Johan Staaf

Summary

Affiliation: Lund University
Country: Sweden

Publications

  1. doi request reprint Landscape of somatic allelic imbalances and copy number alterations in human lung carcinoma
    Johan Staaf
    Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, Lund, Sweden
    Int J Cancer 132:2020-31. 2013
  2. pmc Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer
    Johan Staaf
    Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
    Breast Cancer Res 13:R129. 2011
  3. pmc Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays
    Johan Staaf
    Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
    Genome Biol 9:R136. 2008
  4. pmc High-resolution genomic and expression analyses of copy number alterations in HER2-amplified breast cancer
    Johan Staaf
    Department of Oncology, Clinical Sciences, Lund University, Barngatan 2B, Lund, Sweden
    Breast Cancer Res 12:R25. 2010
  5. pmc Normalization of array-CGH data: influence of copy number imbalances
    Johan Staaf
    Division of Oncology, Department of Clinical Sciences, Lund University, 221 85 Lund, Sweden
    BMC Genomics 8:382. 2007
  6. pmc Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
    Johan Staaf
    Department of Oncology, Clinical Sciences, Lund University, SE 22185 Lund, Sweden
    BMC Bioinformatics 9:409. 2008
  7. doi request reprint Identification of subtypes in human epidermal growth factor receptor 2--positive breast cancer reveals a gene signature prognostic of outcome
    Johan Staaf
    Department of Oncology, CREATE Health Strategic Center for TranslationalCancer Research, Lund University, Lund, Sweden
    J Clin Oncol 28:1813-20. 2010
  8. pmc Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns
    Karolina Holm
    Department of Oncology, Clinical Sciences, Lund University, Barngatan 2B, Lund, Sweden
    Breast Cancer Res 12:R36. 2010
  9. doi request reprint Detecting EGFR alterations in clinical specimens-pitfalls and necessities
    Sofi Isaksson
    Department of Clinical Sciences, Division of Oncology, Lund University, Medicon Village, SE 223 81, Lund, Sweden
    Virchows Arch 463:755-64. 2013
  10. doi request reprint Characterisation of amplification patterns and target genes at chromosome 11q13 in CCND1-amplified sporadic and familial breast tumours
    Karolina Holm
    Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
    Breast Cancer Res Treat 133:583-94. 2012

