{"entity": "journal", "iuid": "b5d0210cbf66403595f5026a5318ce5a", "timestamp": "2026-09-23T21:35:20.377Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/NPJ%20Breast%20Cancer.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/NPJ%20Breast%20Cancer"}}, "title": "NPJ Breast Cancer", "issn": "2374-4677", "issn-l": null, "publications_count": 2, "publications": [{"entity": "publication", "iuid": "4c56a7cae50341b6b4d0d88ea1e07748", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4c56a7cae50341b6b4d0d88ea1e07748.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4c56a7cae50341b6b4d0d88ea1e07748"}}, "title": "High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing.", "authors": [{"family": "Kostecka", "given": "Anna", "initials": "A", "orcid": "0000-0001-5705-0795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/155382b49119451eac0270139acfd2aa.json"}}, {"family": "Nowikiewicz", "given": "Tomasz", "initials": "T"}, {"family": "Olszewski", "given": "Pawe\u0142", "initials": "P"}, {"family": "Koczkowska", "given": "Magdalena", "initials": "M"}, {"family": "Horbacz", "given": "Monika", "initials": "M", "orcid": "0000-0003-1644-2957", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebc9e942f42f447ea2e53323b168b892.json"}}, {"family": "Heinzl", "given": "Monika", "initials": "M"}, {"family": "Andreou", "given": "Maria", "initials": "M", "orcid": "0000-0002-2197-597X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a049e2ddeb954bdba0767cd9e757d8ee.json"}}, {"family": "Salazar", "given": "Renato", "initials": "R", "orcid": "0000-0001-8436-9304", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/50a4e416e16e4e32b6fe9e674707c986.json"}}, {"family": "Mair", "given": "Theresa", "initials": "T"}, {"family": "Madanecki", "given": "Piotr", "initials": "P"}, {"family": "Gucwa", "given": "Magdalena", "initials": "M"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Skokowski", "given": "Jaros\u0142aw", "initials": "J", "orcid": "0000-0002-3079-3502", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/67ad090d46744a7b8daed4d8cf2cd130.json"}}, {"family": "Buckley", "given": "Patrick G", "initials": "PG"}, {"family": "P\u0119ksa", "given": "Rafa\u0142", "initials": "R"}, {"family": "\u015arutek", "given": "Ewa", "initials": "E"}, {"family": "Szylberg", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Jankowski", "given": "Micha\u0142", "initials": "M"}, {"family": "Zegarski", "given": "Wojciech", "initials": "W"}, {"family": "Tiemann-Boege", "given": "Irene", "initials": "I"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Piotrowski", "given": "Arkadiusz", "initials": "A", "orcid": "0000-0002-0823-0607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e64d7b68df2421f9456085fa4a41467.json"}}], "type": "journal article", "published": "2022-06-29", "journal": {"title": "NPJ Breast Cancer", "issn": "2374-4677", "volume": "8", "issue": "1", "pages": "76", "issn-l": null}, "abstract": "The mammary gland undergoes hormonally stimulated cycles of proliferation, lactation, and involution. We hypothesized that these factors increase the mutational burden in glandular tissue and may explain high cancer incidence rate in the general population, and recurrent disease. Hence, we investigated the DNA sequence variants in the normal mammary gland, tumor, and peripheral blood from 52 reportedly sporadic breast cancer patients. Targeted resequencing of 542 cancer-associated genes revealed subclonal somatic pathogenic variants of: PIK3CA, TP53, AKT1, MAP3K1, CDH1, RB1, NCOR1, MED12, CBFB, TBX3, and TSHR in the normal mammary gland at considerable allelic frequencies (9 \u00d7 10-2- 5.2 \u00d7 10-1), indicating clonal expansion. Further evaluation of the frequently damaged PIK3CA and TP53 genes by ultra-sensitive duplex sequencing demonstrated a diversified picture of multiple low-level subclonal (in 10-2-10-4 alleles) hotspot pathogenic variants. Our results raise a question about the oncogenic potential in non-tumorous mammary gland tissue of breast-conserving surgery patients.", "doi": "10.1038/s41523-022-00443-9", "pmid": "35768433", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9243094"}, {"db": "pii", "key": "10.1038/s41523-022-00443-9"}], "notes": [], "created": "2026-09-23T10:08:01.924Z", "modified": "2026-09-23T10:46:07.686Z"}, {"entity": "publication", "iuid": "021d6e3671944964845d5bd3ff8a4f2b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/021d6e3671944964845d5bd3ff8a4f2b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/021d6e3671944964845d5bd3ff8a4f2b"}}, "title": "Interplay