CLL Tables: Regions of Recurrent Copy Number Change and CN-LOH

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Table 1 - Regions of Recurrent Copy Number Change in CLL (Literature Review). The list of clinically significant and/or recurrent CNAs selected and evaluated based on a systematic literature search performed on 72 peer-reviewed manuscripts focusing on CNAs and CN-LOH assessment in CLL published between 2000 and 2017. Table derived from Chun et al., 2018 [PMID 30554732] with permission from Cancer Genetics.

Chromosome/

Region

Abnormality Type Prevalence (%) Relevant Genes Strength of Evidence for Gene Prognostic Significance Strength of Evidence for Prognosis (Level*) Comments References
1p Gain ?2-5 Unknown N/A Favorable Suspected (2) [1] [2] [3]
1q23.2q23.3 Loss 15 Unknown N/A Unknown N/A (3) [4] [5] [6]
2p12p25.3 Gain 5-30 ACP1, MYCN, ALK, REL, BCL11A MYCN (Established), REL, BCL11A (Candidate) Unfavorable Established (if MYCN included) (1) [1] [2] [3] [4] [5] [7] [8] [9] [10] [11] [12] [13]
3p21.31 Loss 1-5 ATRIP, CDC25A Candidate Unknown N/A (3) [4] [14] [15]
3q Gain 2-19 Unknown N/A Unfavorable Suspected (2) Appears to be particularly prevalent in Japanese [2] [16] [17]
4p15.2p16.3 Loss 14 Unknown N/A Unfavorable (occurred with del(11q) or del(17p)) Suspected (2) [18]
6p25.3 Gain 1 Unknown N/A Unknown N/A (3) [4]
6p22.1 Loss 1 Histone cluster, HFE Candidate Unknown N/A (3) [4]
6q Loss 3-6 FOXO3 Candidate Intermediate Suspected (2) [19] [20] [21] [22]
7p Gain 5-6 Unknown N/A Intermediate Suspected (2) [2]
7q Loss 1-2 Unknown N/A Unknown N/A (3) [2] [10]
8p21 Loss 2-5 TRIM35 Candidate Unfavorable Suspected (2) Associated with established unfavorable changes (11q- and 17p-). Not established as an independent prognosticator [2] [23]
8q24.1 Gain 5 MYC Candidate Unfavorable Suspected (2) Often associated with 11q and 17p deletion; may not be independent [2] [2] [4]
9q13q21.11 Loss 1 Unknown N/A Unknown N/A (3) [4]
10q24 Loss 2 Unknown N/A Unknown N/A (3) Clustered around NFKB2 gene locus [4] [9] [24]
11q22.3 Loss 10-20 ATM, BIRC3, MRE11, H2AFX ATM established, Others Candidate Unfavorable Established (1) [25]
12 Gain 10-20 Unknown N/A Intermediate Established (1) Unfavorable if NOTCH1 mutation is present [25]
13q14 Loss 50-60 DLEU2, MIR15A, MIR16-1, DLEU1 Established Favorable Established (1) Co-deletion of RB1 may negatively impact time to treatment [25] [26] [27]
14q24.1q32.3 Loss 2 Unknown N/A Unknown N/A (3) Associated with trisomy 12 [4] [28] [29]
15q15.1 Loss 4 MGA Candidate Unknown N/A (3) [4] [9]
17p13.1 Loss 5-15 TP53 Established Unfavorable Established (1) [25]
17q Gain 1 Unknown N/A Unfavorable Suspected (2) [2]
18p Loss 3 Unknown N/A Unfavorable Suspected (2) [2] [4]
18 Gain 4 Unknown N/A Unfavorable Established (1) Associated with trisomy 12 [30]
19 Gain 2-5 Unknown N/A Unfavorable Established (1) Associated with trisomy 12 [4] [9] [18] [24] [30]
Genomic complexity 3 or more CNAs 10-15 N/A Unfavorable Established (1) [9] [10] [14] [31]
Chromothripsis (>10 copy number states of 2 and 3) 5 SETD2, other markers across genome not defined Established Unfavorable Established (1) [4] [27] [32]

*Level 1: present in WHO classification or professional practice guidelines; Level 2: recurrent in well-powered studies with suspected clinical significance; Level 3: recurrent, but uncertain prognostic significance.

