HAEM5:B-lymphoblastic leukaemia/lymphoma with hypodiploidy: Difference between revisions

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Revision as of 09:57, 20 November 2025


Haematolymphoid Tumours (WHO Classification, 5th ed.)

editContent Update To WHO 5th Edition Classification Is In Process; Content Below is Based on WHO 4th Edition Classification
This page was converted to the new template on 2023-12-07. The original page can be found at HAEM4:B-Lymphoblastic Leukemia/Lymphoma with Hypodiploidy.

(General Instructions – The focus of these pages is the clinically significant genetic alterations in each disease type. This is based on up-to-date knowledge from multiple resources such as PubMed and the WHO classification books. The CCGA is meant to be a supplemental resource to the WHO classification books; the CCGA captures in a continually updated wiki-stye manner the current genetics/genomics knowledge of each disease, which evolves more rapidly than books can be revised and published. If the same disease is described in multiple WHO classification books, the genetics-related information for that disease will be consolidated into a single main page that has this template (other pages would only contain a link to this main page). Use HUGO-approved gene names and symbols (italicized when appropriate), HGVS-based nomenclature for variants, as well as generic names of drugs and testing platforms or assays if applicable. Please complete tables whenever possible and do not delete them (add N/A if not applicable in the table and delete the examples); to add (or move) a row or column in a table, click nearby within the table and select the > symbol that appears. Please do not delete or alter the section headings. The use of bullet points alongside short blocks of text rather than only large paragraphs is encouraged. Additional instructions below in italicized blue text should not be included in the final page content. Please also see Author_Instructions and FAQs as well as contact your Associate Editor or Technical Support.)

Primary Author(s)*

Miguel Gonzalez Mancera, MD

WHO Classification of Disease

Structure Disease
Book Haematolymphoid Tumours (5th ed.)
Category B-cell lymphoid proliferations and lymphomas
Family Precursor B-cell neoplasms
Type B-lymphoblastic leukaemias/lymphomas
Subtype(s) B-lymphoblastic leukaemia/lymphoma with hypodiploidy

Related Terminology

Acceptable N/A
Not Recommended N/A

Gene Rearrangements

No recurrent gene rearrangements have been described[1].

Driver Gene Fusion(s) and Common Partner Genes Molecular Pathogenesis Typical Chromosomal Alteration(s) Prevalence -Common >20%, Recurrent 5-20% or Rare <5% (Disease) Diagnostic, Prognostic, and Therapeutic Significance - D, P, T Established Clinical Significance Per Guidelines - Yes or No (Source) Clinical Relevance Details/Other Notes
EXAMPLE: ABL1 EXAMPLE: BCR::ABL1 EXAMPLE: The pathogenic derivative is the der(22) resulting in fusion of 5’ BCR and 3’ABL1. EXAMPLE: t(9;22)(q34;q11.2) EXAMPLE: Common (CML) EXAMPLE: D, P, T EXAMPLE: Yes (WHO, NCCN) EXAMPLE:

The t(9;22) is diagnostic of CML in the appropriate morphology and clinical context (add reference). This fusion is responsive to targeted therapy such as Imatinib (Gleevec) (add reference). BCR::ABL1 is generally favorable in CML (add reference).


Individual Region Genomic Gain/Loss/LOH

Please refer to section "Characteristic Chromosomal or Other Global Mutational Patterns" below.

Chr # Gain, Loss, Amp, LOH Minimal Region Cytoband and/or Genomic Coordinates [Genome Build; Size] Relevant Gene(s) Diagnostic, Prognostic, and Therapeutic Significance - D, P, T Established Clinical Significance Per Guidelines - Yes or No (Source) Clinical Relevance Details/Other Notes
EXAMPLE:

7

EXAMPLE: Loss EXAMPLE:

chr7

EXAMPLE:

Unknown

EXAMPLE: D, P EXAMPLE: No EXAMPLE:

Presence of monosomy 7 (or 7q deletion) is sufficient for a diagnosis of AML with MDS-related changes when there is ≥20% blasts and no prior therapy (add reference).  Monosomy 7/7q deletion is associated with a poor prognosis in AML (add references).


