Skip to main content
SpringerLink
Log in

Insights of Acute Lymphoblastic Leukemia with Development of Genomic Investigation

  • Protocol
Computational Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1754))

Abstract

Treatment outcomes for acute lymphoblastic leukemia (ALL), especially pediatric ALL, have greatly improved due to the risk-adapted therapy. Combination of drug development, clinical practice, as well as basic genetic researches has brought the survival rate of ALL from less than 10% to more than 90% today, not only increasing the treatment efficacy but also limiting adverse drug reactions (ADRs). In this review, we summarized the landscape identification of ALL genetic alterations, which provided the opportunity to increase the survival rate and especially minimize the relapse risk of ALL, and highlighted the importance of the development of new technologies of genomic investigation for translational medicine.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Pui CH (1995) Childhood leukemias. N Engl J Med 332(24):1618–1630

    Article  CAS  PubMed  Google Scholar 

  2. Pui CH, Evans WE (1998) Acute lymphoblastic leukemia. N Engl J Med 339(9):605–615

    Article  CAS  PubMed  Google Scholar 

  3. Pui CH, Campana D, Evans WE (2001) Childhood acute lymphoblastic leukaemia—current status and future perspectives. Lancet Oncol 2(10):597–607

    Article  CAS  PubMed  Google Scholar 

  4. Inaba H, Greaves M, Mullighan CG (2013) Acute lymphoblastic leukaemia. Lancet 381(9881):1943–1955

    Article  PubMed  Google Scholar 

  5. Pui C-H, Crist WM, Look AT (1990) Biology and clinical significance of cytogenetic abnormalities in childhood acute lymphoblastic leukemia. Blood 76(8):1449–1463

    CAS  PubMed  Google Scholar 

  6. Pui CH, Relling MV, Downing JR (2004) Acute lymphoblastic leukemia. N Engl J Med 350(15):1535–1548

    Article  CAS  PubMed  Google Scholar 

  7. Mullighan CG (2013) Genomic characterization of childhood acute lymphoblastic leukemia. Semin Hematol 50(4):314–324

    Article  CAS  PubMed  Google Scholar 

  8. Mullighan CG (2012) Molecular genetics of B-precursor acute lymphoblastic leukemia. J Clin Invest 122(10):3407–3415

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Mullighan CG (2011) New strategies in acute lymphoblastic leukemia: translating advances in genomics into clinical practice. Clin Cancer Res 17(3):396–400

    Article  CAS  PubMed  Google Scholar 

  10. Pui C-H, Evans WE (2006) Treatment of acute lymphoblastic leukemia. N Engl J Med 354(2):166–178

    Article  CAS  PubMed  Google Scholar 

  11. Roberts KG, Mullighan CG (2015) Genomics in acute lymphoblastic leukaemia: insights and treatment implications. Nat Rev Clin Oncol 12(6):344–357

    Article  CAS  PubMed  Google Scholar 

  12. Pui C-H, Robison LL, Look AT (2008) Acute lymphoblastic leukaemia. Lancet 371(9617):1030–1043

    Article  CAS  PubMed  Google Scholar 

  13. Bhojwani D, Pui CH (2013) Relapsed childhood acute lymphoblastic leukaemia. Lancet Oncol 14(6):e205–e217

    Article  PubMed  Google Scholar 

  14. Fielding AK et al (2007) Outcome of 609 adults after relapse of acute lymphoblastic leukemia (ALL); an MRC UKALL12/ECOG 2993 study. Blood 109(3):944–950

    Article  CAS  PubMed  Google Scholar 

  15. Einsiedel HG et al (2005) Long-term outcome in children with relapsed ALL by risk-stratified salvage therapy: results of trial acute lymphoblastic leukemia-relapse study of the Berlin-Frankfurt-Munster Group 87. J Clin Oncol 23(31):7942–7950

    Article  PubMed  Google Scholar 

  16. Rivera GK et al (2005) Bone marrow recurrence after initial intensive treatment for childhood acute lymphoblastic leukemia. Cancer 103(2):368–376

    Article  PubMed  Google Scholar 

  17. Mullighan CG (2014) The genomic landscape of acute lymphoblastic leukemia in children and young adults. ASH Edu Progr Book 2014(1):174–180

    Google Scholar 

  18. Moriyama T, Relling MV, Yang JJ (2015) Inherited genetic variation in childhood acute lymphoblastic leukemia. Blood 125(26):3988–3995

