Acute Lymphoblastic Leukemia - ALL

Acute lymphoblastic leukemia (ALL) is a malignant disease of the lymphoid cell line occurring predominantly in children. An ALL workup typically includes CBC testing, coagulation studies, and chemistry profiles; definitive diagnosis requires bone marrow biopsy.

  • Diagnosis
  • Monitoring
  • Pharmacogenetics
  • Background
  • Lab Tests
  • References
  • Related Topics
  • Videos

Indications for Testing

  • Abnormal blood count/peripheral smear
  • Constitutional symptoms without other etiology

Laboratory Testing

  • CBC with peripheral smear – leukocytosis and blasts are common
  • Cytochemical staining – used infrequently due to availability of immunophenotyping
    • MPO – usually negative
  • Immunophenotyping – determine antigen markers for identifying cell lineage and predicting outcome
    • CD expression – helps establish ALL lineage
    • B-ALL characterized by B-cell antigens – PAX5, CD19, CD20, CD22, CD24, CD79a
      • CD20 – only partially expressed in non-mature forms
      • CD10 – frequently expressed
    • T-ALL characterized by T-cell antigens – CD2, CD3, CD4, CD5, CD7, CD8
      • Others – CD1a, CD10, CD34, CD55, CD99, HLA-DR, and TdT
      • May also express myeloid antigens – CD11b, CD13, CD15, CD33
  • Cytogenetic studies – diagnostic and prognostic workup
    • Treatment protocols are stratified by age and the presence of t(9;22)
    • Most B-ALL contains genetic abnormalities – usually translocations
      • Genetics correlate with prognosis
    • T-ALL/LBL contains TCR gene rearrangements
    • See Genetics section in Clinical Background for specific abnormalities
  • FISH – more sensitive than conventional cytogenetics in detecting genomic aberrations
    • For initial diagnostic workup, prognostic stratification (especially in children), and determination of treatment approach
    • Adult probes – BCR/ABL1, E2A, MLL, IGH, and MYC
    • Childhood probes – BCR-ABL1, TEL/AML (ETV6-RUNX1), CEP4 and CEP10, and MLL/11q23 rearrangements
  • Cytogenomic SNP microarray – detects abnormalities that may not be detected by FISH or cytogenetics including deletions in the regions of CDKN2A/B, BTG1, IKZF1, and EBF1
    • Does not detect BCR-ABL1, TEL/AML (ETV6/RUNX1), or balanced rearrangement of MLL, IGH, MYC, and TCF3
      • BCR-ABL1 by next generation sequencing offers advantages over Sanger sequencing


  • Bone marrow biopsy – enumerate blasts and collect material for ancillary testing (eg, cytogenetics)
  • Immunohistochemistry – most useful stains include TdT; CD3; CD10 (CALLA); CD20, L26; CD79A


