Identification of mutational patterns in different oncogenes and tumor suppressor genes play role in human breast cancer. A study from Punjab, Pakistan

Main Article Content

Yasir Nawaz
Saba Munir
Fouzia Tanvir
Imran Majeed
Asma Umar
Aqeela Nawaz
Hafiza Fizzah Riaz
Alia Iqbal
Ambar Ayoub
Sadaf Ambreen
Muhammad Wajid


Breast cancer, Oncogenes, Tumor suppressor genes, Somatic mutations, Exons, Whole exome sequencing, Breast cancer, Oncogenes, Tumor suppressor genes, Somatic mutations, Exons, Whole exome sequencing


Background: Cancer is an unequal growth of cells that have capability to invade and spread in parts of an organism. It starts from the breast tissues, frequently from inner covering of milk channels. Objective: The objective of study was to identify novel somatic alternations in oncogenes and tumor suppressor genes of breast cancer.

Methods: Whole-exome sequencing was performed in DNA extracted from tumor samples of people from Jinnah hospital Lahore, Pakistan.

Results: There were nineteen people of age group 27 to 73 and tissue specimens were collected from six patients. Age group, ER and PR status both show non-significant difference. The frequency of 20 mutated tumor suppressor genes includes BRCA1 (66.67%), BRCA2 (83.33%), CARS (50%), CHEK2 (33.33%), DDX5 (50%), FH (66.67%), MEN1 (33.33%), NF1 (66.67%), NF2 (33.33%), NUP98 (66.67%), PALB2 (66.67%), PTEN (50%), SUFU (33.33%), TP53 (50%) and VHL (33.33%, and 22 mutated oncogenes were ABL1 (33.33%), AKT2 (83.33%), ATF1 (83.33%), BCL2 (50%), BCL3 (50%), BCL6 (50%), BCR (50%), BRAF (50%), NUP214 (83.33%), PIK3CA (83.33%), PIM1 (50%), and USP6 (50%). More number of Synonymous SNV mutations was observed in both oncogenes and tumor suppressor genes. Amino acid variations and deletion was detected in various exonic regions of genes.

Conclusion: All people show invasive ductal breast carcinoma. Synonymous SNV mutations show high frequency. BRCA2 as tumor suppressor and AKT2, ATF1, NUP214 and PIK3CA as oncogene show high mutated frequency.  More data is needed to clearly state the role of these altered genes in breast cancer patients.