Abbreviations: CNA = copy number aberration; CLL = chronic lymphocytic leukemia; CN-LOH = copy-neutral loss-of-heterozygosity

Reference

  1. ↑ 1.0 1.1 D, Pfeifer; et al. (2007). "Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays". PMID 17053054.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 J, Houldsworth; et al. (2014). "Genomic imbalance defines three prognostic groups for risk stratification of patients with chronic lymphocytic leukemia". doi:10.3109/10428194.2013.845882. PMC 6905429. PMID 24047479.CS1 maint: PMC format (link)
  3. ↑ 3.0 3.1 E, Chapiro; et al. (2010). "Gain of the short arm of chromosome 2 (2p) is a frequent recurring chromosome aberration in untreated chronic lymphocytic leukemia (CLL) at advanced stages". PMID 19406473.
  4. ↑ 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 4.11 4.12 J, Edelmann; et al. (2012). "High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations". PMID 23047824.
  5. ↑ 5.0 5.1 D, Ma; et al. (2011). "Array comparative genomic hybridization analysis identifies recurrent gain of chromosome 2p25.3 involving the ACP1 and MYCN genes in chronic lymphocytic leukemia". doi:10.1016/j.clml.2011.03.031. PMC 4845643. PMID 22035742.CS1 maint: PMC format (link)
  6. ↑ A, Tyybakinoja; et al. (2007). "High-resolution oligonucleotide array-CGH pinpoints genes involved in cryptic losses in chronic lymphocytic leukemia". PMID 17901694.
  7. ↑ L, Shao; et al. (2010). "Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogenetics". doi:10.2353/jmoldx.2010.090192. PMC 2928432. PMID 20724749.CS1 maint: PMC format (link)
  8. ↑ A, Patel; et al. (2008). "Validation of a targeted DNA microarray for the clinical evaluation of recurrent abnormalities in chronic lymphocytic leukemia". PMID 18161787.
  9. ↑ 9.0 9.1 9.2 9.3 9.4 Mj, Stevens-Kroef; et al. (2014). "Identification of prognostic relevant chromosomal abnormalities in chronic lymphocytic leukemia using microarray-based genomic profiling". doi:10.1186/1755-8166-7-3. PMC 3905918. PMID 24401281.CS1 maint: PMC format (link)
  10. ↑ 10.0 10.1 10.2 Cd, Schweighofer; et al. (2013). "Genomic variation by whole-genome SNP mapping arrays predicts time-to-event outcome in patients with chronic lymphocytic leukemia: a comparison of CLL and HapMap genotypes". doi:10.1016/j.jmoldx.2012.09.006. PMC 3586684. PMID 23273604.CS1 maint: PMC format (link)
  11. ↑ S, Fabris; et al. (2013). "Chromosome 2p gain in monoclonal B-cell lymphocytosis and in early stage chronic lymphocytic leukemia". PMID 23044996.
  12. ↑ F, Forconi; et al. (2008). "Genome-wide DNA analysis identifies recurrent imbalances predicting outcome in chronic lymphocytic leukaemia with 17p deletion". PMID 18752589.
  13. ↑ M, Jarosova; et al. (2010). "Gain of chromosome 2p in chronic lymphocytic leukemia: significant heterogeneity and a new recurrent dicentric rearrangement". PMID 20078324.
  14. ↑ 14.0 14.1 Ka, Kolquist; et al. (2011). "Evaluation of chronic lymphocytic leukemia by oligonucleotide-based microarray analysis uncovers novel aberrations not detected by FISH or cytogenetic analysis". doi:10.1186/1755-8166-4-25. PMC 3253687. PMID 22087757.CS1 maint: PMC format (link)
  15. ↑ I, Salaverria; et al. (2015). "Detection of chromothripsis-like patterns with a custom array platform for chronic lymphocytic leukemia". doi:10.1002/gcc.22277. PMC 4832286. PMID 26305789.CS1 maint: PMC format (link)