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Mullighan CG (2012) The molecular genetic makeup of acute lymphoblastic leukemia. ASH Edu Progr Book 2012(1):389–396

    Google Scholar 

  20. Pui C-H, Behm FG, Crist WM (1993) Clinical and biologic relevance of immunologic marker studies in childhood acute lymphoblastic leukemia. Blood 82(2):343–362

    CAS  PubMed  Google Scholar 

  21. Mancini M et al (2005) A comprehensive genetic classification of adult acute lymphoblastic leukemia (ALL): analysis of the GIMEMA 0496 protocol. Blood 105(9):3434–3441

    Article  CAS  PubMed  Google Scholar 

  22. Armstrong SA, Look AT (2005) Molecular genetics of acute lymphoblastic leukemia. J Clin Oncol 23(26):6306–6315

    Article  CAS  PubMed  Google Scholar 

  23. Mullighan CG (2012) The molecular genetic makeup of acute lymphoblastic leukemia. Hematology Am Soc Hematol Educ Program 2012:389–396

    PubMed  Google Scholar 

  24. Sutcliffe M et al (2005) High concordance from independent studies by the Children’s Cancer Group (CCG) and Pediatric Oncology Group (POG) associating favorable prognosis with combined trisomies 4, 10, and 17 in children with NCI Standard-Risk B-precursor Acute Lymphoblastic Leukemia: a Children’s Oncology Group (COG) initiative. Leukemia 19(5):734–740

    Article  CAS  PubMed  Google Scholar 

  25. Gleißner B et al (2002) Leading prognostic relevance of the BCR-ABL translocation in adult acute B-lineage lymphoblastic leukemia: a prospective study of the German Multicenter Trial Group and confirmed polymerase chain reaction analysis. Blood 99(5):1536–1543

    Article  PubMed  Google Scholar 

  26. Weng AP et al (2004) Activating mutations of NOTCH1 in human T cell acute lymphoblastic leukemia. Science 306(5694):269–271

    Article  CAS  PubMed  Google Scholar 

  27. Aricò M et al (2000) Outcome of treatment in children with Philadelphia chromosome–positive acute lymphoblastic leukemia. N Engl J Med 342(14):998–1006

    Article  PubMed  Google Scholar 

  28. Pui C-H et al (2002) Outcome of treatment in childhood acute lymphoblastic leukaemia with rearrangements of the 11q23 chromosomal region. Lancet 359(9321):1909–1915

    Article  PubMed  Google Scholar 

  29. Ferrando AA et al (2002) Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell 1(1):75–87

    Article  CAS  PubMed  Google Scholar 

  30. Ferrando AA et al (2004) Prognostic importance of TLX1 (HOX11) oncogene expression in adults with T-cell acute lymphoblastic leukaemia. Lancet 363(9408):535–536

    Article  CAS  PubMed  Google Scholar 

  31. Vijayakrishnan J, Houlston R (2010) Candidate gene association studies and risk of childhood acute lymphoblastic leukemia: a systematic review and meta-analysis. Haematologica 95(8):1405–1414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Chang JS et al (2010) Genetic polymorphisms in adaptive immunity genes and childhood acute lymphoblastic leukemia. Cancer Epidemiol Biomarkers Prev 19(9):2152–2163

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Relling MV et al (1999) Mercaptopurine therapy intolerance and heterozygosity at the thiopurine S-methyltransferase gene locus. J Natl Cancer Inst 91(23):2001–2008

    Article  CAS  PubMed  Google Scholar 

  34. Relling MV, Evans WE (2015) Pharmacogenomics in the clinic. Nature 526(7573):343

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Schena M et al (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270(5235):467

    Article  CAS  PubMed  Google Scholar 

  36. McCarroll SA et al (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40(10):1166–1174

    Article  CAS  PubMed  Google Scholar 

  37. Davies JJ, Wilson IM, Lam WL (2005) Array CGH technologies and their applications to cancer genomes. Chromosom Res 13(3):237–248

    Article  CAS  Google Scholar 

  38. Southern E, Mir K, Shchepinov M (1999) Molecular interactions on microarrays. Nat Genet 21:5–9

    Article  CAS  PubMed  Google Scholar 

  39. Zhang L, Miles MF, Aldape KD (2003) A model of molecular interactions on short oligonucleotide microarrays. Nat Biotechnol 21(7):818–821

