Jeanette E Eckel-Passow

Summary

Affiliation: Mayo Clinic
Country: USA

Publications

  1. ncbi request reprint Normalization of two-channel microarray experiments: a semiparametric approach
    J E Eckel
    Department of Health Sciences Research, Mayo Clinic Rochester, MN 55905, USA
    Bioinformatics 21:1078-83. 2005
  2. ncbi request reprint Experimental design and analysis of antibody microarrays: applying methods from cDNA arrays
    Jeanette E Eckel-Passow
    Department of Health Sciences Research, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
    Cancer Res 65:2985-9. 2005
  3. ncbi request reprint Regression analysis for comparing protein samples with 16O/18O stable-isotope labeled mass spectrometry
    J E Eckel-Passow
    Division of Biostatistics, Department of Health Sciences Research 200 First Street SW, Rochester, MN 55905, USA
    Bioinformatics 22:2739-45. 2006
  4. pmc Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform
    Jeanette E Eckel-Passow
    Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
    BMC Bioinformatics 12:220. 2011
  5. doi request reprint Clear Cell Type A and B Molecular Subtypes in Metastatic Clear Cell Renal Cell Carcinoma: Tumor Heterogeneity and Aggressiveness
    Daniel J Serie
    Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
    Eur Urol . 2016
  6. pmc Quality assessment metrics for whole genome gene expression profiling of paraffin embedded samples
    Douglas W Mahoney
    Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
    BMC Res Notes 6:33. 2013
  7. ncbi request reprint A method for automatically interpreting mass spectra of 18O-labeled isotopic clusters
    Christopher J Mason
    Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
    Mol Cell Proteomics 6:305-18. 2007
  8. pmc Genomic analysis reveals that immune function genes are strongly linked to clinical outcome in the North Central Cancer Treatment Group n9831 Adjuvant Trastuzumab Trial
    Edith A Perez
    Edith A Perez, E Aubrey Thompson, Yan W Asmann, and Xochiquetzal J Geiger, Mayo Clinic, Jacksonville, FL Karla V Ballman, S Keith Anderson, Krishna R Kalari, Jeanette E Eckel Passow, Kathleen S Tenner, Jin Jen, Beiyun Chen, Robert B Jenkins, and Monica M Reinholz, Mayo Clinic, Rochester, MN Amylou C Dueck, and Ann E McCullough, Mayo Clinic, Scottsdale, AZ Jian Bing Fan, Illumina, San Diego, CA George W Sledge, Stanford School of Medicine, Palo Alto, CA Eric P Winer, Harvard Medical School, Boston, MA and Julie R Gralow, Seattle Cancer Care Alliance, Seattle, WA
    J Clin Oncol 33:701-8. 2015
  9. pmc Higher expression of topoisomerase II alpha is an independent marker of increased risk of cancer-specific death in patients with clear cell renal cell carcinoma
    Alexander S Parker
    Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA Electronic address
    Eur Urol 66:929-35. 2014
  10. pmc Somatic expression of ENRAGE is associated with obesity status among patients with clear cell renal cell carcinoma
    Jeanette E Eckel-Passow
    Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
    Carcinogenesis 35:822-7. 2014