Abstract 96 | PDF Downloads 46


1. Siegel R, Ma J, Zou Z, Jemal AJCacjfc. Cancer statistics, 2014. 2014;64(1):9-29.
2. Ferlay J, Soerjomataram I, Dikshit R, Eser S, Mathers C, Rebelo M, et al. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. 2015;136(5):E359-E86.
3. Parkin D, Pisani P, Ferlay JJIjoc. Estimates of the worldwide incidence of eighteen major cancers in 1985. 1993;54(4):594-606.
4. Mahmood S, Rana TF, Ahmad MJAoKEMU. Common determinants of Ca breast-a case control study in Lahore. 2006;12(2).
5. Porter PLJSpdM. Global trends in breast cancer incidence and mortality. 2009;51:s141-s6.
6. Babu GR, Lakshmi SB, Thiyagarajan JAJAPJoCP. Epidemiological correlates of breast cancer in South India. 2013;14(9):5077-83.
7. Ali I, Wani WA, Saleem KJCt. Cancer scenario in India with future perspectives. 2011;8.
8. Balasubramaniam S, Rotti S, Vivekanandam SJIjoc. Risk factors of female breast carcinoma: a case control study at Puducherry. 2013;50(1):65-70.
9. Brigham, Hospital Ws, 13 HMSCLPPJKR, 25 GdaBCoMCCJDLA, Ilya IfSBRSKRBBBBRETLJTVZWS. Comprehensive molecular portraits of human breast tumours. 2012;490(7418):61-70.
10. Perou CM, Sørlie T, Eisen MB, Van De Rijn M, Jeffrey SS, Rees CA, et al. Molecular portraits of human breast tumours. 2000;406(6797):747-52.
11. Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, et al. The landscape of cancer genes and mutational processes in breast cancer. 2012;486(7403):400-4.
12. Zhang Y, Cai Q, Shu X-O, Gao Y-T, Li C, Zheng W, et al. Whole-exome sequencing identifies novel somatic mutations in chinese breast cancer patients. 2015;9(4).
13. Dalgliesh GL, Furge K, Greenman C, Chen L, Bignell G, Butler A, et al. Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. 2010;463(7279):360-3.
14. Van Haaften G, Dalgliesh GL, Davies H, Chen L, Bignell G, Greenman C, et al. Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer. 2009;41(5):521-3.
15. Melchor L, Benítez JJHg. The complex genetic landscape of familial breast cancer. 2013;132:845-63.
16. Claus EB, Schildkraut JM, Thompson WD, Risch NJJCIIJotACS. The genetic attributable risk of breast and ovarian cancer. 1996;77(11):2318-24.
17. Roy R, Chun J, Powell SNJNRC. BRCA1 and BRCA2: different roles in a common pathway of genome protection. 2012;12(1):68-78.
18. Mavaddat N, Antoniou AC, Easton DF, Garcia-Closas MJMo. Genetic susceptibility to breast cancer. 2010;4(3):174-91.
19. Michailidou K, Beesley J, Lindstrom S, Canisius S, Dennis J, Lush MJ, et al. Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer. 2015;47(4):373-80.
20. Dai X, Li T, Bai Z, Yang Y, Liu X, Zhan J, et al. Breast cancer intrinsic subtype classification, clinical use and future trends. 2015;5(10):2929.
21. Feng Y, Spezia M, Huang S, Yuan C, Zeng Z, Zhang L, et al. Breast cancer development and progression: Risk factors, cancer stem cells, signaling pathways, genomics, and molecular pathogenesis. Genes & diseases. 2018;5(2):77-106.
22. Bertucci F, Finetti P, Birnbaum D. Basal breast cancer: a complex and deadly molecular subtype. Current molecular medicine. 2012;12(1):96-110.
23. Easton DFJBCR. How many more breast cancer predisposition genes are there? 1999;1(1):1-4.
24. Risch HA, McLaughlin JR, Cole DE, Rosen B, Bradley L, Fan I, et al. Population BRCA1 and BRCA2 mutation frequencies and cancer penetrances: a kin–cohort study in Ontario, Canada. 2006;98(23):1694-706.
25. Begg CB, Haile RW, Borg Å, Malone KE, Concannon P, Thomas DC, et al. Variation of breast cancer risk among BRCA1/2 carriers. 2008;299(2):194-201.
26. Chen S, Parmigiani GJJocoojotASoCO. Meta-analysis of BRCA1 and BRCA2 penetrance. 2007;25(11):1329.
27. Brose MS, Rebbeck TR, Calzone KA, Stopfer JE, Nathanson KL, Weber BLJJotNCI. Cancer risk estimates for BRCA1 mutation carriers identified in a risk evaluation program. 2002;94(18):1365-72.
28. van der Kolk DM, de Bock GH, Leegte BK, Schaapveld M, Mourits MJ, de Vries J, et al. Penetrance of breast cancer, ovarian cancer and contralateral breast cancer in BRCA1 and BRCA2 families: high cancer incidence at older age. 2010;124:643-51.
29. Hall JM, Lee MK, Newman B, Morrow JE, Anderson LA, Huey B, et al. Linkage of early-onset familial breast cancer to chromosome 17q21. 1990;250(4988):1684-9.
30. Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, Tavtigian S, et al. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science. 1994;266(5182):66-71.
31. Wooster R, Bignell G, Lancaster J, Swift S, Seal S, Mangion J, et al. Identification of the breast cancer susceptibility gene BRCA2. Nature. 1995;378(6559):789-92.