    Article  CAS  PubMed  Google Scholar 

  40. Schena M (1999) DNA microarrays: a practical approach. Oxford University Press, New York, NY

    Google Scholar 

  41. Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet 32:496–501

    Article  CAS  PubMed  Google Scholar 

  42. Johnson JM et al (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302(5653):2141–2144

    Article  CAS  PubMed  Google Scholar 

  43. Matsuzaki H et al (2004) Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods 1(2):109–111

    Article  CAS  PubMed  Google Scholar 

  44. Mullighan CG, Downing JR (2009) Genome-wide profiling of genetic alterations in acute lymphoblastic leukemia: recent insights and future directions. Leukemia 23(7):1209–1218

    Article  CAS  PubMed  Google Scholar 

  45. Yang YH et al (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30(4):e15–e15

    Article  PubMed  PubMed Central  Google Scholar 

  46. Irving JA et al (2005) Loss of heterozygosity in childhood acute lymphoblastic leukemia detected by genome-wide microarray single nucleotide polymorphism analysis. Cancer Res 65(8):3053–3058

    Article  CAS  PubMed  Google Scholar 

  47. Huyghe JR et al (2013) Exome array analysis identifies new loci and low-frequency variants influencing insulin processing and secretion. Nat Genet 45(2):197–201

    Article  CAS  PubMed  Google Scholar 

  48. Bertone P et al (2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306(5705):2242–2246

    Article  CAS  PubMed  Google Scholar 

  49. Rhodes DR, Chinnaiyan AM (2005) Integrative analysis of the cancer transcriptome. Nat Genet 37:S31–S37

    Article  CAS  PubMed  Google Scholar 

  50. Bullinger L et al (2004) Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N Engl J Med 350(16):1605–1616

    Article  CAS  PubMed  Google Scholar 

  51. Metzeler KH et al (2011) TET2 mutations improve the new European LeukemiaNet risk classification of acute myeloid leukemia: a Cancer and Leukemia Group B study. J Clin Oncol 29(10):1373–1381

    Article  PubMed  PubMed Central  Google Scholar 

  52. Yang JJ et al (2009) Genome-wide interrogation of germline genetic variation associated with treatment response in childhood acute lymphoblastic leukemia. JAMA 301(4):393–403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Bassan R, Hoelzer D (2011) Modern therapy of acute lymphoblastic leukemia. J Clin Oncol 29(5):532–543

    Article  PubMed  Google Scholar 

  54. Pui C-H et al (2004) Improved outcome for children with acute lymphoblastic leukemia: results of total therapy study XIIIB at St Jude Children’s Research Hospital. Blood 104(9):2690–2696

    Article  CAS  PubMed  Google Scholar 

  55. Simon RM (2003) Design and analysis of DNA microarray investigations. Springer Science & Business Media, New York, NY

    Google Scholar 

  56. Rabbee N, Speed TP (2006) A genotype calling algorithm for affymetrix SNP arrays. Bioinformatics 22(1):7–12

    Article  CAS  PubMed  Google Scholar 

  57. Korn JM et al (2008) Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet 40(10):1253–1260

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Hubbell E, Liu W-M, Mei R (2002) Robust estimators for expression analysis. Bioinformatics 18(12):1585–1592

    Article  CAS  PubMed  Google Scholar 

  59. Xu H et al (2013) Novel susceptibility variants at 10p12.31-12.2 for childhood acute lymphoblastic leukemia in ethnically diverse populations. J Natl Cancer Inst 105(10):733–742

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Neale BM et al (2010) Meta-analysis of genome-wide association studies of attention-deficit/hyperactivity disorder. J Am Acad Child Adolesc Psychiatry 49(9):884–897

    Article  PubMed  PubMed Central  Google Scholar 

  61. Mullighan CG et al (2007) Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446(7137):758–764

    Article  CAS  PubMed  Google Scholar 

  62. Mullighan CG et al (2008) BCR–ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros. Nature 453(7191):110–114

    Article  CAS  PubMed  Google Scholar 

  63. Mullighan CG et al (2009) Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med 360(5):470–480

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Mullighan CG et al (2009) Rearrangement of CRLF2 in B-progenitor–and Down syndrome–associated acute lymphoblastic leukemia. Nat Genet 41(11):1243–1246

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Kawamata N et al (2008) Molecular allelokaryotyping of pediatric acute lymphoblastic leukemias by high-resolution single nucleotide polymorphism oligonucleotide genomic microarray. Blood 111(2):776–784

