Whole-exome sequencing of a rare case of familial childhood acute lymphoblastic leukemia reveals putative predisposing mutations in Fanconi anemia genes

BMC Cancer

Volumn 15, Issue 1, 2015, Pages

  Spinella, Jean François ^a   Healy, Jasmine ^a   Saillour, Virginie ^a   Richer, Chantal ^a   Cassart, Pauline ^a   Ouimet, Manon ^a   Sinnett, Daniel ^a,b  

^a UNIVERSITY OF MONTREAL   (Canada)

^b UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

Childhood leukemia predisposition; Familial acute lymphoblastic leukemia; Fanconi anemia genes

Indexed keywords

FANCONI ANEMIA GROUP A PROTEIN; FANCONI ANEMIA PROTEIN; HISTONE LYSINE METHYLTRANSFERASE; PRDM9 PROTEIN, HUMAN;

ACUTE LYMPHOBLASTIC LEUKEMIA; ADOLESCENT; ALGORITHM; ARTICLE; CHILD; CHILDHOOD LEUKEMIA; COMPUTER MODEL; DNA SEQUENCE; EXOME; FAMILIAL CANCER; FAMILIAL CHILDHOOD ACUTE LYMPHOBLASTIC LEUKEMIA; FANCA GENE; FANCP GENE; FEMALE; GEN1 GENE; GENE; GENE MUTATION; GENETIC PREDISPOSITION; GENETIC VARIABILITY; HETEROZYGOTE; HOMOZYGOTE; HUMAN; MALE; NEXT GENERATION SEQUENCING; PHENOTYPE; PRESCHOOL CHILD; SINGLE NUCLEOTIDE POLYMORPHISM; SLX4 GENE; ALLELE; GENETICS; HIGH THROUGHPUT SEQUENCING; MUTATION; PEDIGREE; PRECURSOR B-CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; SIBLING;

ADOLESCENT; ALLELES; CHILD, PRESCHOOL; EXOME; FANCONI ANEMIA COMPLEMENTATION GROUP PROTEINS; GENETIC PREDISPOSITION TO DISEASE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTONE-LYSINE N-METHYLTRANSFERASE; HUMANS; MALE; MUTATION; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; PRECURSOR B-CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; SIBLINGS;

EID: 84937693478     PISSN: None     EISSN: 14712407     Source Type: Journal    
DOI: 10.1186/s12885-015-1549-6     Document Type: Article

References (47)

