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Genotyping concordance in DNA extracted from formalin‐fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses

dc.contributor.authorHertz, Daniel L.
dc.contributor.authorKidwell, Kelley M.
dc.contributor.authorThibert, Jacklyn N.
dc.contributor.authorGersch, Christina
dc.contributor.authorRegan, Meredith M.
dc.contributor.authorSkaar, Todd C.
dc.contributor.authorHenry, N. Lynn
dc.contributor.authorHayes, Daniel F.
dc.contributor.authorVan Poznak, Catherine H.
dc.contributor.authorRae, James M.
dc.date.accessioned2017-01-10T20:52:20Z
dc.date.available2017-01-10T20:52:20Z
dc.date.issued2015-11
dc.identifier.citation(2015). "Genotyping concordance in DNA extracted from formalin‐fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses." Molecular Oncology 9(9): 1868-1876.
dc.identifier.issn1574-7891
dc.identifier.issn1878-0261
dc.identifier.urihttps://hdl.handle.net/2027.42/135708
dc.publisherSpringer
dc.publisherWiley Periodicals, Inc.
dc.subject.otherCancer
dc.subject.otherPharmacogenetics
dc.subject.otherSomatic genome
dc.subject.otherFormalin-fixed paraffin embedded
dc.subject.otherFFPE
dc.subject.otherGermline genome
dc.titleGenotyping concordance in DNA extracted from formalin‐fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses
dc.typeArticleen_US
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelHematology and Oncology
dc.subject.hlbtoplevelHealth Sciences
dc.description.peerreviewedPeer Reviewed
dc.contributor.affiliationumBreast Oncology Program, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA
dc.contributor.affiliationumDepartment of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI, USA
dc.contributor.affiliationumDepartment of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
dc.contributor.affiliationumDepartment of Internal Medicine, Division of Hematology/Oncology, University of Michigan Health System, Ann Arbor, MI, USA
dc.contributor.affiliationotherDepartment of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
dc.contributor.affiliationotherDepartment of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN, USA
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/135708/1/mol22015991868.pdf
dc.identifier.doi10.1016/j.molonc.2015.07.002
dc.identifier.sourceMolecular Oncology
dc.identifier.citedreferenceNakamura, Y., Ratain, M.J., Cox, N.J., McLeod, H.L., Kroetz, D.L., Flockhart, D.A., 2012. Re: CYP2D6 genotype and tamoxifen response in postmenopausal women with endocrine-responsive breast cancer: the breast international group 1-98 trial. (Electronic version) J. Natl. Cancer Inst. 104, ( 16 ) 1264 author reply 1266–8
dc.identifier.citedreferenceCannon-Albright, L.A., Cooper, K.G., Georgelas, A., Bernard, P.S., 2011. High quality and quantity genome-wide germline genotypes from FFPE normal tissue. (Electronic version) BMC Res. Notes. 4, 159
dc.identifier.citedreferenceGoetz, M.P., Sun, J.X., Suman, V.J., Silva, G.O., Perou, C.M., Nakamura, Y., 2014. Loss of heterozygosity at the CYP2D6 locus in breast cancer: implications for germline pharmacogenetic studies. (Electronic version) J. Natl. Cancer Inst. 107, ( 2 ) 10.1093/jnci/dju401
dc.identifier.citedreferenceGoetz, M.P., Rae, J.M., Suman, V.J., Safgren, S.L., Ames, M.M., Visscher, D.W., 2005. Pharmacogenetics of tamoxifen biotransformation is associated with clinical outcomes of efficacy and hot flashes. (Electronic version) J. Clin. Oncol. 23, ( 36 ) 9312 – 9318.
dc.identifier.citedreferenceGreytak, S.R., Engel, K.B., Bass, B.P., Moore, H.M., 2015. Accuracy of molecular data generated with FFPE biospecimens: lessons from the literature. (Electronic version) Cancer Res. 75, ( 8 ) 1541 – 1547.
dc.identifier.citedreferenceHagleitner, M.M., Coenen, M.J., Jeuken, J.W., Flucke, U., Schreuder, H.W., te Loo, D.M., 2011. Taqman genotyping assays can be used on decalcified and paraffin-embedded tissue from patients with osteosarcoma. (Electronic version) Pediatr. Blood Cancer. 56, ( 1 ) 35 – 38.
