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CLL Tables: Regions of Recurrent Copy Number Change and CN-LOH (view source)

Revision as of 22:14, 7 November 2020

14,261 bytes added ,  22:14, 7 November 2020
adding table 3 references
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Abbreviations: CNA = copy number aberration; CLL = chronic lymphocytic leukemia; CN-LOH = copy-neutral loss-of-heterozygosity
 
Abbreviations: CNA = copy number aberration; CLL = chronic lymphocytic leukemia; CN-LOH = copy-neutral loss-of-heterozygosity
−
      
'''Table 2.  Recurring regions of CN-LOH in CLL'''
 
'''Table 2.  Recurring regions of CN-LOH in CLL'''
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|N/A (3)
 
|N/A (3)
 
|<ref name=":14" /><ref>{{Cite journal|last=Xu|first=Xinjie|last2=Johnson|first2=Eric B.|last3=Leverton|first3=Lisa|last4=Arthur|first4=Ashley|last5=Watson|first5=Quinn|last6=Chang|first6=Faye L.|last7=Raca|first7=Gordana|last8=Laffin|first8=Jennifer J.|date=2013-09|title=The advantage of using SNP array in clinical testing for hematological malignancies--a comparative study of three genetic testing methods|url=https://pubmed.ncbi.nlm.nih.gov/24269304|journal=Cancer Genetics|volume=206|issue=9-10|pages=317–326|doi=10.1016/j.cancergen.2013.09.001|issn=2210-7762|pmid=24269304}}</ref>
 
