1
|
Gillis N, Etheridge AS, Patil SA, Hayes DN, Hayward MC, Auman JT, Parker JS, Innocenti F. Sequencing of genes of drug response in tumor DNA and implications for precision medicine in cancer patients. THE PHARMACOGENOMICS JOURNAL 2023:10.1038/s41397-023-00299-7. [PMID: 36709390 DOI: 10.1038/s41397-023-00299-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/30/2023]
Abstract
Tumor DNA sequencing is becoming standard-of-care for patient treatment decisions. We evaluated genotype concordance between tumor DNA and genomic DNA from blood and catalogued functional effects of somatic mutations in 21 drug response genes in 752 solid tumor patients. Using a threshold of 10% difference between tumor and blood DNA variant allele fraction (VAF), concordance for heterogenous genotype calls was 78% and increased to 97.5% using a 30% VAF threshold. Somatic mutations were observed in all 21 drug response genes, and 44% of patients had at least one somatic mutation in these genes. In tumor DNA, eight patients had a frameshift mutation in CYP2C8, which metabolizes taxanes. Overall, somatic copy number losses were more frequent than gains, including for CYP2C19 and CYP2D6 which had the most frequent copy number losses. However, copy number gains in TPMT were more than four times as common as losses. Seven % of patients had copy number gains in ABCB1, a multidrug resistance transporter of anti-cancer agents. These results demonstrate tumor-only DNA sequencing might not be reliable to call germline genotypes of drug response variants.
Collapse
Affiliation(s)
- Nancy Gillis
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.,Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Amy S Etheridge
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
| | - Sushant A Patil
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - D Neil Hayes
- Department of Medicine, Hematology/Oncology, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.,Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Michele C Hayward
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - J Todd Auman
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Federico Innocenti
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
2
|
Porta C, Cosmai L, Rizzo M, Melazzini M. Single nucleotide polymorphisms in angiogenesis-related genes and outcomes from antiangiogenic therapies in renal cell carcinoma: really a step towards personalized oncology, or not at all? ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:S15. [PMID: 31032296 DOI: 10.21037/atm.2019.01.51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Camillo Porta
- Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy.,Division of Translational Oncology, I.R.C.C.S. Istituti Clinici Scientifici Maugeri, Pavia, Italy
| | - Laura Cosmai
- Division of Nephrology and Dialysis, A.S.S.T. Santi Paolo e Carlo, San Carlo Borromeo Hospital, Milan, Italy
| | - Mimma Rizzo
- Division of Translational Oncology, I.R.C.C.S. Istituti Clinici Scientifici Maugeri, Pavia, Italy
| | - Mario Melazzini
- Scientific Direction, I.R.C.C.S. Istituti Clinici Scientifici Maugeri, Pavia, Italy
| |
Collapse
|
3
|
Smyth E, Zhang S, Cunningham D, Wotherspoon A, Soong R, Peckitt C, Valeri N, Fassan M, Rugge M, Okines A, Allum W, Stenning S, Nankivell M, Langley R, Tan P. Pharmacogenetic Analysis of the UK MRC (Medical Research Council) MAGIC Trial: Association of Polymorphisms with Toxicity and Survival in Patients Treated with Perioperative Epirubicin, Cisplatin, and 5-fluorouracil (ECF) Chemotherapy. Clin Cancer Res 2017; 23:7543-7549. [PMID: 28972045 PMCID: PMC6175041 DOI: 10.1158/1078-0432.ccr-16-3142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/21/2017] [Accepted: 09/26/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Germline polymorphisms may affect chemotherapy efficacy and toxicity. We examined the effect of polymorphisms in drug metabolism and DNA repair genes on pathologic response rates, survival, and toxicity for patients randomized to surgery alone or perioperative ECF chemotherapy in the MRC MAGIC trial.Experimental Design: DNA was extracted from nontumor resection formalin-fixed paraffin-embedded (FFPE) blocks. ERCC1, ERCC2, XRCC1, DYPD, and OPRT SNPs were evaluated using Sequenom, GSTP1, GSTT1 deletion, and TYMS (TS) 5' 2R/3R using multiplex PCR. Post PCR amplification, TS 2R/3R and GSTT1 samples underwent gel electrophoresis.Results: Polymorphism data were available for 289 of 456 (63.4%) operated patients. No polymorphism was statistically significantly associated with pathologic response to chemotherapy. Median overall survival (OS) for patients treated with surgery alone with any TS genotype was not different (1.76 years 2R/2R, 1.68 years 2R/3R, 2.09 years 3R/3R). Median OS for patients with a TS 2R/2R genotype treated with chemotherapy was not reached, whereas median OS for 2R/3R and 3R/3R patients were 1.44 and 1.60 years, respectively (log rank P value = 0.0053). The P value for the interaction between treatment arm and genotype (3R/3R and 3R/2R vs. 2R/2R) was 0.029. No polymorphism was statistically significantly associated with chemotherapy toxicity.Conclusions: In MAGIC, patients with a TS 2R/2R genotype appeared to derive a larger benefit from perioperative ECF chemotherapy than patients with 3R containing genotypes. Further exploration of this potential predictive biomarker in this patient population is warranted. Clin Cancer Res; 23(24); 7543-9. ©2017 AACR.