dc.identifier.citedreferenceHedegaard, J., Thorsen, K., Lund, M.K., Hein, A.M., Hamilton-Dutoit, S.J., Vang, S., 2014. Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue. (Electronic version) PloS One. 9, ( 5 ) e98187
dc.identifier.citedreferenceHertz, D.L., McLeod, H.L., 2013. Use of pharmacogenetics for predicting cancer prognosis and treatment exposure, response and toxicity. (Electronic version) J. Hum. Genet. 58, ( 6 ) 346 – 352.
dc.identifier.citedreferenceHertz, D.L., Rae, J., 2015. Pharmacogenetics of cancer drugs. (Electronic version) Annu. Rev. Med. 66, 65 – 81.
dc.identifier.citedreferenceHorn, H., Pott, C., Kalla, J., Dreyling, M., Rosenwald, A., Ott, G., 2010. A multiplex MALDI-TOF MS approach facilitates genotyping of DNA from formalin-fixed paraffin-embedded tumour specimens. (Electronic version) Pharmacogenet. Genomics. 20, ( 10 ) 598 – 604.
dc.identifier.citedreferenceKandoth, C., McLellan, M.D., Vandin, F., Ye, K., Niu, B., Lu, C., 2013. Mutational landscape and significance across 12 major cancer types. (Electronic version) Nature. 502, ( 7471 ) 333 – 339.
dc.identifier.citedreferenceMarisi, G., Passardi, A., Calistri, D., Zoli, W., Amadori, D., Ulivi, P., 2014. Discrepancies between VEGF -1154 G>A polymorphism analysis performed in peripheral blood samples and FFPE tissue. (Electronic version) Int. J. Mol. Sci. 15, ( 8 ) 13333 – 13343.
dc.identifier.citedreferenceMarsh, S., Mallon, M.A., Goodfellow, P., McLeod, H.L., 2005. Concordance of pharmacogenetic markers in germline and colorectal tumor DNA. (Electronic version) Pharmacogenomics. 6, ( 8 ) 873 – 877.
dc.identifier.citedreferenceMcLeod, H.L., 2013. Cancer pharmacogenomics: early promise, but concerted effort needed. (Electronic version) Science (New York, N.Y.). 339, ( 6127 ) 1563 – 1566.
dc.identifier.citedreferenceNasri, S., Anjomshoaa, A., Song, S., Guilford, P., McNoe, L., Black, M., 2010. Oligonucleotide array outperforms SNP array on formalin-fixed paraffin-embedded clinical samples. (Electronic version) Cancer Genet. Cytogenet. 198, ( 1 ) 1 – 6.
dc.identifier.citedreferencePatterson, S.D., Cohen, N., Karnoub, M., Truter, S.L., Emison, E., Khambata-Ford, S., 2011. Prospective-retrospective biomarker analysis for regulatory consideration: white paper from the industry pharmacogenomics working group. (Electronic version) Pharmacogenomics. 12, ( 7 ) 939 – 951.
dc.identifier.citedreferenceRae, J.M., Cordero, K.E., Scheys, J.O., Lippman, M.E., Flockhart, D.A., Johnson, M.D., 2003. Genotyping for polymorphic drug metabolizing enzymes from paraffin-embedded and immunohistochemically stained tumor samples. (Electronic version) Pharmacogenetics. 13, ( 8 ) 501 – 507.
dc.identifier.citedreferenceRae, J.M., Regan, M.M., Thibert, J.N., Gersch, C., Thomas, D., Leyland-Jones, B., 2013. Concordance between CYP2D6 genotypes obtained from tumor-derived and germline DNA. (Electronic version) J. Natl. Cancer Inst. 105, ( 17 ) 1332 – 1334.
dc.identifier.citedreferenceSchneider, B.P., Skaar, T.C., Sledge, G.W., Badve, S., Li, L., Flockhart, D.A., 2006. Analysis of angiogenesis genes from paraffin-embedded breast tumor and lymph nodes. (Electronic version) Breast Cancer Res. Treat. 96, ( 3 ) 209 – 215.
dc.identifier.citedreferenceSikora, M.J., Thibert, J.N., Salter, J., Dowsett, M., Johnson, M.D., Rae, J.M., 2011. High-efficiency genotype analysis from formalin-fixed, paraffin-embedded tumor tissues. (Electronic version) Pharmacogenomics J. 11, ( 5 ) 348 – 358.
