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CLL Tables: Regions of Recurrent Copy Number Change and CN-LOH (view source)
Revision as of 16:48, 8 August 2020
, 16:48, 8 August 2020Created page with "'''Table 1 -''' '''Regions of recurrent copy number change in CLL''' '''(Literature Review)'''. The list of clinically significant and/or recurrent CNAs selected and evaluate..."
'''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.
{| class="wikitable"
|'''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)
|
|<ref name=":0">{{Cite journal|last=D|first=Pfeifer|last2=M|first2=Pantic|last3=I|first3=Skatulla|last4=J|first4=Rawluk|last5=C|first5=Kreutz|last6=Um|first6=Martens|last7=P|first7=Fisch|last8=J|first8=Timmer|last9=H|first9=Veelken|date=2007|title=Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays|url=https://pubmed.ncbi.nlm.nih.gov/17053054/|language=en|pmid=17053054}}</ref> <ref name=":1">{{Cite journal|last=J|first=Houldsworth|last2=A|first2=Guttapalli|last3=V|first3=Thodima|last4=Xj|first4=Yan|last5=G|first5=Mendiratta|last6=T|first6=Zielonka|last7=G|first7=Nanjangud|last8=W|first8=Chen|last9=S|first9=Patil|date=2014|title=Genomic imbalance defines three prognostic groups for risk stratification of patients with chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/24047479/|language=en|doi=10.3109/10428194.2013.845882|pmc=PMC6905429|pmid=24047479}}</ref> <ref name=":2">{{Cite journal|last=E|first=Chapiro|last2=N|first2=Leporrier|last3=I|first3=Radford-Weiss|last4=C|first4=Bastard|last5=H|first5=Mossafa|last6=D|first6=Leroux|last7=I|first7=Tigaud|last8=M|first8=De Braekeleer|last9=C|first9=Terré|date=2010|title=Gain of the short arm of chromosome 2 (2p) is a frequent recurring chromosome aberration in untreated chronic lymphocytic leukemia (CLL) at advanced stages|url=https://pubmed.ncbi.nlm.nih.gov/19406473/|language=en|pmid=19406473}}</ref>
|-
|1q23.2q23.3
|Loss
|15
|Unknown
|N/A
|Unknown
|N/A (3)
|
|<ref name=":3">{{Cite journal|last=J|first=Edelmann|last2=K|first2=Holzmann|last3=F|first3=Miller|last4=D|first4=Winkler|last5=A|first5=Bühler|last6=T|first6=Zenz|last7=L|first7=Bullinger|last8=Mw|first8=Kühn|last9=A|first9=Gerhardinger|date=2012|title=High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations|url=https://pubmed.ncbi.nlm.nih.gov/23047824/|language=en|pmid=23047824}}</ref> <ref name=":4">{{Cite journal|last=D|first=Ma|last2=Z|first2=Chen|last3=Kp|first3=Patel|last4=Bm|first4=Mishra|last5=H|first5=Yao|last6=Lv|first6=Abruzzo|last7=Lj|first7=Medeiros|last8=W|first8=Wierda|last9=M|first9=Keating|date=2011|title=Array comparative genomic hybridization analysis identifies recurrent gain of chromosome 2p25.3 involving the ACP1 and MYCN genes in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/22035742/|language=en|doi=10.1016/j.clml.2011.03.031|pmc=PMC4845643|pmid=22035742}}</ref> <ref>{{Cite journal|last=A|first=Tyybakinoja|last2=J|first2=Vilpo|last3=S|first3=Knuutila|date=2007|title=High-resolution oligonucleotide array-CGH pinpoints genes involved in cryptic losses in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/17901694/|language=en|pmid=17901694}}</ref>
|-
|2p12p25.3
|Gain
|5-30
|''[[ACP1]], [[MYCN]], [[ALK]], [[REL]], [[BCL11A]]''
|''MYCN'' (Established), ''REL, BCL11A'' (Candidate)
|Unfavorable
|Established (if ''MYCN'' included) (1)
|
|<ref name=":0" /> <ref name=":1" /> <ref name=":2" /> <ref name=":3" /> <ref name=":4" /> <ref>{{Cite journal|last=L|first=Shao|last2=Sh|first2=Kang|last3=J|first3=Li|last4=P|first4=Hixson|last5=J|first5=Taylor|last6=Sa|first6=Yatsenko|last7=Ca|first7=Shaw|last8=A|first8=Milosavljevic|last9=Cc|first9=Chang|date=2010|title=Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogenetics|url=https://pubmed.ncbi.nlm.nih.gov/20724749/|language=en|doi=10.2353/jmoldx.2010.090192|pmc=PMC2928432|pmid=20724749}}</ref> <ref>{{Cite journal|last=A|first=Patel|last2=Sh|first2=Kang|last3=Pa|first3=Lennon|last4=Yf|first4=Li|last5=Pn|first5=Rao|last6=L|first6=Abruzzo|last7=C|first7=Shaw|last8=Ac|first8=Chinault|last9=Sw|first9=Cheung|date=2008|title=Validation of a targeted DNA microarray for the clinical evaluation of recurrent abnormalities in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/18161787/|language=en|pmid=18161787}}</ref> <ref name=":5">{{Cite journal|last=Mj|first=Stevens-Kroef|last2=E|first2=van