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Breast cancer risk prediction models
Re: Breast cancer risk prediction models
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Mano S Selvan, Department of Biostatistics and Applied Mathematics The University of Texas M. D. Anderson Cancer Center
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mselvan{at}mdanderson.org Mano S Selvan
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Dear Editor I would like to bring to your attention an error with respect to the original article by Amir et al.[1] The paper validated a few available breast cancer risk prediction models and compared them to the Tyrer-Cuzick model.[2] From the paper by Amir et al., I understand that they used the Cyrillic plug-in to estimate breast cancer risk (Cyrillic 3.1 Version). Although, I am only familiar with Cyrillic version 2.1, according to the home page for Cyrillic 3.1, it calculates risk assessments according to the BRCAPRO and Mendel models. In their paper, the authors referred to the Ford model [3] and at times to the Claus models as the BRCAPro model, which is not correct. It will be good to clarify on this to the research community, as this paper is an important reference in breast cancer research in perspectives of risk estimation and model development. BRCAPRO [4,5] is one of the eight models available through the CancerGene program [6,7] Amir et al.[1] consistently made this mistake in their paper: in the introduction, study tools section, Table 4, Table 5, Table 9, and in Figure 1. Clarification of what models were validated for their data is needed. The risk models most widely used in breast cancer research, and in clinical and genetic counseling are the Gail model,[8] the Claus model, [9,10] BRCAPRO,[4,5] Myriad I, also called the Shattuck-Eidens model,[11] Myriad II, also called the Frank model,[12] the Couch model,[13] also known as the UPenn model, the NCI model,[14] and the Family History Assessment Tool.[15] Among them, BRCAPRO estimates the probability of an individual being a carrier of a deleterious BRCA-1 or -2 mutation, along with estimating the predicted breast cancer risk, while the Gail and Claus models are empirical models developed prior to the identification of the BRCA genes. The Myriad and Couch models are empirical models to estimate the probability of BRCA1 or BRCA2 mutations. CancerGene,[6,7] is a software program that incorporates all the aforementioned models into a single software package. After all the pedigree information and other epidemiological risk factors required for each of these models have been entered, CancerGene calculates the risk for each model separately. The best feature of the program is its ability to calculate an individual woman’s predicted risk values and outputs from all these models, allowing an oncologist, genetic counselor, researcher, or physician to compare the values of predicted risk. References 1. Amir E, Evans DG, Shenton A, Lalloo F, Moran A, Boggis C, Wilson M, Howell A. Evaluation of breast cancer risk assessment packages in the family history evaluation and screening programme. J Med Genet. 2003 Nov;40(11):807-14. 2. Tyrer JP, Duffy SW, Cuzick J. A breast cancer prediction model incorporating familial and personal risk factors. Statist. Med. 2004; 23:1111–1130 3. Ford D, Easton DF, Bishop DT, Narod SA, Goldgar DE, the Breast Cancer Linkage Consortium. Risk of cancer in BRCA-1 mutation carriers. Lancet 1994;343:692–5. 4. Berry DA, Parmigiani G, Sanchez J, et al. Probability of carrying a mutation of breast-ovarian cancer gene BRCA1 based on family history. J Natl Cancer Inst 1997; 89(3):227-238. 5. Parmigiani G, Berry D, Aguilar O. Determining carrier probabilities for breast cancer-susceptibility genes BRCA1 and BRCA2. Am J Hum Genet 1998; 62(1): 145-158. 6. Euhus DM. Understanding mathematical models for breast cancer risk assessment and counseling. Breast J 2001; 7(4):224-232. 