Chromosomal Microarray, Hematologic Malignancy, ClariSure Oligo-SNP

Chromosomal Microarray, Hematologic Malignancy, ClariSure Oligo-SNP

This test is used to establish the presence of a clonal abnormality and to assess prognosis and monitor disease progression in various hematologic malignancies.

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Chromosomal Microarray, Hematologic Malignancy, ClariSure<span class="super-script">®</span> Oligo-SNP

Test Summary

 

Chromosomal Microarray, Hematologic Malignancy, ClariSure® Oligo-SNP 

Test Code: 90961

 

Clinical use

  • Establish presence of a clonal abnormality when myeloid neoplasm, such as myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), or myeloproliferative neoplasm (MPN), is suspected and conventional cytogenetic (CC) studies are normal or failed
  • Assess genomic risk stratification for patients with hematologic malignancies
  • Monitor disease evolution and clonal progression in hematologic malignancies

Clinical background

The presence of multiple genomic imbalances (genomic complexity) is associated with disease progression and reduced survival in patients with various hematologic malignancies, including MDS,1,2 AML,3–5 chronic lymphocytic leukemia,4,6 diffuse large B-cell lymphoma,7,8 acute lymphoblastic leukemia (ALL),9 and several others.10–14 Acquisition of new chromosomal abnormalities over the course of the disease (clonal evolution) is also associated with unfavorable prognosis in these conditions.

The oligonucleotide-single nucleotide–polymorphism (oligo-SNP) array is a genome-wide DNA assay that detects deletions and duplications at high resolution as well as allelic imbalance. Oligo-SNP is complementary to CC analysis (ie, karyotyping) and fluorescence in situ hybridization (FISH). CC and oligo-SNP testing are better suited for detecting unknown abnormalities than FISH, which is limited to probing specific chromosomal regions. Oligo-SNP array is especially useful when karyotyping fails (eg, when there is no or insufficient growth in cell culture).

Oligo-SNP resolution for detecting unbalanced genomic abnormalities is greater than that of CC analysis; however, oligo-SNP testing cannot detect any balanced rearrangements such as translocations and inversions. Oligo-SNP complements CC by defining cryptic lesions and genomic complexity, while CC detects balanced events and overall karyotype architecture. CC or FISH should be used to detect balanced abnormalities that have diagnostic or prognostic significance. Both FISH and oligo-SNP testing can detect cryptic dosage genomic alterations not identified by karyotyping.9,15

By detecting genomic gains and losses throughout the genome, the Chromosomal Microarray, Hematologic Malignancy, ClariSure® Oligo-SNP (test code 90961) is well suited to detect and characterize genomic complexity characteristic of leukemia, lymphoma, MDS, or MPN. This genomic complexity can be used to stratify risk associated with malignancies such as high-grade B-cell lymphoma with 11q aberration, ALL with masked hypodiploidy, and allelic state of TP53 mutation (monoallelic vs biallelic).3,8,13,16,17 Furthermore, the test can be used to monitor increases in the number of genomic imbalances over time that are associated with disease progression.9

Individuals suitable for testing

  • Individuals suspected of having leukemia, lymphoma, MDS, or MPN especially after normal or failed CC and/or negative FISH results
  • Patients with leukemia, lymphoma, MDS, or MPN who are being evaluated for disease progression

Method

  • DNA extraction from cultured cells, blood, or bone marrow and digestion by restriction enzymes
  • Polymerase chain reaction (PCR) amplification of digested DNA
  • Hybridization of amplified products to oligo-SNP microarray
  • ˜750,000 SNP probes designed to detect copy number neutral events, eg, loss of heterozygosity (LOH) and copy number variations (CNVs)
  • ˜1.9 million copy number probes to detect CNVs
  • Microarray analysis: resolution set at >50 kb for copy number loss, >200 kb for copy number gain, and 10 Mb for segments of homozygosity
  • Results reported by a board-certified geneticist: International System for Human Cytogenomic Nomenclature (ISCN)18 description of any genomic abnormality detected and clinical interpretation (CNVs known to have no phenotypic consequence not reported)

Interpretive information

In general, an increased number of unbalanced genomic abnormalities is associated with disease progression and unfavorable prognosis (ie, reduced survival). For patient-specific interpretive information, refer to the test report. Test reports will incorporate published clinical correlation data when available. Test results should be interpreted in conjunction with clinical and laboratory findings that may include CC and/or FISH test results.

Oligo-SNP testing does not detect balanced polyploidy, balanced rearrangements, low-level mosaicism, or dosage abnormalities that are not represented in the array. Also, false-negative results may occur when a low percentage of abnormal cells are in the specimen. Thus, negative results do not completely rule out the possibility of dosage genomic alterations.

Additional assistance in interpretation of results is available from our genomic science specialists by calling 1.866.GENE.INFO (1.866.436.3463).

