Display options
Cite
Rotunno M, Barajas R, Clyne M, et al. A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer. Cancer Epidemiol Biomarkers Prev. 2020;29(8):1519-1534doi: 10.1158/1055-9965.EPI-19-1551.
Rotunno, M., Barajas, R., Clyne, M., Hoover, E., Simonds, N. I., Lam, T. K., Mechanic, L. E., Goldstein, A. M., & Gillanders, E. M. (2020). A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 29(8), 1519-1534. https://doi.org/10.1158/1055-9965.EPI-19-1551
Rotunno, Melissa, et al. "A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer." Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology vol. 29,8 (2020): 1519-1534. doi: https://doi.org/10.1158/1055-9965.EPI-19-1551
Rotunno M, Barajas R, Clyne M, Hoover E, Simonds NI, Lam TK, Mechanic LE, Goldstein AM, Gillanders EM. A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer. Cancer Epidemiol Biomarkers Prev. 2020 Aug;29(8):1519-1534. doi: 10.1158/1055-9965.EPI-19-1551. Epub 2020 May 28. PMID: 32467344; PMCID: PMC8279039.
Copy Download .nbib Format: NLM
Share it on

Cancer Epidemiol Biomarkers Prev. 2020 Aug;29(8):1519-1534. doi: 10.1158/1055-9965.EPI-19-1551. Epub 2020 May 28.

A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer.

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

Melissa Rotunno, Rolando Barajas, Mindy Clyne, Elise Hoover, Naoko I Simonds, Tram Kim Lam, Leah E Mechanic, Alisa M Goldstein, Elizabeth M Gillanders

Affiliations

  1. National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland. [email protected].
  2. National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland.
  3. Scientific Consulting Group, Inc., Gaithersburg, Maryland.

PMID: 32467344 PMCID: PMC8279039 DOI: 10.1158/1055-9965.EPI-19-1551

Abstract

The application of next-generation sequencing (NGS) technologies in cancer research has accelerated the discovery of somatic mutations; however, progress in the identification of germline variation associated with cancer risk is less clear. We conducted a systematic literature review of cancer genetic susceptibility studies that used NGS technologies at an exome/genome-wide scale to obtain a fuller understanding of the research landscape to date and to inform future studies. The variability across studies on methodologies and reporting was considerable. Most studies sequenced few high-risk (mainly European) families, used a candidate analysis approach, and identified potential cancer-related germline variants or genes in a small fraction of the sequenced cancer cases. This review highlights the importance of establishing consensus on standards for the application and reporting of variants filtering strategies. It also describes the progress in the identification of cancer-related germline variation to date. These findings point to the untapped potential in conducting studies with appropriately sized and racially diverse families and populations, combining results across studies and expanding beyond a candidate analysis approach to advance the discovery of genetic variation that accounts for the unexplained cancer heritability.

©2020 American Association for Cancer Research.