7. Euhus DM, Smith KC, Robinson L, Stucky A, Olopade OI, Cummings S, Garber JE, Chittenden A, Mills GB, Rieger P, Esserman L, Crawford B, Hughes KS, Roche CA, Ganz PA, Seldon J, Fabian CJ, Klemp J, Tomlinson G. Pretest prediction of BRCA1 or BRCA2 mutation by risk counselors and the computer model BRCAPRO. J Natl Cancer Inst 2002; 94(11):844-851. 8. Gail MH, Brinton LA, Byar DP, et al.: Projecting individualized probabilities of developing breast cancer for white females who are being examined annually. J Natl Cancer Inst 1989; 81(24):1879-1886. 9. Claus EB, Risch N, Thompson WD. Genetic analysis of breast cancer in the cancer and steroid hormone study. Am J Hum Genet. 1991;48(2):232-42. 10. Claus EB, Risch N, Thompson WD. Autosomal dominant inheritance of early onset breast cancer:implications for risk prediction. Cancer 1994;73:643-51 11. Shattuck-Eidens D, Oliphant A, McClure M et al. BRCA1 sequence analysis in women at high risk for susceptibility mutations. Risk factor analysis and implications for genetic testing. JAMA 1997; 278:1242-1250. 12. Frank TS, Manley SA, Olopade OI et al. Sequence analysis of BRCA1 and BRCA2: Correlation of mutations with family history and ovarian cancer risk. J Clin Oncol 1998; 16:2417-2425. 13. Couch FJ, DeShano ML, Blackwood MA, et al. BRCA1 mutations in women attending clinics that evaluate the risk of breast cancer. N Engl J Med 1997; 336:1409-1415. 14. Hartge P, Struewing JP, Wacholder S, Brody LC, Tucker MA. The prevalence of common BRCA1 and BRCA2 mutations among Ashkenazi Jews. Am J Hum Genet. 1999 Apr;64(4):963-70. 15. Gilpin CA, Carson N, Hunter AG. A preliminary validation of a family history assessment form to select women at risk for breast or ovarian cancer for referral to a genetics center. Clin Genet 2000; 58(4):299-308. Cyrillic 3.0 pedigree software. Accessed on: March 30th, 2004. Details available at: http://www.exetersoftware.com/cat/cyrillic/cyrillic.html
The University of Texas Southwestern Medical Center at Dallas. CancerGene. Available at: http://www3.utsouthwestern.edu/cancergene/index.htm |
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D Gareth Evans, Professor St. Mary’s Hospital, Manchester, E Amir, A Shenton, A Howell
Send letter to journal:
gareth.evans{at}cmmc.nhs.uk D Gareth Evans, et al.
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Dear Editor We thank Dr Selvan for his comments [1] on our paper.[2] Cyrillic 3 does indeed use the BRCAPRO and MENDEL models. With regards to our use of BRCAPRO, we would like to draw his attention to the official Cyrillic 3 homepage [3] where it states clearly that the BRCAPRO plug-in calculates risk based on the “Bayes’ rules of determination of the probability of a mutation, given family history. An estimate of the mutation frequencies in the normal population [4,5] and among Ashkenazi Jews [6] provides the probability of the mutation in the proband, prior to the ascertainment of family history.” In summary, the BRCAPRO software included in Cyrillic 3 gives the option of using three population models on which it bases its results - Claus et al 1994, Ford et al 1998 and Streuwing et al 1997. The guidelines for using BRCAPRO within Cyrillic 3 were followed and we generated results for unaffected family members using both the Ford and Claus results. As was clearly stated in our paper "Claus and Ford risks were calculated using a plug-in for the Cyrillic 3 package, a software package designed to display family pedigrees for use in clinical genetics and genetic counselling." All results were subsequently described as Claus or Ford. Having to state that they had been derived from a BRCAPRO plug-in every time would have been unwieldy. In the Study tools section we clearly state: "Computerized risk assessment packages Gail, BRCAPRO (Claus and Ford) and Tyrer-Cuzick were tested on this population". While we were a little ambiguous in the paragraphs before