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Kuiper R et al (2007) High-resolution genomic profiling of childhood ALL reveals novel recurrent genetic lesions affecting pathways involved in lymphocyte differentiation and cell cycle progression. Leukemia 21(6):1258–1266

    Article  CAS  PubMed  Google Scholar 

  67. Kuiper R et al (2010) IKZF1 deletions predict relapse in uniformly treated pediatric precursor B-ALL. Leukemia 24(7):1258–1264

    Article  CAS  PubMed  Google Scholar 

  68. Den Boer ML et al (2009) A subtype of childhood acute lymphoblastic leukaemia with poor treatment outcome: a genome-wide classification study. Lancet Oncol 10(2):125–134

    Article  CAS  Google Scholar 

  69. Roberts KG et al (2012) Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell 22(2):153–166

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Wood B et al (2009) Patients with early T-cell precursor (ETP) acute lymphoblastic leukemia (ALL) have high levels of minimal residual disease (MRD) at the end of induction—a Children’s Oncology Group (COG) study. Blood 114(22):9–9

    Google Scholar 

  71. Coustan-Smith E et al (2009) Early T-cell precursor leukaemia: a subtype of very high-risk acute lymphoblastic leukaemia. Lancet Oncol 10(2):147–156

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Paugh SW et al (2015) NALP3 inflammasome upregulation and CASP1 cleavage of the glucocorticoid receptor cause glucocorticoid resistance in leukemia cells. Nat Genet 47(6):607–614

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Wang Y, Armstrong SA (2007) Genome-wide SNP analysis in cancer: leukemia shows the way. Cancer Cell 11(4):308–309

    Article  CAS  PubMed  Google Scholar 

  74. Beroukhim R et al (2010) The landscape of somatic copy-number alteration across human cancers. Nature 463(7283):899–905

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Irving JA et al (2005) Loss of heterozygosity and somatic mutations of the glucocorticoid receptor gene are rarely found at relapse in pediatric acute lymphoblastic leukemia but may occur in a subpopulation early in the disease course. Cancer Res 65(21):9712–9718

    Article  CAS  PubMed  Google Scholar 

  76. Nebral K et al (2009) Incidence and diversity of PAX5 fusion genes in childhood acute lymphoblastic leukemia. Leukemia 23(1):134–143

    Article  CAS  PubMed  Google Scholar 

  77. Iacobucci I et al (2009) Identification and molecular characterization of recurrent genomic deletions on 7p12 in the IKZF1 gene in a large cohort of BCR-ABL1–positive acute lymphoblastic leukemia patients: on behalf of Gruppo Italiano Malattie Ematologiche dell'Adulto Acute Leukemia Working Party (GIMEMA AL WP). Blood 114(10):2159–2167

    Article  CAS  PubMed  Google Scholar 

  78. Lilljebjörn H et al (2010) The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias. Hum Mol Genet 19(16):3150–3158

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  79. Russell LJ et al (2009) Deregulated expression of cytokine receptor gene, CRLF2, is involved in lymphoid transformation in B-cell precursor acute lymphoblastic leukemia. Blood 114(13):2688–2698

    Article  CAS  PubMed  Google Scholar 

  80. Yoda A et al (2010) Functional screening identifies CRLF2 in precursor B-cell acute lymphoblastic leukemia. Proc Natl Acad Sci 107(1):252–257

    Article  CAS  PubMed  Google Scholar 

  81. Mullighan CG et al (2009) JAK mutations in high-risk childhood acute lymphoblastic leukemia. Proc Natl Acad Sci 106(23):9414–9418

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Van Vlierberghe P et al (2006) The cryptic chromosomal deletion del (11)(p12p13) as a new activation mechanism of LMO2 in pediatric T-cell acute lymphoblastic leukemia. Blood 108(10):3520–3529

    Article  PubMed  CAS  Google Scholar 

  83. Lahortiga I et al (2007) Duplication of the MYB oncogene in T cell acute lymphoblastic leukemia. Nat Genet 39(5):593–595

    Article  CAS  PubMed  Google Scholar 

  84. Clappier E et al (2007) The C-MYB locus is involved in chromosomal translocation and genomic duplications in human T-cell acute leukemia (T-ALL), the translocation defining a new T-ALL subtype in very young children. Blood 110(4):1251–1261

