes were CDKN2A deletion (11.7%) and ERBB2 amplification (13.3%). 23% of the patients displayed gene fusion; 17 fusion events were identified, and 14 of the 17 fusion events co-occurred with mutations in driver genes. In total, 46 of the 60 (76%) patients were identified as possessing at least one actionable target to proceed precision oncology.

Conclusions

The present study revealed the mutational profile for the clinical practice of precision oncology in GBC patients.

Cancer Informatics in 2018: The Mysteries of the Cancer Genome Continue to Unravel, Deep Learning Approaches the Clinic, and Passive Data Collection Demonstrates Utility

Objective : To summarize significant research contributions on cancer informatics published in 2018.

Methods : An extensive search using PubMed/Medline, Google Scholar, and manual review was conducted to identify the scientific contributions published in 2018 that address topics in cancer informatics. The selection process comprised three steps: (i) 15 candidate best papers were first selected by the two section editors, (ii) external reviewers from internationally renowned research teams reviewed each candidate best paper, and (iii) the final selection of four best papers was conducted by the editorial board of the International Medical Informatics Association (IMIA) Yearbook.

Results : The four selected best papers present studies addressing many facets of cancer informatics, with immediate applicability in the translational and clinical domains.

Conclusion : Cancer informatics is a broad and vigorous subfield of biomedical informatics. Progress in cancer genomics, artificial intelligence, and passively collected data is especially notable in 2018.

Alterations in DNA Damage Repair Genes in Primary Liver Cancer

PURPOSE

Alterations in DNA damage repair (DDR) genes produce therapeutic biomarkers. However, the characteristics and significance of DDR alterations remain undefined in primary liver cancer (PLC).

EXPERIMENTAL DESIGN

Patients diagnosed with PLC were enrolled in the trial (PTHBC, NCT02715089). Tumors and matched blood samples from participants were collected for a targeted next-generation sequencing assay containing exons of 450 cancer-related genes, including 31 DDR genes. The OncoKB knowledge database was used to identify and classify actionable alterations, and therapeutic regimens were determined after discussion by a multidisciplinary tumor board.

RESULTS

A total of 357 patients with PLC were enrolled, including 214 with hepatocellular carcinoma, 122 with ICC, and 21 with mixed hepatocellular-cholangiocarcinoma. A total of 92 (25.8%) patients had at least one DDR gene mutation, 15 of whom carried germline mutations. The most commonly altered DDR genes were ATM (5%) and BRCA1/2 (4.8%). The occurrence of DDR mutations was significantly correlated with a higher tumor mutation burden regardless of the PLC pathologic subtype. For DDR-mutated PLC, 26.1% (24/92) of patients possessed at least one actionable alteration, and the actionable frequency in DDR wild-type PLC was 18.9% (50/265). Eight patients with the BRCA mutation were treated by olaparib, and patients with BRCA2 germline truncation mutations showed an objective response.

CONCLUSIONS

The landscape of DDR mutations and their association with genetic and clinicopathologic features demonstrated that patients with PLC with altered DDR genes may be rational candidates for precision oncology treatment.

IPCT: Integrated Pharmacogenomic Platform of Human Cancer Cell Lines and Tissues

: (1) Motivation: The exponential increase in multilayered data, including omics, pathways, chemicals, and experimental models, requires innovative strategies to identify new linkages between drug response information and omics features. Despite the availability of databases such as the Cancer Cell Line Encyclopedia (CCLE), the Cancer Therapeutics Response Portal (CTRP), and The Cancer Genome Atlas (TCGA), it is still challenging for biologists to explore the relationship between drug response and underlying genomic features due to the heterogeneity of the data. In light of this, the Integrated Pharmacogenomic Database of Cancer Cell Lines and Tissues (IPCT) has been developed as a user-friendly way to identify new linkages between drug responses and genomic features, as these findings can lead not only to new biological discoveries but also to new clinical trials. (2) Results: The IPCT allows biologists to compare the genomic features of sensitive cell lines or small molecules with the genomic features of tumor tissues by integrating the CTRP and CCLE databases with the REACTOME, cBioPortal, and Expression Atlas databases. The input consists of a list of small molecules, cell lines, or genes, and the output is a graph containing data entities connected with the queried input. Users can apply filters to the databases, pathways, and genes as well as select computed sensitivity values and mutation frequency scores to generate a relevant graph. Different objects are differentiated based on the background color of the nodes. Moreover, when multiple small molecules, cell lines, or genes are input, users can see their shared connections to explore the data entities common between them. Finally, users can view the resulting graphs in the online interface or download them in multiple image or graph formats. (3) Availability and Implementation: The IPCT is available as a web application with an integrated MySQL database. The web application was developed using Java and deployed on the Tomcat server. The user interface was developed using HTML5, JQuery v.3.1.0 , and the Cytoscape Graph API v.1.0.4. The IPCT can be accessed at http://ipct.ewostech.net. The source code is available at https://github.com/muhammadshoaib/ipct.

Atrial Structural Remodeling Gene Variants in Patients with Atrial Fibrillation

Atrial fibrillation (AF) is a common arrhythmia for which the genetic studies mainly focused on the genes involved in electrical remodeling, rather than left atrial muscle remodeling. To identify rare variants involved in atrial myopathy using mutational screening, a high-throughput next-generation sequencing (NGS) workflow was developed based on a custom AmpliSeq™ panel of 55 genes potentially involved in atrial myopathy. This workflow was applied to a cohort of 94 patients with AF, 76 with atrial dilatation and 18 without. Bioinformatic analyses used NextGENe® software and in silico tools for variant interpretation. The AmpliSeq custom-made panel efficiently explored 96.58% of the targeted sequences. Based on in silico analysis, 11 potentially pathogenic missense variants were identified that were not previously associated with AF. These variants were located in genes involved in atrial tissue structural remodeling. Three patients were also carriers of potential variants in prevalent arrhythmia-causing genes, usually associated with AF. Most of the variants were found in patients with atrial dilatation (n=9, 82%). This NGS approach was a sensitive and specific method that identified 11 potentially pathogenic variants, which are likely to play roles in the predisposition to left atrial myopathy. Functional studies are needed to confirm their pathogenicity.