Concordance between single-nucleotide polymorphism-based genomic instability assays and a next-generation sequencing-based homologous recombination deficiency test.

Background: We evaluated the performance of single-nucleotide polymorphism (SNP) genotyping arrays OncoScan (Thermo Fisher Scientific, San Diego, CA) and Infinium CytoSNP-850K (CytoSNP; Illumina, Waltham, MA) for assessing homologous recombination deficiency (HRD) genomic instability.

Methods: DNA (pretreatment samples) across 20 tumor types was evaluated with OncoScan, CytoSNP, and the clinically validated HRD test. Copy number variation (CNV) and loss of heterozygosity (LOH) analyses were performed with ASCATv2.

Baseline and post-treatment biomarkers of resistance to anti-PD-1 therapy in acral and mucosal melanoma: an observational study.

Background: Immunotherapies targeting programmed cell death-1 (PD-1) and its ligands have improved clinical outcomes for advanced melanoma. However, many tumors exhibit primary resistance or acquire secondary resistance after an initial positive response. The mechanisms of resistance are not well understood, and no validated predictive biomarkers are available.

Immune Biomarkers in Metastatic Castration-resistant Prostate Cancer.

Background: Metastatic castration-resistant prostate cancer (mCRPC) is a heterogeneous disease in which molecular stratification is needed to improve clinical outcomes. The identification of predictive biomarkers can have a major impact on the care of these patients, but the availability of metastatic tissue samples for research in this setting is limited.

Objective: To study the prevalence of immune biomarkers of potential clinical utility to immunotherapy in mCRPC and to determine their association with overall survival (OS).

Tumor mutational burden predicts the efficacy of pembrolizumab monotherapy: a pan-tumor retrospective analysis of participants with advanced solid tumors.

Background: Several studies have evaluated the relationship between tumor mutational burden (TMB) and outcomes of immune checkpoint inhibitors. In the phase II KEYNOTE-158 study of pembrolizumab monotherapy for previously treated recurrent or metastatic cancer, high TMB as assessed by the FoundationOne CDx was associated with an improved objective response rate (ORR).

Methods: We retrospectively assessed the relationship between TMB and efficacy in participants with previously treated advanced solid tumors enrolled in 12 trials that evaluated pembrolizumab monotherapy, including 3 randomized trials that compared pembrolizumab with chemotherapy.

Temperature change and electricity consumption of the group living: A case study of college students.

The relationship between energy use and climate change is the center of analysis about mitigation and adaptation. Yet current studies of the electricity-climate relationship focus on developed countries. Little was known about the energy-use behavior in group living.

Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy.

Programmed cell death protein-1 (PD-1) and programmed cell death ligand-1 (PD-L1) checkpoint blockade immunotherapy elicits durable antitumor effects in multiple cancers, yet not all patients respond. We report the evaluation of >300 patient samples across 22 tumor types from four KEYNOTE clinical trials. Tumor mutational burden (TMB) and a T cell-inflamed gene expression profile (GEP) exhibited joint predictive utility in identifying responders and nonresponders to the PD-1 antibody pembrolizumab.

Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer.

Clinical studies support the efficacy of programmed cell death 1 (PD-1) targeted therapy in a subset of patients with metastatic gastric cancer (mGC). With the goal of identifying determinants of response, we performed molecular characterization of tissues and circulating tumor DNA (ctDNA) from 61 patients with mGC who were treated with pembrolizumab as salvage treatment in a prospective phase 2 clinical trial. In patients with microsatellite instability-high and Epstein-Barr virus-positive tumors, which are mutually exclusive, dramatic responses to pembrolizumab were observed (overall response rate (ORR) 85.

[The effects of different occluder selection on cardiac remodeling post transcatheter closure in patients with secundum atrial septal defect].

Objective: To evaluate the effects on cardiac remodeling post transcatheter closure by Amplatzer septal occluder selected by oval circumference formula in patients with atrial septal defect (ASD).

Methods: A total of 146 patients with ASD (68 males,mean 33.5 years) treated by transcatheter closure with the Amplatzer occluder were enrolled in this study.

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.

Recent transcriptome studies have revealed that a large number of transcripts in mammals and other organisms do not encode proteins but function as noncoding RNAs (ncRNAs) instead. As millions of transcripts are generated by large-scale cDNA and EST sequencing projects every year, there is a need for automatic methods to distinguish protein-coding RNAs from noncoding RNAs accurately and quickly. We developed a support vector machine-based classifier, named Coding Potential Calculator (CPC), to assess the protein-coding potential of a transcript based on six biologically meaningful sequence features.

Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP).

Motivation: The rapid accumulation of single amino acid polymorphisms (SAPs), also known as non-synonymous single nucleotide polymorphisms (nsSNPs), brings the opportunities and needs to understand and predict their disease association. Currently published attributes are limited, the detailed mechanisms governing the disease association of a SAP remain unclear and thus, further investigation of new attributes and improvement of the prediction are desired.

Results: A SAP dataset was compiled from the Swiss-Prot variant pages.