Research Topics
Genomes and GenesSpecies | Johan StaafSummaryAffiliation: Lund University Country: Sweden Publications
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Publications
Landscape of somatic allelic imbalances and copy number alterations in human lung carcinomaJohan Staaf
Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, Lund, Sweden
Int J Cancer 132:2020-31. 2013..In summary, these analyses provide a comprehensive overview of the landscape of genomic alterations in lung cancer, highlighting differences but also similarities between subgroups of the disease...
Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancerJohan Staaf
Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
Breast Cancer Res 13:R129. 2011....- Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arraysJohan Staaf
Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
Genome Biol 9:R136. 2008.... - High-resolution genomic and expression analyses of copy number alterations in HER2-amplified breast cancerJohan Staaf
Department of Oncology, Clinical Sciences, Lund University, Barngatan 2B, Lund, Sweden
Breast Cancer Res 12:R25. 2010.... - Normalization of array-CGH data: influence of copy number imbalancesJohan Staaf
Division of Oncology, Department of Clinical Sciences, Lund University, 221 85 Lund, Sweden
BMC Genomics 8:382. 2007..We therefore sought to investigate the effect on normalization imposed by copy number imbalances... - Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratiosJohan Staaf
Department of Oncology, Clinical Sciences, Lund University, SE 22185 Lund, Sweden
BMC Bioinformatics 9:409. 2008..Therefore, we examined the effects of the conventionally used normalization method for Illumina Infinium arrays when applied to cancer samples... - Identification of subtypes in human epidermal growth factor receptor 2--positive breast cancer reveals a gene signature prognostic of outcomeJohan Staaf
Department of Oncology, CREATE Health Strategic Center for TranslationalCancer Research, Lund University, Lund, Sweden
J Clin Oncol 28:1813-20. 2010.... - Molecular subtypes of breast cancer are associated with characteristic DNA methylation patternsKarolina Holm
Department of Oncology, Clinical Sciences, Lund University, Barngatan 2B, Lund, Sweden
Breast Cancer Res 12:R36. 2010..Each subtype has a characteristic expression pattern suggested to partly depend on cellular origin. We aimed to investigate whether the molecular subtypes also display distinct methylation profiles... - Characterisation of amplification patterns and target genes at chromosome 11q13 in CCND1-amplified sporadic and familial breast tumoursKarolina Holm
Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
Breast Cancer Res Treat 133:583-94. 2012..Amplification was equally prevalent in familial and sporadic tumours, but strikingly rare in BRCA1- and BRCA2-mutated tumours. We conclude that 11q13 includes many potential target genes in addition to CCND1... - Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristicsGoran Jonsson
Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, 5 Lund, Sweden
Breast Cancer Res 12:R42. 2010..Additionally, breast tumors occurring in individuals with germline BRCA1 or BRCA2 mutations typically fall into distinct subtypes... - Molecular profiling reveals low- and high-grade forms of primary melanomaKatja Harbst
Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
Clin Cancer Res 18:4026-36. 2012..This raises the possibility that a molecular structure exists even in the early stages of melanoma and that molecular determinants could underlie histophenotype and eventual patient outcome... 