Differential Diagnosis

  • Repeat PCR or FISH testing using leukemia-associated phenotype defined at diagnosis for detection of minimal residual disease (MRD)
    • MRD by PCR or FISH defined as >10-4 cells or >0.01% blasts
    • Qualitative/quantitative PCR testing is very sensitive and may detect MRD that is not of clinical concern
      •  PCR has lower sensitivity than FISH
    • >10% MRD portends higher relapse rate
    • B-cell lines MRD detected using bone marrow; T-cell lines MRD can be detected using peripheral blood
      • T-ALL – detection of TdT or CD34 confirms MRD
    • Relapse mandates new immunophenotyping and molecular testing – karyotype may change and, rarely, second de novo ALL may be discovered
  • Thiopurine S-methyltransferase (TPMT)
    • Thiopurine prodrugs are metabolized via TPMT enzymatic activity
    • Deficiency of TPMT predicts hematopoietic toxicity after thiopurine treatment
    • Increased risk of therapy-related acute myeloid leukemia and radiation-induced brain tumors in patients receiving intensive thiopurine therapy
    • Testing to determine activity level may be helpful in dosing thiopurine drugs and also help avert bone marrow suppression
      • For deficient activity – dose reduction of 80-90% may be required
      • For intermediate activity – dose reduction of 20-50% may be required
  • Other pharmacogenetic pathways (no testing currently available)
    • During induction therapy for ALL
      • Predominant drug metabolism pathway is via CYP3A
      • CYP3A5 GG genotype (lower CYP3A5 activity) predicts gastrointestinal (GI) toxicity and rates of infection
    • During consolidation and continuation phase of therapy
      • Reduced folate carrier AA or AG genotype predicts GI toxicity
    • During all phases
      • UGT1A1 promotor repeat polymorphism (UGT1A1 7h) predicts hyperbilirubinemia
    • MTHFR polymorphism
      • Probably affects methotrexate toxicity
      • MTHFR C677T variant associated with higher rate of relapse
    • Therapy molecular targets
      • Investigational use of Imatinib for BCR-ABL1-positive ALL
    • Adverse drug effects
      • Polymorphism in eight genes significantly associated with glucocorticoid-induced hypertension (CNTNAP2, LEPR, CRHR1, NTAN1, SLCI2A3, ALPL, BGLAP, and APOB)
      • PAI-1 polymorphism associated with GA/AA genotype – increased risk of glucocorticoid-induced osteonecrosis


  • Incidence – 1.7/100,000 (NCCN, 2015)
    • Most common leukemia in childhood – 75-85% of acute leukemias
      • ~3/100,000 (Hunger, 2015)
  • Age – peak incidence 3-5 years; second peak >50 years
  • Sex – M<F; ~1:3
  • Ethnicity
    • <3 years – Caucasian predominance
    • ≥3 years – African Americans have higher risk

Risk Factors


Clinical Presentation

  • Nonspecific constitutional symptoms – fever, lethargy, dizziness
  • Pallor – due to anemia
  • Failure to thrive
  • Bruising – due to thrombocytopenia
  • Infections
  • Pain in extremities – most prominent in children
Tests generally appear in the order most useful for common clinical situations. Click on number for test-specific information in the ARUP Laboratory Test Directory.

Leukemia/Lymphoma Phenotyping by Flow Cytometry 2008003
Method: Flow Cytometry


Some hematopoietic neoplasms do not show phenotypic abnormalities and therefore may not be detected by flow cytometry

Poor cell viability may adversely affect antigens and impede the ability to properly identify neoplastic cells

Flow results cannot be used alone to diagnose malignancy; should be interpreted in conjunction with morphology, clinical information, and other necessary ancillary tests for a definitive diagnosis

Chromosome FISH, Interphase 2002298
Method: Fluorescence in situ Hybridization

Chromosome Analysis, Bone Marrow with Reflex to Genomic Microarray 2007130
Method: Giemsa Band/Genomic Microarray (Oligo-SNP array)

Chromosome Analysis, Leukemic Blood with Reflex to Genomic Microarray 2007131
Method: Giemsa Band/Genomic Microarray (Oligo-SNP array)

Cytogenomic SNP Microarray - Oncology 2006325
Method: Genomic Microarray (Oligo-SNP Array)


Low-level mosaicism (<15%-20%) may not be detected; test may not be appropriate for individuals with expected lower levels of malignant cells

Not recommended for minimal residual disease

Does not detect balanced rearrangements; FISH should be used to evaluate specific balanced rearrangements according to indication

Does not detect base pair mutations and very small deletions/duplications; imbalances of the mitochondrial genome; positional information for chromosome rearrangements; low level clones

Acute Lymphocytic Leukemia (ALL) Panel by FISH, Adult 2002647
Method: Fluorescence in situ Hybridization


Panel detects only the specific aberrations targeted by the probes

Chromosome alterations outside the regions complementary to these FISH probes will not be detected 

Acute Lymphocytic Leukemia (ALL) Panel by FISH, Pediatric 2002719
Method: Fluorescence in situ Hybridization


Panel detects only the specific aberrations targeted by the probes

Chromosome alterations outside the regions complementary to these FISH probes will not be detected