References

  1. Nat Genet. 2011 Jun 19;43(7):663-7 - PubMed
  2. Cold Spring Harb Mol Case Stud. 2016 Nov;2(6):a001032 - PubMed
  3. Lancet Gastroenterol Hepatol. 2018 Jul;3(7):489-498 - PubMed
  4. BMC Cancer. 2018 Feb 8;18(1):165 - PubMed
  5. Nat Genet. 2013 Oct;45(10):1226-1231 - PubMed
  6. Bioinformatics. 2009 Jul 15;25(14):1754-60 - PubMed
  7. Nat Genet. 2014 May;46(5):482-6 - PubMed
  8. J Hum Genet. 2015 Oct;60(10):597-603 - PubMed
  9. Iran J Public Health. 2016 Mar;45(3):346-52 - PubMed
  10. Nat Genet. 2013 Mar;45(3):295-8 - PubMed
  11. Genes Chromosomes Cancer. 2017 Feb;56(2):128-134 - PubMed
  12. Hum Mutat. 2013 Jul;34(7):1026-34 - PubMed
  13. Hum Mutat. 2018 Mar;39(3):371-377 - PubMed
  14. Clin Cancer Res. 2018 Apr 1;24(7):1594-1603 - PubMed
  15. Am J Hum Genet. 2015 Feb 5;96(2):301-8 - PubMed
  16. J Hum Genet. 2012 Oct;57(10):621-32 - PubMed
  17. Nat Genet. 2013 Feb;45(2):136-44 - PubMed
  18. J Infect Dis. 2015 Jun 1;211(11):1842-51 - PubMed
  19. JAMA. 2016 Jan 5;315(1):68-76 - PubMed
  20. Breast Cancer Res Treat. 2017 Feb;161(3):597-604 - PubMed
  21. Curr Protoc Bioinformatics. 2016 Jun 20;54:5.6.1-5.6.37 - PubMed
  22. Hum Mol Genet. 2015 May 15;24(10):2914-22 - PubMed
  23. Endocr Relat Cancer. 2017 Aug;24(8):427-443 - PubMed
  24. Oncotarget. 2017 Mar 3;8(31):50930-50940 - PubMed
  25. Blood. 2013 Apr 25;121(17):3428-30 - PubMed
  26. DNA Repair (Amst). 2018 Jun - Jul;66-67:50-63 - PubMed
  27. Hum Mutat. 2018 Nov;39(11):1623-1630 - PubMed
  28. Nat Commun. 2015 Dec 22;6:10086 - PubMed
  29. J Clin Oncol. 2015 Jul 10;33(20):2303-10 - PubMed
  30. Mol Syst Biol. 2016 Mar 10;12(3):860 - PubMed
  31. Fam Cancer. 2015 Dec;14(4):621-8 - PubMed
  32. Oncotarget. 2015 Sep 22;6(28):26335-46 - PubMed
  33. Hum Mol Genet. 2017 Nov 15;26(22):4481-4493 - PubMed
  34. Am J Hum Genet. 2012 Apr 6;90(4):734-9 - PubMed
  35. Hum Mol Genet. 2018 Mar 1;27(5):853-859 - PubMed
  36. PLoS Med. 2009 Jul 21;6(7):e1000097 - PubMed
  37. Brain Pathol. 2018 Jan;28(1):94-102 - PubMed
  38. J Pathol. 2013 Mar;229(4):621-9 - PubMed
  39. Int J Oncol. 2014 Jul;45(1):77-81 - PubMed
  40. Gastroenterology. 2018 Feb;154(3):719-722.e3 - PubMed
  41. Leukemia. 2014 Jun;28(6):1235-41 - PubMed
  42. Blood. 2011 Jul 21;118(3):493-8 - PubMed
  43. Front Genet. 2018 May 07;9:161 - PubMed
  44. JAMA Oncol. 2019 Jan 1;5(1):51-57 - PubMed
  45. Gastroenterology. 2018 Jan;154(1):181-194.e20 - PubMed
  46. Cancer Epidemiol Biomarkers Prev. 2015 Aug;24(8):1222-8 - PubMed
  47. Haematologica. 2016 Jul;101(7):846-52 - PubMed
  48. Nucleic Acids Res. 2001 Jan 1;29(1):308-11 - PubMed
  49. J Med Genet. 2017 Sep;54(9):607-612 - PubMed
  50. Fam Cancer. 2015 Sep;14(3):437-48 - PubMed
  51. Science. 2009 Apr 10;324(5924):217 - PubMed
  52. Endocr Relat Cancer. 2016 Mar;23(3):171-9 - PubMed
  53. Carcinogenesis. 2017 Sep 1;38(9):938-943 - PubMed
  54. BMC Med Genet. 2015 May 13;16:34 - PubMed
  55. Oncotarget. 2015 Nov 24;6(37):39614-33 - PubMed
  56. Genome Res. 2010 Sep;20(9):1297-303 - PubMed
  57. PLoS One. 2017 Jun 7;12(6):e0178450 - PubMed