den Berg|last3=D|first3=Olde Weghuis|last4=A|first4=Geurts van Kessel|last5=R|first5=Pfundt|last6=M|first6=Linssen-Wiersma|last7=M|first7=Benjamins|last8=T|first8=Dijkhuizen|last9=Pj|first9=Groenen|date=2014|title=Identification of prognostic relevant chromosomal abnormalities in chronic lymphocytic leukemia using microarray-based genomic profiling|url=https://pubmed.ncbi.nlm.nih.gov/24401281/|language=en|doi=10.1186/1755-8166-7-3|pmc=PMC3905918|pmid=24401281}}</ref> <ref name=":6">{{Cite journal|last=Cd|first=Schweighofer|last2=Kr|first2=Coombes|last3=T|first3=Majewski|last4=Ll|first4=Barron|last5=S|first5=Lerner|last6=Rl|first6=Sargent|last7=S|first7=O'Brien|last8=A|first8=Ferrajoli|last9=Wg|first9=Wierda|date=2013|title=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|url=https://pubmed.ncbi.nlm.nih.gov/23273604/|language=en|doi=10.1016/j.jmoldx.2012.09.006|pmc=PMC3586684|pmid=23273604}}</ref> <ref>{{Cite journal|last=S|first=Fabris|last2=L|first2=Mosca|last3=G|first3=Cutrona|last4=M|first4=Lionetti|last5=L|first5=Agnelli|last6=G|first6=Ciceri|last7=M|first7=Barbieri|last8=F|first8=Maura|last9=S|first9=Matis|date=2013|title=Chromosome 2p gain in monoclonal B-cell lymphocytosis and in early stage chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/23044996/|language=en|pmid=23044996}}</ref> <ref>{{Cite journal|last=F|first=Forconi|last2=A|first2=Rinaldi|last3=I|first3=Kwee|last4=E|first4=Sozzi|last5=D|first5=Raspadori|last6=Pm|first6=Rancoita|last7=M|first7=Scandurra|last8=D|first8=Rossi|last9=C|first9=Deambrogi|date=2008|title=Genome-wide DNA analysis identifies recurrent imbalances predicting outcome in chronic lymphocytic leukaemia with 17p deletion|url=https://pubmed.ncbi.nlm.nih.gov/18752589/|language=en|pmid=18752589}}</ref> <ref>{{Cite journal|last=M|first=Jarosova|last2=H|first2=Urbankova|last3=R|first3=Plachy|last4=T|first4=Papajik|last5=M|first5=Holzerova|last6=J|first6=Balcarkova|last7=Z|first7=Pikalova|last8=V|first8=Divoky|last9=K|first9=Indrak|date=2010|title=Gain of chromosome 2p in chronic lymphocytic leukemia: significant heterogeneity and a new recurrent dicentric rearrangement|url=https://pubmed.ncbi.nlm.nih.gov/20078324/|language=en|pmid=20078324}}</ref>
|-
|3p21.31
|Loss
|1-5
|''[[ATRIP]], [[CDC25A]]''
|Candidate
|Unknown
|N/A (3)
|
|<ref name=":3" /> <ref name=":7">{{Cite journal|last=Ka|first=Kolquist|last2=Ra|first2=Schultz|last3=Ml|first3=Slovak|last4=Ld|first4=McDaniel|last5=Tc|first5=Brown|last6=Rr|first6=Tubbs|last7=Jr|first7=Cook|last8=Ks|first8=Theil|last9=V|first9=Cawich|date=2011|title=Evaluation of chronic lymphocytic leukemia by oligonucleotide-based microarray analysis uncovers novel aberrations not detected by FISH or cytogenetic analysis|url=https://pubmed.ncbi.nlm.nih.gov/22087757/|language=en|doi=10.1186/1755-8166-4-25|pmc=PMC3253687|pmid=22087757}}</ref> <ref>{{Cite journal|last=I|first=Salaverria|last2=D|first2=Martín-Garcia|last3=C|first3=López|last4=G|first4=Clot|last5=M|first5=García-Aragonés|last6=A|first6=Navarro|last7=J|first7=Delgado|last8=T|first8=Baumann|last9=M|first9=Pinyol|date=2015|title=Detection of chromothripsis-like patterns with a custom array platform for chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/26305789/|language=en|doi=10.1002/gcc.22277|pmc=PMC4832286|pmid=26305789}}</ref>
|-
|3q
|Gain
|2-19
|Unknown
|N/A
|Unfavorable
|Suspected (2)
|Appears to be particularly prevalent in Japanese
|<ref name=":1" /> <ref>{{Cite journal|last=N|first=Kawamata|last2=C|first2=Moreilhon|last3=T|first3=Saitoh|last4=M|first4=Karasawa|last5=Bk|first5=Bernstein|last6=A|first6=Sato-Otsubo|last7=S|first7=Ogawa|last8=S|first8=Raynaud|last9=Hp|first9=Koeffler|date=2013|title=Genetic differences between Asian and Caucasian chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/23708256/|language=en|doi=10.3892/ijo.2013.1966|pmc=PMC3775563|pmid=23708256}}</ref> <ref>{{Cite journal|last=K|first=Tsukasaki|last2=D|first2=Lohr|last3=K|first3=Sugahara|last4=S|first4=Kamihira|last5=M|first5=Tomonaga|last6=Cr|first6=Bartram|last7=A|first7=Jauch|date=2006|title=Comparative genomic hybridization analysis of Japanese B-cell chronic lymphocytic leukemia: correlation with clinical course|url=https://pubmed.ncbi.nlm.nih.gov/16321855/|language=en|pmid=16321855}}</ref>
|-
|4p15.2p16.3
|Loss
|14
|Unknown
|N/A