|<ref name=":14" /><ref>{{Cite journal|last=Xu|first=Xinjie|last2=Johnson|first2=Eric B.|last3=Leverton|first3=Lisa|last4=Arthur|first4=Ashley|last5=Watson|first5=Quinn|last6=Chang|first6=Faye L.|last7=Raca|first7=Gordana|last8=Laffin|first8=Jennifer J.|date=2013-09|title=The advantage of using SNP array in clinical testing for hematological malignancies--a comparative study of three genetic testing methods|url=https://pubmed.ncbi.nlm.nih.gov/24269304|journal=Cancer Genetics|volume=206|issue=9-10|pages=317–326|doi=10.1016/j.cancergen.2013.09.001|issn=2210-7762|pmid=24269304}}</ref>
 +
|}
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<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
 +
 +
 +
'''Table 3. Recurrent mutated genes in CLL'''
 +
{| class="wikitable"
 +
|'''Gene'''
 +
|'''Locus'''
 +
|'''Function'''
 +
|'''Mutation Type'''
 +
|'''Prevalence (%)'''
 +
|'''Prognostic Significance'''
 +
|'''Strength of Evidence (Level*)'''
 +
|'''Comments'''
 +
|'''References'''
 +
|-
 +
|''[[ATM]]''
 +
|11q22.3
 +
|DNA repair and cell-cycle control
 +
|Missense, nonsense, indel
 +
|10-14
 +
|Unfavorable
 +
|Established (1)
 +
|Associated with unmut''IGHV'' and 11q-; Candidate driver gene
 +
|<ref name=":17">{{Cite journal|last=Wierda|first=William G.|last2=Zelenetz|first2=Andrew D.|last3=Gordon|first3=Leo I.|last4=Abramson|first4=Jeremy S.|last5=Advani|first5=Ranjana H.|last6=Andreadis|first6=C. Babis|last7=Bartlett|first7=Nancy|last8=Byrd|first8=John C.|last9=Caimi|first9=Paolo|date=03 2017|title=NCCN Guidelines Insights: Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma, Version 1.2017|url=https://pubmed.ncbi.nlm.nih.gov/28275031|journal=Journal of the National Comprehensive Cancer Network: JNCCN|volume=15|issue=3|pages=293–311|doi=10.6004/jnccn.2017.0030|issn=1540-1413|pmid=28275031}}</ref><ref name=":18">{{Cite journal|last=Campregher|first=Paulo Vidal|last2=Hamerschlak|first2=Nelson|date=2014-08|title=Novel prognostic gene mutations identified in chronic lymphocytic leukemia and their impact on clinical practice|url=https://pubmed.ncbi.nlm.nih.gov/24548608|journal=Clinical Lymphoma, Myeloma & Leukemia|volume=14|issue=4|pages=271–276|doi=10.1016/j.clml.2013.12.016|issn=2152-2669|pmid=24548608}}</ref>
 +
|-
 +
|''[[BIRC3]]''
 +
|11q22.2
 +
|Apoptosis inhibitor
 +
|Frameshift, nonsense, whole gene deletion
 +
|1-10
 +
 +
(higher in previously treated patients)
 +
|Unfavorable
 +
|Established (1)
 +
|In ~25% of fludarabine-refractory CLL; Candidate driver gene
 +
|<ref name=":19">{{Cite journal|last=Strefford|first=Jonathan C.|date=2015-04|title=The genomic landscape of chronic lymphocytic leukaemia: biological and clinical implications|url=https://pubmed.ncbi.nlm.nih.gov/25496136|journal=British Journal of Haematology|volume=169|issue=1|pages=14–31|doi=10.1111/bjh.13254|issn=1365-2141|pmid=25496136}}</ref><ref>{{Cite journal|last=Alsolami|first=Reem|last2=Knight|first2=Samantha Jl|last3=Schuh|first3=Anna|date=2013-06-01|title=Clinical application of targeted and genome-wide technologies: can we predict treatment responses in chronic lymphocytic leukemia?|url=https://pubmed.ncbi.nlm.nih.gov/24611071|journal=Personalized Medicine|volume=10|issue=4|pages=361–376|doi=10.2217/pme.13.33|issn=1741-0541|pmc=3943176|pmid=24611071}}</ref><ref name=":20">{{Cite journal|last=Baliakas|first=P.|last2=Hadzidimitriou|first2=A.|last3=Sutton|first3=L.-A.|last4=Rossi|first4=D.|last5=Minga|first5=E.|last6=Villamor|first6=N.|last7=Larrayoz|first7=M.|last8=Kminkova|first8=J.|last9=Agathangelidis|first9=A.