1. Pui CH, Mullighan CG, Evans WE, Relling MV. Pediatric acute lymphoblastic leukemia: where are we going and how do we get there? Blood. 2012;120(6):1165-74. doi: 10.1182/blood-2012-05-378943.
2. Horwitz M. The genetics of familial leukemia. Leukemia. 1997;11(8):1347-59.
3. Papaemmanuil E, Hosking FJ, Vijayakrishnan J, Price A, Olver B, Sheridan E, et al. Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia. Nat Genet. 2009;41(9):1006-10. doi: 10.1038/ng.430.
4. Treviño LR, Shimasaki N, Yang W, Panetta JC, Cheng C, Pei D, et al. Germline genetic variation in an organic anion transporter polypeptide associated with methotrexate pharmacokinetics and clinical effects. J Clin Oncol. 2009;27(35):5972-8. doi: 10.1200/JCO.2008.20.4156.
5. Prasad RB, Hosking FJ, Vijayakrishnan J, Papaemmanuil E, Koehler R, Greaves M, et al. Verification of the susceptibility loci on 7p12.2, 10q21.2, and 14q11.2 in precursor B-cell acute lymphoblastic leukemia of childhood. Blood. 2010;115(9):1765-7. doi: 10.1182/blood-2009-09-241513.
6. Sherborne AL, Hosking FJ, Prasad RB, Kumar R, Koehler R, Vijayakrishnan J, et al. Variation in CDKN2A at 9p21.3 influences childhood acute lymphoblastic leukemia risk. Nat Genet. 2010;42(6):492-4. doi: 10.1038/ng.585.
7. Kharazmi E, da Silva Filho MI, Pukkala E, Sundquist K, Thomsen H, Hemminki K. Familial risks for childhood acute lymphocytic leukaemia in Sweden and Finland: Far exceeding the effects of known germline variants. Br J Haematol. 2012;159(5):585-8. doi: 10.1111/bjh.12069.
8. Schmiegelow K, Lausten Thomsen U, Baruchel A, Pacheco CE, Pieters R, Pombo-de-Oliveira MS, et al. High concordance of subtypes of childhood acute lymphoblastic leukemia within families: lessons from sibships with multiple cases of leukemia. Leukemia. 2012;26(4):675-81. doi: 10.1038/leu.2011.274.
9. Pombo-de-Oliveira MS, Emerenciano M, Winn AP, Costa I, Mansur MB, Ford AM. Concordant B-cell precursor acute lymphoblastic leukemia in non-twinned siblings. Blood Cells Mol Dis. 2015;54(1):110-5. doi: 10.1016/j.bcmd.2014.07.011.
10. Bateman CM, Alpar D, Ford AM, Colman SM, Wren D, Morgan M, Kearney L, Greaves M. Evolutionary trajectories of hyperdiploid ALL in monozygotic twins. Leukemia. 2015;29(1):58-65. doi: 10.1038/leu.2014.177.
11. Hussin J, Sinnett D, Casals F, Idaghdour Y, Bruat V, Saillour V, et al. Rare allelic forms of PRDM9 associated with childhood leukemogenesis. Genome Res. 2013;23(3):419-30. doi: 10.1101/gr.144188.112.
12. Baker CL, Walker M, Kajita S, Petkov PM, Paigen K. PRDM9 binding organizes hotspot nucleosomes and limits Holliday junction migration. Genome Res. 2014;24(5):724-32. doi: 10.1101/gr.170167.113.
13. Fekairi S, Scaglione S, Chahwan C, Taylor ER, Tissier A, Coulon S, et al. Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. Cell. 2009;138(1):78-89. doi: 10.1016/j.cell.2009.06.029.
14. Kim H, Andrea ADD. Regulation of DNA cross-link repair by the Fanconi anemia/BRCA pathway. Genes Dev. 2012;26(13):1393-408. doi: 10.1101/gad.195248.112.
15. Hysert M, Bruyère H, Côté GB, Dawson AJ, Dolling JA, Fetni R, et al. Prenatal cytogenetic assessment and inv(2)(p11.2q13). Prenat Diagn. 2006;26(9):810-3.
16. Baccichet A, Qualman SK, Sinnett D. Allelic loss in childhood acute lymphoblastic leukemia. Leuk Res. 1997;21(9):817-23.
17. http://picard.sourceforge.net
18. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-303. doi: 10.1101/gr.107524.110.
19. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. 1000 Genome Project Data Processing Subgroup. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics. 2009;25:2078-9. doi: 10.1093/bioinformatics/btp352.
20. 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, et al. A map of human genome variation from population-scale sequencing. Nature. 2010;467(7319):1061-73. doi: 10.1038/nature09534.
21. http://evs.gs.washington.edu/EVS/
22. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16):e164. doi: 10.1093/nar/gkq603.
23. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4(7):1073-81. doi: 10.1038/nprot.2009.86.
24. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7(4):248-9. doi: 10.1038/nmeth0410-248.
25. Shihab HA, Gough J, Cooper DN, Day IN, Gaunt TR. Predicting the functional consequences of cancer-associated amino acid substitutions. Bioinformatics. 2013;29(12):1504-10. doi: 10.1093/bioinformatics/btt182.
26. Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics. 2009;25(12):i54-62. doi: 10.1093/bioinformatics/btp190.
