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PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.
Olson ND, Wagner J, McDaniel J, Stephens SH, Westreich ST, Prasanna AG, Johanson E, Boja E, Maier EJ, Serang O, Jáspez D, Lorenzo-Salazar JM, Muñoz-Barrera A, Rubio-Rodríguez LA, Flores C, Kyriakidis K, Malousi A, Shafin K, Pesout T, Jain M, Paten B, Chang PC, Kolesnikov A, Nattestad M, Baid G, Goel S, Yang H, Carroll A, Eveleigh R, Bourgey M, Bourque G, Li G, Ma C, Tang L, Du Y, Zhang S, Morata J, Tonda R, Parra G, Trotta JR, Brueffer C, Demirkaya-Budak S, Kabakci-Zorlu D, Turgut D, Kalay Ö, Budak G, Narcı K, Arslan E, Brown R, Johnson IJ, Dolgoborodov A, Semenyuk V, Jain A, Tetikol HS, Jain V, Ruehle M, Lajoie B, Roddey C, Catreux S, Mehio R, Ahsan MU, Liu Q, Wang K, Sahraeian SME, Fang LT, Mohiyuddin M, Hung C, Jain C, Feng H, Li Z, Chen L, Sedlazeck FJ, Zook JM. Olson ND, et al. Among authors: brueffer c. Cell Genom. 2022 May 11;2(5):100129. doi: 10.1016/j.xgen.2022.100129. Epub 2022 Apr 27. Cell Genom. 2022. PMID: 35720974 Free PMC article.
A crowdsourced set of curated structural variants for the human genome.
Chapman LM, Spies N, Pai P, Lim CS, Carroll A, Narzisi G, Watson CM, Proukakis C, Clarke WE, Nariai N, Dawson E, Jones G, Blankenberg D, Brueffer C, Xiao C, Kolora SRR, Alexander N, Wolujewicz P, Ahmed AE, Smith G, Shehreen S, Wenger AM, Salit M, Zook JM. Chapman LM, et al. Among authors: brueffer c. PLoS Comput Biol. 2020 Jun 19;16(6):e1007933. doi: 10.1371/journal.pcbi.1007933. eCollection 2020 Jun. PLoS Comput Biol. 2020. PMID: 32559231 Free PMC article.
Remarkable similarities of chromosomal rearrangements between primary human breast cancers and matched distant metastases as revealed by whole-genome sequencing.
Tang MH, Dahlgren M, Brueffer C, Tjitrowirjo T, Winter C, Chen Y, Olsson E, Wang K, Törngren T, Sjöström M, Grabau D, Bendahl PO, Rydén L, Niméus E, Saal LH, Borg Å, Gruvberger-Saal SK. Tang MH, et al. Among authors: brueffer c. Oncotarget. 2015 Nov 10;6(35):37169-84. doi: 10.18632/oncotarget.5951. Oncotarget. 2015. PMID: 26439695 Free PMC article.
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.
Saal LH, Vallon-Christersson J, Häkkinen J, Hegardt C, Grabau D, Winter C, Brueffer C, Tang MH, Reuterswärd C, Schulz R, Karlsson A, Ehinger A, Malina J, Manjer J, Malmberg M, Larsson C, Rydén L, Loman N, Borg Å. Saal LH, et al. Among authors: brueffer c. Genome Med. 2015 Feb 2;7(1):20. doi: 10.1186/s13073-015-0131-9. eCollection 2015. Genome Med. 2015. PMID: 25722745 Free PMC article.
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.
Alkner S, Tang MH, Brueffer C, Dahlgren M, Chen Y, Olsson E, Winter C, Baker S, Ehinger A, Rydén L, Saal LH, Fernö M, Gruvberger-Saal SK. Alkner S, et al. Among authors: brueffer c. Breast Cancer Res. 2015 Aug 5;17(1):102. doi: 10.1186/s13058-015-0608-x. Breast Cancer Res. 2015. PMID: 26242876 Free PMC article.
Detection 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.
Förnvik D, Aaltonen KE, Chen Y, George AM, Brueffer C, Rigo R, Loman N, Saal LH, Rydén L. Förnvik D, et al. Among authors: brueffer c. Breast Cancer Res Treat. 2019 Sep;177(2):447-455. doi: 10.1007/s10549-019-05326-5. Epub 2019 Jun 24. Breast Cancer Res Treat. 2019. PMID: 31236809 Free PMC article.
Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network-Breast Initiative.
Brueffer C, Vallon-Christersson J, Grabau D, Ehinger A, Häkkinen J, Hegardt C, Malina J, Chen Y, Bendahl PO, Manjer J, Malmberg M, Larsson C, Loman N, Rydén L, Borg Å, Saal LH. Brueffer C, et al. JCO Precis Oncol. 2018 Mar 9;2:PO.17.00135. doi: 10.1200/PO.17.00135. eCollection 2018. JCO Precis Oncol. 2018. PMID: 32913985 Free PMC article.
The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome.
Brueffer C, Gladchuk S, Winter C, Vallon-Christersson J, Hegardt C, Häkkinen J, George AM, Chen Y, Ehinger A, Larsson C, Loman N, Malmberg M, Rydén L, Borg Å, Saal LH. Brueffer C, et al. EMBO Mol Med. 2020 Oct 7;12(10):e12118. doi: 10.15252/emmm.202012118. Epub 2020 Sep 14. EMBO Mol Med. 2020. PMID: 32926574 Free PMC article.
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