Radiation Oncology Journal

  • 제33권2호
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  • Pages.149-154
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  • 2015
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  • 2234-1900(pISSN)
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  • 2234-3156(eISSN)
대한방사선종양학회 (The Korean Society for Radiation Oncology)
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Exome sequencing in a breast cancer family without BRCA mutation

  • Noh, Jae Myoung (Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine) ;
  • Kim, Jihun (LabGenomics Clinical Research Institute, LabGenomics) ;
  • Cho, Dae Yeon (LabGenomics Clinical Research Institute, LabGenomics) ;
  • Choi, Doo Ho (Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine) ;
  • Park, Won (Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine) ;
  • Huh, Seung Jae (Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine)
  • 투고 : 2015.05.12
  • 심사 : 2015.06.09
  • 발행 : 2015.06.30
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초록

Purpose: We performed exome sequencing in a breast cancer family without BRCA mutations. Materials and Methods: A family that three sisters have a history of breast cancer was selected for analysis. There were no family members with breast cancer in the previous generation. Genetic testing for BRCA mutation was negative, even by the multiplex ligation-dependent probe amplification method. Two sisters with breast cancer were selected as affected members, while the mother of the sisters was a non-affected member. Whole exome sequencing was performed on the HiSeq 2000 platform with paired-end reads of 101 bp in the three members. Results: We identified 19,436, 19,468, and 19,345 single-nucleotide polymorphisms (SNPs) in the coding regions. Among them, 8,759, 8,789, and 8,772 were non-synonymous SNPs, respectively. After filtering out 12,843 synonymous variations and 12,105 known variations with indels found in the dbSNP135 or 1000 Genomes Project database, we selected 73 variations in the samples from the affected sisters that did not occur in the sample from the unaffected mother. Using the Sorting Intolerant From Tolerant (SIFT), PolyPhen-2, and MutationTaster algorithms to predict amino acid substitutions, the XCR1, DLL1, TH, ACCS, SPPL3, CCNF, and SRL genes were risky among all three algorithms, while definite candidate genes could not be conclusively determined. Conclusion: Using exome sequencing, we found 7 variants for a breast cancer family without BRCA mutations. Genetic evidence of disease association should be confirmed by future studies.