Characteristic Chromosomal or Other Global Mutational Patterns

This entity is defined by the presence of neoplastic lymphoblasts containing less than 46 chromosomes[2], and can be subdivided into near-haploid B-ALL/LBL with hypodiploidy (24–31 chromosomes); low-hypodiploid B-ALL/LBL with hypodiploidy (32–39 chromosomes); and high-hypodiploid B-ALL/LBL with hypodiploidy (40–43 chromosomes)[1][3]. Of note, near-diploid cases (44–45 chromosomes) are not included in the hypodiploid category in clinical therapy–directed classification schemes because they do not share the poor prognosis observed[4]. In a study, for patients with 44 chromosomes, monosomy 7, the presence of a dicentric chromosome, or both predicted a worse event-free survival (EFS) but similar overall survival (OS)[5].

Chromosomal Pattern Molecular Pathogenesis Prevalence -

Common >20%, Recurrent 5-20% or Rare <5% (Disease)

Diagnostic, Prognostic, and Therapeutic Significance - D, P, T Established Clinical Significance Per Guidelines - Yes or No (Source) Clinical Relevance Details/Other Notes
Near-haploid B-ALL/LBL with hypodiploidy (24–31 chromosomes) Near haploidy may be the primary event with loss of chromosomes, followed by a secondary event of doubling of chromosomes indicating uniparental isodisomy (UPID), microdeletions if any may occur after the secondary event[6]. The chromosomal loss alone may be enough for leukemogenesis and the unconserved random chromosomes may contain specific genes that increase the oncogenic potential of leukemic cells[7][8]. Rare (0.5%)[9] D: Needs demonstration of hypodiploidy (≤ 43 chromosomes) by karyotyping and/or FISH analysis; flow cytometry DNA index analysis and/or single nucleotide polymorphism (SNP) array analysis to identify masked hypodiploidy.

P: Associated with poor prognosis[5][10]. 5-year EFS 25–40%[9].

No (NCCN) It has been observed in the pediatric population with virtually no adult cases reported. Nonrandom retention of the X chromosome plus chromosomes 8, 14, 18, and 21 are frequently observed. The most common targets of aneuploidy are chromosomes 1–7, 9, 11–13, 15–17, 19–20 and 22[11][12][13][14][15].

Near-haploid and low-hypodiploid B-ALL/LBL may undergo doubling, resulting in a pseudohyperdiploid or near-triploid clone containing up to 78 chromosomes, and can present as a diagnostic challenge. If the original hypodiploid clone is not present, the hypodiploidy is regarded as masked, and the case may be mistaken for high-hyperdiploid B-ALL/LBL, resulting in an inappropriate prognostication[10][16][17]. The two subtypes may be differentiated by SNP array analysis, demonstrating copy-neutral loss of heterozygosity for doubled monosomic chromosomes. The DNA index assessed by flow cytometry may also be helpful if distinct peaks representing the hypodiploid and doubled clones are both detectable[18].

Low-hypodiploid B-ALL/LBL with hypodiploidy (32–39 chromosomes) More than 90% of low-hypodiploid patients have been identified with TP53 mutations, which occur in virtually all low-hypodiploid B-ALL cases due to the very recurrent loss of chromosome 17[14][19][20]. p53 is one of the most prominent tumor suppressors. Its activation as a transcription factor stimulates downstream pathways leading to protective cellular processes, including cell-cycle arrest, apoptosis, and senescence, to prevent the propagation of genetically altered cells[21]. Rare in children, recurrent in adolescents, young adults, and adults P: Associated with poor prognosis. EFS 30–50%[9][10]. No (NCCN) Low-hypodiploid B-ALL/LBL is rare in children (< 1%); however, the frequency increases with age, accounting for 5% of B-ALL/LBL cases in adolescents and young adults, and > 10% of cases in adults. Nonrandom retention of two copies of chromosomes from the following: the sex chromosomes plus chromosomes 1,6, 8, 10, 14, 18, and19. Chromosome 21 is almost always retained in two copies.

The most common targets of aneuploidy are chromosomes 2–4, 7, 9, 12–13, 15–17 and 20[15].