Detail Information

Publications37

  1. ncbi request reprint Normalization of two-channel microarray experiments: a semiparametric approach
    J E Eckel
    Department of Health Sciences Research, Mayo Clinic Rochester, MN 55905, USA
    Bioinformatics 21:1078-83. 2005
    ....
  2. ncbi request reprint Experimental design and analysis of antibody microarrays: applying methods from cDNA arrays
    Jeanette E Eckel-Passow
    Department of Health Sciences Research, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
    Cancer Res 65:2985-9. 2005
    ..The objective of this article is to discuss statistical methods that have been developed for cDNA arrays and describe how the methods can be directly applied to antibody arrays...
  3. ncbi request reprint Regression analysis for comparing protein samples with 16O/18O stable-isotope labeled mass spectrometry
    J E Eckel-Passow
    Division of Biostatistics, Department of Health Sciences Research 200 First Street SW, Rochester, MN 55905, USA
    Bioinformatics 22:2739-45. 2006
    ..Although discussed in the context of (16)O/(18)O stable-isotope labeled data, the multivariable regression models are generalizable to other stable-isotope labeled technologies...
  4. pmc Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform
    Jeanette E Eckel-Passow
    Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
    BMC Bioinformatics 12:220. 2011
    ..0. We compared bias and variance in the locus-level copy number data, the concordance amongst regions of copy number gains/deletions and the false-positive rate amongst deleted segments...
  5. doi request reprint Clear Cell Type A and B Molecular Subtypes in Metastatic Clear Cell Renal Cell Carcinoma: Tumor Heterogeneity and Aggressiveness
    Daniel J Serie
    Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
    Eur Urol . 2016
    ..Intratumor molecular heterogeneity has been reported for primary clear cell renal cell carcinoma (ccRCC) tumors; however, heterogeneity in metastatic ccRCC tumors has not been explored...
  6. pmc Quality assessment metrics for whole genome gene expression profiling of paraffin embedded samples
    Douglas W Mahoney
    Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
    BMC Res Notes 6:33. 2013
    ....
  7. ncbi request reprint A method for automatically interpreting mass spectra of 18O-labeled isotopic clusters
    Christopher J Mason
    Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
    Mol Cell Proteomics 6:305-18. 2007
    ..We describe in detail the operation of the algorithm and demonstrate its use on datasets with known and unknown ratios...
  8. pmc Genomic analysis reveals that immune function genes are strongly linked to clinical outcome in the North Central Cancer Treatment Group n9831 Adjuvant Trastuzumab Trial
    Edith A Perez
    Edith A Perez, E Aubrey Thompson, Yan W Asmann, and Xochiquetzal J Geiger, Mayo Clinic, Jacksonville, FL Karla V Ballman, S Keith Anderson, Krishna R Kalari, Jeanette E Eckel Passow, Kathleen S Tenner, Jin Jen, Beiyun Chen, Robert B Jenkins, and Monica M Reinholz, Mayo Clinic, Rochester, MN Amylou C Dueck, and Ann E McCullough, Mayo Clinic, Scottsdale, AZ Jian Bing Fan, Illumina, San Diego, CA George W Sledge, Stanford School of Medicine, Palo Alto, CA Eric P Winer, Harvard Medical School, Boston, MA and Julie R Gralow, Seattle Cancer Care Alliance, Seattle, WA
    J Clin Oncol 33:701-8. 2015
    ..To develop a genomic signature that predicts benefit from trastuzumab in human epidermal growth factor receptor 2-positive breast cancer...
  9. pmc Higher expression of topoisomerase II alpha is an independent marker of increased risk of cancer-specific death in patients with clear cell renal cell carcinoma
    Alexander S Parker
    Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA Electronic address
    Eur Urol 66:929-35. 2014
    ..Type IIa topoisomerase (TOPOIIa) is a well-known biomarker of DNA replication and a target for antineoplastic agents, but it has not been evaluated as a biomarker of ccRCC outcome...
  10. pmc Somatic expression of ENRAGE is associated with obesity status among patients with clear cell renal cell carcinoma
    Jeanette E Eckel-Passow
    Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
    Carcinogenesis 35:822-7. 2014
    ..Upregulation of ENRAGE could lead to local, autocrine stimulation of the RAGE receptor and thus support cancer progression. ..
  11. pmc Loss of histone H3 lysine 36 trimethylation is associated with an increased risk of renal cell carcinoma-specific death
    Thai H Ho
    Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
    Mod Pathol 29:34-42. 2016
    ..This association remains significant after stratifying for the SSIGN score, particularly among those patients with low-risk tumors. ..
  12. pmc The association of copy number variation and percent mammographic density
    Elizabeth J Atkinson
    Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
    BMC Res Notes 8:297. 2015
    ..Segmentation was subsequently performed on the probe-level test statistics to identify candidate CNV regions that were associated with PD...
  13. doi request reprint Assessing the clinical use of clear cell renal cell carcinoma molecular subtypes identified by RNA expression analysis
    Jeanette E Eckel-Passow
    Department of Health Sciences Researches, Mayo Clinic, Rochester, MN
    Urol Oncol 33:68.e17-23. 2015
    ....
  14. pmc An integrated model of the transcriptome of HER2-positive breast cancer
    Krishna R Kalari
    Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