TdT by Immunohistochemistry 2004142
Method: Immunohistochemistry

CD10 (CALLA) by Immunohistochemistry 2003523
Method: Immunohistochemistry

CD19 by Immunohistochemistry 2005114
Method: Immunohistochemistry

CD20, L26 by Immunohistochemistry 2003532
Method: Immunohistochemistry

CD79A by Immunohistochemistry 2003800
Method: Immunohistochemistry

CD3 by Immunohistochemistry 2003508
Method: Immunohistochemistry

BCR-ABL1 Mutation Analysis for Tyrosine Kinase Inhibitor Resistance by Next Generation Sequencing 2008420
Method: Massively Parallel Sequencing


A negative result does not exclude mutations below the level of detection or mutations outside the sequenced region of this test

BCR-ABL1, Major (p210), Quantitative 2005017
Method: Quantitative Reverse Transcription Polymerase Chain Reaction


Does not detect p190 or p230 form 

BCR-ABL1, Minor (p190), Quantitative 2005016
Method: Quantitative Reverse Transcription Polymerase Chain Reaction


Does not detect p210 or p230 form 

BCR-ABL1, Qualitative with Reflex to BCR-ABL1 Quantitative 2005010
Method: Reverse Transcription Polymerase Chain Reaction


Brüggemann M, Schrauder A, Raff T, Pfeifer H, Dworzak M, Ottmann OG, Asnafi V, Baruchel A, Bassan R, Benoit Y, Biondi A, Cavé H, Dombret H, Fielding AK, Foà R, Gökbuget N, Goldstone AH, Goulden N, Henze G, Hoelzer D, Janka-Schaub GE, Macintyre EA, Pieters R, Rambaldi A, Ribera J, Schmiegelow K, Spinelli O, Stary J, von Stackelberg A, Kneba M, Schrappe M, van Dongen JJ, European Working Group for Adult Acute Lymphoblastic Leukemia (EWALL), International Berlin-Frankfurt-Münster Study Group (I-BFM-SG). Standardized MRD quantification in European ALL trials: proceedings of the Second International Symposium on MRD assessment in Kiel, Germany, 18-20 September 2008. Leukemia. 2010; 24(3): 521-35. PubMed

Hampel H, Bennett RL, Buchanan A, Pearlman R, Wiesner GL, Guideline Development Group, American College of Medical Genetics and Genomics Professional Practice and Guidelines Committee and National Society of Genetic Counselors Practice Guidelines Committee. A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. Genet Med. 2015; 17(1): 70-87. PubMed

NCCN Clinical Practice Guidelines in Oncology, Acute Lymphoblastic Leukemia. National Comprehensive Cancer Network. Fort Washington, PA [Accessed: Jun 2015]

Protocol for the Examination of Specimens From Patients With Hematopoietic Neoplasms Involving the Bone Marrow. Based on AJCC/UICC TNM, 7th ed. Protocol web posting date: Jun 2012. College of American Pathologists (CAP). Northfield, IL [Revised: Jun 2012; Accessed: May 2017]

General References

Brüggemann M, Gökbuget N, Kneba M. Acute lymphoblastic leukemia: monitoring minimal residual disease as a therapeutic principle. Semin Oncol. 2012; 39(1): 47-57. PubMed

Cornell RF, Palmer J. Adult acute leukemia. Dis Mon. 2012; 58(4): 219-38. PubMed

Digiuseppe JA. Acute lymphoblastic leukemia: diagnosis and detection of minimal residual disease following therapy. Clin Lab Med. 2007; 27(3): 533-49, vi. PubMed

Harrison CJ. Acute lymphoblastic leukemia. Clin Lab Med. 2011; 31(4): 631-47, ix. PubMed

Hunger SP, Mullighan CG. Acute Lymphoblastic Leukemia in Children. N Engl J Med. 2015; 373(16): 1541-52. PubMed