|Unfavorable (occurred with del(11q) or del(17p))
|Suspected (2)
|
|<ref name=":8">{{Cite journal|last=R|first=Gunnarsson|last2=L|first2=Mansouri|last3=A|first3=Isaksson|last4=H|first4=Göransson|last5=N|first5=Cahill|last6=M|first6=Jansson|last7=M|first7=Rasmussen|last8=J|first8=Lundin|last9=S|first9=Norin|date=2011|title=Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/21546498/|language=en|doi=10.3324/haematol.2010.039768|pmc=PMC3148910|pmid=21546498}}</ref>
|-
|6p25.3
|Gain
|1
|Unknown
|N/A
|Unknown
|N/A (3)
|
|<ref name=":3" />
|-
|6p22.1
|Loss
|1
|Histone cluster, ''[[HFE]]''
|Candidate
|Unknown
|N/A (3)
|
|<ref name=":3" />
|-
|6q
|Loss
|3-6
|''[[FOXO3]]''
|Candidate
|Intermediate
|Suspected (2)
|
|<ref>{{Cite journal|last=A|first=Cuneo|last2=Gm|first2=Rigolin|last3=R|first3=Bigoni|last4=C|first4=De Angeli|last5=A|first5=Veronese|last6=F|first6=Cavazzini|last7=A|first7=Bardi|last8=Mg|first8=Roberti|last9=E|first9=Tammiso|date=2004|title=Chronic lymphocytic leukemia with 6q- shows distinct hematological features and intermediate prognosis|url=https://pubmed.ncbi.nlm.nih.gov/14712287/|language=en|pmid=14712287}}</ref> <ref>{{Cite journal|last=Dm|first=Wang|last2=Kr|first2=Miao|last3=L|first3=Fan|last4=Hr|first4=Qiu|last5=C|first5=Fang|last6=Dx|first6=Zhu|last7=Hx|first7=Qiu|last8=W|first8=Xu|last9=Jy|first9=Li|date=2011|title=Intermediate prognosis of 6q deletion in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/21281237/|language=en|pmid=21281237}}</ref> <ref>{{Cite journal|last=M|first=Jarosova|last2=M|first2=Hruba|last3=A|first3=Oltova|last4=K|first4=Plevova|last5=L|first5=Kruzova|last6=E|first6=Kriegova|last7=R|first7=Fillerova|last8=E|first8=Koritakova|last9=M|first9=Doubek|date=2017|title=Chromosome 6q deletion correlates with poor prognosis and low relative expression of FOXO3 in chronic lymphocytic leukemia patients|url=https://pubmed.ncbi.nlm.nih.gov/28699185/|language=en|pmid=28699185}}</ref> <ref>{{Cite journal|last=C|first=Nabhan|last2=G|first2=Raca|last3=Yl|first3=Wang|date=2015|title=Predicting Prognosis in Chronic Lymphocytic Leukemia in the Contemporary Era|url=https://pubmed.ncbi.nlm.nih.gov/26181643/|language=en|pmid=26181643}}</ref>
|-
|7p
|Gain
|5-6
|Unknown
|N/A
|Intermediate
|Suspected (2)
|
|<ref name=":1" />
|-
|7q
|Loss
|1-2
|Unknown
|N/A
|Unknown
|N/A (3)
|
|<ref name=":1" /> <ref name=":6" />
|-
|8p21
|Loss
|2-5
|''[[TRIM35]]''
|Candidate
|Unfavorable
|Suspected (2)
|Associated with established unfavorable changes (11q- and 17p-). Not established as an independent prognosticator
|<ref name=":1" /> <ref>{{Cite journal|last=V|first=Grubor|last2=A|first2=Krasnitz|last3=Je|first3=Troge|last4=Jl|first4=Meth|last5=B|first5=Lakshmi|last6=Jt|first6=Kendall|last7=B|first7=Yamrom|last8=G|first8=Alex|last9=D|first9=Pai|date=2009|title=Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA)|url=https://pubmed.ncbi.nlm.nih.gov/18922857/|language=en|pmid=18922857}}</ref>
|-
|8q24.1
|Gain
|5
|''[[MYC]]''
|Candidate
|Unfavorable
|Suspected (2)
|Often associated with 11q and 17p deletion; may not be independent <ref name=":1" />
|<ref name=":1" /> <ref name=":3" />
|-
|9q13q21.11
|Loss
|1
|Unknown
|N/A
|Unknown
|N/A (3)
|
|<ref name=":3" />
|-
|10q24
|Loss
|2
|Unknown
|N/A
|Unknown
|N/A (3)
|Clustered around ''NFKB2'' gene locus
|<ref name=":3" /> <ref name=":5" /> <ref name=":9">{{Cite journal|last=C|first=Schwaenen|last2=M|first2=Nessling|last3=S|first3=Wessendorf|last4=T|first4=Salvi|last5=G|first5=Wrobel|last6=B|first6=Radlwimmer|last7=Ha|first7=Kestler|last8=C|first8=Haslinger|last9=S|first9=Stilgenbauer|date=2004|title=Automated array-based genomic profiling in chronic lymphocytic leukemia: development of a clinical tool and discovery of recurrent genomic alterations|url=https://pubmed.ncbi.nlm.nih.gov/14730057/|language=en|doi=10.1073/pnas.0304717101|pmc=PMC327147|pmid=14730057}}</ref>
|-
|11q22.3
|Loss
|10-20
|''[[ATM]], [[BIRC3]], [[MRE11]], [[H2AFX]]''
|''ATM'' established, Others Candidate
|Unfavorable
|Established (1)
|
|<ref name=":10">{{Cite journal|last=Wg|first=Wierda|last2=Ad|first2=Zelenetz|last3=Li|first3=Gordon|last4=Js|first4=Abramson|last5=Rh|first5=Advani|last6=Cb|first6=Andreadis|last7=N|first7=Bartlett|last8=Jc|first8=Byrd|last9=P|first9=Caimi|date=2017|title=NCCN Guidelines Insights: Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma, Version 1.2017|url=https://pubmed.ncbi.nlm.nih.gov/28275031/|language=en|pmid=28275031}}</ref>