|date=2015-02|title=Recurrent mutations refine prognosis in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/24943832|journal=Leukemia|volume=29|issue=2|pages=329–336|doi=10.1038/leu.2014.196|issn=1476-5551|pmid=24943832}}</ref><ref name=":21">{{Cite journal|last=Rossi|first=Davide|last2=Rasi|first2=Silvia|last3=Spina|first3=Valeria|last4=Bruscaggin|first4=Alessio|last5=Monti|first5=Sara|last6=Ciardullo|first6=Carmela|last7=Deambrogi|first7=Clara|last8=Khiabanian|first8=Hossein|last9=Serra|first9=Roberto|date=2013-02-21|title=Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/23243274|journal=Blood|volume=121|issue=8|pages=1403–1412|doi=10.1182/blood-2012-09-458265|issn=1528-0020|pmc=3578955|pmid=23243274}}</ref>
 +
|-
 +
|''[[CHD2]]''
 +
|15q26.1
 +
|Chromatin remodeler
 +
|Missense, truncation
 +
|5-10
 +
|Unknown
 +
|N/A (3)
 +
|
 +
|<ref name=":19" /><ref>{{Cite journal|last=Rodríguez|first=David|last2=Bretones|first2=Gabriel|last3=Quesada|first3=Víctor|last4=Villamor|first4=Neus|last5=Arango|first5=Javier R.|last6=López-Guillermo|first6=Armando|last7=Ramsay|first7=Andrew J.|last8=Baumann|first8=Tycho|last9=Quirós|first9=Pedro M.|date=2015-07-09|title=Mutations in CHD2 cause defective association with active chromatin in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/26031915|journal=Blood|volume=126|issue=2|pages=195–202|doi=10.1182/blood-2014-10-604959|issn=1528-0020|pmid=26031915}}</ref>
 +
|-
 +
|''[[FBXW7]]''
 +
|4q31.3
 +
|Ubiquitin ligase subunit/targets include ''[[NOTCH1]]''
 +
|Missense
 +
|4
 +
|Unknown
 +
|N/A (3)
 +
|Exclusive to ''[[NOTCH1]]'' mutation patients; Negatively regulates ''[[NOTCH1]]''
 +
|<ref>{{Cite journal|last=Wang|first=Lili|last2=Lawrence|first2=Michael S.|last3=Wan|first3=Youzhong|last4=Stojanov|first4=Petar|last5=Sougnez|first5=Carrie|last6=Stevenson|first6=Kristen|last7=Werner|first7=Lillian|last8=Sivachenko|first8=Andrey|last9=DeLuca|first9=David S.|date=2011-12-29|title=SF3B1 and other novel cancer genes in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/22150006|journal=The New England Journal of Medicine|volume=365|issue=26|pages=2497–2506|doi=10.1056/NEJMoa1109016|issn=1533-4406|pmc=3685413|pmid=22150006}}</ref>
 +
|-
 +
|''[[MYD88]]''
 +
|3p22.2
 +
|Inflammatory pathway signal transducer
 +
|Missense
 +
|2-10
 +
|Favorable/
 +
 +
No effect
 +
|Suspected (2)
 +
|Candidate driver gene
 +
|<ref name=":20" /><ref name=":21" /><ref name=":22">{{Cite journal|last=Filip|first=Agata A.|date=2013-09|title=New boys in town: prognostic role of SF3B1, NOTCH1 and other cryptic alterations in chronic lymphocytic leukemia and how it works|url=https://pubmed.ncbi.nlm.nih.gov/23343182|journal=Leukemia & Lymphoma|volume=54|issue=9|pages=1876–1881|doi=10.3109/10428194.2013.769049|issn=1029-2403|pmid=23343182}}</ref>
 +
|-
 +
|''[[NOTCH1]]''
 +
|9q34.3
 +
|Intercellular signaling
 +
|Missense, nonsense, insertion, duplication, frameshift
 +
|4-10
 +
 +
(diagnosis)
 +
 +
12-30
 +
 +
(progression)
 +
|Unfavorable
 +
|Established (1)
 +
|Associated with +12; Candidate driver gene
 +
|<ref>{{Cite journal|last=Nabhan|first=Chadi|last2=Raca|first2=Gordana|last3=Wang|first3=Y. Lynn|date=2015-10|title=Predicting Prognosis in Chronic Lymphocytic Leukemia in the Contemporary Era|url=https://pubmed.ncbi.nlm.nih.gov/26181643|journal=JAMA oncology|volume=1|issue=7|pages=965–974|doi=10.1001/jamaoncol.2015.0779|issn=2374-2445|pmid=26181643}}</ref><ref name=":18" /><ref name=":21" /><ref>{{Cite journal|last=Balatti|first=Veronica|last2=Bottoni|first2=Arianna|last3=Palamarchuk|first3=Alexey|last4=Alder|first4=Hansjuerg|last5=Rassenti|first5=Laura Z.|last6=Kipps|first6=Thomas J.|last7=Pekarsky|first7=Yuri|last8=Croce|first8=Carlo M.|date=2012-01-12|title=NOTCH1 mutations in CLL associated with trisomy 12|url=https://pubmed.ncbi.nlm.nih.gov/22086416|journal=Blood|volume=119|issue=2|pages=329–331|doi=10.1182/blood-2011-10-386144|issn=1528-0020|pmc=3257004|pmid=22086416}}</ref><ref>{{Cite journal|last=Del Giudice|first=Ilaria|last2=Rossi|first2=Davide|last3=Chiaretti|first3=Sabina|last4=Marinelli|first4=Marilisa|last5=Tavolaro|first5=Simona|last6=Gabrielli|first6=Sara|last7=Laurenti|first7=Luca|last8=Marasca|first8=Roberto|last9=Rasi|first9=Silvia|date=2012-03|title=NOTCH1 mutations in +12 chronic lymphocytic leukemia (CLL) confer an unfavorable prognosis, induce a distinctive transcriptional profiling and refine the intermediate prognosis of +12 CLL|url=https://pubmed.ncbi.nlm.nih.gov/22207691|journal=Haematologica|volume=97|issue=3|pages=437–441|doi=10.3324/haematol.2011.060129|issn=1592-8721|pmc=3291600|pmid=22207691}}</ref>
 +
|-
 +
|''[[POT1]]''
 +
|7q31.33
 +
|Telomere protector/
 +
 +
stabilizer; component of telomerase RNP complex
 +
|Missense, frameshift, splicing
 +
|5-10
 +
|Unfavorable
 +
|Suspected (2)
 +
|Associated with familial CLL
 +
|<ref>{{Cite journal|last=Herling|first=Carmen Diana|last2=Klaumünzer|first2=Marion|last3=Rocha|first3=Cristiano Krings|last4=Altmüller|first4=Janine|last5=Thiele|first5=Holger|last6=Bahlo|first6=Jasmin|last7=Kluth|first7=Sandra|last8=Crispatzu|first8=Giuliano|last9=Herling|first9=Marco|date=07 21, 2016|title=Complex karyotypes and KRAS and POT1 mutations impact outcome in CLL after chlorambucil-based chemotherapy or chemoimmunotherapy|url=https://pubmed.ncbi.nlm.nih.gov/27226433|journal=Blood|volume=128|issue=3|pages=395–404|doi=10.1182/blood-2016-01-691550|issn=1528-0020|pmid=27226433}}</ref><ref>{{Cite journal|last=Ramsay|first=Andrew J.|last2=Quesada|first2=Víctor|last3=Foronda|first3=Miguel|last4=Conde|first4=Laura|last5=Martínez-Trillos|first5=Alejandra|last6=Villamor|first6=Neus|last7=Rodríguez|first7=David|last8=Kwarciak|first8=Agnieszka|last9=Garabaya|first9=Cecilia|date=2013-05|title=POT1 mutations cause telomere dysfunction in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/23502782|journal=Nature Genetics|volume=45|issue=5|pages=526–530|doi=10.1038/ng.2584|issn=1546-1718|pmid=23502782}}</ref><ref>{{Cite journal|last=Speedy|first=Helen E.|last2=Kinnersley|first2=Ben|last3=Chubb|first3=Daniel|last4=Broderick|first4=Peter|last5=Law|first5=Philip J.|last6=Litchfield|first6=Kevin|last7=Jayne|first7=Sandrine|last8=Dyer|first8=Martin J. S.|last9=Dearden|first9=Claire|date=11 10, 2016|title=Germ line mutations in shelterin complex genes are associated with familial chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/27528712|journal=Blood|volume=128|issue=19|pages=2319–2326|doi=10.1182/blood-2016-01-695692|issn=1528-0020|pmc=5271173|pmid=27528712}}</ref>
 +
|-
 +
|''[[SF3B1]]''
 +
|2q33.1
 +
|Spliceosome component
 +
|Missense
 +
|10 -18
 +
|Unfavorable
 +
|Established (1)
 +
|Enriched in patients with del(11q) and unmut''IGHV''; Candidate driver gene for disease progression
 +
|<ref name=":20" /><ref name=":21" /><ref>{{Cite journal|last=Mitsui|first=Takeki|last2=Koiso|first2=Hiromi|last3=Nakahashi|first3=Hirotaka|last4=Saitoh|first4=Akio|last5=Shimizu|first5=Hiroaki|last6=Ishizaki|first6=Takuma|last7=Ogawa|first7=Yoshiyuki|last8=Takizawa|first8=Makiko|last9=Yokohama|first9=Akihiko|date=2016-02|title=SF3B1 and IGHV gene mutation status predict poor prognosis in Japanese CLL patients|url=https://pubmed.ncbi.nlm.nih.gov/26588928|journal=International Journal of Hematology|volume=103|issue=2|pages=219–226|doi=10.1007/s12185-015-1912-z|issn=1865-3774|pmid=26588928}}</ref><ref>{{Cite journal|last=Quesada|first=Víctor|last2=Conde|first2=Laura|last3=Villamor|first3=Neus|last4=Ordóñez|first4=Gonzalo R.|last5=Jares|first5=Pedro|last6=Bassaganyas|first6=Laia|last7=Ramsay|first7=Andrew J.|last8=Beà|first8=Sílvia|last9=Pinyol|first9=Magda|date=2011-12-11|title=Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/22158541|journal=Nature Genetics|volume=44|issue=1|pages=47–52|doi=10.1038/ng.1032|issn=1546-1718|pmid=22158541}}</ref><ref>{{Cite journal|last=Wan|first=Youzhong|last2=Wu|first2=Catherine J.|date=2013-06-06|title=SF3B1 mutations in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/23568491|journal=Blood|volume=121|issue=23|pages=4627–4634|doi=10.1182/blood-2013-02-427641|issn=1528-0020|pmc=3674664|pmid=23568491}}</ref>
 +
|-
 +
|''[[TP53]]''
 +
|17p13.1
 +
|DNA repair and cell-cycle control
 +
|Missense
 +
|5-10
 +
 +
(higher with progressive disease)
 +
|Unfavorable
 +
|Established (1)
 +
|
 +
|<ref name=":17" /><ref name=":19" /><ref>{{Cite journal|last=Rossi|first=Davide|last2=Khiabanian|first2=Hossein|last3=Spina|first3=Valeria|last4=Ciardullo|first4=Carmela|last5=Bruscaggin|first5=Alessio|last6=Famà|first6=Rosella|last7=Rasi|first7=Silvia|last8=Monti|first8=Sara|last9=Deambrogi|first9=Clara|date=2014-04-03|title=Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/24501221|journal=Blood|volume=123|issue=14|pages=2139–2147|doi=10.1182/blood-2013-11-539726|issn=1528-0020|pmc=4017291|pmid=24501221}}</ref><ref>{{Cite journal|last=Zenz|first=Thorsten|last2=Eichhorst|first2=Barbara|last3=Busch|first3=Raymonde|last4=Denzel|first4=Tina|last5=Häbe|first5=Sonja|last6=Winkler|first6=Dirk|last7=Bühler|first7=Andreas|last8=Edelmann|first8=Jennifer|last9=Bergmann|first9=Manuela|date=2010-10-10|title=TP53 mutation and survival in chronic lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/20697090|journal=Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology|volume=28|issue=29|pages=4473–4479|doi=10.1200/JCO.2009.27.8762|issn=1527-7755|pmid=20697090}}</ref><ref>{{Cite journal|last=Stilgenbauer|first=Stephan|last2=Schnaiter|first2=Andrea|last3=Paschka|first3=Peter|last4=Zenz|first4=Thorsten|last5=Rossi|first5=Marianna|last6=Döhner|first6=Konstanze|last7=Bühler|first7=Andreas|last8=Böttcher|first8=Sebastian|last9=Ritgen|first9=Matthias|date=2014-05-22|title=Gene mutations and treatment outcome in chronic lymphocytic leukemia: results from the CLL8 trial|url=https://pubmed.ncbi.nlm.nih.gov/24652989|journal=Blood|volume=123|issue=21|pages=3247–3254|doi=10.1182/blood-2014-01-546150|issn=1528-0020|pmid=24652989}}</ref>
 +
|-
 +
|''[[XPO1]]''
 +
|2p15
 +
|Exports proteins/RNA fragments from nucleus into cytoplasm
 +
|Missense
 +
|5-7.5
 +
|Unfavorable/
 +
 +
high risk of progression
 +
|Suspected (2)
 +
|Associated with unmut''IGHV''
 +
|<ref>{{Cite journal|last=Cosson|first=A.|last2=Chapiro|first2=E.|last3=Bougacha|first3=N.|last4=Lambert|first4=J.|last5=Herbi|first5=L.|last6=Cung|first6=H.-A.|last7=Algrin|first7=C.|last8=Keren|first8=B.|last9=Damm|first9=F.|date=07 2017|title=Gain in the short arm of chromosome 2 (2p+) induces gene overexpression and drug resistance in chronic lymphocytic leukemia: analysis of the central role of XPO1|url=https://pubmed.ncbi.nlm.nih.gov/28344316|journal=Leukemia|volume=31|issue=7|pages=1625–1629|doi=10.1038/leu.2017.100|issn=1476-5551|pmid=28344316}}</ref><ref name=":22" /><ref>{{Cite journal|last=Jain|first=Nitin|last2=O'Brien|first2=Susan|date=2015-07-23|title=Initial treatment of CLL: integrating biology and functional status|url=https://pubmed.ncbi.nlm.nih.gov/26065656|journal=Blood|volume=126|issue=4|pages=463–470|doi=10.1182/blood-2015-04-585067|issn=1528-0020|pmc=4624441|pmid=26065656}}</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
 
<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
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