    PLoS ONE 8:e79298. 2013
    ....
  15. pmc A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis
    Sarah E Reese
    Department of Biostatistics, Biostatistics Shared Resource Core, VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23284, USA, Division of Biomedical Statistics and Informatics and Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
    Bioinformatics 29:2877-83. 2013
    ..However, PCA yields linear combinations of the variables that contribute maximum variance and thus will not necessarily detect batch effects if they are not the largest source of variability in the data...
  16. pmc Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing
    Zhifu Sun
    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
    PLoS ONE 6:e17490. 2011
    ..The role of gene amplification/deletion appears to more modest, although several potentially significant genes appear to be regulated by copy number aberrations...
  17. pmc Understanding inherited genetic risk of adult glioma - a review
    Terri Rice
    Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, 1450 3rd Street, San Francisco, CA 94158 T R, A M M, K M W, S S F, J W, J K W, M R W Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905 D H L, R B J Department of Neurology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905 D H L Department of Epidemiology and Biostatistics, University of California, San Francisco, 1450 3rd Street, San Francisco, CA 94158 A M M, J W Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905 J E E P Program in Cancer Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, San Francisco, CA 94158 K M W, J W, J K W, M R W Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 11100 Euclid Avenue
    Neurooncol Pract 3:10-16. 2016
    ..This review also provides an information sheet for primary adult glioma patients and their families...
  18. pmc ANKS1B is a smoking-related molecular alteration in clear cell renal cell carcinoma
    Jeanette E Eckel-Passow
    Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
    BMC Urol 14:14. 2014
    ..We used a multi-stage design to identify and validate genes that are associated with smoking-related ccRCC...
  19. pmc Incidence of Pseudomonas aeruginosa bacteremia: a population-based study
    Majdi N Al-Hasan
    Department of Medicine, Division of Infectious Diseases, College of Medicine, Mayo Clinic, Rochester, MN 55905, USA
    Am J Med 121:702-8. 2008
    ..The incidence of Pseudomonas aeruginosa bacteremia has not been defined in a population-based investigation...
  20. pmc An insight into high-resolution mass-spectrometry data
    J E Eckel-Passow
    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
    Biostatistics 10:481-500. 2009
    ..Areas in need of statistical research for proteomic data include alignment, experimental design, abundance normalization, and statistical analysis...
  21. pmc Determining the frequency of pathogenic germline variants from exome sequencing in patients with castrate-resistant prostate cancer
    Steven N Hart
    Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
    BMJ Open 6:e010332. 2016
    ..To determine the frequency of pathogenic inherited mutations in 157 select genes from patients with metastatic castrate-resistant prostate cancer (mCRPC)...
  22. pmc Statistical considerations on prognostic models for glioma
    Annette M Molinaro
    Department of Neurological Surgery, University of California San Francisco UCSF, San Francisco, California A M M, M R W Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California A M M, M R W Institute of Human Genetics, University of California San Francisco, San Francisco, California M R W Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota R B J Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota J E E P
    Neuro Oncol 18:609-23. 2016
    ..As editors, reviewers, and readers of the relevant literature, we should be cognizant of the needed statistical considerations and insist on their use. ..
  23. pmc Exome sequencing reveals frequent deleterious germline variants in cancer susceptibility genes in women with invasive breast cancer undergoing neoadjuvant chemotherapy
    Marissa S Ellingson
    Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
    Breast Cancer Res Treat 153:435-43. 2015
    ..Deleterious variants in cancer susceptibility genes are highly prevalent in patients with invasive breast cancer referred for neoadjuvant chemotherapy undergoing exome sequencing. Detection of these variants impacts medical management...
  24. pmc Loss of PBRM1 and BAP1 expression is less common in non-clear cell renal cell carcinoma than in clear cell renal cell carcinoma
    Thai H Ho
    Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN Electronic address
    Urol Oncol 33:23.e9-14. 2015
    ..We evaluated loss of PBRM1 and BAP1 staining in ccRCC, papillary RCC (pRCC), chromophobe RCC (chRCC), and RO tumors using an immunohistochemistry assay in which negative staining was associated with loss-of-function mutations...
  25. pmc Expression of endothelin 2 and localized clear cell renal cell carcinoma
    Brian M Bot
    Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
    Hum Pathol 43:843-9. 2012
    ..If supportive mechanistic data can be produced, endothelin 2 could represent a potential target for chemopreventive or neoadjuvant therapeutics for clear cell renal cell carcinoma...
  26. pmc Statistical analysis of relative labeled mass spectrometry data from complex samples using ANOVA
    Ann L Oberg
    Division of Biostatistics, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, USA
