SCONCE2: jointly inferring single cell copy number profiles and tumor evolutionary distances.

Background: Single cell whole genome tumor sequencing can yield novel insights into the evolutionary history of somatic copy number alterations. Existing single cell copy number calling methods do not explicitly model the shared evolutionary process of multiple cells, and generally analyze cells independently. Additionally, existing methods for estimating tumor cell phylogenies using copy number profiles are sensitive to profile estimation errors.

SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing.

Motivation: Copy number alterations (CNAs) are a significant driver in cancer growth and development, but remain poorly characterized on the single cell level. Although genome evolution in cancer cells is Markovian through evolutionary time, CNAs are not Markovian along the genome. However, existing methods call copy number profiles with Hidden Markov Models or change point detection algorithms based on changes in observed read depth, corrected by genome content and do not account for the stochastic evolutionary process.

Chronic Cough With Non-Resolving Mass-like Consolidation.

A 72-year-old Chinese man presented with a 5-month history of chronic dry cough, weight loss, and progressive dyspnea. There was no associated hemoptysis, hoarseness, epistaxis, or fever on systemic review. He was a nonsmoker and had no family history of malignancy.

Haploinsufficiency networks identify targetable patterns of allelic deficiency in low mutation ovarian cancer.

Identification of specific oncogenic gene changes has enabled the modern generation of targeted cancer therapeutics. In high-grade serous ovarian cancer (OV), the bulk of genetic changes is not somatic point mutations, but rather somatic copy-number alterations (SCNAs). The impact of SCNAs on tumour biology remains poorly understood.

Does this patient really have chronic obstructive pulmonary disease?

Chronic obstructive pulmonary disease (COPD) is a condition commonly encountered by primary care practitioners. The disease should be detected in its early stages to prevent disease progression and to reduce the burden of symptoms. Early treatment also results in improved mortality and reduced morbidity.