    Article  CAS  PubMed  Google Scholar 

  85. Graux C et al (2004) Fusion of NUP214 to ABL1 on amplified episomes in T-cell acute lymphoblastic leukemia. Nat Genet 36(10):1084

    Article  CAS  PubMed  Google Scholar 

  86. Palomero T et al (2007) Mutational loss of PTEN induces resistance to NOTCH1 inhibition in T-cell leukemia. Nat Med 13(10):1203–1210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Tosello V et al (2009) WT1 mutations in T-all. Blood 114(5):1038–1045

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Xavier RJ, Rioux JD (2008) Genome-wide association studies: a new window into immune-mediated diseases. Nat Rev Immunol 8(8):631–643

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Sherborne AL et al (2010) Variation in CDKN2A at 9p21.3 influences childhood acute lymphoblastic leukemia risk. Nat Genet 42(6):492–494

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Perez-Andreu V et al (2013) Inherited GATA3 variants are associated with Ph-like childhood acute lymphoblastic leukemia and risk of relapse. Nat Genet 45(12):1494–1498

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Papaemmanuil E et al (2009) Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia. Nat Genet 41(9):1006–1010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Xu H et al (2015) Inherited coding variants at the CDKN2A locus influence susceptibility to acute lymphoblastic leukaemia in children. Nat Commun 6:7553

    Article  CAS  PubMed  Google Scholar 

  93. Perez-Andreu V et al (2015) A genome-wide association study of susceptibility to acute lymphoblastic leukemia in adolescents and young adults. Blood 125(4):680–686

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Liao F et al (2016) Association between PIP4K2A polymorphisms and acute lymphoblastic leukemia susceptibility. Medicine (Baltimore) 95(18):e3542

    Article  CAS  Google Scholar 

  95. Xu H et al (2012) ARID5B genetic polymorphisms contribute to racial disparities in the incidence and treatment outcome of childhood acute lymphoblastic leukemia. J Clin Oncol 30(7):751–757

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Linabery AM, Ross JA (2008) Trends in childhood cancer incidence in the U.S. (1992–2004). Cancer 112(2):416–432

    Article  PubMed  Google Scholar 

  97. Dores GM et al (2012) Acute leukemia incidence and patient survival among children and adults in the United States, 2001–2007. Blood 119(1):34–43

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Burmeister T et al (2014) Germline variants in IKZF1, ARID5B, and CEBPE as risk factors for adult-onset acute lymphoblastic leukemia: an analysis from the GMALL study group. Haematologica 99(2):e23–e25

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  99. Hou Q et al (2017) Regulatory network of GATA3 in pediatric acute lymphoblastic leukemia. Oncotarget 8(22):36040–36053

    Article  PubMed  PubMed Central  Google Scholar 

  100. Trevino LR et al (2009) Germline genomic variants associated with childhood acute lymphoblastic leukemia. Nat Genet 41(9):1001–1005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Huang Q (2015) Genetic study of complex diseases in the post-GWAS era. J Genet Genomics 42(3):87–98

    Article  CAS  PubMed  Google Scholar 

  102. Freedman ML et al (2011) Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet 43(6):513–518

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Vijayakrishnan J et al (2015) The 9p21.3 risk of childhood acute lymphoblastic leukaemia is explained by a rare high-impact variant in CDKN2A. Sci Rep 5:15065

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Walsh KM et al (2015) A heritable missense polymorphism in CDKN2A confers strong risk of childhood acute lymphoblastic leukemia and is preferentially selected during clonal evolution. Cancer Res 75(22):4884–4894

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Studd JB et al (2017) Genetic and regulatory mechanism of susceptibility to high-hyperdiploid acute lymphoblastic leukaemia at 10p21.2. Nat Commun 8:14616

    Article  PubMed  PubMed Central  Google Scholar 

  106. Hungate EA et al (2016) A variant at 9p21.3 functionally implicates CDKN2B in paediatric B-cell precursor acute lymphoblastic leukaemia aetiology. Nat Commun 7:10635

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Yin D et al (2017) Impact of NUDT15 polymorphisms on thiopurines-induced myelotoxicity and thiopurines tolerance dose. Oncotarget 8(8):13575–13585

    Article  PubMed  PubMed Central  Google Scholar 

  108. Yang JJ et al (2015) Inherited NUDT15 variant is a genetic determinant of mercaptopurine intolerance in children with acute lymphoblastic leukemia. J Clin Oncol 33(11):1235–1242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Moriyama T et al (2016) NUDT15 polymorphisms alter thiopurine metabolism and hematopoietic toxicity. Nat Genet 48(4):367–373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Xu H et al (2015) Common variants in ACYP2 influence susceptibility to cisplatin-induced hearing loss. Nat Genet 47(3):263–266