Collapse
Affiliation(s)
- Elizabeth Smyth
- Department of Gastrointestinal Oncology and Lymphoma, Royal Marsden Hospital, London & Sutton, United Kingdom
| | - Shenli Zhang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - David Cunningham
- Department of Gastrointestinal Oncology and Lymphoma, Royal Marsden Hospital, London & Sutton, United Kingdom.
| | - Andrew Wotherspoon
- Department of Pathology, Royal Marsden Hospital, London & Sutton, United Kingdom
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Clare Peckitt
- Department of Clinical Research and Development, Royal Marsden Hospital, London & Sutton, United Kingdom
| | - Nicola Valeri
- Department of Gastrointestinal Oncology and Lymphoma, Royal Marsden Hospital, London & Sutton, United Kingdom
- Department of Molecular Pathology, The Institute of Cancer Research London & Sutton, United Kingdom
| | - Matteo Fassan
- Department of Medicine, Surgical Pathology & Cytopathology Unit, University of Padua, Padua, Italy
| | - Massimo Rugge
- Department of Medicine, Surgical Pathology & Cytopathology Unit, University of Padua, Padua, Italy
| | - Alicia Okines
- Department of Gastrointestinal Oncology and Lymphoma, Royal Marsden Hospital, London & Sutton, United Kingdom
| | - William Allum
- Department of Medicine, Surgical Pathology & Cytopathology Unit, University of Padua, Padua, Italy
| | - Sally Stenning
- Department of Surgery, Royal Marsden Hospital, London & Sutton, United Kingdom
| | - Matthew Nankivell
- Department of Surgery, Royal Marsden Hospital, London & Sutton, United Kingdom
| | - Ruth Langley
- Medical Research Council Clinical Trials Unit at UCL, London, United Kingdom
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Cellular and Molecular Research, National Cancer Centre, Singapore, Singapore
- Cancer Therapeutics and Stratified Oncology Group, Genome Institute of Singapore, Singapore, Singapore
| |
Collapse
|
4
|
Emami NC, Leong L, Wan E, Van Blarigan EL, Cooperberg MR, Tenggara I, Carroll PR, Chan JM, Witte JS, Simko JP. Tissue Sources for Accurate Measurement of Germline DNA Genotypes in Prostate Cancer Patients Treated With Radical Prostatectomy. Prostate 2017; 77:425-434. [PMID: 27900799 PMCID: PMC5479703 DOI: 10.1002/pros.23283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/03/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Benign tissue from a tumor-containing organ is commonly the only available source for obtaining a patient's unmutated genome for use in cancer research. While it is critical to identify histologically normal tissue that is independent of the tumor lineage, few additional considerations are applied to the choice of this material for such measurements. METHODS Normal formalin-fixed, paraffin-embedded seminal vesicle, and urethral tissues, in addition to whole blood, were collected from 31 prostate cancer patients having undergone radical prostatectomy. Genotype concordance was evaluated for DNA from each tissue source in relation to whole blood. RESULTS Overall, there was a greater genotype call rate for DNA derived from urethral tissue (97.0%) in comparison with patient-matched seminal vesicle tissues (95.9%, P = 0.0015). Furthermore, with reference to patient-matched whole blood, urethral samples exhibited higher genotype concordance (94.1%) than that of seminal vesicle samples (92.5%, P = 0.035). CONCLUSIONS These findings highlight the heterogeneity between diverse sources of DNA in genotype measurement and motivate the consideration of normal tissue biases in tumor-normal analyses. Prostate 77: 425-434, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Nima C. Emami
- Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Lancelote Leong