High-hypodiploid B-ALL/LBL with hypodiploidy (40–43 chromosomes) Genetic alterations involve CDKN2A and TP53[19]. Rare, occurring in approximately 4% of diagnosed cases of hypodiploidy in both children and adults, but with a predominance of the younger group[13][22]. P: Associated with poor prognosis. EFS 75%[4]. No (NCCN) Chromosome abnormalities include whole chromosome loss, specifically one sex chromosome and often chromosomes 7, 9, and/or 13. Also detected are structural anomalies especially dicentric chromosomes involving chromosomes 7, 9 or 12.
End of V4 Section

Gene Mutations (SNV/INDEL)

Gene Genetic Alteration Tumor Suppressor Gene, Oncogene, Other Prevalence -

Common >20%, Recurrent 5-20% or Rare <5% (Disease)

Diagnostic, Prognostic, and Therapeutic Significance - D, P, T   Established Clinical Significance Per Guidelines - Yes or No (Source) Clinical Relevance Details/Other Notes
TP53
The majority are missense mutations located in exon 7, exon 8, exon 6, and exon 5. Less frequent frameshift mutations in exon 4 and 7 have been described[14]. In general are predicted to be loss of function (LOF) mutations. Tumor supressor gene Common (>90%) No established significance No (NCCN) These alterations correlate with low-hypodiploid ALL (32–39 chromosomes) and poorer clinical outcomes[11]. Approximately 50% of children with low-hypodiploid B-ALL/LBL carry germline TP53 variants associated with Li–Fraumeni syndrome. Accordingly, genetic counseling is recommended for children with low-hypodiploid B-ALL carrying TP53 mutations, and their relatives[23]. In contrast to childhood cases, TP53 mutations in low-hypodiploid adult B-ALL are somatic, are not found in healthy hematopoietic cells, and not detectable in remission samples[11][14].
RB1 Focal deletion and mutation[11][24] Tumor supressor gene Common No established significance No (NCCN) Associated with low-hypodiploid B-ALL.
NF1 Mutations and focal deletions. In 68% of the cases, the NF1 deletions were intragenic involving exons 15 through 35[11]. Tumor supressor gene Mutations: Recurrent

Focal deletions: Common[11]

No established significance No (NCCN) Involved in RTK/RAS cellular pathway, and associated primarily with near-haploid B-ALL[11][24].
FLT3 Mutations[11] Oncogene Recurrent No established significance No (NCCN)
NRAS Mutations[11] Oncogene Recurrent No established significance No (NCCN)
KRAS Mutation[11] Oncogene Rare No established significance No (NCCN)
MAPK1 Mutation[11] Oncogene Rare No established significance No (NCCN)
PTPN11 Mutation[11] Oncoogene Rare No established significance No (NCCN)
CDKN2A/B Focal deletion[11] Tumor supressor Common No established significance No (NCCN) Associated with near-haploid B-ALL and low-hypodiploid B-ALL.
IKZF2 Focal deletion[24] Tumor supressor Common No established significance No (NCCN) Associated with low-hypodiploid B-ALL.
IKZF3


Focal deletion[24] Tumor supressor Recurrent No established significance No (NCCN) Associated with near-haploid B-ALL.
PAG1 Focal deletion[11] Tumor supressor Recurrent No established significance No (NCCN) Associated with near-haploid B-ALL. It was identified as a putative RAS signaling inhibitor and have a negative regulatory function in proximal B-cell receptor signaling[11].

Note: A more extensive list of mutations can be found in cBioportal, COSMIC, and/or other databases. When applicable, gene-specific pages within the CCGA site directly link to pertinent external content.


Epigenomic Alterations

In near haploid 19% of the cases had focal deletions of histone gene cluster at 6p22, however, non-hypodiploid ALL had 8%, lower frequency of these deletions[11].

Of the 25 next generation sequenced haploid cases 16 (64%) cases had twenty six histone modifier gene mutations and of the 15 low hypodiploid ALL cases 9 (60%) cases had 9 mutations; the most common mutation (32%) of the near haploid cases was transcriptional co-activator and histone acetyltransferase CREBBP[11].

