Difference between revisions of "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.
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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.
 
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|'''Chromosome/'''

Revision as of 16:49, 8 August 2020

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.

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)