between copy number alterations and immune profiles in the early breast cancer Scandinavian Breast Group 2004-1 randomized phase II trial: results from a feasibility study.", "authors": [{"family": "Zerdes", "given": "Ioannis", "initials": "I", "orcid": "0000-0002-8304-2462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f4ce5f98b0640778e21d53349e3a468.json"}}, {"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac01283eacef4f2e81675653202782a5.json"}}, {"family": "Matikas", "given": "Alexios", "initials": "A", "orcid": "0000-0002-4122-9624", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/694cc730bb754271a18b029ec0c1eadf.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9967939c5d5494a85fac56173a49821.json"}}, {"family": "Acs", "given": "Balazs", "initials": "B"}, {"family": "Boyaci", "given": "Ceren", "initials": "C", "orcid": "0000-0001-5598-0243", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea42415f08204e299bce41f767982d98.json"}}, {"family": "Zhang", "given": "Ning", "initials": "N", "orcid": "0000-0002-6430-4236", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f8c46858ed4641639ae4cfb6996a9ee5.json"}}, {"family": "Salgkamis", "given": "Dimitrios", "initials": "D", "orcid": "0000-0002-3020-0359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e76cfdf1a2004e1fb8808dc3372c2d4b.json"}}, {"family": "Agartz", "given": "Susanne", "initials": "S"}, {"family": "Moreno-Ruiz", "given": "Pablo", "initials": "P"}, {"family": "Bai", "given": "Yalai", "initials": "Y"}, {"family": "Rimm", "given": "David L", "initials": "DL", "orcid": "0000-0001-5820-4397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8391cca478a441d68e9d3b092983cb48.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Mezheyeuski", "given": "Artur", "initials": "A", "orcid": "0000-0002-4394-2634", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/227a0142881848f4a1635d66cf52e673.json"}}, {"family": "Bergh", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5526-1847", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a462537d526a4259b9c68da95bd4aae4.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b1cef698ae749749b4017dbacb9e3db.json"}}, {"family": "Foukakis", "given": "Theodoros", "initials": "T", "orcid": "0000-0001-8952-9987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8d949ec9ece444da6676f68f062c787.json"}}], "type": "journal article", "published": "2021-11-19", "journal": {"title": "NPJ Breast Cancer", "issn": "2374-4677", "volume": "7", "issue": "1", "pages": "144", "issn-l": null}, "abstract": "Emerging data indicate that genomic alterations can shape immune cell composition in early breast cancer. However, there is a need for complementary imaging and sequencing methods for the quantitative assessment of combined somatic copy number alteration (SCNA) and immune profiling in pathological samples. Here, we tested the feasibility of three approaches-CUTseq, for high-throughput low-input SCNA profiling, multiplexed fluorescent immunohistochemistry (mfIHC) and digital-image analysis (DIA) for quantitative immuno-profiling- in archival formalin-fixed paraffin-embedded (FFPE) tissue samples from patients enrolled in the randomized SBG-2004-1 phase II trial. CUTseq was able to reproducibly identify amplification and deletion events with a resolution of 100 kb using only 6 ng of DNA extracted from FFPE tissue and pooling together 77 samples into the same sequencing library. In the same samples, mfIHC revealed that CD4 + T-cells and CD68 + macrophages were the most abundant immune cells and they mostly expressed PD-L1 and PD-1. Combined analysis showed that the SCNA burden was inversely associated with lymphocytic infiltration. Our results set the basis for further applications of CUTseq, mfIHC and DIA to larger cohorts of early breast cancer patients.", "doi": "10.1038/s41523-021-00352-3", "pmid": "34799582", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8604966"}, {"db": "pii", "key": "10.1038/s41523-021-00352-3"}], "notes": [], "created": "2026-09-23T12:07:28.425Z", "modified": "2026-09-23T12:07:28.665Z"}], "created": "2026-09-23T10:08:02.010Z", "modified": "2026-09-23T10:08:02.010Z"}