Detail Information

Publications42

  1. doi request reprint Landscape of somatic allelic imbalances and copy number alterations in human lung carcinoma
    Johan 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...
  2. pmc Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer
    Johan Staaf
    Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
    Breast Cancer Res 13:R129. 2011
    ....
  3. pmc Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays
    Johan Staaf
    Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
    Genome Biol 9:R136. 2008
    ....
  4. pmc High-resolution genomic and expression analyses of copy number alterations in HER2-amplified breast cancer
    Johan Staaf
    Department of Oncology, Clinical Sciences, Lund University, Barngatan 2B, Lund, Sweden
    Breast Cancer Res 12:R25. 2010
    ....
  5. pmc Normalization of array-CGH data: influence of copy number imbalances
    Johan 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...
  6. pmc Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
    Johan 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...
  7. doi request reprint Identification of subtypes in human epidermal growth factor receptor 2--positive breast cancer reveals a gene signature prognostic of outcome
    Johan Staaf
    Department of Oncology, CREATE Health Strategic Center for TranslationalCancer Research, Lund University, Lund, Sweden
    J Clin Oncol 28:1813-20. 2010
    ....
  8. pmc Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns
    Karolina 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...
  9. doi request reprint Detecting EGFR alterations in clinical specimens-pitfalls and necessities
    Sofi Isaksson
    Department of Clinical Sciences, Division of Oncology, Lund University, Medicon Village, SE 223 81, Lund, Sweden
    Virchows Arch 463:755-64. 2013
    ....
  10. doi request reprint Characterisation of amplification patterns and target genes at chromosome 11q13 in CCND1-amplified sporadic and familial breast tumours
    Karolina 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...
  11. pmc Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics
    Goran 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...
  12. pmc Molecular profiling reveals low- and high-grade forms of primary melanoma
    Katja 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...
  13. ncbi request reprint Multiple metastases from cutaneous malignant melanoma patients may display heterogeneous genomic and epigenomic patterns
    Katja 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...
  14. ncbi request reprint The retinoblastoma gene undergoes rearrangements in BRCA1-deficient basal-like breast cancer
    Goran 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...
  15. doi request reprint Effect of polyamine deficiency on proteins involved in Okazaki fragment maturation
    Veronica 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...
  16. ncbi request reprint High-resolution genomic profiles of breast cancer cell lines assessed by tiling BAC array comparative genomic hybridization
    Goran 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...
  17. pmc Integrated genomic and gene expression profiling identifies two major genomic circuits in urothelial carcinoma
    David 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...
  18. ncbi request reprint Cytogenetic characterization and gene expression profiling of the trastuzumab-resistant breast cancer cell line JIMT-1
    Karin 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...
  19. doi request reprint Identification of new microRNAs in paired normal and tumor breast tissue suggests a dual role for the ERBB2/Her2 gene
    Helena 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...
  20. pmc Relation between smoking history and gene expression profiles in lung adenocarcinomas
    Johan 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...
  21. doi request reprint 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-31
    Srinivas 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...
  22. ncbi request reprint Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization
    Goran 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...
  23. ncbi request reprint Genetic profiles distinguish different types of hereditary ovarian cancer
    Katarina 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...
  24. doi request reprint High-resolution genomic profiling of male breast cancer reveals differences hidden behind the similarities with female breast cancer
    Ida 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...
  25. doi request reprint Heterogeneous genetic profiles in soft tissue myoepitheliomas
    Karolin H Hallor
    Department of Clinical Genetics, Lund University Hospital, Lund, Sweden
    Mod Pathol 21:1311-9. 2008
    ....
  26. doi request reprint Molecular mechanisms underlying N1, N11-diethylnorspermine-induced apoptosis in a human breast cancer cell line
    C 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...
  27. doi request reprint 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...
  28. doi request reprint Histological specificity of alterations and expression of KIT and KITLG in non-small cell lung carcinoma
    Annette Salomonsson
    Division of Oncology, Department of Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
    Genes Chromosomes Cancer 52:1088-96. 2013
    ....
  29. doi request reprint Nonfamilial breast cancer subtypes
    Markus 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...
  30. doi request reprint Genetic profiles of gastroesophageal cancer: combined analysis using expression array and tiling array--comparative genomic hybridization
    Anna 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...
  31. doi request reprint Zoom-in array comparative genomic hybridization (aCGH) to detect germline rearrangements in cancer susceptibility genes
    Johan 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...
  32. doi request reprint Different cell cycle kinetic effects of N1,N11-diethylnorspermine-induced polyamine depletion in four human breast cancer cell lines
    Louise 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...
  33. pmc GOBO: gene expression-based outcome for breast cancer online
    Markus 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...
  34. doi request reprint Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms
    Rebeqa 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...
  35. doi request reprint Two genetic pathways, t(1;10) and amplification of 3p11-12, in myxoinflammatory fibroblastic sarcoma, haemosiderotic fibrolipomatous tumour, and morphologically similar lesions
    Karolin 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...
  36. ncbi request reprint Mapping of a novel ocular and cutaneous malignant melanoma susceptibility locus to chromosome 9q21.32
    Goran Jonsson
    Department of Oncology, University Hospital, Lund, Sweden
    J Natl Cancer Inst 97:1377-82. 2005
    ....
  37. pmc Genomic and transcriptional alterations in lung adenocarcinoma in relation to EGFR and KRAS mutation status
    Maria Planck
    Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Medicon Village, Lund, Sweden
    PLoS ONE 8:e78614. 2013
    ..Improved knowledge about genomic and transcriptional alterations in and between mutation-defined subgroups may identify genes involved in disease development or progression...
  38. pmc Non-coding antisense transcription detected by conventional and single-stranded cDNA microarray
    Johan 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...
  39. ncbi request reprint Continuous-index hidden Markov modelling of array CGH copy number data
    Susann Stjernqvist
    Centre for Mathematical Sciences, Lund University, Lund, Sweden
    Bioinformatics 23:1006-14. 2007
    ..For array designs in which clones are of unequal lengths, are unevenly spaced or overlap, the discrete-index view typically adopted by such methods may be questionable or improved...
  40. doi request reprint Identification of transcriptional subgroups in EGFR-mutated and EGFR/KRAS wild-type lung adenocarcinoma reveals gene signatures associated with patient outcome
    Maria Planck
    Authors Affiliations Department of Oncology, Clinical Sciences, Skåne University Hospital and CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
    Clin Cancer Res 19:5116-26. 2013
    ..We sought to determine whether transcriptional subgroups of clinical relevance exist within EGFR-mutated, KRAS-mutated, or EGFR and KRAS wild-type (EGFRwt/KRASwt) adenocarcinomas...
  41. doi request reprint Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors
    Karolin 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...
  42. ncbi request reprint ACID: a database for microarray clone information
    Markus 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...