Genes and Main Pathways Involved

Gene; Genetic Alteration Pathway Pathophysiologic Outcome
NF1, NRAS, KRAS, MAPK1, FLT3 or PTPN11; Activating mutations[11] RTK or Ras signaling Constitutive activation of mitogenic and anti-apoptotic pathways, driving uncontrolled cell proliferation, survival, and malignant transformation.
IKZF1, IKZF2, IKZF3, PAX5, EBF1, VPREB1 B-cell development
CDKN2A/B, TP53, RB1; Loss of function mutations Cell cycle and apoptosis Propagation of genetically altered cells.
ETV6 Hematopoiesis
PAG1 BCR signaling
ARPP21 Calmodulin signaling
SLX4IP Telomere length maintenance
CUL5 Ubiquitin pathway
FAM53B Wnt signaling
PDS5B Cohesis complex
ANKRD11, DMD Cell adhesion

Genetic Diagnostic Testing Methods

Karyotype, flow cytometry DNA index, FISH, and SNP arrays are all useful in establishing the diagnosis[1]. When using FISH or karyotype, approximately 16% to 30% of the ALL cases yield no or inadequate cytogenetic results due to inadequate specimens and absent or few mitotic cells. Among those with a cytogenetic result, 15% to 25% have a normal karyotype[25]. High-resolution SNP array can detect IKZF1 deletions and other cryptic copy number aberrations as well as CN-LOH that are not detectable by chromosome analysis[26].

Familial Forms

In Low hypodiploid (LH), several studies have not only identified a high percentage of pediatric patients with TP53 mutations, but close to half displayed germline mutations, suggesting that LH ALL is a manifestation of Li-Fraumeni syndrome in children[11][20][23].

Adults also showed a high incidence of TP53 mutations, but these mutations appear to be somatic in origin. In NH, mutations of genes of receptor tyrosine kinase (RTK) pathway, Ras signaling, IKZF3 (17q21.1) and histone clusters, but mutations of IZFK2, RB1, or TP53 were rare.

Additional Information

Genetic abnormalities involving TP53, RB1 and IKZF2 are hallmarks of low hypodiploid ALL, where as near haploid ALL has RTK, RAS and IKZF3 alterations[11].