|-
|12
|Gain
|10-20
|Unknown
|N/A
|Intermediate
|Established (1)
|Unfavorable if ''NOTCH1'' mutation is present
|<ref name=":10" />
|-
|13q14
|Loss
|50-60
|''[[DLEU2]], [[MIR15A]], [[MIR16-1]],'' ''[[DLEU1]]''
|Established
|Favorable
|Established (1)
|Co-deletion of ''RB1'' may negatively impact time to treatment
|<ref name=":10" /> <ref>{{Cite journal|last=M|first=Dal Bo|last2=Fm|first2=Rossi|last3=D|first3=Rossi|last4=C|first4=Deambrogi|last5=F|first5=Bertoni|last6=I|first6=Del Giudice|last7=G|first7=Palumbo|last8=M|first8=Nanni|last9=A|first9=Rinaldi|date=2011|title=13q14 deletion size and number of deleted cells both influence prognosis in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/21563234/|language=en|pmid=21563234}}</ref> <ref name=":11">{{Cite journal|last=Sn|first=Malek|date=2013|title=The biology and clinical significance of acquired genomic copy number aberrations and recurrent gene mutations in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/23001040/|language=en|doi=10.1038/onc.2012.411|pmc=PMC3676480|pmid=23001040}}</ref>
|-
|14q24.1q32.3
|Loss
|2
|Unknown
|N/A
|Unknown
|N/A (3)
|Associated with trisomy 12
|<ref name=":3" /> <ref>{{Cite journal|last=Pt|first=Greipp|last2=Sa|first2=Smoley|last3=Ds|first3=Viswanatha|last4=Ls|first4=Frederick|last5=Kg|first5=Rabe|last6=Rg|first6=Sharma|last7=Sl|first7=Slager|last8=Dl|first8=Van Dyke|last9=Td|first9=Shanafelt|date=2013|title=Patients with chronic lymphocytic leukaemia and clonal deletion of both 17p13.1 and 11q22.3 have a very poor prognosis|url=https://pubmed.ncbi.nlm.nih.gov/24032430/|language=en|doi=10.1111/bjh.12534|pmc=PMC3907074|pmid=24032430}}</ref> <ref>{{Cite journal|last=A|first=Cosson|last2=E|first2=Chapiro|last3=N|first3=Belhouachi|last4=Ha|first4=Cung|last5=B|first5=Keren|last6=F|first6=Damm|last7=C|first7=Algrin|last8=C|first8=Lefebvre|last9=S|first9=Fert-Ferrer|date=2014|title=14q deletions are associated with trisomy 12, NOTCH1 mutations and unmutated IGHV genes in chronic lymphocytic leukemia and small lymphocytic lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/24729385/|language=en|pmid=24729385}}</ref>
|-
|15q15.1
|Loss
|4
|''[[MGA]]''
|Candidate
|Unknown
|N/A (3)
|
|<ref name=":3" /> <ref name=":5" />
|-
|17p13.1
|Loss
|5-15
|''[[TP53]]''
|Established
|Unfavorable
|Established (1)
|
|<ref name=":10" />
|-
|17q
|Gain
|1
|Unknown
|N/A
|Unfavorable
|Suspected (2)
|
|<ref name=":1" />
|-
|18p
|Loss
|3
|Unknown
|N/A
|Unfavorable
|Suspected (2)
|
|<ref name=":1" /> <ref name=":3" />
|-
|18
|Gain
|4
|Unknown
|N/A
|Unfavorable
|Established (1)
|Associated with trisomy 12
|<ref name=":12">{{Cite journal|last=R|first=Ibbotson|last2=A|first2=Athanasiadou|last3=La|first3=Sutton|last4=Z|first4=Davis|last5=A|first5=Gardiner|last6=P|first6=Baliakas|last7=R|first7=Gunnarsson|last8=A|first8=Anagnostopoulos|last9=G|first9=Juliusson|date=2012|title=Coexistence of trisomies of chromosomes 12 and 19 in chronic lymphocytic leukemia occurs exclusively in the rare IgG-positive variant|url=https://pubmed.ncbi.nlm.nih.gov/21788947/|language=en|pmid=21788947}}</ref>
|-
|19
|Gain
|2-5
|Unknown
|N/A
|Unfavorable
|Established (1)
|Associated with trisomy 12
|<ref name=":3" /> <ref name=":5" /> <ref name=":8" /> <ref name=":9" /> <ref name=":12" />
|-
|Genomic complexity
|3 or more CNAs
|10-15
|
|N/A
|Unfavorable
|Established (1)
|
|<ref name=":5" /> <ref name=":6" /> <ref name=":7" /> <ref>{{Cite journal|last=Sr|first=Gunn|last2=Ms|first2=Mohammed|last3=Ch|first3=Mellink|last4=Lv|first4=Abruzzo|last5=Rs|first5=Robetorye|date=2008|title=The HemeScan test for genomic prognostic marker assessment in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/23495782/|language=en|pmid=23495782}}</ref>
|-
|Chromothripsis
|(>10 copy number states of 2 and 3)
|5
|''[[SETD2]]'', other markers across genome not defined
|Established
|Unfavorable
|Established (1)
|
|<ref name=":3" /> <ref name=":11" /> <ref>{{Cite journal|last=H|first=Parker|last2=Mj|first2=Rose-Zerilli|last3=M|first3=Larrayoz|last4=R|first4=Clifford|last5=J|first5=Edelmann|last6=S|first6=Blakemore|last7=J|first7=Gibson|last8=J|first8=Wang|last9=V|first9=Ljungström|date=2016|title=Genomic disruption of the histone methyltransferase SETD2 in chronic lymphocytic leukaemia|url=https://pubmed.ncbi.nlm.nih.gov/27282254/|language=en|doi=10.1038/leu.2016.134|pmc=PMC5023049|pmid=27282254}}</ref>