27. Ip SC, Rass U, Blanco MG, Flynn HR, Skehel JM, West SC. Identification of Holliday junction resolvases from humans and yeast. Nature. 2008;456(7220):357-61. doi: 10.1038/nature07470.
28. Healy J, Richer C, Bourgey M, Kritikou EA, Sinnett D. Replication analysis confirms the association of ARID5B with childhood B-cell acute lymphoblastic leukemia. Haematologica. 2010;95(9):1608-11. doi: 10.3324/haematol.2010.022459.
29. Wang AT, Smogorzewska A. SnapShot: Fanconi anemia and associated proteins. Cell. 2015;160(1-2):354-354.e1. doi: 10.1016/j.cell.2014.12.031.
30. Wang W. Emergence of a DNA-damage response network consisting of Fanconi anaemia and BRCA proteins. Nat Rev Genet. 2007;8(10):735-48.
31. Fernández-Rodríguez J, Quiles F, Blanco I, Teulé A, Feliubadaló L, Valle JD, et al. Analysis of SLX4/FANCP in non-BRCA1/2-mutated breast cancer families. BMC Cancer. 2012;12:84. doi: 10.1186/1471-2407-12-84.
32. Catucci I1, Colombo M, Verderio P, Bernard L, Ficarazzi F, Mariette F, et al. Sequencing analysis of SLX4/FANCP gene in Italian familial breast cancer cases. PLoS One. 2012;7(2):e31038. doi: 10.1371/journal.pone.0031038.
33. Litim N, Labrie Y, Desjardins S, Ouellette G, Plourde K. Belleau P; INHERIT BRCAs, Durocher F. Polymorphic variations in the FANCA gene in high-risk non-BRCA1/2 breast cancer individuals from the French Canadian population. Mol Oncol. 2013;7(1):85-100. doi: 10.1016/j.molonc.2012.08.002.
34. Seal S, Barfoot R, Jayatilake H, Smith P, Renwick A, Bascombe L, et al. Rahman N; Breast Cancer Susceptibility Collaboration. Evaluation of Fanconi Anemia genes in familial breast cancer predisposition. Cancer Res. 2003;63(24):8596-9.
35. Kottemann MC, Smogorzewska A. Fanconi anaemia and the repair of Watson and Crick DNA crosslinks. Nature. 2013;493(7432):356-63. doi: 10.1038/nature11863.
36. Tischkowitz MD, Morgan NV, Grimwade D, Eddy C, Ball S, Vorechovsky I, et al. Deletion and reduced expression of the Fanconi anemia FANCA gene in sporadic acute myeloid leukemia. Leukemia. 2004;18(3):420-5.
37. Svendsen JM, Smogorzewska A, Sowa ME, O'Connell BC, Gygi SP, Elledge SJ, et al. Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair. Cell. 2009;138(1):63-77. doi: 10.1016/j.cell.2009.06.030.
38. Kim Y, Spitz GS, Veturi U, Lach FP, Auerbach AD, Smogorzewska A. Regulation of multiple DNA repair pathways by the Fanconi anemia protein SLX4. Blood. 2013;121(1):54-63. doi: 10.1182/blood-2012-07-441212.
39. Gao M, Rendtlew Danielsen J, Wei LZ, Zhou DP, Xu Q, Li MM, et al. A novel role of human holliday junction resolvase GEN1 in the maintenance of centrosome integrity. PLoS One. 2012;7(11):e49687. doi: 10.1371/journal.pone.0049687.
40. Kuligina ES, Sokolenko AP, Mitiushkina NV, Abysheva SN, Preobrazhenskaya EV, Gorodnova TV, et al. Value of bilateral breast cancer for identification of rare recessive at-risk alleles: evidence for the role of homozygous GEN1 c.2515_2519delAAGTT mutation. Familial Cancer. 2013;12(1):129-32. doi: 10.1007/s10689-012-9575-x.
41. Wechsler T, Newman S, West SC. Aberrant chromosome morphology in human cells defective for Holliday junction resolution. Nature. 2011;471(7340):642-6. doi: 10.1038/nature09790.
42. Rodrigue A, Coulombe Y, Jacquet K, Gagné JP, Roques C, Gobeil S, et al. The RAD51 paralogs ensure cellular protection against mitotic defects and aneuploidy. J Cell Sci. 2013;126(Pt 1):348-59. doi: 10.1242/jcs.114595.
43. Giampietro PF, Adler-Brecher B, Verlander PC, Pavlakis SG, Davis JG, Auerbach AD. The need for more accurate and timely diagnosis in Fanconi anemia: a report from the International Fanconi Anemia Registry. Pediatrics. 1993;91(6):1116-20.
44. Welshimer K, Swift M. Congenital malformations and developmental disabilities in ataxia-telangiectasia, Fanconi anemia, and xeroderma pigmentosum families. Am J Hum Genet. 1982;34(5):781-93.
45. Wilkinson K, Velloso ER, Lopes LF, Lee C, Aster JC, Shipp MA, et al. Cloning of the t(1;5)(q23;q33) in a myeloproliferative disorder associated with eosinophilia: involvement of PDGFRB and response to imatinib. Blood. 2003;102(12):4187-90.
46. Jeffery J, Sinha D, Srihari S, Kalimutho M, Khanna KK. Beyond cytokinesis: the emerging roles of CEP55 in tumorigenesis. Oncogene. 2015. doi: 10.1038/onc.2015.128.
47. Paulsson K, Lilljebjörn H, Biloglav A, Olsson L, Rissler M, Castor A, et al. The genomic landscape of high hyperdiploid childhood acute lymphoblastic leukemia. Nat Genet. 2015;47(6):672-6. doi: 10.1038/ng.3301.