Iacobucci I, Papayannidis C, Lonetti A, Ferrari A, Baccarani M, Martinelli G. Cytogenetic and molecular predictors of outcome in acute lymphocytic leukemia: recent developments. Curr Hematol Malig Rep. 2012; 7(2): 133-43. PubMed

Inaba H, Greaves M, Mullighan CG. Acute lymphoblastic leukaemia. Lancet. 2013; 381(9881): 1943-55. PubMed

Margolin JF. Molecular diagnosis and risk-adjusted therapy in pediatric hematologic malignancies: a primer for pediatricians. Eur J Pediatr. 2011; 170(4): 419-25. PubMed

Morrissette JJ, Bagg A. Acute myeloid leukemia: conventional cytogenetics, FISH, and moleculocentric methodologies. Clin Lab Med. 2011; 31(4): 659-86, x. PubMed

Mrózek K, Harper DP, Aplan PD. Cytogenetics and molecular genetics of acute lymphoblastic leukemia. Hematol Oncol Clin North Am. 2009; 23(5): 991-1010, v. PubMed

Peters JM, Ansari Q. Multiparameter flow cytometry in the diagnosis and management of acute leukemia. Arch Pathol Lab Med. 2011; 135(1): 44-54. PubMed

Swerdlow S, Campo E, Harris N, Jaffe E, Pileri S, Harald S, Thiele J, Vardiman J. WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues, 4th ed. Lyon, France: International Agency for Research on Cancer, 2008.

Zweidler-McKay PA, Hilden JM. The ABCs of infant leukemia. Curr Probl Pediatr Adolesc Health Care. 2008; 38(3): 78-94. PubMed

References from the ARUP Institute for Clinical and Experimental Pathology®

Baughn LB, Biegel JA, South ST, Smolarek TA, Volkert S, Carroll AJ, Heerema NA, Rabin KR, Zweidler-McKay PA, Loh M, Hirsch B. Integration of cytogenomic data for furthering the characterization of pediatric B-cell acute lymphoblastic leukemia: a multi-institution, multi-platform microarray study Cancer Genet. 2015; 208(1-2): 1-18. PubMed

Gu G, Sederberg MC, Drachenberg MR, South ST. IGF2BP1: a novel IGH translocation partner in B acute lymphoblastic leukemia. Cancer Genet. 2014; 207(7-8): 332-4. PubMed

Jones D, Kamel-Reid S, Bahler D, Dong H, Elenitoba-Johnson K, Press R, Quigley N, Rothberg P, Sabath D, Viswanatha D, Weck K, Zehnder J. Laboratory practice guidelines for detecting and reporting BCR-ABL drug resistance mutations in chronic myelogenous leukemia and acute lymphoblastic leukemia: a report of the Association for Molecular Pathology. J Mol Diagn. 2009; 11(1): 4-11. PubMed

Lowe EJ, Sposto R, Perkins SL, Gross TG, Finlay J, Zwick D, Abromowitch M, Children's Cancer Group Study 5941. Intensive chemotherapy for systemic anaplastic large cell lymphoma in children and adolescents: final results of Children's Cancer Group Study 5941. Pediatr Blood Cancer. 2009; 52(3): 335-9. PubMed

Ridges S, Heaton WL, Joshi D, Choi H, Eiring A, Batchelor L, Choudhry P, Manos EJ, Sofla H, Sanati A, Welborn S, Agarwal A, Spangrude GJ, Miles RR, Cox JE, Frazer K, Deininger M, Balan K, Sigman M, Müschen M, Perova T, Johnson R, Montpellier B, Guidos CJ, Jones DA, Trede NS. Zebrafish screen identifies novel compound with selective toxicity against leukemia. Blood. 2012; 119(24): 5621-31. PubMed

Staddon JH, Smock KJ, Schiffman JD, Fluchel MN, Engel ME, Weyrich AS, Campbell RA. Pegasparaginase treatment alters thrombin generation by modulating the protein C and S system in acute lymphoblastic leukaemia/lymphoma Blood Coagul Fibrinolysis. 2015; 26(7): 840-3. PubMed

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Last Update: October 2017