Links

N/A

References

  1. 1.0 1.1 1.2 WHO Classification of Tumours: Haematolymphoid Tumours [Internet; Beta Version Ahead of Print](5th ed.), International Agency for Research on Cancer (2022)
  2. Borowitz MJ, et al., (2017). B-Lymphoblastic leukaemia/lymphoma with recurrent genetic abnormalities, in World Health Organization Classification of Tumours of Haematopoietic and Lymphoid Tissues, Revised 4th edition. Swerdlow SH, Campo E, Harris NL, Jaffe ES, Pileri SA, Stein H, Thiele J, Arber DA, Hasserjian RP, Le Beau MM, Orazi A, and Siebert R, Editors. IARC Press: Lyon, France, p206.
  3. Harrison, Christine J.; et al. (2004). "Three distinct subgroups of hypodiploidy in acute lymphoblastic leukaemia". British Journal of Haematology. 125 (5): 552–559. doi:10.1111/j.1365-2141.2004.04948.x. ISSN 0007-1048. PMID 15147369.
  4. 4.0 4.1 Pui, Ching-Hon; et al. (2019-04-01). "Outcome of Children With Hypodiploid Acute Lymphoblastic Leukemia: A Retrospective Multinational Study". Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology. 37 (10): 770–779. doi:10.1200/JCO.18.00822. ISSN 1527-7755. PMC 7051863 Check |pmc= value (help). PMID 30657737.
  5. 5.0 5.1 Nachman, James B.; et al. (2007). "Outcome of treatment in children with hypodiploid acute lymphoblastic leukemia". Blood. 110 (4): 1112–1115. doi:10.1182/blood-2006-07-038299. ISSN 0006-4971. PMC 1939895. PMID 17473063.
  6. Safavi, S.; et al. (2013). "Loss of chromosomes is the primary event in near-haploid and low-hypodiploid acute lymphoblastic leukemia". Leukemia. 27 (1): 248–250. doi:10.1038/leu.2012.227. ISSN 1476-5551. PMID 22889820.
  7. Harrison, Christine J.; et al. (2005-05). "Interphase molecular cytogenetic screening for chromosomal abnormalities of prognostic significance in childhood acute lymphoblastic leukaemia: a UK Cancer Cytogenetics Group Study". British Journal of Haematology. 129 (4): 520–530. doi:10.1111/j.1365-2141.2005.05497.x. ISSN 0007-1048. PMID 15877734. Check date values in: |date= (help)
  8. Raimondi, Susana C.; et al. (2003-12-15). "Reassessment of the prognostic significance of hypodiploidy in pediatric patients with acute lymphoblastic leukemia". Cancer. 98 (12): 2715–2722. doi:10.1002/cncr.11841. ISSN 0008-543X. PMID 14669294.
  9. 9.0 9.1 9.2 Panuciak, Kinga; et al. (2023-05-15). "Overview on Aneuploidy in Childhood B-Cell Acute Lymphoblastic Leukemia". International Journal of Molecular Sciences. 24 (10): 8764. doi:10.3390/ijms24108764. ISSN 1422-0067. PMC 10218510 Check |pmc= value (help). PMID 37240110 Check |pmid= value (help).
  10. 10.0 10.1 10.2 Safavi, Setareh; et al. (2017). "Near-haploid and low-hypodiploid acute lymphoblastic leukemia: two distinct subtypes with consistently poor prognosis". Blood. 129 (4): 420–423. doi:10.1182/blood-2016-10-743765. ISSN 1528-0020. PMID 27903530.
  11. 11.00 11.01 11.02 11.03 11.04 11.05 11.06 11.07 11.08 11.09 11.10 11.11 11.12 11.13 11.14 11.15 11.16 11.17 11.18 11.19 Holmfeldt, Linda; et al. (2013). "The genomic landscape of hypodiploid acute lymphoblastic leukemia". Nature Genetics. 45 (3): 242–252. doi:10.1038/ng.2532. ISSN 1546-1718. PMC 3919793. PMID 23334668.
  12. Creasey, Thomas; et al. (2021-09). "Single nucleotide polymorphism array-based signature of low hypodiploidy in acute lymphoblastic leukemia". Genes, Chromosomes & Cancer. 60 (9): 604–615. doi:10.1002/gcc.22956. ISSN 1098-2264. PMC 8600946 Check |pmc= value (help). PMID 33938069 Check |pmid= value (help). Check date values in: |date= (help)
  13. 13.0 13.1 Harrison, Christine J.; et al. (2004-06). "Three distinct subgroups of hypodiploidy in acute lymphoblastic leukaemia". British Journal of Haematology. 125 (5): 552–559. doi:10.1111/j.1365-2141.2004.04948.x. ISSN 0007-1048. PMID 15147369. Check date values in: |date= (help)
  14. 14.0 14.1 14.2 14.3 Mühlbacher, Verena; et al. (2014). "Acute lymphoblastic leukemia with low hypodiploid/near triploid karyotype is a specific clinical entity and exhibits a very high TP53 mutation frequency of 93%". Genes, Chromosomes & Cancer. 53 (6): 524–536. doi:10.1002/gcc.22163. ISSN 1098-2264. PMID 24619868.