  16. ↑ N, Kawamata; et al. (2013). "Genetic differences between Asian and Caucasian chronic lymphocytic leukemia". doi:10.3892/ijo.2013.1966. PMC 3775563. PMID 23708256.CS1 maint: PMC format (link)
  17. ↑ K, Tsukasaki; et al. (2006). "Comparative genomic hybridization analysis of Japanese B-cell chronic lymphocytic leukemia: correlation with clinical course". PMID 16321855.
  18. ↑ 18.0 18.1 R, Gunnarsson; et al. (2011). "Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia". doi:10.3324/haematol.2010.039768. PMC 3148910. PMID 21546498.CS1 maint: PMC format (link)
  19. ↑ A, Cuneo; et al. (2004). "Chronic lymphocytic leukemia with 6q- shows distinct hematological features and intermediate prognosis". PMID 14712287.
  20. ↑ Dm, Wang; et al. (2011). "Intermediate prognosis of 6q deletion in chronic lymphocytic leukemia". PMID 21281237.
  21. ↑ M, Jarosova; et al. (2017). "Chromosome 6q deletion correlates with poor prognosis and low relative expression of FOXO3 in chronic lymphocytic leukemia patients". PMID 28699185.
  22. ↑ C, Nabhan; et al. (2015). "Predicting Prognosis in Chronic Lymphocytic Leukemia in the Contemporary Era". PMID 26181643.
  23. ↑ V, Grubor; et al. (2009). "Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA)". PMID 18922857.
  24. ↑ 24.0 24.1 C, Schwaenen; et al. (2004). "Automated array-based genomic profiling in chronic lymphocytic leukemia: development of a clinical tool and discovery of recurrent genomic alterations". doi:10.1073/pnas.0304717101. PMC 327147. PMID 14730057.CS1 maint: PMC format (link)
  25. ↑ 25.0 25.1 25.2 25.3 Wg, Wierda; et al. (2017). "NCCN Guidelines Insights: Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma, Version 1.2017". PMID 28275031.
  26. ↑ M, Dal Bo; et al. (2011). "13q14 deletion size and number of deleted cells both influence prognosis in chronic lymphocytic leukemia". PMID 21563234.
  27. ↑ 27.0 27.1 Sn, Malek (2013). "The biology and clinical significance of acquired genomic copy number aberrations and recurrent gene mutations in chronic lymphocytic leukemia". doi:10.1038/onc.2012.411. PMC 3676480. PMID 23001040.CS1 maint: PMC format (link)
  28. ↑ Pt, Greipp; et al. (2013). "Patients with chronic lymphocytic leukaemia and clonal deletion of both 17p13.1 and 11q22.3 have a very poor prognosis". doi:10.1111/bjh.12534. PMC 3907074. PMID 24032430.CS1 maint: PMC format (link)
  29. ↑ A, Cosson; et al. (2014). "14q deletions are associated with trisomy 12, NOTCH1 mutations and unmutated IGHV genes in chronic lymphocytic leukemia and small lymphocytic lymphoma". PMID 24729385.
  30. ↑ 30.0 30.1 R, Ibbotson; et al. (2012). "Coexistence of trisomies of chromosomes 12 and 19 in chronic lymphocytic leukemia occurs exclusively in the rare IgG-positive variant". PMID 21788947.
  31. ↑ Sr, Gunn; et al. (2008). "The HemeScan test for genomic prognostic marker assessment in chronic lymphocytic leukemia". PMID 23495782.
  32. ↑ H, Parker; et al. (2016). "Genomic disruption of the histone methyltransferase SETD2 in chronic lymphocytic leukaemia". doi:10.1038/leu.2016.134. PMC 5023049. PMID 27282254.CS1 maint: PMC format (link)
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