{"entity": "researcher", "timestamp": "2026-07-14T03:41:29.578Z", "family": "Zhang", "given": "Ning", "initials": "N", "orcid": "0000-0002-6430-4236", "affiliations": ["Bienko-Crosetto Lab for Quantitative Genome Biology, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.", "Science for Life Laboratory, Solna, Sweden.", "Department of Breast Surgery, Qilu hospital of Shandong University, Ji'nan, China."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/a3fdde99294d422694c7a8a00c9811ed.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/a3fdde99294d422694c7a8a00c9811ed"}}, "publications": [{"entity": "publication", "iuid": "f9f4da192abc41a59c7dbafd427b7cd0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9f4da192abc41a59c7dbafd427b7cd0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9f4da192abc41a59c7dbafd427b7cd0"}}, "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.scilifelab.se/researcher/f786763a4a0e4b5bb865ebb199eb6ca2.json"}}, {"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/839bf10741044782aecdc77b3f06fc88.json"}}, {"family": "Matikas", "given": "Alexios", "initials": "A", "orcid": "0000-0002-4122-9624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0af6483a77d746c2b838414692f1f4ed.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Acs", "given": "Balazs", "initials": "B"}, {"family": "Boyaci", "given": "Ceren", "initials": "C", "orcid": "0000-0001-5598-0243", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1a803107a224c578bf01ef65aba69ff.json"}}, {"family": "Zhang", "given": "Ning", "initials": "N", "orcid": "0000-0002-6430-4236", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3fdde99294d422694c7a8a00c9811ed.json"}}, {"family": "Salgkamis", "given": "Dimitrios", "initials": "D", "orcid": "0000-0002-3020-0359", "researcher": {"href": "https://publications.scilifelab.se/researcher/826836fefcf5440ebef1c404e046a0ca.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.scilifelab.se/researcher/5bb1180d52564c48876ecc4b7e635d52.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Mezheyeuski", "given": "Artur", "initials": "A", "orcid": "0000-0002-4394-2634", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd907ed1df0441b99789d3e045c4d890.json"}}, {"family": "Bergh", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5526-1847", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd38f4f7704144ed9e3f869e197175e6.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Foukakis", "given": "Theodoros", "initials": "T", "orcid": "0000-0001-8952-9987", "researcher": {"href": "https://publications.scilifelab.se/researcher/7683c0280e9b4145aa54305fb08936a7.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": {"Clinical Genomics Stockholm": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41523-021-00352-3"}, {"db": "pmc", "key": "PMC8604966"}], "notes": [], "created": "2021-12-01T19:52:21.708Z", "modified": "2024-01-16T13:48:38.062Z"}, {"entity": "publication", "iuid": "e18b31942e41465999c590cac3365408", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e18b31942e41465999c590cac3365408.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e18b31942e41465999c590cac3365408"}}, "title": "COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.", "authors": [{"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/839bf10741044782aecdc77b3f06fc88.json"}}, {"family": "Zhang", "given": "Ning", "initials": "N", "orcid": "0000-0002-6430-4236", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3fdde99294d422694c7a8a00c9811ed.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Milia", "given": "Maria Grazia", "initials": "MG"}, {"family": "Brossa", "given": "Silvia", "initials": "S"}, {"family": "Huong Nguyen", "given": "Thi Thu", "initials": "TT", "orcid": "0000-0002-9089-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/57451410c8ac4547a4b09111a020e396.json"}}, {"family": "Cerutti", "given": "Francesco", "initials": "F", "orcid": "0000-0003-0480-8296", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a243dc846624a8a8292dde5416fa402.json"}}, {"family": "Berrino", "given": "Enrico", "initials": "E"}, {"family": "Sapino", "given": "Anna", "initials": "A"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Sottile", "given": "Antonino", "initials": "A"}, {"family": "Ghisetti", "given": "Valeria", "initials": "V", "orcid": "0000-0002-4698-598X", "researcher": {"href": "https://publications.scilifelab.se/researcher/75237266d0b1496f909cb0c53ff87920.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2021-06-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "3903", "issn-l": "2041-1723"}, "abstract": "While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow-COVseq-which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We benchmark COVseq against a standard library preparation method (NEBNext) on 29 SARS-CoV-2 positive samples, reaching 95.4% of concordance between single-nucleotide variants detected by both methods. Application of COVseq to 245 additional SARS-CoV-2 positive samples demonstrates the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis shows that COVseq could be used to sequence thousands of samples at less than 15 USD per sample, including library preparation and sequencing costs. We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses.", "doi": "10.1038/s41467-021-24078-9", "pmid": "34162869", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-24078-9"}, {"db": "pmc", "key": "PMC8222401"}], "notes": [], "created": "2021-10-01T09:02:30.491Z", "modified": "2024-01-16T13:48:39.472Z"}]}