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Eunice Wan
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
| | - Erin L. Van Blarigan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Matthew R. Cooperberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Imelda Tenggara
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Peter R. Carroll
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - June M. Chan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - John S. Witte
- Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Correspondence to: Jeffry P. Simko, 1825 4th St., Room M2360, San Francisco, CA 94158, 415-353-7171 (Phone), 415-353-7094 (Fax), . John S. Witte, 1450 3rd St., San Francisco, CA 94158, 415-502-6882 (Phone), 415-476-1356 (Fax),
| | - Jeffry P. Simko
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Anatomic Pathology, University of California, San Francisco, San Francisco, California
- Correspondence to: Jeffry P. Simko, 1825 4th St., Room M2360, San Francisco, CA 94158, 415-353-7171 (Phone), 415-353-7094 (Fax), . John S. Witte, 1450 3rd St., San Francisco, CA 94158, 415-502-6882 (Phone), 415-476-1356 (Fax),
| |
Collapse
|
5
|
Shao W, Ge Y, Ma G, Du M, Chu H, Qiang F, Zhang Z, Wang M. Evaluation of genome-wide genotyping concordance between tumor tissues and peripheral blood. Genomics 2017; 109:108-112. [DOI: 10.1016/j.ygeno.2017.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 01/04/2017] [Accepted: 01/24/2017] [Indexed: 11/29/2022]
|
6
|
Piqueret-Stephan L, Marcaillou C, Reyes C, Honoré A, Letexier M, Gentien D, Droin N, Lacroix L, Scoazec JY, Vielh P. Massively parallel DNA sequencing from routinely processed cytological smears. Cancer Cytopathol 2015; 124:241-53. [DOI: 10.1002/cncy.21639] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 10/03/2015] [Accepted: 10/05/2015] [Indexed: 11/07/2022]
Affiliation(s)
| | | | - Cécile Reyes
- Genomic Platform, Translational Research Department; Institut Curie; Paris France
| | - Aurélie Honoré
- Analyse Moléculaire, Modélisation et Imagerie de la maladie Cancéreuse (AMMICa) CNRS Unité Mixte de Service 3655, INSERM US23, Paris Sud University), Translational Research Laboratory; Gustave Roussy Villejuif France
| | | | - David Gentien
- Genomic Platform, Translational Research Department; Institut Curie; Paris France
| | - Nathalie Droin
- Gustave Roussy; Villejuif France
- Unit 1009, INSERM; Villejuif France
| | - Ludovic Lacroix
- Analyse Moléculaire, Modélisation et Imagerie de la maladie Cancéreuse (AMMICa) CNRS Unité Mixte de Service 3655, INSERM US23, Paris Sud University), Translational Research Laboratory; Gustave Roussy Villejuif France
- Department of Biopathology; Gustave Roussy Villejuif France
| | - Jean-Yves Scoazec
- Analyse Moléculaire, Modélisation et Imagerie de la maladie Cancéreuse (AMMICa) CNRS Unité Mixte de Service 3655, INSERM US23, Paris Sud University), Translational Research Laboratory; Gustave Roussy Villejuif France
- Department of Biopathology; Gustave Roussy Villejuif France
| | - Philippe Vielh
- Gustave Roussy; Villejuif France
- Unité Mixte de Recherche 981, INSERM; Villejuif France
- Analyse Moléculaire, Modélisation et Imagerie de la maladie Cancéreuse (AMMICa) CNRS Unité Mixte de Service 3655, INSERM US23, Paris Sud University), Translational Research Laboratory; Gustave Roussy Villejuif France
- Department of Biopathology; Gustave Roussy Villejuif France
| |
Collapse
|
7
|
Genotyping concordance in DNA extracted from formalin-fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses. Mol Oncol 2015; 9:1868-76. [PMID: 26276228 DOI: 10.1016/j.molonc.2015.07.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 01/01/2023] Open
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.
Collapse
|