The retinoblastoma gene undergoes rearrangements in BRCA1-deficient basal-like breast cancerGoran Jonsson
Department of Oncology, CREATE Health Strategic Center for Translational Cancer Research, Lund University, Skåne Department of Oncology, Skane University Hospital, Lund, Sweden
Cancer Res 72:4028-36. 2012..Together, our findings show the existence of genetic heterogeneity within the basal-like breast cancer subtype that is based upon BRCA1 status...- Effect of polyamine deficiency on proteins involved in Okazaki fragment maturationVeronica M Johansson
Department of Cell and Organism Biology, Lund University, Helgonavagen 3B, SE 223 62 Lund, Sweden
Cell Biol Int 32:1467-77. 2008..DENSPM treatment affects the cellular distribution of FEN1 in L56Br-C1 cells, but not in MCF-7 cells, implying that FEN1 is affected by or involved in DENSPM-induced apoptosis... - Integrated genomic and gene expression profiling identifies two major genomic circuits in urothelial carcinomaDavid Lindgren
Department of Molecular Pathology, Lund University, Malmo, Sweden
PLoS ONE 7:e38863. 2012..Taken together, our integrative approach revealed at least two separate networks of genomic alterations linked to the molecular diversity seen in UC, and that these circuits may reflect distinct pathways of tumor development... - Cytogenetic characterization and gene expression profiling of the trastuzumab-resistant breast cancer cell line JIMT-1Karin Rennstam
Department of Oncology, Clinical Sciences, Lund University, Barngatan 2 1, SE 221 85 Lund, Sweden
Cancer Genet Cytogenet 172:95-106. 2007..We conclude that cytogenetic and expression profiling of JIMT-1 revealed several new features that need further characterization and may shed light on trastuzumab resistance... - Relation between smoking history and gene expression profiles in lung adenocarcinomasJohan Staaf
Department of Oncology, Lund University, Lund, Sweden
BMC Med Genomics 5:22. 2012..However, the genetic aberrations that differ between smokers and never-smokers' lung carcinomas remain to a large extent unclear... - Multiple metastases from cutaneous malignant melanoma patients may display heterogeneous genomic and epigenomic patternsKatja Harbst
Department of Oncology, Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, Lund, Sweden
Melanoma Res 20:381-91. 2010..These data are further corroborated by a switch in CDH1 and CDH2 expression between metastases from the same patient. In conclusion, our results provide evidence for different models of metastatic progression in melanoma... - High-resolution genomic profiles of breast cancer cell lines assessed by tiling BAC array comparative genomic hybridizationGoran Jonsson
Department of Oncology, University Hospital, Lund, Sweden
Genes Chromosomes Cancer 46:543-58. 2007..The tiling BAC-arrays constitute a powerful tool for high-resolution genomic profiling suitable for cancer research and clinical diagnostics... - MiRNA expression in urothelial carcinomas: important roles of miR-10a, miR-222, miR-125b, miR-7 and miR-452 for tumor stage and metastasis, and frequent homozygous losses of miR-31Srinivas Veerla
Department of Clinical Genetics, Lund University Hospital, Lund, Sweden
Int J Cancer 124:2236-42. 2009..In addition, these latter miRNAs were shown to be excellent prognostic markers for death by disease as outcome. The presented data shows that pathological subtypes of urothelial carcinoma show distinct miRNA gene expression signatures... - Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridizationGoran Jonsson
Department of Oncology, University Hospital, Lund, Sweden
Cancer Res 65:7612-21. 2005..00005, respectively). Further validation may prove this tumor classifier to be useful for selecting familial breast cancer cases for further mutation screening, particularly, as these data can be obtained using archival tissue... - Identification of new microRNAs in paired normal and tumor breast tissue suggests a dual role for the ERBB2/Her2 geneHelena Persson
Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
Cancer Res 71:78-86. 2011..In summary, our work substantially expands the number of known miRNAs and highlights the complexity of small RNA expression in breast cancer... - Genetic profiles distinguish different types of hereditary ovarian cancerKatarina Domanska
Institute of Clinical Sciences, Department of Oncology, Lund University, 22185 Lund, Sweden
Oncol Rep 24:885-95. 2010..The results indicate that HBOC and HNPCC associated ovarian cancer develop along distinct genetic pathways and genetic profiles can thus be applied to distinguish between different types of hereditary ovarian cancer... - High-resolution genomic profiling of male breast cancer reveals differences hidden behind the similarities with female breast cancerIda Johansson
Department of Oncology, Clinical Sciences, Lund University, BMC C13, 22184 Lund, Sweden
Breast Cancer Res Treat 129:747-60. 2011..MBC can be divided into two comprehensive genomic subgroups, which may be of prognostic value. The male-simple subgroup appears notably different from any genomic subgroup so far defined in FBC... - Detection and precise mapping of germline rearrangements in BRCA1, BRCA2, MSH2, and MLH1 using zoom-in array comparative genomic hybridization (aCGH)Johan Staaf
Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
