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Article
Open AccessProteomic profiling reveals that ESR1 mutations enhance cyclin-dependent kinase signaling
Three quarters of all breast cancers express the estrogen receptor (ER, ESR1 gene), which promotes tumor growth and constitutes a direct target for endocrine therapies. ESR1 mutations have been implicated in ther...
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Article
Open AccessDigital PCR quantification of ultrahigh ERBB2 copy number identifies poor breast cancer survival after trastuzumab
HER2/ERBB2 evaluation is necessary for treatment decision-making in breast cancer (BC), however current methods have limitations and considerable variability exists. DNA copy number (CN) evaluation by droplet ...
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Article
Open AccessMitochondrial heteroplasmic shifts reveal a positive selection of breast cancer
Breast cancer is, despite screening, not always detected early enough and is together with other tumor types known to shed genetic information in circulation. Unlike single-copy nuclear DNA, mitochondrial DNA ...
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Article
Open AccessMatched analysis of circulating selenium with the breast cancer selenotranscriptome: a multicentre prospective study
Low serum selenium and altered tumour RNA expression of certain selenoproteins are associated with a poor breast cancer prognosis. Selenoprotein expression stringently depends on selenium availability, hence c...
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Article
Open AccessCITED1 as a marker of favourable outcome in anti-endocrine treated, estrogen-receptor positive, lymph-node negative breast cancer
To investigate CITED1 as a potential biomarker of anti-endocrine response and breast cancer recurrence, given its previously determined role in mediating estrogen-dependant transcription. The study is a contin...
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Article
Lung adenocarcinoma promotion by air pollutants
A complete understanding of how exposure to environmental substances promotes cancer formation is lacking. More than 70 years ago, tumorigenesis was proposed to occur in a two-step process: an initiating step ...
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Article
Open AccessRNA sequencing-based single sample predictors of molecular subtype and risk of recurrence for clinical assessment of early-stage breast cancer
Multigene assays for molecular subtypes and biomarkers can aid management of early invasive breast cancer. Using RNA-sequencing we aimed to develop single-sample predictor (SSP) models for clinical markers, su...
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Article
Open AccessClinical associations of ESR2 (estrogen receptor beta) expression across thousands of primary breast tumors
Estrogen receptor alpha (ERα, encoded by ESR1) is a well-characterized transcription factor expressed in more than 75% of breast tumors and is the key biomarker to direct endocrine therapies. On the other hand, m...
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Article
Open AccessComprehensive molecular comparison of BRCA1 hypermethylated and BRCA1 mutated triple negative breast cancers
Homologous recombination deficiency (HRD) is a defining characteristic in BRCA-deficient breast tumors caused by genetic or epigenetic alterations in key pathway genes. We investigated the frequency of BRCA1 prom...
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Article
Open AccessAgreement between molecular subty** and surrogate subtype classification: a contemporary population-based study of ER-positive/HER2-negative primary breast cancer
Oestrogen receptor-positive (ER+) and human epidermal receptor 2-negative (HER2–) breast cancers are classified as Luminal A or B based on gene expression, but immunohistochemical markers are used for surrogat...
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Article
Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study
Whole-genome sequencing (WGS) brings comprehensive insights to cancer genome interpretation. To explore the clinical value of WGS, we sequenced 254 triple-negative breast cancers (TNBCs) for which associated t...
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Article
Open AccessDetection of circulating tumor cells and circulating tumor DNA before and after mammographic breast compression in a cohort of breast cancer patients scheduled for neoadjuvant treatment
It is not known if mammographic breast compression of a primary tumor causes shedding of tumor cells into the circulatory system. Little is known about how the detection of circulating biomarkers such as circu...
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Article
Open AccessCross comparison and prognostic assessment of breast cancer multigene signatures in a large population-based contemporary clinical series
Multigene expression signatures provide a molecular subdivision of early breast cancer associated with patient outcome. A gap remains in the validation of such signatures in clinical treatment groups of patien...
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Article
Open AccessGermline mutations in BRCA1 and BRCA2 incidentally revealed in a biobank research study: experiences from re-contacting mutation carriers and relatives
Once an incidental finding (IF) is discovered in the course of genomic research, the researchers are faced with the question of whether or not that finding should be reported back to the study participant. A l...
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Article
Microenvironmental control of breast cancer subtype elicited through paracrine platelet-derived growth factor-CC signaling
Paracrine signaling networks in the breast cancer microenvironment uncover determinants of hormone receptor status and offer opportunities for therapeutic intervention.
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Identification and Use of Personalized Genomic Markers for Monitoring Circulating Tumor DNA
Digital PCR techniques are ideally suited for accurately quantifying trace amounts of target DNA sequences, such as tumor-derived mutant DNA that is present in the blood circulation of patients with cancer. He...
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Article
Open AccessEfficacy versus effectiveness of clinical genetic testing criteria for BRCA1 and BRCA2 hereditary mutations in incident breast cancer
Increasing evidence supports the benefit of identifying BRCA1 and BRCA2 germline mutations in early breast cancer. Selection of patients for genetic testing is based on defined criteria taking individual and fami...
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Article
Open AccessIntegrated molecular pathway analysis informs a synergistic combination therapy targeting PTEN/PI3K and EGFR pathways for basal-like breast cancer
The basal-like breast cancer (BLBC) subtype is characterized by positive staining for basal mammary epithelial cytokeratin markers, lack of hormone receptor and HER2 expression, and poor prognosis with current...
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Article
Open AccessTopHat-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 ...
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Article
Open AccessPTEN and NEDD4 in Human Breast Carcinoma
PTEN is an important tumor suppressor gene that antagonizes the oncogenic PI3K/AKT signaling pathway and has functions in the nucleus for maintaining genome integrity. Although PTEN inactivation by mutation is...