|}
<nowiki>*</nowiki>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==
<references />
{| class="wikitable"
|'''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)
|
|<ref name=":0">{{Cite journal|last=D|first=Pfeifer|last2=M|first2=Pantic|last3=I|first3=Skatulla|last4=J|first4=Rawluk|last5=C|first5=Kreutz|last6=Um|first6=Martens|last7=P|first7=Fisch|last8=J|first8=Timmer|last9=H|first9=Veelken|date=2007|title=Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays|url=https://pubmed.ncbi.nlm.nih.gov/17053054/|language=en|pmid=17053054}}</ref> <ref name=":1">{{Cite journal|last=J|first=Houldsworth|last2=A|first2=Guttapalli|last3=V|first3=Thodima|last4=Xj|first4=Yan|last5=G|first5=Mendiratta|last6=T|first6=Zielonka|last7=G|first7=Nanjangud|last8=W|first8=Chen|last9=S|first9=Patil|date=2014|title=Genomic imbalance defines three prognostic groups for risk stratification of patients with chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/24047479/|language=en|doi=10.3109/10428194.2013.845882|pmc=PMC6905429|pmid=24047479}}</ref> <ref name=":2">{{Cite journal|last=E|first=Chapiro|last2=N|first2=Leporrier|last3=I|first3=Radford-Weiss|last4=C|first4=Bastard|last5=H|first5=Mossafa|last6=D|first6=Leroux|last7=I|first7=Tigaud|last8=M|first8=De Braekeleer|last9=C|first9=Terré|date=2010|title=Gain of the short arm of chromosome 2 (2p) is a frequent recurring chromosome aberration in untreated chronic lymphocytic leukemia (CLL) at advanced stages|url=https://pubmed.ncbi.nlm.nih.gov/19406473/|language=en|pmid=19406473}}</ref>
|-
|1q23.2q23.3
|Loss
|15
|Unknown
|N/A
|Unknown
|N/A (3)
|
|<ref name=":3">{{Cite journal|last=J|first=Edelmann|last2=K|first2=Holzmann|last3=F|first3=Miller|last4=D|first4=Winkler|last5=A|first5=Bühler|last6=T|first6=Zenz|last7=L|first7=Bullinger|last8=Mw|first8=Kühn|last9=A|first9=Gerhardinger|date=2012|title=High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations|url=https://pubmed.ncbi.nlm.nih.gov/23047824/|language=en|pmid=23047824}}</ref> <ref name=":4">{{Cite journal|last=D|first=Ma|last2=Z|first2=Chen|last3=Kp|first3=Patel|last4=Bm|first4=Mishra|last5=H|first5=Yao|last6=Lv|first6=Abruzzo|last7=Lj|first7=Medeiros|last8=W|first8=Wierda|last9=M|first9=Keating|date=2011|title=Array comparative genomic hybridization analysis identifies recurrent gain of chromosome 2p25.3 involving the ACP1 and MYCN genes in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/22035742/|language=en|doi=10.1016/j.clml.2011.03.031|pmc=PMC4845643|pmid=22035742}}</ref> <ref>{{Cite journal|last=A|first=Tyybakinoja|last2=J|first2=Vilpo|last3=S|first3=Knuutila|date=2007|title=High-resolution oligonucleotide array-CGH pinpoints genes involved in cryptic losses in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/17901694/|language=en|pmid=17901694}}</ref>
|-
|2p12p25.3
|Gain
|5-30
|''[[ACP1]], [[MYCN]], [[ALK]], [[REL]], [[BCL11A]]''
|''MYCN'' (Established), ''REL, BCL11A'' (Candidate)
|Unfavorable
|Established (if ''MYCN'' included) (1)
|
|<ref name=":0" /> <ref name=":1" /> <ref name=":2" /> <ref name=":3" /> <ref name=":4" /> <ref>{{Cite journal|last=L|first=Shao|last2=Sh|first2=Kang|last3=J|first3=Li|last4=P|first4=Hixson|last5=J|first5=Taylor|last6=Sa|first6=Yatsenko|last7=Ca|first7=Shaw|last8=A|first8=Milosavljevic|last9=Cc|first9=Chang|date=2010|title=Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogenetics|url=https://pubmed.ncbi.nlm.nih.gov/20724749/|language=en|doi=10.2353/jmoldx.2010.090192|pmc=PMC2928432|pmid=20724749}}</ref> <ref>{{Cite journal|last=A|first=Patel|last2=Sh|first2=Kang|last3=Pa|first3=Lennon|last4=Yf|first4=Li|last5=Pn|first5=Rao|last6=L|first6=Abruzzo|last7=C|first7=Shaw|last8=Ac|first8=Chinault|last9=Sw|first9=Cheung|date=2008|title=Validation of a targeted DNA microarray for the clinical evaluation of recurrent abnormalities in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/18161787/|language=en|pmid=18161787}}</ref> <ref name=":5">{{Cite journal|last=Mj|first=Stevens-Kroef|last2=E|first2=van den Berg|last3=D|first3=Olde Weghuis|last4=A|first4=Geurts van Kessel|last5=R|first5=Pfundt|last6=M|first6=Linssen-Wiersma|last7=M|first7=Benjamins|last8=T|first8=Dijkhuizen|last9=Pj|first9=Groenen|date=2014|title=Identification