dc.identifier.citedreferenceThompson, A., Johnson, A., Quinlan, P., Hillman, G., Fontecha, M., Bray, S., 2010. Comprehensive CYP2D6 Genotype and Adherence Affect Outcome in Breast Cancer Patients Treated with Tamoxifen Monotherapy. Springer Netherlands
dc.identifier.citedreferenceThompson, E.R., Herbert, S.C., Forrest, S.M., Campbell, I.G., 2005. Whole genome SNP arrays using DNA derived from formalin-fixed, paraffin-embedded ovarian tumor tissue. (Electronic version) Hum. Mutat. 26, ( 4 ) 384 – 389.
dc.identifier.citedreferencevan Huis-Tanja, L., Kweekel, D., Gelderblom, H., Koopman, M., Punt, K., Guchelaar, H.J., 2013. Concordance of genotype for polymorphisms in DNA isolated from peripheral blood and colorectal cancer tumor samples. (Electronic version) Pharmacogenomics. 14, ( 16 ) 2005 – 2012.
dc.identifier.citedreferenceVos, H.I., van der Straaten, T., Coenen, M.J., Flucke, U., te Loo, D.M., Guchelaar, H.J., 2015. High-quality genotyping data from formalin-fixed, paraffin-embedded tissue on the drug metabolizing enzymes and transporters plus array. (Electronic version) J. Mol. Diagn. 17, ( 1 ) 4 – 9.
dc.identifier.citedreferenceXie, B., Freudenheim, J.L., Cummings, S.S., Singh, B., He, H., McCann, S.E., 2006. Accurate genotyping from paraffin-embedded normal tissue adjacent to breast cancer. (Electronic version) Carcinogenesis. 27, ( 2 ) 307 – 310.
dc.identifier.citedreferenceZhang, S., Tan, I.B., Sapari, N.S., Grabsch, H.I., Okines, A., Smyth, E.C., 2015. Technical reproducibility of single-nucleotide and size-based DNA biomarker assessment using DNA extracted from formalin-fixed, paraffin-embedded tissues. (Electronic version) J. Mol. Diagn. 17, ( 3 ) 242 – 250.
dc.identifier.citedreferenceAdank, M.A., Brogi, E., Bogomolniy, F., Wadsworth, E.A., Lafaro, K.J., Yee, C.J., 2006. Accuracy of BRCA1 and BRCA2 founder mutation analysis in formalin-fixed and paraffin-embedded (FFPE) tissue. (Electronic version) Fam. Cancer. 5, ( 4 ) 337 – 342.
dc.identifier.citedreferenceAhern, T.P., Christensen, M., Cronin-Fenton, D.P., Lunetta, K.L., Rosenberg, C.L., Sorensen, H.T., 2010. Concordance of metabolic enzyme genotypes assayed from paraffin-embedded, formalin-fixed breast tumors and normal lymphatic tissue. (Electronic version) Clin. Epidemiol. 2, 241 – 246.
dc.identifier.citedreferenceBaak-Pablo, R., Dezentje, V., Guchelaar, H.J., van der Straaten, T., 2010. Genotyping of DNA samples isolated from formalin-fixed paraffin-embedded tissues using preamplification. (Electronic version) J. Mol. Diagn. 12, ( 6 ) 746 – 749.
dc.identifier.citedreferenceBass, B.P., Engel, K.B., Greytak, S.R., Moore, H.M., 2014. A review of preanalytical factors affecting molecular, protein, and morphological analysis of formalin-fixed, paraffin-embedded (FFPE) tissue: how well do you know your FFPE specimen?. (Electronic version) Arch. Pathol. Lab. Med. 138, ( 11 ) 1520 – 1530.
dc.identifier.citedreferenceCancer Genome Atlas Network, 2012. Comprehensive molecular characterization of human colon and rectal cancer. (Electronic version) Nature. 487, ( 7407 ) 330 – 337.
dc.identifier.citedreferenceCancer Genome Atlas Network, 2012. Comprehensive molecular portraits of human breast tumours. (Electronic version) Nature. 490, ( 7418 ) 61 – 70.
dc.identifier.citedreferenceCancer Genome Atlas Research Network, 2012. Comprehensive genomic characterization of squamous cell lung cancers. (Electronic version) Nature. 489, ( 7417 ) 519 – 525.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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