  58. Sci Rep. 2016 May 24;6:26440 - PubMed
  59. Nat Rev Genet. 2010 Jan;11(1):31-46 - PubMed
  60. BMC Med Genomics. 2018 Mar 27;11(1):35 - PubMed
  61. J Med Genet. 2016 Jun;53(6):385-8 - PubMed
  62. J Natl Cancer Inst. 2018 Dec 1;110(12):1380-1385 - PubMed
  63. Cancer Genet. 2015 Jan-Feb;208(1-2):35-40 - PubMed
  64. Eur Urol. 2018 Jun;73(6):828-831 - PubMed
  65. Fam Cancer. 2015 Jun;14(2):297-306 - PubMed
  66. PLoS Genet. 2012 Sep;8(9):e1002894 - PubMed
  67. Nucleic Acids Res. 2012 Jan;40(Database issue):D930-4 - PubMed
  68. Lancet Oncol. 2015 Dec;16(16):1659-66 - PubMed
  69. Cold Spring Harb Mol Case Stud. 2018 Apr 2;4(2): - PubMed
  70. Hum Genet. 2013 Aug;132(8):845-63 - PubMed
  71. Gastroenterology. 2014 Sep;147(3):595-598.e5 - PubMed
  72. Prostate. 2014 Oct;74(14):1371-8 - PubMed
  73. Head Neck Pathol. 2017 Dec;11(4):546-551 - PubMed
  74. Oncotarget. 2015 Mar 20;6(8):5918-31 - PubMed
  75. Hum Mol Genet. 2017 Jan 15;26(2):243-257 - PubMed
  76. J Transl Med. 2018 Jun 7;16(1):158 - PubMed
  77. Nat Genet. 2018 Dec;50(12):1650-1657 - PubMed
  78. Nat Genet. 2015 Jun;47(6):643-6 - PubMed
  79. J Allergy Clin Immunol. 2013 Jun;131(6):1594-603 - PubMed
  80. Nat Methods. 2015 Jan;12(1):7-8 - PubMed
  81. Hum Genomics. 2017 Apr 20;11(1):6 - PubMed
  82. Hum Mol Genet. 2016 Jan 15;25(2):371-81 - PubMed
  83. Eur J Hum Genet. 2012 May;20(5):490-7 - PubMed
  84. N Engl J Med. 2015 Dec 10;373(24):2336-2346 - PubMed
  85. BMC Genomics. 2015;16 Suppl 1:S3 - PubMed
  86. Nat Rev Genet. 2011 Sep 27;12(11):745-55 - PubMed
  87. Nat Commun. 2016 Jun 22;7:11883 - PubMed
  88. Cell. 2019 Mar 21;177(1):70-84 - PubMed
  89. Int J Cancer. 2015 May 1;136(9):2109-19 - PubMed
  90. Int J Cancer. 2018 Jun 15;142(12):2512-2517 - PubMed
  91. Gastroenterology. 2017 Apr;152(5):983-986.e6 - PubMed
  92. PLoS One. 2017 Jan 11;12(1):e0167581 - PubMed
  93. BMC Cancer. 2013 Feb 04;13:55 - PubMed
  94. Gastroenterology. 2015 Dec;149(7):1872-1883.e9 - PubMed
  95. Gene. 2013 Sep 10;526(2):164-9 - PubMed
  96. Lung Cancer. 2014 Aug;85(2):168-74 - PubMed
  97. Genet Med. 2016 Aug;18(8):823-32 - PubMed
  98. Hum Genomics. 2013 Apr 05;7:11 - PubMed
  99. Nat Commun. 2016 Dec 20;7:13840 - PubMed
  100. Am J Hum Genet. 2013 Jun 6;92(6):974-80 - PubMed
  101. Blood. 2016 Nov 3;128(18):2261-2263 - PubMed
  102. Nature. 2016 Aug 17;536(7616):285-91 - PubMed
  103. Urol Oncol. 2016 Mar;34(3):120.e9-16 - PubMed
  104. Clin Cancer Res. 2019 Mar 1;25(5):1517-1525 - PubMed
  105. Cancer Sci. 2017 Jun;108(6):1263-1270 - PubMed
  106. Cancer Discov. 2016 Nov;6(11):1267-1275 - PubMed
  107. Breast Cancer Res Treat. 2017 Feb;162(1):31-37 - PubMed
  108. Cancer. 2017 Jan 1;123(2):210-218 - PubMed
  109. Fam Cancer. 2019 Jan;18(1):113-119 - PubMed
  110. Gastroenterology. 2015 Sep;149(3):563-6 - PubMed
  111. Breast Cancer Res Treat. 2011 Dec;130(3):1043-9 - PubMed
  112. J Pathol. 2013 Sep;231(1):35-43 - PubMed
  113. Nucleic Acids Res. 2010 Sep;38(16):e164 - PubMed
  114. J Genet Genomics. 2018 Jan 20;45(1):41-45 - PubMed
  115. Genes Chromosomes Cancer. 2018 Jun;57(6):294-303 - PubMed