of prognostic relevant chromosomal abnormalities in chronic lymphocytic leukemia using microarray-based genomic profiling|url=https://pubmed.ncbi.nlm.nih.gov/24401281/|language=en|doi=10.1186/1755-8166-7-3|pmc=PMC3905918|pmid=24401281}}</ref> <ref name=":6">{{Cite journal|last=Cd|first=Schweighofer|last2=Kr|first2=Coombes|last3=T|first3=Majewski|last4=Ll|first4=Barron|last5=S|first5=Lerner|last6=Rl|first6=Sargent|last7=S|first7=O'Brien|last8=A|first8=Ferrajoli|last9=Wg|first9=Wierda|date=2013|title=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|url=https://pubmed.ncbi.nlm.nih.gov/23273604/|language=en|doi=10.1016/j.jmoldx.2012.09.006|pmc=PMC3586684|pmid=23273604}}</ref> <ref>{{Cite journal|last=S|first=Fabris|last2=L|first2=Mosca|last3=G|first3=Cutrona|last4=M|first4=Lionetti|last5=L|first5=Agnelli|last6=G|first6=Ciceri|last7=M|first7=Barbieri|last8=F|first8=Maura|last9=S|first9=Matis|date=2013|title=Chromosome 2p gain in monoclonal B-cell lymphocytosis and in early stage chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/23044996/|language=en|pmid=23044996}}</ref> <ref>{{Cite journal|last=F|first=Forconi|last2=A|first2=Rinaldi|last3=I|first3=Kwee|last4=E|first4=Sozzi|last5=D|first5=Raspadori|last6=Pm|first6=Rancoita|last7=M|first7=Scandurra|last8=D|first8=Rossi|last9=C|first9=Deambrogi|date=2008|title=Genome-wide DNA analysis identifies recurrent imbalances predicting outcome in chronic lymphocytic leukaemia with 17p deletion|url=https://pubmed.ncbi.nlm.nih.gov/18752589/|language=en|pmid=18752589}}</ref> <ref>{{Cite journal|last=M|first=Jarosova|last2=H|first2=Urbankova|last3=R|first3=Plachy|last4=T|first4=Papajik|last5=M|first5=Holzerova|last6=J|first6=Balcarkova|last7=Z|first7=Pikalova|last8=V|first8=Divoky|last9=K|first9=Indrak|date=2010|title=Gain of chromosome 2p in chronic lymphocytic leukemia: significant heterogeneity and a new recurrent dicentric rearrangement|url=https://pubmed.ncbi.nlm.nih.gov/20078324/|language=en|pmid=20078324}}</ref>
|-
|3p21.31
|Loss
|1-5
|''[[ATRIP]], [[CDC25A]]''
|Candidate
|Unknown
|N/A (3)
|
|<ref name=":3" /> <ref name=":7">{{Cite journal|last=Ka|first=Kolquist|last2=Ra|first2=Schultz|last3=Ml|first3=Slovak|last4=Ld|first4=McDaniel|last5=Tc|first5=Brown|last6=Rr|first6=Tubbs|last7=Jr|first7=Cook|last8=Ks|first8=Theil|last9=V|first9=Cawich|date=2011|title=Evaluation of chronic lymphocytic leukemia by oligonucleotide-based microarray analysis uncovers novel aberrations not detected by FISH or cytogenetic analysis|url=https://pubmed.ncbi.nlm.nih.gov/22087757/|language=en|doi=10.1186/1755-8166-4-25|pmc=PMC3253687|pmid=22087757}}</ref> <ref>{{Cite journal|last=I|first=Salaverria|last2=D|first2=Martín-Garcia|last3=C|first3=López|last4=G|first4=Clot|last5=M|first5=García-Aragonés|last6=A|first6=Navarro|last7=J|first7=Delgado|last8=T|first8=Baumann|last9=M|first9=Pinyol|date=2015|title=Detection of chromothripsis-like patterns with a custom array platform for chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/26305789/|language=en|doi=10.1002/gcc.22277|pmc=PMC4832286|pmid=26305789}}</ref>
|-
|3q
|Gain
|2-19
|Unknown
|N/A
|Unfavorable
|Suspected (2)
|Appears to be particularly prevalent in Japanese
|<ref name=":1" /> <ref>{{Cite journal|last=N|first=Kawamata|last2=C|first2=Moreilhon|last3=T|first3=Saitoh|last4=M|first4=Karasawa|last5=Bk|first5=Bernstein|last6=A|first6=Sato-Otsubo|last7=S|first7=Ogawa|last8=S|first8=Raynaud|last9=Hp|first9=Koeffler|date=2013|title=Genetic differences between Asian and Caucasian chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/23708256/|language=en|doi=10.3892/ijo.2013.1966|pmc=PMC3775563|pmid=23708256}}</ref> <ref>{{Cite journal|last=K|first=Tsukasaki|last2=D|first2=Lohr|last3=K|first3=Sugahara|last4=S|first4=Kamihira|last5=M|first5=Tomonaga|last6=Cr|first6=Bartram|last7=A|first7=Jauch|date=2006|title=Comparative genomic hybridization analysis of Japanese B-cell chronic lymphocytic leukemia: correlation with clinical course|url=https://pubmed.ncbi.nlm.nih.gov/16321855/|language=en|pmid=16321855}}</ref>
|-
|4p15.2p16.3
|Loss
|14
|Unknown
|N/A
|Unfavorable (occurred with del(11q) or del(17p))
|Suspected (2)
|