32. Wooster R, Neuhausen SL, Mangion J, Quirk Y, Ford D, Collins N, et al. Localization of a breast cancer susceptibility gene, BRCA2, to chromosome 13q12-13. Science. 1994;265(5181):2088-90.
33. Chai X, Friebel TM, Singer CF, Evans DG, Lynch HT, Isaacs C, et al. Use of risk-reducing surgeries in a prospective cohort of 1,499 BRCA1 and BRCA2 mutation carriers. 2014;148:397-406.
34. Finch AP, Lubinski J, Møller P, Singer CF, Karlan B, Senter L, et al. Impact of oophorectomy on cancer incidence and mortality in women with a BRCA1 or BRCA2 mutation. 2014;32(15):1547.
35. Easton D. Breast cancer genes—what are the real risks? Nature genetics. 1997;16(3):210-1.
36. De Jong M, Nolte I, Te Meerman G, Van der Graaf W, Oosterwijk J, Kleibeuker J, et al. Genes other than BRCA1 and BRCA2 involved in breast cancer susceptibility. Journal of medical genetics. 2002;39(4):225-42.
37. Nusbaum R, Vogel KJ, Ready K. Susceptibility to breast cancer: hereditary syndromes and low penetrance genes. Breast disease. 2007;27(1):21-50.
38. Hoskins KF, Stopfer JE, Calzone KA, Merajver SD, Rebbeck TR, Garber JE, et al. Assessment and counseling for women with a family history of breast cancer: a guide for clinicians. Jama. 1995;273(7):577-85.
39. Tung N, Lin NU, Kidd J, Allen BA, Singh N, Wenstrup RJ, et al. Frequency of germline mutations in 25 cancer susceptibility genes in a sequential series of patients with breast cancer. 2016;34(13):1460.
40. Rafnar T, Gudbjartsson DF, Sulem P, Jonasdottir A, Sigurdsson A, Jonasdottir A, et al. Mutations in BRIP1 confer high risk of ovarian cancer. 2011;43(11):1104-7.
41. Ramus SJ, Song H, Dicks E, Tyrer JP, Rosenthal AN, Intermaggio MP, et al. Germline mutations in the BRIP1, BARD1, PALB2, and NBN genes in women with ovarian cancer. 2015;107(11):djv214.
42. Loveday C, Turnbull C, Ruark E, Xicola RMM, Ramsay E, Hughes D, et al. Germline RAD51C mutations confer susceptibility to ovarian cancer. 2012;44(5):475-6.
43. Song H, Dicks E, Ramus SJ, Tyrer JP, Intermaggio MP, Hayward J, et al. Contribution of germline mutations in the RAD51B, RAD51C, and RAD51D genes to ovarian cancer in the population. 2015;33(26):2901.
44. Pelttari LM, Heikkinen T, Thompson D, Kallioniemi A, Schleutker J, Holli K, et al. RAD51C is a susceptibility gene for ovarian cancer. 2011;20(16):3278-88.
45. Meindl A, Hellebrand H, Wiek C, Erven V, Wappenschmidt B, Niederacher D, et al. Germline mutations in breast and ovarian cancer pedigrees establish RAD51C as a human cancer susceptibility gene. 2010;42(5):410-4.
46. Loveday C, Turnbull C, Ramsay E, Hughes D, Ruark E, Frankum JR, et al. Germline mutations in RAD51D confer susceptibility to ovarian cancer. 2011;43(9):879-82.
47. Churpek JE, Walsh T, Zheng Y, Moton Z, Thornton AM, Lee MK, et al. Inherited predisposition to breast cancer among African American women. 2015;149:31-9.
48. Couch FJ, Hart SN, Sharma P, Toland AE, Wang X, Miron P, et al. Inherited mutations in 17 breast cancer susceptibility genes among a large triple-negative breast cancer cohort unselected for family history of breast cancer. 2015;33(4):304.
49. Kurian AW, Hare EE, Mills MA, Kingham KE, McPherson L, Whittemore AS, et al. Clinical evaluation of a multiple-gene sequencing panel for hereditary cancer risk assessment. 2014;32(19):2001.
50. Tung N, Battelli C, Allen B, Kaldate R, Bhatnagar S, Bowles K, et al. Frequency of mutations in individuals with breast cancer referred for BRCA 1 and BRCA 2 testing using next‐generation sequencing with a 25‐gene panel. 2015;121(1):25-33.
51. Castéra L, Krieger S, Rousselin A, Legros A, Baumann J-J, Bruet O, et al. Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes. 2014;22(11):1305-13.
52. Desmond A, Kurian AW, Gabree M, Mills MA, Anderson MJ, Kobayashi Y, et al. Clinical actionability of multigene panel testing for hereditary breast and ovarian cancer risk assessment. 2015;1(7):943-51.
53. Goodwin S, McPherson JD, McCombie WRJNRG. Coming of age: ten years of next-generation sequencing technologies. 2016;17(6):333-51.
54. Chandler MR, Bilgili EP, Merner NDJHm. A review of whole‐exome sequencing efforts toward hereditary breast cancer susceptibility gene discovery. 2016;37(9):835-46.
55. Sun J, Meng H, Yao L, Lv M, Bai J, Zhang J, et al. Germline Mutations in Cancer Susceptibility Genes in a Large Series of Unselected Breast Cancer PatientsMutations in Cancer Susceptibility Genes in Breast Cancer. 2017;23(20):6113-9.