  116. Nat Genet. 2014 May;46(5):438-43 - PubMed
  117. Gene. 2018 Jan 30;641:94-104 - PubMed
  118. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W452-7 - PubMed
  119. Br J Haematol. 2015 Aug;170(3):428-31 - PubMed
  120. Biochem Biophys Res Commun. 2017 Jan 22;482(4):590-596 - PubMed
  121. Pigment Cell Melanoma Res. 2012 Nov;25(6):815-8 - PubMed
  122. Gastroenterology. 2015 Jul;149(1):67-78 - PubMed
  123. Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15172-7 - PubMed
  124. Nat Commun. 2015 Sep 25;6:8383 - PubMed
  125. Eur J Hum Genet. 2016 Jan;25(1):85-93 - PubMed
  126. Genes Chromosomes Cancer. 2017 Jun;56(6):453-459 - PubMed
  127. Genet Med. 2015 Feb;17(2):131-42 - PubMed
  128. Fam Cancer. 2015 Jun;14(2):241-6 - PubMed
  129. Genome Res. 2012 Sep;22(9):1790-7 - PubMed
  130. Haematologica. 2016 Jul;101(7):853-60 - PubMed
  131. Cancer Lett. 2016 Jan 28;370(2):302-12 - PubMed
  132. Cancer Epidemiol Biomarkers Prev. 2013 Jul;22(7):1239-51 - PubMed
  133. Fam Cancer. 2017 Oct;16(4):561-566 - PubMed
  134. J Natl Cancer Inst. 2017 Dec 1;109(12): - PubMed
  135. Nat Genet. 2012 May 29;44(6):623-30 - PubMed
  136. Mol Cancer. 2014 Jan 31;13:19 - PubMed
  137. Br J Cancer. 2018 Jul;119(1):96-104 - PubMed
  138. Nat Genet. 2015 Dec;47(12):1471-4 - PubMed
  139. Int J Cancer. 2018 Oct 15;143(8):2076-2078 - PubMed
  140. Nat Genet. 2014 May;46(5):478-481 - PubMed
  141. Breast Cancer Res Treat. 2012 Jul;134(1):429-33 - PubMed
  142. Br J Haematol. 2018 May;181(3):372-377 - PubMed
  143. J Hepatol. 2018 May;68(5):959-969 - PubMed
  144. Genet Med. 2013 Sep;15(9):733-47 - PubMed
  145. Cell. 2018 Apr 5;173(2):355-370.e14 - PubMed
  146. Pediatr Blood Cancer. 2017 Jan;64(1):100-102 - PubMed
  147. Pediatr Blood Cancer. 2013 Jun;60(6):E1-3 - PubMed
  148. Eur J Hum Genet. 2017 Nov;25(11):1246-1252 - PubMed
  149. Am J Hum Genet. 2012 Sep 7;91(3):520-6 - PubMed
  150. PLoS Genet. 2015 May 06;11(5):e1005228 - PubMed
  151. Curr Opin Genet Dev. 2014 Feb;24:52-60 - PubMed
  152. BMJ Open. 2016 Apr 15;6(4):e010332 - PubMed
  153. Clin Genet. 2015 Oct;88(4):366-70 - PubMed
  154. Sci Rep. 2015 Jul 02;5:10566 - PubMed
  155. Oncotarget. 2017 Jun 20;8(25):40896-40905 - PubMed
  156. Int J Cancer. 2019 Mar 15;144(6):1321-1330 - PubMed
  157. J Clin Oncol. 2014 Mar 1;32(7):687-98 - PubMed
  158. BMC Cancer. 2014 Jun 26;14:470 - PubMed
  159. J Clin Immunol. 2016 Oct;36(7):684-92 - PubMed
  160. Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3317-22 - PubMed
  161. Nat Methods. 2014 Apr;11(4):361-2 - PubMed
  162. Nat Genet. 2014 Mar;46(3):310-5 - PubMed
  163. Nature. 2015 Oct 1;526(7571):68-74 - PubMed
  164. Blood. 2016 Nov 10;128(19):2319-2326 - PubMed
  165. Genome Med. 2014 Mar 31;6(3):26 - PubMed
  166. Tumour Biol. 2017 May;39(5):1010428317699115 - PubMed
  167. Int J Cancer. 2014 May 15;134(10):2352-8 - PubMed
  168. Blood. 2016 May 26;127(21):2598-606 - PubMed
  169. Cancer Discov. 2014 Jul;4(7):804-15 - PubMed
  170. Nat Methods. 2010 Apr;7(4):248-9 - PubMed
  171. Breast J. 2013 Sep-Oct;19(5):520-8 - PubMed