|<ref name=":8">{{Cite journal|last=R|first=Gunnarsson|last2=L|first2=Mansouri|last3=A|first3=Isaksson|last4=H|first4=Göransson|last5=N|first5=Cahill|last6=M|first6=Jansson|last7=M|first7=Rasmussen|last8=J|first8=Lundin|last9=S|first9=Norin|date=2011|title=Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/21546498/|language=en|doi=10.3324/haematol.2010.039768|pmc=PMC3148910|pmid=21546498}}</ref>
|-
|6p25.3
|Gain
|1
|Unknown
|N/A
|Unknown
|N/A (3)
|
|<ref name=":3" />
|-
|6p22.1
|Loss
|1
|Histone cluster, ''[[HFE]]''
|Candidate
|Unknown
|N/A (3)
|
|<ref name=":3" />
|-
|6q
|Loss
|3-6
|''[[FOXO3]]''
|Candidate
|Intermediate
|Suspected (2)
|
|<ref>{{Cite journal|last=A|first=Cuneo|last2=Gm|first2=Rigolin|last3=R|first3=Bigoni|last4=C|first4=De Angeli|last5=A|first5=Veronese|last6=F|first6=Cavazzini|last7=A|first7=Bardi|last8=Mg|first8=Roberti|last9=E|first9=Tammiso|date=2004|title=Chronic lymphocytic leukemia with 6q- shows distinct hematological features and intermediate prognosis|url=https://pubmed.ncbi.nlm.nih.gov/14712287/|language=en|pmid=14712287}}</ref> <ref>{{Cite journal|last=Dm|first=Wang|last2=Kr|first2=Miao|last3=L|first3=Fan|last4=Hr|first4=Qiu|last5=C|first5=Fang|last6=Dx|first6=Zhu|last7=Hx|first7=Qiu|last8=W|first8=Xu|last9=Jy|first9=Li|date=2011|title=Intermediate prognosis of 6q deletion in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/21281237/|language=en|pmid=21281237}}</ref> <ref>{{Cite journal|last=M|first=Jarosova|last2=M|first2=Hruba|last3=A|first3=Oltova|last4=K|first4=Plevova|last5=L|first5=Kruzova|last6=E|first6=Kriegova|last7=R|first7=Fillerova|last8=E|first8=Koritakova|last9=M|first9=Doubek|date=2017|title=Chromosome 6q deletion correlates with poor prognosis and low relative expression of FOXO3 in chronic lymphocytic leukemia patients|url=https://pubmed.ncbi.nlm.nih.gov/28699185/|language=en|pmid=28699185}}</ref> <ref>{{Cite journal|last=C|first=Nabhan|last2=G|first2=Raca|last3=Yl|first3=Wang|date=2015|title=Predicting Prognosis in Chronic Lymphocytic Leukemia in the Contemporary Era|url=https://pubmed.ncbi.nlm.nih.gov/26181643/|language=en|pmid=26181643}}</ref>
|-
|7p
|Gain
|5-6
|Unknown
|N/A
|Intermediate
|Suspected (2)
|
|<ref name=":1" />
|-
|7q
|Loss
|1-2
|Unknown
|N/A
|Unknown
|N/A (3)
|
|<ref name=":1" /> <ref name=":6" />
|-
|8p21
|Loss
|2-5
|''[[TRIM35]]''
|Candidate
|Unfavorable
|Suspected (2)
|Associated with established unfavorable changes (11q- and 17p-). Not established as an independent prognosticator
|<ref name=":1" /> <ref>{{Cite journal|last=V|first=Grubor|last2=A|first2=Krasnitz|last3=Je|first3=Troge|last4=Jl|first4=Meth|last5=B|first5=Lakshmi|last6=Jt|first6=Kendall|last7=B|first7=Yamrom|last8=G|first8=Alex|last9=D|first9=Pai|date=2009|title=Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA)|url=https://pubmed.ncbi.nlm.nih.gov/18922857/|language=en|pmid=18922857}}</ref>
|-
|8q24.1
|Gain
|5
|''[[MYC]]''
|Candidate
|Unfavorable
|Suspected (2)
|Often associated with 11q and 17p deletion; may not be independent <ref name=":1" />
|<ref name=":1" /> <ref name=":3" />
|-
|9q13q21.11
|Loss
|1
|Unknown
|N/A
|Unknown
|N/A (3)
|
|<ref name=":3" />
|-
|10q24
|Loss
|2
|Unknown
|N/A
|Unknown
|N/A (3)
|Clustered around ''NFKB2'' gene locus
|<ref name=":3" /> <ref name=":5" /> <ref name=":9">{{Cite journal|last=C|first=Schwaenen|last2=M|first2=Nessling|last3=S|first3=Wessendorf|last4=T|first4=Salvi|last5=G|first5=Wrobel|last6=B|first6=Radlwimmer|last7=Ha|first7=Kestler|last8=C|first8=Haslinger|last9=S|first9=Stilgenbauer|date=2004|title=Automated array-based genomic profiling in chronic lymphocytic leukemia: development of a clinical tool and discovery of recurrent genomic alterations|url=https://pubmed.ncbi.nlm.nih.gov/14730057/|language=en|doi=10.1073/pnas.0304717101|pmc=PMC327147|pmid=14730057}}</ref>
|-
|11q22.3
|Loss
|10-20
|''[[ATM]], [[BIRC3]], [[MRE11]], [[H2AFX]]''
|''ATM'' established, Others Candidate
|Unfavorable
|Established (1)
|
|<ref name=":10">{{Cite journal|last=Wg|first=Wierda|last2=Ad|first2=Zelenetz|last3=Li|first3=Gordon|last4=Js|first4=Abramson|last5=Rh|first5=Advani|last6=Cb|first6=Andreadis|last7=N|first7=Bartlett|last8=Jc|first8=Byrd|last9=P|first9=Caimi|date=2017|title=NCCN Guidelines Insights: Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma, Version 1.2017|url=https://pubmed.ncbi.nlm.nih.gov/28275031/|language=en|pmid=28275031}}</ref>
|-
|12
|Gain
|10-20
|Unknown
|N/A
|Intermediate
|Established (1)
|Unfavorable if ''NOTCH1'' mutation is present
|<ref name=":10" />