56. Wang C, Zhang J, Wang Y, Ouyang T, Li J, Wang T, et al. Prevalence of BRCA1 mutations and responses to neoadjuvant chemotherapy among BRCA1 carriers and non-carriers with triple-negative breast cancer. 2015;26(3):523-8.
57. Lipponen P, Aaltomaa S, Kosma V-M, Syrjänen KJEJoC. Apoptosis in breast cancer as related to histopathological characteristics and prognosis. 1994;30(14):2068-73.
58. Engstrøm MJ, Opdahl S, Hagen AI, Romundstad PR, Akslen LA, Haugen OA, et al. Molecular subtypes, histopathological grade and survival in a historic cohort of breast cancer patients. 2013;140(3):463-73.
59. Onitilo AA, Engel JM, Greenlee RT, Mukesh BNJCm, research. Breast cancer subtypes based on ER/PR and Her2 expression: comparison of clinicopathologic features and survival. 2009;7(1-2):4-13.
60. Köchl S, Niederstätter H, Parson W. DNA extraction and quantitation of forensic samples using the phenol-chloroform method and real-time PCR. Forensic DNA typing protocols: Springer; 2005. p. 13-29.
61. Sambrook J, Russell DWJCSHP. Purification of nucleic acids by extraction with phenol: chloroform. 2006;2006(1):pdb. prot4455.
62. Ghatak S, Muthukumaran RB, Nachimuthu SKJJobtJ. A simple method of genomic DNA extraction from human samples for PCR-RFLP analysis. 2013;24(4):224.
63. Joshi M, Deshpande JJIJoBR. Polymerase chain reaction: methods, principles and application. 2010;2(1):81-97.
64. Waye J, Presley L, Budowle B, Shutler G, Fourney RJB. A simple and sensitive method for quantifying human genomic DNA in forensic specimen extracts. 1989;7(8):852-5.
65. Chang Y-S, Chang C-M, Lin C-Y, Chao D-S, Huang H-Y, Chang J-GJOr. Pathway mutations in breast cancer using whole-exome sequencing. 2020;28(2):107.
66. Goggins WB, Wong GJCC, Control. Cancer among Asian Indians/Pakistanis living in the United States: low incidence and generally above average survival. Cancer Causes & Control volume. 2009;20(5):635-43.
67. Rastogi T, Devesa S, Mangtani P, Mathew A, Cooper N, Kao R, et al. Cancer incidence rates among South Asians in four geographic regions: India, Singapore, UK and US. International Journal of Epidemiology. 2008;37(1):147-60.
68. Kakarala M, Rozek L, Cote M, Liyanage S, Brenner DEJBc. Breast cancer histology and receptor status characterization in Asian Indian and Pakistani women in the US-a SEER analysis. BMC Cancer volume 2010;10(1):1-8.
69. Carey LA, Perou CM, Livasy CA, Dressler LG, Cowan D, Conway K, et al. Race, breast cancer subtypes, and survival in the Carolina Breast Cancer Study. JAMA. 2006;295(21):2492-502.
70. Bauer KR, Brown M, Cress RD, Parise CA, Caggiano VJc. Descriptive analysis of estrogen receptor (ER)‐negative, progesterone receptor (PR)‐negative, and HER2‐negative invasive breast cancer, the so‐called triple‐negative phenotype: a population‐based study from the California cancer Registry. Cancer. 2007;109(9):1721-8.
71. Bertolo C, Guerrero D, Vicente F, Cordoba A, Esteller M, Ropero S, et al. Differences and molecular immunohistochemical parameters in the subtypes of infiltrating ductal breast cancer. American Journal of Clinical Pathology. 2008;130(3):414-24.
72. Del Casar J, Martin A, Garcia C, Corte M, Alvarez A, Junquera S, et al. Characterization of breast cancer subtypes by quantitative assessment of biological parameters: relationship with clinicopathological characteristics, biological features and prognosis. European Journal of Obstetrics & Gynecology and Reproductive Biology. 2008;141(2):147-52.
73. Sims AH, Howell A, Howell SJ, Clarke RBJNCPO. Origins of breast cancer subtypes and therapeutic implications. Nature Clinical Practice Oncology volume. 2007;4(9):516-25.
74. Ivshina AV, George J, Senko O, Mow B, Putti TC, Smeds J, et al. Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res 2006;66(21):10292-301.
75. Rosenberg LU, Magnusson C, Lindström E, Wedrén S, Hall P, Dickman PWJBCR. Menopausal hormone therapy and other breast cancer risk factors in relation to the risk of different histological subtypes of breast cancer: a case-control study. Breast Cancer Research 2006;8(1):1-13.
76. Kwong A, Shin VY, Au CH, Law FB, Ho DN, Ip BK, et al. Detection of germline mutation in hereditary breast and/or ovarian cancers by next-generation sequencing on a four-gene panel. The Journal of Molecular Diagnostics. 2016;18(4):580-94.
77. Langerød A, Zhao H, Borgan Ø, Nesland JM, Bukholm IR, Ikdahl T, et al. TP53mutation status and gene expression profiles are powerful prognostic markers of breast cancer. Breast Cancer Research volume. 2007;9(3):1-16.