Hum Mutat 29:555-64. 2008..g., focusing on breast cancer susceptibility genes, with increased capacity using multiformat design, and represents a valuable new tool and complement for genetic screening in clinical diagnostics... - Heterogeneous genetic profiles in soft tissue myoepitheliomasKarolin H Hallor
Department of Clinical Genetics, Lund University Hospital, Lund, Sweden
Mod Pathol 21:1311-9. 2008.... - Molecular mechanisms underlying N1, N11-diethylnorspermine-induced apoptosis in a human breast cancer cell lineC Martina Holst
Department of Cell and Organism Biology, Lund University, Lund, Sweden
Anticancer Drugs 19:871-83. 2008..The results also indicate that it should be possible to find molecular markers for sensitivity to DENSPM that could be used in the clinic to predict sensitivity to a polyamine analogue... - Genetic profiles of gastroesophageal cancer: combined analysis using expression array and tiling array--comparative genomic hybridizationAnna Isinger-Ekstrand
Department of Oncology, Clinical Sciences, Lund University, Barngatan 2B, Lund, Sweden
Cancer Genet Cytogenet 200:120-6. 2010..These data suggest that molecular diagnostics and targeted therapies can be applied to adenocarcinomas of the distal esophagus and gastroesophageal junction alike... - Zoom-in array comparative genomic hybridization (aCGH) to detect germline rearrangements in cancer susceptibility genesJohan Staaf
Department of Oncology, Clinical Sciences, CREATE Health Strategic Centre For Translational Cancer Research, Lund University, Lund, Sweden
Methods Mol Biol 653:221-35. 2010..Furthermore, zoom-in aCGH can be streamlined for a particular application, for example, focusing on breast cancer susceptibility genes, with increased capacity using multiformat design... - Different cell cycle kinetic effects of N1,N11-diethylnorspermine-induced polyamine depletion in four human breast cancer cell linesLouise Myhre
Department of Cell and Organism Biology, Lund University, Lund, Sweden
Anticancer Drugs 19:359-68. 2008..The two cell lines that were most sensitive to DENSPM treatment belong to the basal-like subtype of breast cancer and they were deficient with respect to p53, BRCA1, and RB1... - GOBO: gene expression-based outcome for breast cancer onlineMarkus Ringner
Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
PLoS ONE 6:e17911. 2011..The design and implementation of GOBO facilitate easy incorporation of additional query functions and applications, as well as additional data sets irrespective of tumor type and array platform... - Mapping of a novel ocular and cutaneous malignant melanoma susceptibility locus to chromosome 9q21.32Goran Jonsson
Department of Oncology, University Hospital, Lund, Sweden
J Natl Cancer Inst 97:1377-82. 2005.... - Two genetic pathways, t(1;10) and amplification of 3p11-12, in myxoinflammatory fibroblastic sarcoma, haemosiderotic fibrolipomatous tumour, and morphologically similar lesionsKarolin H Hallor
Department of Clinical Genetics, University Hospital, Lund, Sweden
J Pathol 217:716-27. 2009..The identified genetic aberrations were not confined to MIFS; an identical t(1;10) was also found in a case of HFT and the amplicon in 3p was seen in an IMFH... - Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platformsRebeqa Gunnarsson
Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Hematology and Transplantation, Lund University, Lund, Sweden
Genes Chromosomes Cancer 47:697-711. 2008..Large-scale studies of genomic aberrations are now feasible, but new tools for LOH analysis are requested... - Continuous-index hidden Markov modelling of array CGH copy number dataSusann Stjernqvist
Centre for Mathematical Sciences, Lund University, Lund, Sweden
Bioinformatics 23:1006-14. 2007..Bioinformatics, 21, 3763-3370.) giving result similar to theirs but with certain features highlighted in the continuous-index setting... - Non-coding antisense transcription detected by conventional and single-stranded cDNA microarrayJohan Vallon-Christersson
Department of Oncology, Institute of Clinical Sciences, and SWEGENE DNA microarray resource center, Lund University, Barngatan 2 1, SE 221 85 Lund, Sweden
BMC Genomics 8:295. 2007..Therefore, we profiled transcription of sense and antisense independently by using strand-specific cDNA microarrays... - Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumorsKarolin H Hallor
Department of Clinical Genetics, Lund University Hospital, Lund, Sweden
Clin Cancer Res 15:2685-94. 2009..Hence, we have investigated DNA copy numbers in chondrosarcomas with the purpose of identifying markers useful for prognosis and subclassification... - Nonfamilial breast cancer subtypesMarkus Ringner
Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
Methods Mol Biol 973:279-95. 2013..Additionally, inherited BRCA1- and BRCA2-mutated tumors were significantly correlated to specific subtypes. In this chapter, we will review the current status regarding genomic subtypes of nonfamilial breast cancer... - ACID: a database for microarray clone informationMarkus Ringner
Complex Systems Division, Lund University, Sweden
Bioinformatics 20:2305-6. 2004..For each clone, the database contents include assigned UniGene cluster(s), location in the full-length transcript, assigned gene ontology terms and position in the genome assembly. AVAILABILITY: http://bioinfo.thep.lu.se/acid.html..