|-
|13q14
|Loss
|50-60
|''[[DLEU2]], [[MIR15A]], [[MIR16-1]],'' ''[[DLEU1]]''
|Established
|Favorable
|Established (1)
|Co-deletion of ''RB1'' may negatively impact time to treatment
|<ref name=":10" /> <ref>{{Cite journal|last=M|first=Dal Bo|last2=Fm|first2=Rossi|last3=D|first3=Rossi|last4=C|first4=Deambrogi|last5=F|first5=Bertoni|last6=I|first6=Del Giudice|last7=G|first7=Palumbo|last8=M|first8=Nanni|last9=A|first9=Rinaldi|date=2011|title=13q14 deletion size and number of deleted cells both influence prognosis in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/21563234/|language=en|pmid=21563234}}</ref> <ref name=":11">{{Cite journal|last=Sn|first=Malek|date=2013|title=The biology and clinical significance of acquired genomic copy number aberrations and recurrent gene mutations in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/23001040/|language=en|doi=10.1038/onc.2012.411|pmc=PMC3676480|pmid=23001040}}</ref>
|-
|14q24.1q32.3
|Loss
|2
|Unknown
|N/A
|Unknown
|N/A (3)
|Associated with trisomy 12
|<ref name=":3" /> <ref>{{Cite journal|last=Pt|first=Greipp|last2=Sa|first2=Smoley|last3=Ds|first3=Viswanatha|last4=Ls|first4=Frederick|last5=Kg|first5=Rabe|last6=Rg|first6=Sharma|last7=Sl|first7=Slager|last8=Dl|first8=Van Dyke|last9=Td|first9=Shanafelt|date=2013|title=Patients with chronic lymphocytic leukaemia and clonal deletion of both 17p13.1 and 11q22.3 have a very poor prognosis|url=https://pubmed.ncbi.nlm.nih.gov/24032430/|language=en|doi=10.1111/bjh.12534|pmc=PMC3907074|pmid=24032430}}</ref> <ref>{{Cite journal|last=A|first=Cosson|last2=E|first2=Chapiro|last3=N|first3=Belhouachi|last4=Ha|first4=Cung|last5=B|first5=Keren|last6=F|first6=Damm|last7=C|first7=Algrin|last8=C|first8=Lefebvre|last9=S|first9=Fert-Ferrer|date=2014|title=14q deletions are associated with trisomy 12, NOTCH1 mutations and unmutated IGHV genes in chronic lymphocytic leukemia and small lymphocytic lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/24729385/|language=en|pmid=24729385}}</ref>
|-
|15q15.1
|Loss
|4
|''[[MGA]]''
|Candidate
|Unknown
|N/A (3)
|
|<ref name=":3" /> <ref name=":5" />
|-
|17p13.1
|Loss
|5-15
|''[[TP53]]''
|Established
|Unfavorable
|Established (1)
|
|<ref name=":10" />
|-
|17q
|Gain
|1
|Unknown
|N/A
|Unfavorable
|Suspected (2)
|
|<ref name=":1" />
|-
|18p
|Loss
|3
|Unknown
|N/A
|Unfavorable
|Suspected (2)
|
|<ref name=":1" /> <ref name=":3" />
|-
|18
|Gain
|4
|Unknown
|N/A
|Unfavorable
|Established (1)
|Associated with trisomy 12
|<ref name=":12">{{Cite journal|last=R|first=Ibbotson|last2=A|first2=Athanasiadou|last3=La|first3=Sutton|last4=Z|first4=Davis|last5=A|first5=Gardiner|last6=P|first6=Baliakas|last7=R|first7=Gunnarsson|last8=A|first8=Anagnostopoulos|last9=G|first9=Juliusson|date=2012|title=Coexistence of trisomies of chromosomes 12 and 19 in chronic lymphocytic leukemia occurs exclusively in the rare IgG-positive variant|url=https://pubmed.ncbi.nlm.nih.gov/21788947/|language=en|pmid=21788947}}</ref>
|-
|19
|Gain
|2-5
|Unknown
|N/A
|Unfavorable
|Established (1)
|Associated with trisomy 12
|<ref name=":3" /> <ref name=":5" /> <ref name=":8" /> <ref name=":9" /> <ref name=":12" />
|-
|Genomic complexity
|3 or more CNAs
|10-15
|
|N/A
|Unfavorable
|Established (1)
|
|<ref name=":5" /> <ref name=":6" /> <ref name=":7" /> <ref>{{Cite journal|last=Sr|first=Gunn|last2=Ms|first2=Mohammed|last3=Ch|first3=Mellink|last4=Lv|first4=Abruzzo|last5=Rs|first5=Robetorye|date=2008|title=The HemeScan test for genomic prognostic marker assessment in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/23495782/|language=en|pmid=23495782}}</ref>
|-
|Chromothripsis
|(>10 copy number states of 2 and 3)
|5
|''[[SETD2]]'', other markers across genome not defined
|Established
|Unfavorable
|Established (1)
|
|<ref name=":3" /> <ref name=":11" /> <ref>{{Cite journal|last=H|first=Parker|last2=Mj|first2=Rose-Zerilli|last3=M|first3=Larrayoz|last4=R|first4=Clifford|last5=J|first5=Edelmann|last6=S|first6=Blakemore|last7=J|first7=Gibson|last8=J|first8=Wang|last9=V|first9=Ljungström|date=2016|title=Genomic disruption of the histone methyltransferase SETD2 in chronic lymphocytic leukaemia|url=https://pubmed.ncbi.nlm.nih.gov/27282254/|language=en|doi=10.1038/leu.2016.134|pmc=PMC5023049|pmid=27282254}}</ref>
|}
<nowiki>*</nowiki>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==
<references />