    J Proteome Res 7:225-33. 2008
    ..The modeling approach, implementation, and useful visualization tools are demonstrated via a case study of complex biological samples assessed using the iTRAQ relative labeling protocol...
  27. doi request reprint Characterizing the clinical benefit of ipilimumab in patients who progressed on high-dose IL-2
    Richard W Joseph
    Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL 32224, USA
    J Immunother 35:711-5. 2012
    ..Prospective trials of HD IL-2 followed by ipilimumab could potentially identify patients most likely to benefit from a sequential approach of HD IL-2 followed by ipilimumab...
  28. doi request reprint Comparison of fluorescence in situ hybridization (FISH) and dual-ISH (DISH) in the determination of HER2 status in breast cancer
    Aaron S Mansfield
    Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
    Am J Clin Pathol 139:144-50. 2013
    ..Using a cohort of difficult specimens, we observed less than 95% concordance between FISH and DISH. DISH may underestimate the HER2/chromosome 17 ratio, or FISH may overestimate this ratio...
  29. pmc Identification of a novel percent mammographic density locus at 12q24
    Kristen N Stevens
    Department of Health Sciences Research, Mayo Clinic, Charlton 6 239, 200 First St SW, Rochester, MN 55905, USA
    Hum Mol Genet 21:3299-305. 2012
    ..Understanding the mechanism underlying this association will provide insight into the genetics of breast tissue composition...
  30. pmc Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASLĀ® platform
    Monica M Reinholz
    Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, Minnesota 55905, USA
    BMC Med Genomics 3:60. 2010
    ..5K) and 24,526-gene panel (24K) platforms at differentiating nine human epidermal growth factor receptor 2- positive (HER2+) and 11 HER2-negative (HER2-) paraffin-embedded breast tumors...
  31. doi request reprint Multiplex matrix network analysis of protein complexes in the human TCR signalosome
    Stephen E P Smith
    Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
    Sci Signal 9:rs7. 2016
    ..Thus, generation of PiSCES biosignatures represents an approach that can provide information about the activity of protein signaling networks in samples including low-abundance primary cells from clinical biopsies. ..
  32. pmc Telomere maintenance and the etiology of adult glioma
    Kyle M Walsh
    Department of Neurological Surgery, University of California San Francisco, San Francisco, California K M W, J K W, A M M, M R W Institute for Human Genetics, University of California San Francisco, San Francisco, California J K W, M R W Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota D H L, R B J Department of Neurology, Mayo Clinic, Rochester, Minnesota D H L Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California J L W, A M M Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota J E E P
    Neuro Oncol 17:1445-52. 2015
    ..Specifically, several inherited and acquired variants underlying gliomagenesis affect telomere pathways and are also associated with increased telomere length. ..
  33. doi request reprint The Mayo prosthetic joint infection risk score: implication for surgical site infection reporting and risk stratification
    Elie F Berbari
    Department of Medicine, Division of Infectious Diseases, Section of Orthopedic Infections, Mayo Clinic, Rochester, Minnesota 55905, USA
    Infect Control Hosp Epidemiol 33:774-81. 2012
    ..The goal of this study was to develop a prognostic scoring system for the development of prosthetic joint infection (PJI) that could risk-stratify patients undergoing total hip (THA) or total knee (TKA) arthroplasties...
  34. pmc Tissue microarrays: one size does not fit all
    Jeanette E Eckel-Passow
    Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
    Diagn Pathol 5:48. 2010
    ..Furthermore, TMA performance across multiple biomarkers has not been systematically explored...
  35. doi request reprint A prospective longitudinal analysis of cytomegalovirus (CMV)-specific CD4+ and CD8+ T cells in kidney allograft recipients at risk of CMV infection
    Albert J Eid
    Divisions of Infectious Diseases, Department of Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
    Transpl Int 23:506-13. 2010
    ..On the other hand, the clinical utility of CMV-specific T cell assays will need to be assessed in a larger cohort of CMV D+/R- kidney recipients who remain at high-risk of delayed-onset CMV disease...
  36. pmc Progressive but previously untreated CLL patients with greater array CGH complexity exhibit a less durable response to chemoimmunotherapy
    Neil E Kay
    Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
    Cancer Genet Cytogenet 203:161-8. 2010
    ..1 deletion and in the more favorable genetic subtype characterized by the presence of 13q14.1 deletion. This aCGH study adds information on the association between poor trial response and increasing genetic complexity as CLL progresses...
  37. doi request reprint Kinetics of interferon-gamma producing cytomegalovirus (CMV)-specific CD4+ and CD8+ T lymphocytes and the risk of subsequent CMV viremia after allogeneic hematopoietic stem cell transplantation
    A J Eid
    Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
    Transpl Infect Dis 11:519-28. 2009
    ..Deficiencies in cytomegalovirus (CMV)-specific T lymphocytes impair the immunologic response against CMV reactivation after allogeneic hematopoietic stem cell transplantation (HSCT)...