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Martinelli G et al (2009) IKZF1 (Ikaros) deletions in BCR-ABL1-positive acute lymphoblastic leukemia are associated with short disease-free survival and high rate of cumulative incidence of relapse: a GIMEMA AL WP report. J Clin Oncol 27(31):5202–5207

    Article  CAS  PubMed  Google Scholar 

  112. Schwab C et al (2010) Evaluation of multiplex ligation-dependent probe amplification as a method for the detection of copy number abnormalities in B-cell precursor acute lymphoblastic leukemia. Genes Chromosom Cancer 49(12):1104–1113

    Article  CAS  PubMed  Google Scholar 

  113. JD MP et al (2001) A physical map of the human genome. Nature 409(6822):934–941

    Article  Google Scholar 

  114. Collins FS, Morgan M, Patrinos A (2003) The Human Genome Project: lessons from large-scale biology. Science 300(5617):286–290

    Article  CAS  PubMed  Google Scholar 

  115. Wetterstrand KA (2013) DNA sequencing costs: data from the NHGRI Genome Sequencing Program (GSP). National Human Genome Research Institute, Bethesda, MD

    Google Scholar 

  116. Tomkinson AE et al (2006) DNA ligases: structure, reaction mechanism, and function. Chem Rev 106(2):687–699

    Article  CAS  PubMed  Google Scholar 

  117. Harismendy O et al (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10(3):R32

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  118. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26(10):1135–1145

    Article  CAS  PubMed  Google Scholar 

  119. Valouev A et al (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18(7):1051–1063

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Margulies M et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376–380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Loman NJ et al (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30(5):434–439

    Article  CAS  PubMed  Google Scholar 

  122. Rothberg JM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475(7356):348–352

    Article  CAS  PubMed  Google Scholar 

  123. Ju J et al (2006) Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci 103(52):19635–19640

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Solexa I (2006) Illumina: protocol for whole genome sequencing using solexa technology. BioTech Protoc Guide 2006:29

    Google Scholar 

  125. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10(10):669–680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Buenrostro JD et al (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10(12):1213–1218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Brunner AL et al (2009) Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res 19(6):1044–1056

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Ding L et al (2012) Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 481(7382):506–510

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Masetti R et al (2013) CBFA2T3-GLIS2 fusion transcript is a novel common feature in pediatric, cytogenetically normal AML, not restricted to FAB M7 subtype. Blood 121(17):3469–3472

    Article  CAS  PubMed  Google Scholar 

  131. Schatz MC, Langmead B (2013) The DNA data deluge. IEEE Spectr 50(7):28–33

    Article  Google Scholar 

  132. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25(14):1754–1760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Langmead B et al (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  134. Li R et al (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15):1966–1967

    Article  CAS  PubMed  Google Scholar 

  135. Burrows, M. and D.J. Wheeler, (1994) A block-sorting lossless data compression algorithm. SRC research report

    Google Scholar 

  136. Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18(11):1851–1858

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Ewing B et al (1998) Base-calling of automated sequencer traces usingPhred. I. Accuracy assessment. Genome Res 8(3):175–185

    Article  CAS  PubMed  Google Scholar 

  138. Martin ER et al (2010) SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies. Bioinformatics 26(22):2803–2810

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. McKenna A et al (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297–1303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Li H et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  141. Ivakhno S et al (2010) CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics 26(24):3051–3058

    Article  CAS  PubMed  Google Scholar 

  142. Chiang DY et al (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 6(1):99–103

    Article  CAS  PubMed  Google Scholar 

  143. Magi A et al (2011) Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm. Nucleic Acids Res 39(10):e65

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Chen X et al (2015) CONSERTING: integrating copy-number analysis with structural-variation detection. Nat Methods 12(6):527–530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Chen K et al (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6(9):677–681

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Wang J et al (2011) CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods 8(8):652–654

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Sun R et al (2012) Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. Bioinformatics 28(7):1024–1025

    Article  CAS  PubMed  Google Scholar 

  148. Zhao H, Zhao F (2015) BreakSeek: a breakpoint-based algorithm for full spectral range INDEL detection. Nucleic Acids Res 43(14):6701–6713