  172. Cancer Discov. 2016 Feb;6(2):166-75 - PubMed
  173. Oncotarget. 2018 Apr 17;9(29):20377-20385 - PubMed
  174. J Natl Cancer Inst. 2014 Dec 07;107(1):384 - PubMed
  175. Cancer Genet. 2018 Feb;221:46-52 - PubMed
  176. Radiat Oncol J. 2015 Jun;33(2):149-54 - PubMed
  177. Genet Med. 2017 Aug;19(8):955-958 - PubMed
  178. Nat Biotechnol. 2011 Jan;29(1):24-6 - PubMed
  179. BMC Med Genomics. 2017 Feb 15;10(1):8 - PubMed
  180. J Hepatol. 2017 Apr;66(4):734-742 - PubMed
  181. Blood. 2013 Feb 21;121(8):1478-9 - PubMed
  182. PLoS One. 2013 Aug 19;8(8):e72144 - PubMed
  183. Am J Pathol. 2014 Sep;184(9):2374-81 - PubMed
  184. Nature. 2014 Jul 10;511(7508):241-5 - PubMed
  185. Cancer Genet. 2015 Jan-Feb;208(1-2):41-6 - PubMed
  186. World J Gastroenterol. 2015 Apr 14;21(14):4136-49 - PubMed
  187. J Pathol. 2017 Nov;243(3):331-341 - PubMed
  188. Annu Rev Genomics Hum Genet. 2016 Aug 31;17:95-115 - PubMed
  189. Nat Genet. 2012 Nov;44(11):1185-7 - PubMed
  190. Nature. 2013 Aug 22;500(7463):415-21 - PubMed
  191. Eur J Hum Genet. 2016 Oct;24(10):1501-5 - PubMed
  192. Gene. 2019 Mar 20;689:34-42 - PubMed
  193. Leukemia. 2017 Apr;31(4):821-828 - PubMed
  194. Fam Cancer. 2015 Jun;14(2):337-40 - PubMed
  195. BMC Genet. 2016 Feb 13;17:41 - PubMed
  196. Iran J Public Health. 2015 Oct;44(10):1348-52 - PubMed
  197. Nucleic Acids Res. 2014 Jan;42(Database issue):D980-5 - PubMed
  198. Genome Res. 2013 Mar;23(3):419-30 - PubMed
  199. Hum Genet. 2016 Nov;135(11):1241-1249 - PubMed
  200. Gut. 2015 Feb;64(2):355-6 - PubMed
  201. Nature. 2009 Oct 8;461(7265):747-53 - PubMed
  202. BMC Med Genomics. 2016 Aug 11;9(1):52 - PubMed
  203. Lung Cancer. 2018 Aug;122:76-82 - PubMed
  204. PLoS One. 2016 Oct 4;11(10):e0164233 - PubMed
  205. J Natl Cancer Inst. 2014 Jan;106(1):djt338 - PubMed
  206. Nature. 2013 Jan 10;493(7431):216-20 - PubMed
  207. Nat Rev Genet. 2014 Sep;15(9):585-98 - PubMed
  208. Oncotarget. 2017 Jan 3;8(1):1495-1507 - PubMed
  209. Cancer Epidemiol Biomarkers Prev. 2016 Nov;25(11):1456-1463 - PubMed
  210. Nat Commun. 2014;5:3156 - PubMed
  211. PLoS One. 2013;8(1):e55734 - PubMed
  212. Cancer Discov. 2012 Jan;2(1):41-6 - PubMed
  213. PLoS Genet. 2016 Feb 22;12(2):e1005880 - PubMed
  214. Nat Commun. 2014 Aug 07;5:4398 - PubMed
  215. Cancer Res Treat. 2019 Jan;51(1):337-344 - PubMed
  216. PLoS One. 2013;8(2):e55681 - PubMed
  217. Leukemia. 2017 Oct;31(10):2244-2247 - PubMed
  218. Int J Cancer. 2018 Oct 1;143(7):1696-1705 - PubMed
  219. Int J Cancer. 2018 Oct 15;143(8):1954-1962 - PubMed
  220. Carcinogenesis. 2016 Feb;37(2):139-144 - PubMed
  221. Cancer Epidemiol Biomarkers Prev. 2013 Sep;22(9):1520-8 - PubMed
  222. BMC Cancer. 2015 Jul 23;15:539 - PubMed
  223. PLoS Genet. 2013;9(10):e1003876 - PubMed
  224. Oncol Lett. 2018 Jun;15(6):9413-9419 - PubMed
  225. N Engl J Med. 2015 Jul 30;373(5):448-55 - PubMed
  226. Hum Genet. 2015 Jul;134(7):775-87 - PubMed
  227. Biochim Biophys Acta Mol Basis Dis. 2018 Jun;1864(6 Pt B):2247-2254 - PubMed

MeSH terms

Publication Types

Grant support