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Articles by Johan Staaf
Genome-wide DNA methylation profiling of triple-negative breast cancer uncovers epigenetic biomarkers of tumor identity and the immune microenvironment
Abstract DNA methylation deregulation is an essential feature of tumor biology, influencing cancer formation and pathogenesis. Analyses of DNA methylation in bulk cancer specimens are challenging due to the high data dimensionality, noise, and mixture of different cell types. Here, we characterized methylation dynamics in cancer by investigating the variance structure of bulk tumor DNA methylation data through the identification of groups of highly correlated CpGs, termed CpG cassettes.
Integrated prediction of lung cancer histology and molecular profiles from small bronchoscopic tumor specimens
Abstract Treatment decisions in lung cancer rely on comprehensive molecular and histological characterization, but the limited amount of tumor tissue available from diagnostic procedures remains a major challenge. In this proof-of-concept study, we investigated whether preserving small bronchoscopic tumor specimens in RNAlater enables integrated molecular and histological profiling.
Tumor microenvironment transcriptional activity enables robust stratification of chemotherapy response in triple-negative breast cancer
Keywords transcriptome plasticity transcriptomic deconvolution prognostic stratification tumor microenvironment Introduction Triple-negative breast cancer (TNBC), which lacks expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2),1,2,3 accounts for 15%–20% of all breast cancers.4 TNBC has the worst prognosis across diverse ethnic groups.4,5,6 While immunotherapy and PARP inhibitors have been integrated into standard-of-care...
Homologous recombination deficiency in primary ER-positive and HER2-negative breast cancer - Communications Medicine
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Abstract Homologous recombination deficiency (HRD) originating from inactivation of genes like BRCA1/BRCA2 is a targetable abnormality common in triple-negative breast cancer (TNBC). In estrogen-receptor (ER)-positive HER2-negative (ERpHER2n) breast cancer (BC), HRD prevalence and clinical impact are unclear.
By Helen Davies, Daniella Black, Anders Kvist, Kristín Magnea Sigurjónsdóttir, Ana Bosch, Ramsay Bowden, Ziqian Chen, Giuseppe Rinaldi, Frida Rosengren, Deborah F. Nacer, Srinivas Veerla, Lennart Hohmann, Jari Häkkinen, Johan Vallon-Christersson, Åke Borg, Serena Nik-Zainal, Johan Staaf, Yasin Memari, Nicklas Nordborg
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Nature
Verified
The analytical and clinical validity of AI algorithms to score TILs in TNBC: can we use different machine learning models interchangeably?
ArticlesVolume 78102928Open access aDepartment of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden bDivision of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-22381, Lund, Sweden cDepartment of Hematology, Oncology and Radiation Physics, Region Skåne, Lund, Sweden dDepartment of Genetics, Pathology and Molecular Diagnostics, Laboratory Medicine, Region Skåne, Lund, Sweden eDivision of Surgery, Department of Clinical Sciences, Lund...
Kataegis in clinical and molecular subgroups of primary breast cancer - npj Breast Cancer
Abstract Kataegis is a hypermutation phenomenon characterized by localized clusters of single base pair substitution (SBS) reported in multiple cancer types. Despite a high frequency in breast cancer, large-scale analyses of kataegis patterns and associations with clinicopathological and molecular variables in established breast cancer subgroups are lacking.
Multi-omic profiling of squamous cell lung cancer identifies metabolites and related genes associated with squamous cell carcinoma
Abstract Background Squamous cell lung carcinoma (SqCC) is the second most common histological subtype of lung cancer. Besides tumor-initiating and promoting DNA, RNA, and epigenetic alterations, aberrant cell metabolism is a hallmark of carcinogenesis. This study aimed to identify SqCC-specific metabolites and key gene regulators that could eventually be used as new anticancer targets. Methods Transcriptional, proteomic, and metabolomic data were gathered for a cohort of resected lung cancers.
Improved detection of clinically relevant fusion transcripts in cancer by machine learning classification - BMC Genomics
To create a dataset where we could identify true and false positive gene fusion events, we ran the fusion prediction software FusionCatcher for sensitive fusion detection on 4760 RNA-seq samples from 11 diverse cancer types in The Cancer Genome Atlas (TCGA) cohort.
Diagnostic Value of Insulinoma-Associated Protein 1 (INSM1) and Comparison With Established Neuroendocrine Markers in Pulmonary Cancers: A Comprehensive Study and Review of the Literature
Article Citation: Johan Staaf, Lena Tran, Linnea Söderlund, Björn Nodin, Karin Jirström, Halla Vidarsdottir, Maria Planck, Johanna S. M. Mattsson, Johan Botling, Patrick Micke, and Hans Brunnström (2020) Diagnostic Value of Insulinoma-Associated Protein 1 (INSM1) and Comparison With Established Neuroendocrine Markers in Pulmonary Cancers: A Comprehensive Study and Review of the Literature. Archives of Pathology & Laboratory Medicine In-Press.
Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study
Abstract 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 treatment and outcome data were collected between 2010 and 2015 via the population-based Sweden Cancerome Analysis Network–Breast (SCAN-B) project (ClinicalTrials.gov ID:NCT02306096).
Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences
Correction to: Nature https://doi.org/10.1038/nature17676, published online 2 May 2016. In the Methods section of this Article, ‘greater than’ should have been ‘less than’ in the sentence ‘Putative regions of clustered rearrangements were identified as having an average inter-rearrangement distance that was at least 10 times greater than the whole-genome average for the individual sample. ’ . The original Article has not been corrected online.
Landscape of somatic mutations in 560 breast cancer whole-genome sequences
This work has been funded through the ICGC Breast Cancer Working group by the Breast Cancer Somatic Genetics Study (BASIS), a European research project funded by the European Community’s Seventh Framework Programme (FP7/2010-2014) under the grant agreement number 242006; the Triple Negative project funded by the Wellcome Trust (grant reference 077012/Z/05/Z) and the HER2+ project funded by Institut National du Cancer (INCa) in France (grant numbers 226-2009, 02-2011, 41-2012, 144-2008, 06-2012).
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