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참고문헌

  1. Wooster R, Bignell G, Lancaster J, et al. Identification of the breast cancer susceptibility gene BRCA2. Nature 1995;378:789-92. https://doi.org/10.1038/378789a0
  2. Miki Y, Swensen J, Shattuck-Eidens D, et al. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 1994;266:66-71. https://doi.org/10.1126/science.7545954
  3. Turnbull C, Rahman N. Genetic predisposition to breast cancer: past, present, and future. Annu Rev Genomics Hum Genet 2008;9:321-45. https://doi.org/10.1146/annurev.genom.9.081307.164339
  4. Easton DF, Pooley KA, Dunning AM, et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 2007;447:1087-93. https://doi.org/10.1038/nature05887
  5. Snape K, Ruark E, Tarpey P, et al. Predisposition gene identification in common cancers by exome sequencing: insights from familial breast cancer. Breast Cancer Res Treat 2012;134:429-33. https://doi.org/10.1007/s10549-012-2057-x
  6. Gracia-Aznarez FJ, Fernandez V, Pita G, et al. Whole exome sequencing suggests much of non-BRCA1/BRCA2 familial breast cancer is due to moderate and low penetrance susceptibility alleles. PLoS One 2013;8:e55681. https://doi.org/10.1371/journal.pone.0055681
  7. Gilissen C, Hoischen A, Brunner HG, Veltman JA. Disease gene identification strategies for exome sequencing. Eur J Hum Genet 2012;20:490-7. https://doi.org/10.1038/ejhg.2011.258
  8. Ahn SH, Yoo KY. Chronological changes of clinical characteristics in 31,115 new breast cancer patients among Koreans during 1996-2004. Breast Cancer Res Treat 2006;99:209-14. https://doi.org/10.1007/s10549-006-9188-x
  9. Kim H, Cho DY, Choi DH, et al. Characteristics and spectrum of BRCA1 and BRCA2 mutations in 3,922 Korean patients with breast and ovarian cancer. Breast Cancer Res Treat 2012;134:1315-26. https://doi.org/10.1007/s10549-012-2159-5
  10. Kim JH, Choi DH, Cho DY, Ahn SH, Son BH, Haffty BG. PALB2 mutations 1592delT and 229delT are not present in Korean breast cancer patients negative for BRCA1 and BRCA2 mutations. Breast Cancer Res Treat 2010;122:303-6. https://doi.org/10.1007/s10549-010-0806-2
  11. Choi DH, Cho DY, Lee MH, et al. The CHEK2 1100delC mutation is not present in Korean patients with breast cancer cases tested for BRCA1 and BRCA2 mutation. Breast Cancer Res Treat 2008;112:569-73. https://doi.org/10.1007/s10549-007-9878-z
  12. Han SA, Kim SW, Kang E, et al. The prevalence of BRCA mutations among familial breast cancer patients in Korea: results of the Korean Hereditary Breast Cancer study. Fam Cancer 2013;12:75-81. https://doi.org/10.1007/s10689-012-9578-7
  13. Jeong D, Jeong Y, Park JH, et al. BRAF (V600E) mutation analysis in papillary thyroid carcinomas by peptide nucleic acid clamp real-time PCR. Ann Surg Oncol 2013;20:759-66. https://doi.org/10.1245/s10434-012-2494-0
  14. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010;38:e164. https://doi.org/10.1093/nar/gkq603
  15. Abecasis GR, Auton A, Brooks LD, et al. An integrated map of genetic variation from 1,092 human genomes. Nature 2012;491:56-65. https://doi.org/10.1038/nature11632
  16. Liu X, Jian X, Boerwinkle E. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat 2011;32:894-9. https://doi.org/10.1002/humu.21517
  17. Lei Y, Takahama Y. XCL1 and XCR1 in the immune system. Microbes Infect 2012;14:262-7. https://doi.org/10.1016/j.micinf.2011.10.003
  18. Yoshida T, Imai T, Kakizaki M, Nishimura M, Takagi S, Yoshie O. Identification of single C motif-1/lymphotactin receptor XCR1. J Biol Chem 1998;273:16551-4. https://doi.org/10.1074/jbc.273.26.16551
  19. Gantsev SK, Umezawa K, Islamgulov DV, et al. The role of inflammatory chemokines in lymphoid neoorganogenesis in breast cancer. Biomed Pharmacother 2013;67:363-6. https://doi.org/10.1016/j.biopha.2013.03.017
  20. Ayyanan A, Civenni G, Ciarloni L, et al. Increased Wnt signaling triggers oncogenic conversion of human breast epithelial cells by a Notch-dependent mechanism. Proc Natl Acad Sci U S A 2006;103:3799-804. https://doi.org/10.1073/pnas.0600065103
  21. Han J, Hendzel MJ, Allalunis-Turner J. Notch signaling as a therapeutic target for breast cancer treatment? Breast Cancer Res 2011;13:210. https://doi.org/10.1186/bcr2875
  22. D'Angiolella V, Donato V, Vijayakumar S, et al. SCF (Cyclin F) controls centrosome homeostasis and mitotic fidelity through CP110 degradation. Nature 2010;466:138-42. https://doi.org/10.1038/nature09140
  23. Roy D, Arason GA, Chowdhury B, Mitra A, Calaf GM. Profiling of cell cycle genes of breast cells exposed to etodolac. Oncol Rep 2010;23:1383-91.
  24. Lynch H, Wen H, Kim YC, et al. Can unknown predisposition in familial breast cancer be family-specific? Breast J 2013;19:520-8.
  25. Noh JM, Choi DH, Baek H, et al. Genetic anticipation of familial breast cancer with or without BRCA mutation in the Korean population. Cancer Genet 2014;207:160-3. https://doi.org/10.1016/j.cancergen.2014.04.002

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