this, we think this sentence is perfectly clear in explaining what we were doing and as the correspondent acknowledges, he is not familiar with Cyrillic 3. We are not sure how much clearer we could have been. With regard to the rest of the correspondence this appears to be an advert to use the CancerGene software programme. Although Dr Selvan does distinguish between models that merely predict the likelihood of a mutation being present (Myriad I and II, [7]), those that just predict breast cancer risk over time [8,9] and those that purport to do both (BRCAPRO) our paper was only addressing breast cancer risk. Although we did not use a direct download of the BRCAPRO, we have no reason to believe that the results would have been any different if we had. BRCAPRO appears to underestimate breast cancer risk over time because it assumes that all inherited breast cancer is due to mutations in BRCA1 or BRCA2. The Ford element of this involves the use of the Ford et al [5] penetrance figures in the BRCAPRO algorithm as opposed to those of Claus [8]. References
1. Selvan, M. Breast cancer risk prediction models. Rapid Respone, www.jmedgenet.com. 2. Amir E, Evans DG, Shenton A, Lalloo F, Moran A, Boggis C, Wilson M, Howell A. Evaluation of breast cancer risk assessment packages in the family history evaluation and screening programme. J Med Genet. 2003 Nov;40(11):807-14. 3. About BRCAPro in Cyrillic 3. Accessed on: 14th April 2004. Details available at: http://www.cyrillicsoftware.com/support/cy3brca.htm 4. Claus EB, Schildkraut JM, Thompson WD, Risch NJ. The genetic attributable risk of breast and ovarian cancer. Cancer. 1996;77(11):2318- 24. 5. Ford D, Easton DF, Stratton M, Narod S, Goldgar D, Devilee P, Bishop DT, Weber B, Lenoir G, Chang-Claude J, Sobol H, Teare MD, Struewing J, Arason A, Scherneck S, Peto J, Rebbeck TR, Tonin P, Neuhausen S, Barkardottir R, Eyfjord J, Lynch H, Ponder BA, Gayther SA, Zelada-Hedman M and the Breast Cancer Linkage Consortium. Genetic Heterogeneity and Penetrance Analysis of the BRCA1 and BRCA2 genes in breast cancer families. Am J Hum Genet 1998;62:676-89 6. Struewing JP, Hartge P, Wacholder S, Baker SM, Berlin M, McAdams M, Timmerman MM, Brody LC, Tucker MA (1997) The risk of cancer associated with specific mutations of BRCA1 and BRCA2 among Ashkenazi Jews. New England Journal of Medicine 336:1401-1408 7. Couch FJ, DeShano ML, Blackwood MA, et al. BRCA1 mutations in women attending clinics that evaluate the risk of breast cancer. N Engl J Med 1997; 336:1409-1415. 8. Claus EB, Risch N, Thompson WD. Autosomal dominant inheritance of early onset breast cancer:implications for risk prediction. Cancer 1994;73:643-51 9. Gail MH, Brinton LA, Byar DP, et al.: Projecting individualized probabilities of developing breast cancer for white females who are being examined annually. J Natl Cancer Inst 1989; 81(24):1879-1886. Berry DA, Parmigiani G, Sanchez J, et al. Probability of carrying a mutation of breast-ovarian cancer gene BRCA1 based on family history. J Natl Cancer Inst 1997; 89(3):227-238. Cyrillic 3.0 pedigree software. Accessed on: March 30th, 2004. Details available at: http://www.exetersoftware.com/cat/cyrillic/cyrillic.html Frank TS, Manley SA, Olopade OI et al. Sequence analysis of BRCA1 and BRCA2: Correlation of mutations with family history and ovarian cancer risk. J Clin Oncol 1998; 16:2417-2425. Parmigiani G, Berry D, Aguilar O. Determining carrier probabilities for breast cancer-susceptibility genes BRCA1 and BRCA2. Am J Hum Genet 1998; 62(1): 145-158. Shattuck-Eidens D, Oliphant A, McClure M et al. BRCA1 sequence analysis in women at high risk for susceptibility mutations. Risk factor analysis and implications for genetic testing. JAMA 1997; 278:1242-1250. The University of Texas Southwestern Medical Center at Dallas. CancerGene. Available at http://www3.utsouthwestern.edu/cancergene/index.ht |
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