RNA Sequencing

Preexisting Somatic Mutations of Estrogen Receptor Alpha (ESR1) in Early-Stage Primary Breast Cancer

More than three-quarters of primary breast cancers are positive for estrogen receptor alpha (ER; encoded by the gene *ESR1*), the most important factor for directing anti-estrogenic endocrine therapy (ET). Recently, mutations in *ESR1* were …

PhD Project: RNA Sequencing-based Tools for Breast Cancer Diagnostics

My PhD work in developing RNA sequencing-based diagnostic tools for breast cancer.

The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome

Breast cancer is a disease of genomic alterations, of which the panorama of somatic mutations and how these relate to subtypes and therapy response is incompletely understood. Within SCAN‐B (ClinicalTrials.gov: NCT02306096), a prospective study …

Features of increased malignancy in eosinophilic clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most common form of renal cancer. Due to inactivation of the von Hippel–Lindau tumour suppressor, the hypoxia‐inducible transcription factors (HIFs) are constitutively activated in these tumours, …

SCAN-B MutationExplorer

A web-based application for exploring tumor somatic mutations.

Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network–Breast Initiative

In early breast cancer (BC), five conventional biomarkers—estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG)—are used to determine prognosis and treatment. …

TopHat-Recondition: A post-processor for TopHat unmapped reads

TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format – the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for aligned sequencing reads, thus correct …

The Sweden Cancerome Analysis Network-Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine

Breast cancer exhibits significant molecular, pathological, and clinical heterogeneity. Current clinicopathological evaluation is imperfect for predicting outcome, which results in overtreatment for many patients, and for others, leads to death from …