Bioinformatics

Abstract P4-09-03: On the development and clinical value of RNA-sequencing-based classifiers for prediction of the five conventional breast cancer biomarkers: A report from the population-based multicenter SCAN-B study
Background
In early breast cancer, five histopathological biomarkers are part of current clinical routines and used for determining …
Christian Brueffer, Johan Vallon-Christersson, Dorthe Grabau, Anna Ehinger, Jari Häkkinen, Cecilia Hegardt, Janne Malina, Yilun Chen, Pär-Ola Bendahl, Jonas Manjer, Martin Malmberg, Christer Larsson, Niklas Loman, Lisa Rydén, Åke Borg, Lao H. Saal
DOI
Abstract P4-09-03: On the development and clinical value of RNA-sequencing-based classifiers for prediction of the five conventional breast cancer biomarkers: A report from the population-based multicenter SCAN-B study
TopHat-Recondition: A post-processor for TopHat unmapped reads
Background
TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format – the binary version …
Christian Brueffer, Lao H. Saal
DOI PDF bioRxiv Preprint Code PhD Project
TopHat-Recondition: A post-processor for TopHat unmapped reads
Remarkable similarities of chromosomal rearrangements between primary human breast cancers and matched distant metastases as revealed by whole-genome sequencing
To better understand and characterize chromosomal structural variation during breast cancer progression, we enumerated chromosomal …
Man-Hung Eric Tang, Malin Dahlgren, Christian Brueffer, Tamara Tjitrowirjo, Christof Winter, Yilun Chen, Eleonor Olsson, Kun Wang, Therese Törngren, Martin Sjöström, Dorthe Grabau, Pär-Ola Bendahl, Lisa Rydén, Emma Niméus, Lao H. Saal, Åke Borg, Sofia K. Gruvberger-Saal
DOI PDF
Remarkable similarities of chromosomal rearrangements between primary human breast cancers and matched distant metastases as revealed by whole-genome sequencing
Contralateral breast cancer can represent a metastatic spread of the first primary tumor: determination of clonal relationship between contralateral breast cancers using next-generation whole genome sequencing
Introduction
By convention, a contralateral breast cancer (CBC) is treated as a new primary tumor, independent of the first cancer …
Sara Alkner, Man-Hung Eric Tang, Christian Brueffer, Malin Dahlgren, Yilun Chen, Eleonor Olsson, Christof Winter, Sara Baker, Anna Ehinger, Lisa Rydén, Lao H. Saal, Mårten Fernö, Sofia K. Gruvberger-Saal
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Contralateral breast cancer can represent a metastatic spread of the first primary tumor: determination of clonal relationship between contralateral breast cancers using next-generation whole genome sequencing
Abstract 4805: Whole genome sequencing of primary breast cancers and matched distant metastases
Metastatic disease is the main cause of death for breast cancer patients, but it is still unclear whether primary tumor characteristics …
Man-Hung Eric Tang, Malin Dahlgren, Christian Brueffer, Christof Winter, Yilun Chen, Eleonor Olsson, Martin Sjöström, Pär-Ola Bendahl, Emma Niméus-Malmström, Lao H. Saal, Åke Borg, Sofia K. Gruvberger-Saal
DOI
Abstract 4805: Whole genome sequencing of primary breast cancers and matched distant metastases
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 …
Lao H. Saal, Johan Vallon-Christersson, Jari Häkkinen, Cecilia Hegardt, Dorthe Grabau, Christof Winter, Christian Brueffer, Man-Hung Eric Tang, Christel Reuterswärd, Ralph Schulz, Anna Karlsson, Anna Ehinger, Janne Malina, Jonas Manjer, Martin Malmberg, Christer Larsson, Lisa Rydén, Niklas Loman, Åke Borg
DOI PDF Dataset PhD Project
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