  15. 15.0 15.1 Holmfeldt, Linda; et al. (2013-03). "The genomic landscape of hypodiploid acute lymphoblastic leukemia". Nature Genetics. 45 (3): 242–252. doi:10.1038/ng.2532. ISSN 1546-1718. PMC 3919793. PMID 23334668. Check date values in: |date= (help)
  16. Carroll, Andrew J.; et al. (2019-10). "Masked hypodiploidy: Hypodiploid acute lymphoblastic leukemia (ALL) mimicking hyperdiploid ALL in children: A report from the Children's Oncology Group". Cancer Genetics. 238: 62–68. doi:10.1016/j.cancergen.2019.07.009. ISSN 2210-7762. PMC 6768693. PMID 31425927. Check date values in: |date= (help)
  17. Creasey, Thomas; et al. (2021-09). "Single nucleotide polymorphism array-based signature of low hypodiploidy in acute lymphoblastic leukemia". Genes, Chromosomes & Cancer. 60 (9): 604–615. doi:10.1002/gcc.22956. ISSN 1098-2264. PMC 8600946 Check |pmc= value (help). PMID 33938069 Check |pmid= value (help). Check date values in: |date= (help)
  18. Yu, Chih-Hsiang; et al. (2020-07-13). "MLPA and DNA index improve the molecular diagnosis of childhood B-cell acute lymphoblastic leukemia". Scientific Reports. 10 (1): 11501. doi:10.1038/s41598-020-68311-9. ISSN 2045-2322. PMC 7359332 Check |pmc= value (help). PMID 32661308 Check |pmid= value (help).
  19. 19.0 19.1 Safavi, Setareh; et al. (2015). "Genetic and epigenetic characterization of hypodiploid acute lymphoblastic leukemia". Oncotarget. 6 (40): 42793–42802. doi:10.18632/oncotarget.6000. ISSN 1949-2553. PMC 4767471. PMID 26544893.
  20. 20.0 20.1 Stengel, Anna; et al. (2014-07-10). "TP53 mutations occur in 15.7% of ALL and are associated with MYC-rearrangement, low hypodiploidy, and a poor prognosis". Blood. 124 (2): 251–258. doi:10.1182/blood-2014-02-558833. ISSN 1528-0020. PMID 24829203.
  21. Vogelstein, B.; et al. (2000-11-16). "Surfing the p53 network". Nature. 408 (6810): 307–310. doi:10.1038/35042675. ISSN 0028-0836. PMID 11099028.
  22. Moorman, Anthony V. (2016). "New and emerging prognostic and predictive genetic biomarkers in B-cell precursor acute lymphoblastic leukemia". Haematologica. 101 (4): 407–416. doi:10.3324/haematol.2015.141101. ISSN 1592-8721. PMC 5004393. PMID 27033238.
  23. 23.0 23.1 Comeaux, Evan Q.; et al. (2017-03-01). "TP53 Mutations in Hypodiploid Acute Lymphoblastic Leukemia". Cold Spring Harbor Perspectives in Medicine. 7 (3): a026286. doi:10.1101/cshperspect.a026286. ISSN 2157-1422. PMC 5334249. PMID 28003275.
  24. 24.0 24.1 24.2 24.3 Molina, Oscar; et al. (2021-12-22). "Near-Haploidy and Low-Hypodiploidy in B-Cell Acute Lymphoblastic Leukemia: When Less Is Too Much". Cancers. 14 (1): 32. doi:10.3390/cancers14010032. ISSN 2072-6694. PMC 8750410 Check |pmc= value (help). PMID 35008193 Check |pmid= value (help).
  25. Moorman, Anthony V.; et al. (2010-05). "Prognostic effect of chromosomal abnormalities in childhood B-cell precursor acute lymphoblastic leukaemia: results from the UK Medical Research Council ALL97/99 randomised trial". The Lancet. Oncology. 11 (5): 429–438. doi:10.1016/S1470-2045(10)70066-8. ISSN 1474-5488. PMID 20409752. Check date values in: |date= (help)
  26. Wang, Yunhong; et al. (2016). "Genome-Wide Single-Nucleotide Polymorphism Array Analysis Improves Prognostication of Acute Lymphoblastic Leukemia/Lymphoma". The Journal of molecular diagnostics: JMD. 18 (4): 595–603. doi:10.1016/j.jmoldx.2016.03.004. ISSN 1943-7811. PMID 27161658.


Notes

*Primary authors will typically be those that initially create and complete the content of a page. If a subsequent user modifies the content and feels the effort put forth is of high enough significance to warrant listing in the authorship section, please contact the CCGA coordinators (contact information provided on the homepage). Additional global feedback or concerns are also welcome.


[[Copy Number and cn-LOH Abnormalities in ALL]

*Citation of this Page: “B-lymphoblastic leukaemia/lymphoma with hypodiploidy”. Compendium of Cancer Genome Aberrations (CCGA), Cancer Genomics Consortium (CGC), updated 11/20/2025, https://ccga.io/index.php/HAEM5:B-lymphoblastic_leukaemia/lymphoma_with_hypodiploidy.