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Cancer PHGKB

Specific PHGKB|Cancer|PHGKB
Last Posted: Aug 10, 2022
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Interactive exploration of a global clinical network from a large breast cancer cohort
N Sella et al, NPJ Diital Medicine, August 10, 2022

Despite unprecedented amount of information now available in medical records, health data remain underexploited due to their heterogeneity and complexity. Simple charts and hypothesis-driven statistics can no longer apprehend the content of information-rich clinical data. There is, therefore, a clear need for powerful interactive visualization tools enabling medical practitioners to perceive the patterns and insights gained by state-of-the-art machine learning algorithms. Here, we report an interactive graphical interface for use as the front end of a machine learning causal inference server (MIIC), to facilitate the visualization and comprehension by clinicians of relationships between clinically relevant variables.

Finding Ways to Improve Patients’ Cancer Immunotherapy Response
HD Larkin, JAMA, August 9, 2022

An investigational tool using whole-exome sequencing (WES) more accurately identified genes and pathways that predict whether patients with cancer will respond to immune checkpoint blockade (ICB) than current tumor mutation burden (TMB) tests alone, a new research study reported. TMB is often used to determine ICB eligibility and is generally calculated from a few hundred genes. The researchers sought to improve its performance by broadening analysis to the nearly 20?000 genes consistently captured by WES.

cfDNA methylome profiling for detection and subtyping of small cell lung cancers.
Chemi Francesca et al. Nature cancer 2022 8

We describe a robust workflow for genome-wide DNA methylation profiling applied to both patient-derived models and to patients' circulating cell-free DNA (cfDNA). Tumor-specific methylation patterns were readily detected in cfDNA samples from patients with SCLC and were correlated with survival outcomes. cfDNA methylation also discriminated between the transcription factor SCLC subtypes, a precedent for a liquid biopsy cfDNA-methylation approach to molecularly subtype SCLC. Our data reveal the potential clinical utility of cfDNA methylation profiling as a universally applicable liquid biopsy approach for the sensitive detection, monitoring and molecular subtyping of patients with SCLC.

Circulating tumour DNA - looking beyond the blood.
Tivey Ann et al. Nature reviews. Clinical oncology 2022 8

To date, the majority of research in the area of liquid biopsies has focused on blood-based biomarkers, predominantly using plasma-derived circulating tumour DNA (ctDNA). However, ctDNA can also be obtained from various non-blood sources and these might offer unique advantages over plasma ctDNA. In this Review, we discuss advances in the analysis of ctDNA from non-blood sources, focusing on urine, cerebrospinal fluid, and pleural or peritoneal fluid, but also consider other sources of ctDNA.

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