Daniel L Hertz1, Kelley M Kidwell2, Jacklyn N Thibert3, Christina Gersch4, Meredith M Regan5, Todd C Skaar6, N Lynn Henry7, Daniel F Hayes8, Catherine H Van Poznak9, James M Rae10. 1. Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI, USA. Electronic address: DLHertz@med.umich.edu. 2. Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA. Electronic address: kidwell@umich.edu. 3. Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Health System, Ann Arbor, MI, USA. Electronic address: jthibert@med.umich.edu. 4. Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Health System, Ann Arbor, MI, USA. Electronic address: clgersch@med.umich.edu. 5. Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. Electronic address: mregan@jimmy.harvard.edu. 6. Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN, USA. Electronic address: tskaar@iu.edu. 7. Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Health System, Ann Arbor, MI, USA; Breast Oncology Program, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA. Electronic address: norahh@med.umich.edu. 8. Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Health System, Ann Arbor, MI, USA; Breast Oncology Program, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA. Electronic address: hayesdf@med.umich.edu. 9. Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Health System, Ann Arbor, MI, USA; Breast Oncology Program, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA. Electronic address: cvanpoz@med.umich.edu. 10. Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Health System, Ann Arbor, MI, USA. Electronic address: jimmyrae@med.umich.edu.
Abstract
BACKGROUND: Cancer pharmacogenetic studies use archival tumor samples as a DNA source when germline DNA is unavailable. Genotyping DNA from formalin-fixed paraffin embedded tumors (FFPE-T) may be inaccurate due to FFPE storage, genetic aberrations, and/or insufficient DNA extraction. Our objective was to assess the extent and source of genotyping inaccuracy from FFPE-T DNA and demonstrate analytical validity of FFPE-T genotyping of candidate single nucleotide polymorphisms (SNPs) for pharmacogenetic analyses. METHODS: Cancer pharmacogenetics SNPs were genotyped by Sequenom MassARRAYs in DNA harvested from matched FFPE-T, FFPE lymph node (FFPE-LN), and whole blood leukocyte samples obtained from breast cancer patients. No- and discordant-call rates were calculated for each tissue type and SNP. Analytical validity was defined as any SNP with <5% discordance between FFPE-T and blood and <10% discordance plus no-calls. RESULTS: Matched samples from 114 patients were genotyped for 247 SNPs. No-call rate in FFPE-T was greater than FFPE-LN and blood (4.3% vs. 3.0% vs. 0.5%, p < 0.001). Discordant-call rate between FFPE-T and blood was very low, but greater than that between FFPE-LN and blood (1.1% vs. 0.3%, p < 0.001). Samples with heterozygous genotypes were more likely to be no- or discordantly-called in either tissue (p < 0.001). Analytical validity of FFPE-T genotyping was demonstrated for 218 (88%) SNPs. CONCLUSIONS: No- and discordant-call rates were below concerning thresholds, confirming that most SNPs can be accurately genotyped from FFPE-T on our Sequenom platform. FFPE-T is a viable DNA source for prospective-retrospective pharmacogenetic analyses of clinical trial cohorts.
BACKGROUND:Cancer pharmacogenetic studies use archival tumor samples as a DNA source when germline DNA is unavailable. Genotyping DNA from formalin-fixed paraffin embedded tumors (FFPE-T) may be inaccurate due to FFPE storage, genetic aberrations, and/or insufficient DNA extraction. Our objective was to assess the extent and source of genotyping inaccuracy from FFPE-T DNA and demonstrate analytical validity of FFPE-T genotyping of candidate single nucleotide polymorphisms (SNPs) for pharmacogenetic analyses. METHODS:Cancer pharmacogenetics SNPs were genotyped by Sequenom MassARRAYs in DNA harvested from matched FFPE-T, FFPE lymph node (FFPE-LN), and whole blood leukocyte samples obtained from breast cancerpatients. No- and discordant-call rates were calculated for each tissue type and SNP. Analytical validity was defined as any SNP with <5% discordance between FFPE-T and blood and <10% discordance plus no-calls. RESULTS: Matched samples from 114 patients were genotyped for 247 SNPs. No-call rate in FFPE-T was greater than FFPE-LN and blood (4.3% vs. 3.0% vs. 0.5%, p < 0.001). Discordant-call rate between FFPE-T and blood was very low, but greater than that between FFPE-LN and blood (1.1% vs. 0.3%, p < 0.001). Samples with heterozygous genotypes were more likely to be no- or discordantly-called in either tissue (p < 0.001). Analytical validity of FFPE-T genotyping was demonstrated for 218 (88%) SNPs. CONCLUSIONS: No- and discordant-call rates were below concerning thresholds, confirming that most SNPs can be accurately genotyped from FFPE-T on our Sequenom platform. FFPE-T is a viable DNA source for prospective-retrospective pharmacogenetic analyses of clinical trial cohorts.
Authors: Soroush Nasri; Ahmad Anjomshoaa; Sarah Song; Parry Guilford; Les McNoe; Michael Black; Vicky Phillips; Anthony Reeve; Bostjan Humar Journal: Cancer Genet Cytogenet Date: 2010-04-01
Authors: Thomas P Ahern; Mariann Christensen; Deirdre P Cronin-Fenton; Kathryn L Lunetta; Carol L Rosenberg; Henrik Toft Sørensen; Timothy L Lash; Stephen Hamilton-Dutoit Journal: Clin Epidemiol Date: 2010-10-22 Impact factor: 4.790
Authors: Daniel L Hertz; Kelley M Kidwell; Jacklyn N Thibert; Christina Gersch; Meredith M Regan; Todd C Skaar; N Lynn Henry; Daniel F Hayes; Catherine H Van Poznak; James M Rae Journal: Mol Oncol Date: 2015-07-29 Impact factor: 6.603
Authors: Emmanuel Amankwaa-Frempong; Francis Agyemang Yeboah; Samuel Blay Nguah; Lisa A Newman Journal: JAMA Surg Date: 2017-08-01 Impact factor: 14.766
Authors: Thomas P Ahern; Daniel L Hertz; Per Damkier; Bent Ejlertsen; Stephen J Hamilton-Dutoit; James M Rae; Meredith M Regan; Alastair M Thompson; Timothy L Lash; Deirdre P Cronin-Fenton Journal: Am J Epidemiol Date: 2016-12-17 Impact factor: 4.897
Authors: Amanda Kravitz; Ron Tyler; B Murali Manohar; B Samuel Masilamoni Ronald; Michael T Collins; Nammalwar Sriranganathan Journal: Vet Res Commun Date: 2022-05-26 Impact factor: 2.459
Authors: Catherine Van Poznak; Evan L Reynolds; Cherry L Estilo; Mimi Hu; Bryan Paul Schneider; Daniel L Hertz; Christina Gersch; Jacklyn Thibert; Dafydd Thomas; Mousumi Banerjee; James M Rae; Daniel F Hayes Journal: Oral Dis Date: 2020-12-14 Impact factor: 3.511
Authors: Cathrine F Hjorth; Per Damkier; Tore B Stage; Søren Feddersen; Stephen Hamilton-Dutoit; Mikael Rørth; Bent Ejlertsen; Timothy L Lash; Thomas P Ahern; Henrik T Sørensen; Deirdre Cronin-Fenton Journal: Breast Cancer Res Treat Date: 2022-04-30 Impact factor: 4.624
Authors: Susana Nunes Silva; Bruno Costa Gomes; Saudade André; Ana Félix; António Sebastião Rodrigues; José Rueff Journal: Breast Cancer Res Treat Date: 2021-05-03 Impact factor: 4.872