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Sindi SS et al (2012) An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biol 13(3):R22

    Article  PubMed  PubMed Central  Google Scholar 

  150. Handsaker RE et al (2015) Large multiallelic copy number variations in humans. Nat Genet 47(3):296–303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Abo RP et al (2015) BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers. Nucleic Acids Res 43(3):e19–e19

    Article  PubMed  CAS  Google Scholar 

  152. Hajirasouliha I et al (2010) Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics 26(10):1277–1283

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Van Vlierberghe P et al (2010) PHF6 mutations in T-cell acute lymphoblastic leukemia. Nat Genet 42(4):338–342

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  154. De Keersmaecker K (2013) Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia. Nat Genet 45:186–190

    Article  PubMed  CAS  Google Scholar 

  155. Holmfeldt L (2013) The genomic landscape of hypodiploid acute lymphoblastic leukemia. Nat Genet 45:242–252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Kalender Atak Z (2013) Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia. PLoS Genet 9:e1003997

    Article  PubMed Central  CAS  Google Scholar 

  157. Li Y (2014) Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia. Nature 508:98–102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Papaemmanuil E (2014) RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia. Nat Genet 46:116–125

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Zhang J (2012) The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 481:157–163

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Huether R et al (2014) The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. Nat Commun 5:3630

    Article  PubMed  CAS  Google Scholar 

  161. O'Neil J (2007) FBW7 mutations in leukemic cells mediate NOTCH pathway activation and resistance to gamma-secretase inhibitors. J Exp Med 204:1813–1824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Van Vlierberghe P et al (2011) PHF6 mutations in adult acute myeloid leukemia. Leukemia 25(1):130–134

    Article  PubMed  CAS  Google Scholar 

  163. Treanor LM (2014) Interleukin-7 receptor mutants initiate early T cell precursor leukemia in murine thymocyte progenitors with multipotent potential. J Exp Med 211:701–713

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  164. Ma X (2015) Rise and fall of subclones from diagnosis to relapse in pediatric B-progenitor acute lymphoblastic leukemia. Nat Commun 6:6604

    Article  CAS  PubMed  Google Scholar 

  165. Andersson AK (2015) The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukaemias. Nat Genet 47(4):330–337

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Roberts KG (2014) Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med 371:1005–1015

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  167. Mullighan CG (2011) CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature 471:235–239

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Hof J (2011) Mutations and deletions of the TP53 gene predict nonresponse to treatment and poor outcome in first relapse of childhood acute lymphoblastic leukemia. J Clin Oncol 29:3185–3193

    Article  PubMed  Google Scholar 

  169. Mar BG (2014) Mutations in epigenetic regulators including SETD2 are gained during relapse in paediatric acute lymphoblastic leukaemia. Nat Commun 5:3469

    Article  PubMed  CAS  Google Scholar 

  170. Tzoneva G (2013) Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL. Nat Med 19:368–371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Yang JJ (2012) Genome-wide association study identifies germline polymorphisms associated with relapse of childhood acute lymphoblastic leukemia. Blood 120:4197–4204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. Li B et al (2015) Negative feedback-defective PRPS1 mutants drive thiopurine resistance in relapsed childhood ALL. Nat Med 21(6):563–571

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  173. Ionita-Laza I et al (2013) Sequence kernel association tests for the combined effect of rare and common variants. Am J Hum Genet 92(6):841–853

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  174. Moriyama T et al (2015) Germline genetic variation in ETV6 and risk of childhood acute lymphoblastic leukaemia: a systematic genetic study. Lancet Oncol 16(16):1659–1666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. Shah S et al (2013) A recurrent germline PAX5 mutation confers susceptibility to pre-B cell acute lymphoblastic leukemia. Nat Genet 45(10):1226–1231

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Precision Medicine Center, State Key Laboratory of Biotherapy, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, No.17, Section 3, South Renmin Road, Chengdu, Sichuan, 610041, China

    Heng Xu & Yang Shu

Authors
  1. Heng Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yang Shu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Heng Xu .

Editor information

Editors and Affiliations

  1. Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

    Tao Huang

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Cite this protocol

Xu, H., Shu, Y. (2018). Insights of Acute Lymphoblastic Leukemia with Development of Genomic Investigation. In: Huang, T. (eds) Computational Systems Biology. Methods in Molecular Biology, vol 1754. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7717-8_21

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7717-8_21

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7716-1

  • Online ISBN: 978-1-4939-7717-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation