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MDS, MDS/MPN and MPN Tables: Recurrent Genomic Alterations Detected by Chromosomal Microarray (view source)
Revision as of 17:10, 30 April 2020
, 17:10, 30 April 2020Jennelleh moved page TestMDS-MPNtable to MDS, MDS/MPN and MPN Tables: Recurrent Genomic Alterations Detected by Chromosomal Microarray without leaving a redirect
'''Table 1.''' Evidence for the clinical utility of chromosomal microarray testing (CMA) in myeloid disorders excluding acute myeloid leukemia
'''Table 1 - Evidence for the Clinical Utility of Chromosomal Microarray (CMA) Testing in Myeloid Disorders Excluding Acute Myeloid Leukemia (Literature Review).''' Table derived from Kanagal-Shawanna et al., 2018 [PMID 30377088] with permission from Cancer Genetics.
{| class="wikitable"
{| class="wikitable"
|'''Disease'''
|'''Disease'''
|
|
|4q loss
|4q loss
|''TET2''
|''[[TET2]]''
|Prognostic for poor survival
|Prognostic for poor survival
|<ref name=":3" /><ref name=":8" /><ref name=":10">Jankowska AM, Szpurka H, Tiu RV, Makishima H, Afable M, Huh J, et al. Loss of heterozygosity 4q24 and TET2 mutations associated with myelodysplastic/myeloproliferative neoplasms. Blood 2009;113:6403-10.[https://www.ncbi.nlm.nih.gov/pubmed/19372255]</ref><ref name=":11">Bacher U, Weissmann S, Kohlmann A, Schindela S, Alpermann T, Schnittger S, et al. TET2 deletions are a recurrent but rare phenomenon in myeloid malignancies and are frequently accompanied by TET2 mutations on the remaining allele. Br J Haematol 2012;156:67-75.[https://www.ncbi.nlm.nih.gov/pubmed/22017486]</ref><ref name=":12">Kolquist KA, Schultz RA, Furrow A, Brown TC, Han JY, Campbell LJ, et al. Microarray-based comparative genomic hybridization of cancer targets reveals novel, recurrent genetic aberrations in the myelodysplastic syndromes. Cancer Genet 2011;204:603-28.[https://www.sciencedirect.com/science/article/pii/S2210776211002973]</ref>
|<ref name=":3" /><ref name=":8" /><ref name=":10">Jankowska AM, Szpurka H, Tiu RV, Makishima H, Afable M, Huh J, et al. Loss of heterozygosity 4q24 and TET2 mutations associated with myelodysplastic/myeloproliferative neoplasms. Blood 2009;113:6403-10.[https://www.ncbi.nlm.nih.gov/pubmed/19372255]</ref><ref name=":11">Bacher U, Weissmann S, Kohlmann A, Schindela S, Alpermann T, Schnittger S, et al. TET2 deletions are a recurrent but rare phenomenon in myeloid malignancies and are frequently accompanied by TET2 mutations on the remaining allele. Br J Haematol 2012;156:67-75.[https://www.ncbi.nlm.nih.gov/pubmed/22017486]</ref><ref name=":12">Kolquist KA, Schultz RA, Furrow A, Brown TC, Han JY, Campbell LJ, et al. Microarray-based comparative genomic hybridization of cancer targets reveals novel, recurrent genetic aberrations in the myelodysplastic syndromes. Cancer Genet 2011;204:603-28.[https://www.sciencedirect.com/science/article/pii/S2210776211002973]</ref>
|
|
|4q CN-LOH
|4q CN-LOH
|''TET2''
|''[[TET2]]''
|Prognostic for poor survival
|Prognostic for poor survival
|<ref name=":13">Gondek LP, Tiu R, O'Keefe CL, Sekeres MA, Theil KS, Maciejewski JP. Chromosomal lesions and uniparental disomy detected by SNP arrays in MDS, MDS/MPD, and MDS-derived AML. Blood 2008;111:1534-42.[https://www.ncbi.nlm.nih.gov/pubmed/17954704]</ref><ref name=":3" /><ref name=":14">Heinrichs S, Kulkarni RV, Bueso-Ramos CE, Levine RL, Loh ML, Li C, et al. Accurate detection of uniparental disomy and microdeletions by SNP array analysis in myelodysplastic syndromes with normal cytogenetics. Leukemia 2009;23:1605-13.[https://www.nature.com/articles/leu200982]</ref><ref name=":8" /><ref name=":9" /><ref name=":1" /><ref name=":5" /><ref name=":15">Mohamedali AM, Smith AE, Gaken J, Lea NC, Mian SA, Westwood NB, et al. Novel TET2 mutations associated with UPD4q24 in myelodysplastic syndrome. J Clin Oncol 2009;27:4002-6.[https://www.ncbi.nlm.nih.gov/pubmed/19528370]</ref><ref name=":16">Mohamedali A, Gaken J, Twine NA, Ingram W, Westwood N, Lea NC, et al. Prevalence and prognostic significance of allelic imbalance by single-nucleotide polymorphism analysis in low-risk myelodysplastic syndromes. Blood 2007;110:3365-73.[https://www.ncbi.nlm.nih.gov/pubmed/17634407]</ref><ref name=":17">Flach J, Dicker F, Schnittger S, Schindela S, Kohlmann A, Haferlach T, et al. An accumulation of cytogenetic and molecular genetic events characterizes the progression from MDS to secondary AML: an analysis of 38 paired samples analyzed by cytogenetics, molecular mutation analysis and SNP microarray profiling. Leukemia 2011;25:713-8.[https://www.nature.com/articles/leu2010304]</ref><ref name=":18">Larsson N, Lilljebjorn H, Lassen C, Johansson B, Fioretos T. Myeloid malignancies with acquired trisomy 21 as the sole cytogenetic change are clinically highly variable and display a heterogeneous pattern of copy number alterations and mutations. Eur J Haematol 2012;88:136-43.[https://www.ncbi.nlm.nih.gov/pubmed/21933280]</ref>
|<ref name=":13">Gondek LP, Tiu R, O'Keefe CL, Sekeres MA, Theil KS, Maciejewski JP. Chromosomal lesions and uniparental disomy detected by SNP arrays in MDS, MDS/MPD, and MDS-derived AML. Blood 2008;111:1534-42.[https://www.ncbi.nlm.nih.gov/pubmed/17954704]</ref><ref name=":3" /><ref name=":14">Heinrichs S, Kulkarni RV, Bueso-Ramos CE, Levine RL, Loh ML, Li C, et al. Accurate detection of uniparental disomy and microdeletions by SNP array analysis in myelodysplastic syndromes with normal cytogenetics. Leukemia 2009;23:1605-13.[https://www.nature.com/articles/leu200982]</ref><ref name=":8" /><ref name=":9" /><ref name=":1" /><ref name=":5" /><ref name=":15">Mohamedali AM, Smith AE, Gaken J, Lea NC, Mian SA, Westwood NB, et al. Novel TET2 mutations associated with UPD4q24 in myelodysplastic syndrome. J Clin Oncol 2009;27:4002-6.[https://www.ncbi.nlm.nih.gov/pubmed/19528370]</ref><ref name=":16">Mohamedali A, Gaken J, Twine NA, Ingram W, Westwood N, Lea NC, et al. Prevalence and prognostic significance of allelic imbalance by single-nucleotide polymorphism analysis in low-risk myelodysplastic syndromes. Blood 2007;110:3365-73.[https://www.ncbi.nlm.nih.gov/pubmed/17634407]</ref><ref name=":17">Flach J, Dicker F, Schnittger S, Schindela S, Kohlmann A, Haferlach T, et al. An accumulation of cytogenetic and molecular genetic events characterizes the progression from MDS to secondary AML: an analysis of 38 paired samples analyzed by cytogenetics, molecular mutation analysis and SNP microarray profiling. Leukemia 2011;25:713-8.[https://www.nature.com/articles/leu2010304]</ref><ref name=":18">Larsson N, Lilljebjorn H, Lassen C, Johansson B, Fioretos T. Myeloid malignancies with acquired trisomy 21 as the sole cytogenetic change are clinically highly variable and display a heterogeneous pattern of copy number alterations and mutations. Eur J Haematol 2012;88:136-43.[https://www.ncbi.nlm.nih.gov/pubmed/21933280]</ref>
|
|
|7q loss
|7q loss
|''CUX1, EZH2''
|''[[CUX1]], [[EZH2]]''
|Prognostic for poor survival
|Prognostic for poor survival
|<ref name=":3" /><ref name=":19" /><ref name=":23">Thiel A, Beier M, Ingenhag D, Servan K, Hein M, Moeller V, et al. Comprehensive array CGH of normal karyotype myelodysplastic syndromes reveals hidden recurrent and individual genomic copy number alterations with prognostic relevance. Leukemia 2011;25:387-99.[https://www.ncbi.nlm.nih.gov/pubmed/21274003]</ref><ref name=":9" /><ref name=":24">Volkert S, Haferlach T, Holzwarth J, Zenger M, Kern W, Staller M, et al. Array CGH identifies copy number changes in 11% of 520 MDS patients with normal karyotype and uncovers prognostically relevant deletions. Leukemia 2016;30:257-60.[https://www.ncbi.nlm.nih.gov/pubmed/26392226]</ref><ref name=":25">Svobodova K, Zemanova Z, Lhotska H, Novakova M, Podskalska L, Belickova M, et al. Copy number neutral loss of heterozygosity at 17p and homozygous mutations of TP53 are associated with complex chromosomal aberrations in patients newly diagnosed with myelodysplastic syndromes. Leuk Res 2016;42:7-12.[https://www.ncbi.nlm.nih.gov/pubmed/26851439]</ref><ref name=":16" /><ref name=":6" /><ref name=":17" /><ref name=":26">Babushok DV, Xie HM, Roth JJ, Perdigones N, Olson TS, Cockroft JD, et al. Single nucleotide polymorphism array analysis of bone marrow failure patients reveals characteristic patterns of genetic changes. Br J Haematol 2014;164:73-82.[https://www.ncbi.nlm.nih.gov/pubmed/24116929]</ref><ref name=":27">Stevens-Kroef MJ, Hebeda KM, Verwiel ET, Kamping EJ, van Cleef PH, Kuiper RP, et al. Microarray-based genomic profiling and in situ hybridization on fibrotic bone marrow biopsies for the identification of numerical chromosomal abnormalities in myelodysplastic syndrome. Mol Cytogenet 2015;8:33.[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447009/]</ref><ref name=":7" /><ref name=":28">Barresi V, Palumbo GA, Musso N, Consoli C, Capizzi C, Meli CR, et al. Clonal selection of 11q CN-LOH and CBL gene mutation in a serially studied patient during MDS progression to AML. Leuk Res 2010;34:1539-42.[https://www.ncbi.nlm.nih.gov/pubmed/20674974]</ref><ref name=":22" />
|<ref name=":3" /><ref name=":19" /><ref name=":23">Thiel A, Beier M, Ingenhag D, Servan K, Hein M, Moeller V, et al. Comprehensive array CGH of normal karyotype myelodysplastic syndromes reveals hidden recurrent and individual genomic copy number alterations with prognostic relevance. Leukemia 2011;25:387-99.[https://www.ncbi.nlm.nih.gov/pubmed/21274003]</ref><ref name=":9" /><ref name=":24">Volkert S, Haferlach T, Holzwarth J, Zenger M, Kern W, Staller M, et al. Array CGH identifies copy number changes in 11% of 520 MDS patients with normal karyotype and uncovers prognostically relevant deletions. Leukemia 2016;30:257-60.[https://www.ncbi.nlm.nih.gov/pubmed/26392226]</ref><ref name=":25">Svobodova K, Zemanova Z, Lhotska H, Novakova M, Podskalska L, Belickova M, et al. Copy number neutral loss of heterozygosity at 17p and homozygous mutations of TP53 are associated with complex chromosomal aberrations in patients newly diagnosed with myelodysplastic syndromes. Leuk Res 2016;42:7-12.[https://www.ncbi.nlm.nih.gov/pubmed/26851439]</ref><ref name=":16" /><ref name=":6" /><ref name=":17" /><ref name=":26">Babushok DV, Xie HM, Roth JJ, Perdigones N, Olson TS, Cockroft JD, et al. Single nucleotide polymorphism array analysis of bone marrow failure patients reveals characteristic patterns of genetic changes. Br J Haematol 2014;164:73-82.[https://www.ncbi.nlm.nih.gov/pubmed/24116929]</ref><ref name=":27">Stevens-Kroef MJ, Hebeda KM, Verwiel ET, Kamping EJ, van Cleef PH, Kuiper RP, et al. Microarray-based genomic profiling and in situ hybridization on fibrotic bone marrow biopsies for the identification of numerical chromosomal abnormalities in myelodysplastic syndrome. Mol Cytogenet 2015;8:33.[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447009/]</ref><ref name=":7" /><ref name=":28">Barresi V, Palumbo GA, Musso N, Consoli C, Capizzi C, Meli CR, et al. Clonal selection of 11q CN-LOH and CBL gene mutation in a serially studied patient during MDS progression to AML. Leuk Res 2010;34:1539-42.[https://www.ncbi.nlm.nih.gov/pubmed/20674974]</ref><ref name=":22" />
|
|
|11q CN-LOH
|11q CN-LOH
|''CBL''
|''[[CBL]]''
|Prognostic/ recurrent
|Prognostic/ recurrent
|<ref name=":13" /><ref name=":3" /><ref name=":19" /><ref name=":4" /> <ref name=":1" /><ref name=":5" /><ref name=":17" /><ref name=":7" />
|<ref name=":13" /><ref name=":3" /><ref name=":19" /><ref name=":4" /> <ref name=":1" /><ref name=":5" /><ref name=":17" /><ref name=":7" />
|
|
|12p loss
|12p loss
|''ETV6''
|''[[ETV6]]''
|Recurrent
|Recurrent
|<ref name=":3" /><ref name=":14" /><ref name=":9" /><ref name=":24" /><ref name=":12" />
|<ref name=":3" /><ref name=":14" /><ref name=":9" /><ref name=":24" /><ref name=":12" />
|
|
|13q loss
|13q loss
|''?RB1''
|''?[[RB1]]''
|Recurrent
|Recurrent
|<ref name=":3" /><ref name=":8" /><ref name=":24" /><ref name=":1" /><ref name=":7" />
|<ref name=":3" /><ref name=":8" /><ref name=":24" /><ref name=":1" /><ref name=":7" />
|
|
|17p loss
|17p loss
|''TP53''
|''[[TP53]]''
|Recurrent
|Recurrent
|<ref name=":3" /><ref name=":9" /><ref name=":30">Zhang R, Kim YM, Wang X, Li Y, Lu X, Sternenberger AR, et al. Genomic Copy Number Variations in the Myelodysplastic Syndrome and Acute Myeloid Leukemia Patients with del(5q) and/or -7/del(7q). Int J Med Sci 2015;12:719-26.[https://www.ncbi.nlm.nih.gov/pubmed/26392809]</ref><ref name=":12" /><ref name=":27" />
|<ref name=":3" /><ref name=":9" /><ref name=":30">Zhang R, Kim YM, Wang X, Li Y, Lu X, Sternenberger AR, et al. Genomic Copy Number Variations in the Myelodysplastic Syndrome and Acute Myeloid Leukemia Patients with del(5q) and/or -7/del(7q). Int J Med Sci 2015;12:719-26.[https://www.ncbi.nlm.nih.gov/pubmed/26392809]</ref><ref name=":12" /><ref name=":27" />
|
|
|17p CN-LOH
|17p CN-LOH
|''TP53''
|''[[TP53]]''
|Diagnostic for advanced MDS/sAML
|Diagnostic for advanced MDS/sAML
|<ref name=":8" /><ref name=":9" /><ref name=":1" /><ref name=":5" /><ref name=":25" />
|<ref name=":8" /><ref name=":9" /><ref name=":1" /><ref name=":5" /><ref name=":25" />
|
|
|21q CN-LOH or deletion
|21q CN-LOH or deletion
|''RUNX1''
|''[[RUNX1]]''
|Prognostic for progression to AML
|Prognostic for progression to AML
|<ref name=":3" /><ref name=":23" /><ref name=":24" /><ref name=":12" /><ref name=":6" /><ref name=":29" />
|<ref name=":3" /><ref name=":23" /><ref name=":24" /><ref name=":12" /><ref name=":6" /><ref name=":29" />
|73%/NA
|73%/NA
|4q CN-LOH
|4q CN-LOH
|''TET2''
|''[[TET2]]''
|Recurrent
|Recurrent
|<ref name=":13" /><ref name=":33">Palomo L, Xicoy B, Garcia O, Mallo M, Adema V, Cabezon M, et al. Impact of SNP array karyotyping on the diagnosis and the outcome of chronic myelomonocytic leukemia with low risk cytogenetic features or no metaphases. Am J Hematol 2016;91:185-92.[https://www.ncbi.nlm.nih.gov/pubmed/26509444]</ref><ref name=":10" /><ref name=":17" /><ref name=":32" />
|<ref name=":13" /><ref name=":33">Palomo L, Xicoy B, Garcia O, Mallo M, Adema V, Cabezon M, et al. Impact of SNP array karyotyping on the diagnosis and the outcome of chronic myelomonocytic leukemia with low risk cytogenetic features or no metaphases. Am J Hematol 2016;91:185-92.[https://www.ncbi.nlm.nih.gov/pubmed/26509444]</ref><ref name=":10" /><ref name=":17" /><ref name=":32" />
|
|
|7q CN-LOH
|7q CN-LOH
|''Likely CUX1''
|''Likely [[CUX1]]''
|Recurrent
|Recurrent
|<ref name=":13" /><ref name=":33" /><ref name=":5" /><ref name=":6" /><ref name=":17" />
|<ref name=":13" /><ref name=":33" /><ref name=":5" /><ref name=":6" /><ref name=":17" />
|
|
|11q CN-LOH
|11q CN-LOH
|''CBL''
|''[[CBL]]''
|Recurrent
|Recurrent
|<ref name=":13" /><ref name=":33" /><ref name=":10" /><ref name=":5" /><ref name=":34">Gondek LP, Dunbar AJ, Szpurka H, McDevitt MA, Maciejewski JP. SNP array karyotyping allows for the detection of uniparental disomy and cryptic chromosomal abnormalities in MDS/MPD-U and MPD. PLoS One 2007;2:e1225. [https://www.ncbi.nlm.nih.gov/pubmed/18030353]</ref>
|<ref name=":13" /><ref name=":33" /><ref name=":10" /><ref name=":5" /><ref name=":34">Gondek LP, Dunbar AJ, Szpurka H, McDevitt MA, Maciejewski JP. SNP array karyotyping allows for the detection of uniparental disomy and cryptic chromosomal abnormalities in MDS/MPD-U and MPD. PLoS One 2007;2:e1225. [https://www.ncbi.nlm.nih.gov/pubmed/18030353]</ref>
|
|
|Recurrent
|Recurrent
|<ref>Singh NR, Morris CM, Koleth M, Wong K, Ward CM, Stevenson WS. Polyploidy in myelofibrosis: analysis by cytogenetic and SNP array indicates association with advancing disease. Mol Cytogenet 2013;6:59.[https://www.ncbi.nlm.nih.gov/pubmed/24341401]</ref><ref name=":37">Hahm C, Huh HJ, Mun YC, Seong CM, Chung WS, Huh J. Genomic aberrations of myeloproliferative and myelodysplastic/myeloproliferative neoplasms in chronic phase and during disease progression. Int J Lab Hematol 2015;37:181-9.[https://www.ncbi.nlm.nih.gov/pubmed/24845343]</ref>
|<ref name=":49">Singh NR, Morris CM, Koleth M, Wong K, Ward CM, Stevenson WS. Polyploidy in myelofibrosis: analysis by cytogenetic and SNP array indicates association with advancing disease. Mol Cytogenet 2013;6:59.[https://www.ncbi.nlm.nih.gov/pubmed/24341401]</ref><ref name=":37">Hahm C, Huh HJ, Mun YC, Seong CM, Chung WS, Huh J. Genomic aberrations of myeloproliferative and myelodysplastic/myeloproliferative neoplasms in chronic phase and during disease progression. Int J Lab Hematol 2015;37:181-9.[https://www.ncbi.nlm.nih.gov/pubmed/24845343]</ref>
|-
|-
|
|
|
|
|4q loss
|4q loss
|''TET2''
|''[[TET2]]''
|Prognostic for progression to AML
|Prognostic for progression to AML
|<ref name=":11" /><ref name=":38">Klampfl T, Harutyunyan A, Berg T, Gisslinger B, Schalling M, Bagienski K, et al. Genome integrity of myeloproliferative neoplasms in chronic phase and during disease progression. Blood 2011;118:167-76.[https://www.ncbi.nlm.nih.gov/pubmed/21531982]</ref>
|<ref name=":11" /><ref name=":38">Klampfl T, Harutyunyan A, Berg T, Gisslinger B, Schalling M, Bagienski K, et al. Genome integrity of myeloproliferative neoplasms in chronic phase and during disease progression. Blood 2011;118:167-76.[https://www.ncbi.nlm.nih.gov/pubmed/21531982]</ref>
|
|
|9p CN-LOH
|9p CN-LOH
|''JAK2''
|''[[JAK2]]''
|Predictive for JAK2 inhibitors; Prognostic for PV progression to MF
|Predictive for JAK2 inhibitors; Prognostic for PV progression to MF
|<ref name=":35">Rumi E, Harutyunyan A, Elena C, Pietra D, Klampfl T, Bagienski K, et al. Identification of genomic aberrations associated with disease transformation by means of high-resolution SNP array analysis in patients with myeloproliferative neoplasm. Am J Hematol 2011;86:974-9.[https://www.ncbi.nlm.nih.gov/pubmed/21953568]</ref><ref name=":34" /><ref name=":35" /><ref name=":37" /><ref name=":39">Stegelmann F, Bullinger L, Griesshammer M, Holzmann K, Habdank M, Kuhn S, et al. High-resolution single-nucleotide polymorphism array-profiling in myeloproliferative neoplasms identifies novel genomic aberrations. Haematologica 2010;95:666-9.[https://www.ncbi.nlm.nih.gov/pubmed/20015882]</ref>
|<ref name=":35">Rumi E, Harutyunyan A, Elena C, Pietra D, Klampfl T, Bagienski K, et al. Identification of genomic aberrations associated with disease transformation by means of high-resolution SNP array analysis in patients with myeloproliferative neoplasm. Am J Hematol 2011;86:974-9.[https://www.ncbi.nlm.nih.gov/pubmed/21953568]</ref><ref name=":34" /><ref name=":35" /><ref name=":37" /><ref name=":39">Stegelmann F, Bullinger L, Griesshammer M, Holzmann K, Habdank M, Kuhn S, et al. High-resolution single-nucleotide polymorphism array-profiling in myeloproliferative neoplasms identifies novel genomic aberrations. Haematologica 2010;95:666-9.[https://www.ncbi.nlm.nih.gov/pubmed/20015882]</ref>
|21-24%/NA
|21-24%/NA
|17p loss
|17p loss
|''TP53''
|''[[TP53]]''
|Recurrent, progression, associated with TKI resistance
|Recurrent, progression, associated with TKI resistance
|<ref name=":41">Nowak D, Ogawa S, Muschen M, Kato M, Kawamata N, Meixel A, et al. SNP array analysis of tyrosine kinase inhibitor-resistant chronic myeloid leukemia identifies heterogeneous secondary genomic alterations. Blood 2010;115:1049-53.[https://www.ncbi.nlm.nih.gov/pubmed/19965645]</ref><ref name=":42">Boultwood J, Perry J, Zaman R, Fernandez-Santamaria C, Littlewood T, Kusec R, et al. High-density single nucleotide polymorphism array analysis and ASXL1 gene mutation screening in chronic myeloid leukemia during disease progression. Leukemia 2010;24:1139-45.[https://www.ncbi.nlm.nih.gov/pubmed/20410925]</ref>
|<ref name=":41">Nowak D, Ogawa S, Muschen M, Kato M, Kawamata N, Meixel A, et al. SNP array analysis of tyrosine kinase inhibitor-resistant chronic myeloid leukemia identifies heterogeneous secondary genomic alterations. Blood 2010;115:1049-53.[https://www.ncbi.nlm.nih.gov/pubmed/19965645]</ref><ref name=":42">Boultwood J, Perry J, Zaman R, Fernandez-Santamaria C, Littlewood T, Kusec R, et al. High-density single nucleotide polymorphism array analysis and ASXL1 gene mutation screening in chronic myeloid leukemia during disease progression. Leukemia 2010;24:1139-45.[https://www.ncbi.nlm.nih.gov/pubmed/20410925]</ref>
|}
|}
'''Table 2.''' A comprehensive list of CNAs and CN-LOH of known or likely clinical significance in MDS detected by CMA testing
AA, Aplastic anemia; BMFS, Bone Marrow Failure Syndrome; MDS, Myelodysplastic Syndrome; MDS/MPN, Myelodysplastic/ myeloproliferative Neoplasm; MPN, Myeloproliferative Neoplasm; CML, Chronic Myelogeneous Leukemia; sAML, secondary AML; TGA, Total genomic aberration; TKI, tyrosine kinase inhibitors.
∗Recurrent indicates recurrent aberration with no established prognostic significance
'''Table 2 -''' '''A Comprehensive List of Copy Number Aberrations and CN-LOH of Known or Likely Clinical Significance in MDS Detected by CMA Testing (Literature Review).''' Table derived from Kanagal-Shawanna et al., 2018 [PMID 30377088] with permission from Cancer Genetics.
{| class="wikitable"
{| class="wikitable"
|'''Chromosome'''
|'''Chromosome'''
|Gain
|Gain
|1p36.33-p33
|1p36.33-p33
|''MPL''
|''[[MPL]]''
|Recurrent
|Recurrent
|3
|3
|CN-LOH
|CN-LOH
|1p
|1p
|''MPL''
|''[[MPL]]''
|Recurrent
|Recurrent
|2
|2
|CN-LOH
|CN-LOH
|2pter-2p13.3
|2pter-2p13.3
|''DNMT3A''
|''[[DNMT3A]]''
|Recurrent
|Recurrent
|2
|2
|CN-LOH
|CN-LOH
|3q21.3-qter
|3q21.3-qter
|''MECOM, GATA2''
|''[[MECOM]], [[GATA2]]''
|Recurrent
|Recurrent
|3
|3
|Loss
|Loss
|4q24
|4q24
|''TET2''
|''[[TET2]]''
|T***
|T***
|2
|2
|CN-LOH
|CN-LOH
|4q12-qter
|4q12-qter
|''TET2''
|''[[TET2]]''
|Recurrent
|Recurrent
|2
|2
|Loss
|Loss
|5q
|5q
|''RPS14''
|''[[RPS14]]''
|D, P (Good when isolated)
|D, P (Good when isolated)
|1
|1
|Loss
|Loss
|7q
|7q
|''EZH2, CUX1''
|''[[EZH2]], [[CUX1]]''
|D, P (Intermediate)
|D, P (Intermediate)
|1
|1
|CN-LOH
|CN-LOH
|7q21.11-qter
|7q21.11-qter
|''EZH2, CUX1''
|''[[EZH2]], [[CUX1]]''
|Recurrent
|Recurrent
|2
|2
|Gain
|Gain
|9p
|9p
|''JAK2''
|''[[JAK2]]''
|Recurrent
|Recurrent
|3
|3
|CN-LOH
|CN-LOH
|9pter-p24.2
|9pter-p24.2
|''JAK2''
|''[[JAK2]]''
|Recurrent
|Recurrent
|2
|2
|Loss
|Loss
|11q14.1-q24.3
|11q14.1-q24.3
|''CBL''
|''[[CBL]]''
|D, P (Very Good)
|D, P (Very Good)
|1
|1
|CN-LOH
|CN-LOH
|11q13.3-qter
|11q13.3-qter
|''CBL''
|''[[CBL]]''
|Recurrent
|Recurrent
|2
|2
|Gain (Trisomy and q-arm)
|Gain (Trisomy and q-arm)
|11 / 11q
|11 / 11q
|''CBL''
|''[[CBL]]''
|Recurrent
|Recurrent
|3
|3
|Loss
|Loss
|12p
|12p
|''ETV6''
|''[[ETV6]]''
|D, P (Good)
|D, P (Good)
|1
|1
|CN-LOH
|CN-LOH
|12pter-p11.23
|12pter-p11.23
|''ETV6''
|''[[ETV6]]''
|Recurrent
|Recurrent
|2
|2
|Loss
|Loss
|13q
|13q
|''RB1''
|''[[RB1]]''
|D, P (Intermediate)
|D, P (Intermediate)
|2
|2
|CN-LOH
|CN-LOH
|13q12.3-qter
|13q12.3-qter
|''FLT3, RB1''
|''[[FLT3]], [[RB1]]''
|Recurrent
|Recurrent
|3
|3
|CN-LOH
|CN-LOH
|14q24.2-qter
|14q24.2-qter
|''CHGA''
|''[[CHGA]]''
|Recurrent
|Recurrent
|3
|3
|Loss (Monosomy and q-arm)
|Loss (Monosomy and q-arm)
|16 / 16q
|16 / 16q
|''CDH1''
|''[[CDH1]]''
|Recurrent
|Recurrent
|3
|3
|CN-LOH
|CN-LOH
|16q22.1-qter
|16q22.1-qter
|''CDH1''
|''[[CDH1]]''
|Recurrent
|Recurrent
|3
|3
|Loss
|Loss
|17p
|17p
|''TP53''
|''[[TP53]]''
|P (Poor)
|P (Poor)
|1
|1
|CN-LOH
|CN-LOH
|17pter-p11.2
|17pter-p11.2
|''TP53''
|''[[TP53]]''
|Recurrent
|Recurrent
|2
|2
|Loss
|Loss
|17q11.2
|17q11.2
|''NF1''
|''[[NF1]]''
|Recurrent
|Recurrent
|3
|3
|CN-LOH
|CN-LOH
|17q11.2-qter
|17q11.2-qter
|''SRSF2, NF1''
|''[[SRSF2]], [[NF1]]''
|Recurrent
|Recurrent
|2
|2
|CN-LOH
|CN-LOH
|19pter-p13.11
|19pter-p13.11
|''DNMT1, PRDX2''
|''[[DNMT1]], [[PRDX2]]''
|Recurrent
|Recurrent
|3
|3
|Loss
|Loss
|19p13.13
|19p13.13
|''PRDX2''
|''[[PRDX2]]''
|Recurrent
|Recurrent
|3
|3
|Loss
|Loss
|20q
|20q
|''ASXL1''
|''[[ASXL1]]''
|P (Good)**
|P (Good)**
|1
|1
|CN-LOH
|CN-LOH
|20q11.21-qter
|20q11.21-qter
|''ASXL1''
|''[[ASXL1]]''
|Recurrent
|Recurrent
|2
|2
|Loss
|Loss
|21q22.12
|21q22.12
|''RUNX1''
|''[[RUNX1]]''
|D, P (Poor)
|D, P (Poor)
|2
|2
|CN-LOH
|CN-LOH
|21q21.1-qter
|21q21.1-qter
|''RUNX1'', ''U2AF1''
|''[[RUNX1]]'', ''[[U2AF1]]''
|Recurrent
|Recurrent
|2
|2
|CN-LOH
|CN-LOH
|22q11.23-qter
|22q11.23-qter
|''MN1, SF3A1, EP300''
|''[[MN1]], [[SF3A1]], [[EP300]]''
|Recurrent
|Recurrent
|3
|3
|<ref name=":3" /><ref name=":7" />
|<ref name=":3" /><ref name=":7" />
|}
|}
'''Table 3. ''' A comprehensive list of CNAs and CN-LOH of known or likely clinical significance in MDS/MPN detected by CMA testing
Legend: d- diagnostic significance; P-prognostic significance; T- therapeutic significance. Recurrent indicates recurrent aberration with no established prognostic significance.
∗ Clinical significance based on WHO classification using IPSS-R<ref>{{Cite journal|last=Greenberg|first=Peter L.|last2=Tuechler|first2=Heinz|last3=Schanz|first3=Julie|last4=Sanz|first4=Guillermo|last5=Garcia-Manero|first5=Guillermo|last6=Solé|first6=Francesc|last7=Bennett|first7=John M.|last8=Bowen|first8=David|last9=Fenaux|first9=Pierre|date=2012|title=Revised international prognostic scoring system for myelodysplastic syndromes|url=https://www.ncbi.nlm.nih.gov/pubmed/22740453|journal=Blood|volume=120|issue=12|pages=2454–2465|doi=10.1182/blood-2012-03-420489|issn=1528-0020|pmc=4425443|pmid=22740453}}</ref><ref>{{Cite journal|last=Schanz|first=Julie|last2=Tüchler|first2=Heinz|last3=Solé|first3=Francesc|last4=Mallo|first4=Mar|last5=Luño|first5=Elisa|last6=Cervera|first6=José|last7=Granada|first7=Isabel|last8=Hildebrandt|first8=Barbara|last9=Slovak|first9=Marilyn L.|date=2012|title=New comprehensive cytogenetic scoring system for primary myelodysplastic syndromes (MDS) and oligoblastic acute myeloid leukemia after MDS derived from an international database merge|url=https://www.ncbi.nlm.nih.gov/pubmed/22331955|journal=Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology|volume=30|issue=8|pages=820–829|doi=10.1200/JCO.2011.35.6394|issn=1527-7755|pmc=4874200|pmid=22331955}}</ref>.
<nowiki>**</nowiki> Isolated trisomy 8 or del(20q) are not diagnostic of MDS in the absence of morphologic findings of disease.
∗∗∗ Potential marker for responsiveness to hypomethylating agents or DNA methyltransferase inhibitors<ref name=":50">{{Cite journal|last=Bejar|first=Rafael|last2=Lord|first2=Allegra|last3=Stevenson|first3=Kristen|last4=Bar-Natan|first4=Michal|last5=Pérez-Ladaga|first5=Albert|last6=Zaneveld|first6=Jacques|last7=Wang|first7=Hui|last8=Caughey|first8=Bennett|last9=Stojanov|first9=Petar|date=2014|title=TET2 mutations predict response to hypomethylating agents in myelodysplastic syndrome patients|url=https://www.ncbi.nlm.nih.gov/pubmed/25224413|journal=Blood|volume=124|issue=17|pages=2705–2712|doi=10.1182/blood-2014-06-582809|issn=1528-0020|pmc=4208285|pmid=25224413}}</ref><ref name=":51">{{Cite journal|last=Traina|first=F.|last2=Visconte|first2=V.|last3=Elson|first3=P.|last4=Tabarroki|first4=A.|last5=Jankowska|first5=A. M.|last6=Hasrouni|first6=E.|last7=Sugimoto|first7=Y.|last8=Szpurka|first8=H.|last9=Makishima|first9=H.|date=2014|title=Impact of molecular mutations on treatment response to DNMT inhibitors in myelodysplasia and related neoplasms|url=https://www.ncbi.nlm.nih.gov/pubmed/24045501|journal=Leukemia|volume=28|issue=1|pages=78–87|doi=10.1038/leu.2013.269|issn=1476-5551|pmid=24045501}}</ref>.
'''Table 3''' '''-''' '''A Comprehensive List of Copy Number Aberrations and CN-LOH of Known or Likely Clinical Significance in MDS/MPN Detected by CMA Testing (Literature Review).''' Table derived from Kanagal-Shawanna et al., 2018 [PMID 30377088] with permission from Cancer Genetics.
{| class="wikitable"
{| class="wikitable"
|'''Chromosome'''
|'''Chromosome'''
|CN-LOH
|CN-LOH
|1p21.3
|1p21.3
|''MPL''
|''[[MPL]]''
|Recurrent
|Recurrent
|2
|2
|Loss
|Loss
|4q24
|4q24
|''TET2''
|''[[TET2]]''
|Recurrent<sup>**</sup>
|Recurrent<sup>**</sup>
|2
|2
|CN-LOH
|CN-LOH
|4q12.4-qter
|4q12.4-qter
|''TET2''
|''[[TET2]]''
|Recurrent
|Recurrent
|2
|2
|Loss (Monosomy and q-arm)
|Loss (Monosomy and q-arm)
|5 / 5q
|5 / 5q
|''RPS14''
|''[[RPS14]]''
|P (Intermediate)
|P (Intermediate)
|1
|1
|Loss
|Loss
|7q
|7q
|''EZH2, CUX1''
|''[[EZH2]], [[CUX1]]''
|P (Poor)
|P (Poor)
|1
|1
|CN-LOH
|CN-LOH
|7q21.11-qter
|7q21.11-qter
|''EZH2, CUX1''
|''[[EZH2]], [[CUX1]]''
|Recurrent
|Recurrent
|2
|2
|CN-LOH
|CN-LOH
|9pter-p13.3
|9pter-p13.3
|''JAK2''
|''[[JAK2]]''
|Recurrent
|Recurrent
|2
|2
|CN-LOH
|CN-LOH
|11q13.2-qter
|11q13.2-qter
|''CBL''
|''[[CBL]]''
|Recurrent
|Recurrent
|2
|2
|Loss
|Loss
|12p
|12p
|''ETV6''
|''[[ETV6]]''
|P (Intermediate)
|P (Intermediate)
|1
|1
|Loss
|Loss
|13q
|13q
|''RB1''
|''[[RB1]]''
|P (Intermediate)
|P (Intermediate)
|1
|1
|CN-LOH
|CN-LOH
|14q
|14q
|''CHGA''
|''[[CHGA]]''
|Recurrent
|Recurrent
|3
|3
|Loss
|Loss
|17p
|17p
|''TP53''
|''[[TP53]]''
|P (Poor)***
|P (Poor)***
|1
|1
|Loss
|Loss
|20q
|20q
|''ASXL1''
|''[[ASXL1]]''
|P (Intermediate)
|P (Intermediate)
|2
|2
|Gain
|Gain
|21q22.12
|21q22.12
|''RUNX1''
|''[[RUNX1]]''
|P (Intermediate)
|P (Intermediate)
|2
|2
|CN-LOH
|CN-LOH
|21q22-qter
|21q22-qter
|''RUNX1''
|''[[RUNX1]]''
|Recurrent
|Recurrent
|2
|2
|<ref name=":33" /><ref name=":5" />
|<ref name=":33" /><ref name=":5" />
|}
|}
Legend: d- diagnostic significance; P-prognostic significance; T- therapeutic significance.
MPN detected by CMA testing
Recurrent indicates recurrent aberration with no established significance.
∗ Clinical significance based on International MDS/MPN Working Group recommendations<ref>{{Cite journal|last=Mughal|first=Tariq I.|last2=Cross|first2=Nicholas C. P.|last3=Padron|first3=Eric|last4=Tiu|first4=Ramon V.|last5=Savona|first5=Michael|last6=Malcovati|first6=Luca|last7=Tibes|first7=Raoul|last8=Komrokji|first8=Rami S.|last9=Kiladjian|first9=Jean-Jacques|date=2015|title=An International MDS/MPN Working Group's perspective and recommendations on molecular pathogenesis, diagnosis and clinical characterization of myelodysplastic/myeloproliferative neoplasms|url=https://www.ncbi.nlm.nih.gov/pubmed/26341525|journal=Haematologica|volume=100|issue=9|pages=1117–1130|doi=10.3324/haematol.2014.114660|issn=1592-8721|pmc=4800699|pmid=26341525}}</ref>; No NCCN guidelines available. Low risk (normal, isolated –Y), Intermediate (others), High risk (+8, abnormal 7, complex).
∗∗ Potential marker for responsiveness to hypomethylating agents or DNA methyltransferase inhibitors<ref name=":50" /><ref name=":51" />.
∗∗∗ Haploinsufficiency of 17p as part of an isolated isochromosome may be a distinct disease entity with further increased risk of AML progression relative to 17p loss in a complex karyotype.
'''Table 4''' '''-''' '''A Comprehensive List of Copy Number Aberrations and CN-LOH of Known or Likely Clinical Significance in MPN Detected by CMA Testing (Literature Review).''' Table derived from Kanagal-Shawanna et al., 2018 [PMID 30377088] with permission from Cancer Genetics.
{| class="wikitable"
{| class="wikitable"
|Chromosome
|Chromosome
|CN-LOH
|CN-LOH
|1p21.3
|1p21.3
|''MPL''
|''[[MPL]]''
|Recurrent
|Recurrent
|2
|2
|Recurrent
|Recurrent
|2
|2
|<ref name=":35" /><ref name=":35" /><ref name=":37" />
|<ref name=":35" /><ref name=":49" /><ref name=":37" />
|-
|-
|4
|4
|Loss
|Loss
|4q24
|4q24
|''TET2''
|''[[TET2]]''
|Recurrent
|Recurrent
|2
|2
|Loss
|Loss
|5q
|5q
|''RPS14''
|''[[RPS14]]''
|P (Poor)
|P (Poor)
|1
|1
|Loss
|Loss
|6p23-22.3
|6p23-22.3
|''JARID2''
|''[[JARID2]]''
|Recurrent
|Recurrent
|3
|3
|Loss
|Loss
|7q
|7q
|''EZH2, CUX1''
|''[[EZH2]], [[CUX1]]''
|P (Poor)
|P (Poor)
|1
|1
|CN-LOH
|CN-LOH
|7q22.1-qter
|7q22.1-qter
|''EZH2, CUX1''
|''[[EZH2]], [[CUX1]]''
|Recurrent
|Recurrent
|2
|2
|Gain
|Gain
|9p
|9p
|''JAK2''
|''[[JAK2]]''
|Recurrent
|Recurrent
|2
|2
|<ref name=":35" /><ref name=":35" /><ref name=":37" />
|<ref name=":35" /><ref name=":49" /><ref name=":37" />
|-
|-
|9
|9
|CN-LOH
|CN-LOH
|9pter-p13.3
|9pter-p13.3
|''JAK2''
|''[[JAK2]]''
|Recurrent
|Recurrent
|2
|2
|<ref name=":35" /><ref name=":34" /><ref name=":35" /><ref name=":37" /><ref name=":39" />
|<ref name=":35" /><ref name=":34" /><ref name=":49" /><ref name=":37" /><ref name=":39" />
|-
|-
|9
|9
|Gain
|Gain
|9q34 (+Ph)
|9q34 (+Ph)
|''ABL1''
|''[[ABL1]]''
|Recurrent
|Recurrent
|1
|1
|CN-LOH
|CN-LOH
|11q13.4-q25
|11q13.4-q25
|''CBL''
|''[[CBL]]''
|Recurrent
|Recurrent
|2
|2
|<ref name=":35" /><ref name=":35" />
|<ref name=":35" /><ref name=":49" />
|-
|-
|12
|12
|Loss
|Loss
|12p13.3-p12.2
|12p13.3-p12.2
|''ETV6''
|''[[ETV6]]''
|P (Poor)
|P (Poor)
|1
|1
|Loss
|Loss
|13q
|13q
|''RB1''
|''[[RB1]]''
|Recurrent
|Recurrent
|1
|1
|CN-LOH
|CN-LOH
|14q
|14q
|''CHGA''
|''[[CHGA]]''
|Recurrent
|Recurrent
|3
|3
|<ref name=":35" /><ref name=":35" /><ref name=":37" /><ref name=":6" />
|<ref name=":35" /><ref name=":49" /><ref name=":37" /><ref name=":6" />
|-
|-
|17
|17
|Loss
|Loss
|17p
|17p
|''TP53''
|''[[TP53]]''
|P (Poor)
|P (Poor)
|1
|1
|Loss
|Loss
|20q
|20q
|''ASXL1''
|''[[ASXL1]]''
|Recurrent
|Recurrent
|1
|1
|Gain
|Gain
|22q11.2 (+Ph)
|22q11.2 (+Ph)
|''BCR''
|''[[BCR]]''
|Recurrent
|Recurrent
|1
|1
|<ref name=":41" />
|<ref name=":41" />
|}
|}
Legend: d- diagnostic significance; P-prognostic significance; T- therapeutic significance.
Recurrent indicates recurrent aberration with no established significance.
∗ Clinical significance based on NCCN guidelines<ref>{{Cite journal|last=Mesa|first=Ruben A.|last2=Jamieson|first2=Catriona|last3=Bhatia|first3=Ravi|last4=Deininger|first4=Michael W.|last5=Fletcher|first5=Christopher D.|last6=Gerds|first6=Aaron T.|last7=Gojo|first7=Ivana|last8=Gotlib|first8=Jason|last9=Gundabolu|first9=Krishna|date=2017|title=NCCN Guidelines Insights: Myeloproliferative Neoplasms, Version 2.2018|url=https://www.ncbi.nlm.nih.gov/pubmed/28982745|journal=Journal of the National Comprehensive Cancer Network: JNCCN|volume=15|issue=10|pages=1193–1207|doi=10.6004/jnccn.2017.0157|issn=1540-1413|pmid=28982745}}</ref>; For myelofibrosis, unfavorable [complex karyotype or sole or two abnormalities that include inv(3), 5/5q-, 7/7q-,+8, 11q23 rearrangement, 12p-, and (17q)].
<references />
<references />