References

  1. Shahjahani M, Hadad EH, Azizidoost S, et al. Complex karyotype in myelodysplastic syndromes: diagnostic procedure and prognostic susceptibility. Oncol Rev. 2018;13(1):389. doi:10.4081/oncol.2019.389
  2. National Comprehensive Cancer Network® Clinical Practice Guidelines in Oncology (NCCN Guidelines®). Myelodysplastic syndromes version1.2026. Published October 9, 2025. Accessed October 31, 2025. http://www.nccn.org
  3. Döhner H, Wei AH, Appelbaum FR, et al. Diagnosis and management of AML in adults: 2022 ELN Recommendations from an International Expert Panel. Blood. 2022;140(12):1345-1377. doi:10.1182/blood.2022016867
  4. Song J, Shao H. SNP array in hematopoietic neoplasms: a review. Microarrays. 2015;5(1):0001. doi:10.3390/microarrays5010001
  5. National Comprehensive Cancer Network® Clinical Practice Guidelines in Oncology (NCCN Guidelines®). Acute myeloid leukemia version2.2026. Published October 2, 2025. Accessed October 31, 2025. http://www.nccn.org
  6. Goergen E, Al-Sawaf O. The prognostic significance of genomic complexity in patients with CLL. Leuk Lymphoma. 2024;65(7):873-881. doi:10.1080/10428194.2024.2333448
  7. Ma C, Siddiqi IN, Xie Y, et al. Genomic complexity in diffuse large B-cell lymphoma is associated with p53 expression and inferior survival. Blood. 2014;124(21):3023. doi:10.1182/blood.v124.21.3023.3023
  8. Bernard E, Tuechler H, Greenberg PL, et al. Molecular international prognostic scoring system for myelodysplastic syndromes. NEJM Évid. 2022;1(7):EVIDoa2200008. doi:10.1056/evidoa2200008
  9. Simons A, Sikkema-Raddatz B, Leeuw N de, et al. Genome-wide arrays in routine diagnostics of hematological malignancies. Hum Mutat. 2012;33(6):941-948. doi:10.1002/humu.22057
  10. Sethi S, Epstein-Peterson Z, Kumar A, et al. Current knowledge in genetics, molecular diagnostic tools, and treatments for mantle cell lymphomas. Front Oncol. 2021;11:739441. doi:10.3389/fonc.2021.739441
  11. Shao L, Akkari Y, Cooley LD, et al. Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2021;23(10):1818-1829. doi:10.1038/s41436-021-01214-w
  12. Wang C, Tang J, Tong K, et al. Chromosomal microarray analysis versus noninvasive prenatal testing in fetuses with increased nuchal translucency. J Hum Genet. 2022;67(9):533-539. doi:10.1038/s10038-022-01041-0
  13. Kurz KS, Ott M, Kalmbach S, et al. Large B-cell lymphomas in the 5th Edition of the WHO-Classification of Haematolymphoid Neoplasms—updated classification and new concepts. Cancers. 2023;15(8):2285. doi:10.3390/cancers15082285
  14. Akkari Y, Baughn LB, Kim A, et al. Section E6.1–6.6 of the American College of Medical Genetics and Genomics (ACMG) Technical Laboratory Standards: cytogenomic studies of acquired chromosomal abnormalities in neoplastic blood, bone marrow, and lymph nodes. Genet Med. 2024;26(4):101054. doi:10.1016/j.gim.2023.101054
  15. Ptashkin RN, Ewalt MD, Jayakumaran G, et al. Enhanced clinical assessment of hematologic malignancies through routine paired tumor and normal sequencing. Nat Commun. 2023;14(1):6895. doi:10.1038/s41467-023-42585-9
  16. National Comprehensive Cancer Network® Clinical Practice Guidelines in Oncology (NCCN Guidelines®). B-cell lymphomas v3.2025. Published August 25, 2025. Accessed November 3, 2025. http://www.nccn.org
  17. Arber DA, Orazi A, Hasserjian RP, et al. International Consensus Classification of Myeloid Neoplasms and Acute Leukemias: integrating morphologic, clinical, and genomic data. Blood. 2022;140(11):1200-1228. doi:10.1182/blood.2022015850
  18. Shaffer LG, Slovak ML, Campbell LJ. ISCN 2009: An International System for Human Cytogenetic Nomenclature (2009). Karger; 2009.

Content reviewed 11/2025

top of page

This test is used to establish the presence of a clonal abnormality and to assess prognosis and monitor disease progression in various hematologic malignancies.

Test Guide List

Chromosomal Microarray, Hematologic Malignancy, ClariSure<span class="super-script">®</span> Oligo-SNP

Test Summary

 

Chromosomal Microarray, Hematologic Malignancy, ClariSure® Oligo-SNP 

Test Code: 90961

 

Clinical use

  • Establish presence of a clonal abnormality when myeloid neoplasm, such as myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), or myeloproliferative neoplasm (MPN), is suspected and conventional cytogenetic (CC) studies are normal or failed
  • Assess genomic risk stratification for patients with hematologic malignancies
  • Monitor disease evolution and clonal progression in hematologic malignancies

Clinical background

The presence of multiple genomic imbalances (genomic complexity) is associated with disease progression and reduced survival in patients with various hematologic malignancies, including MDS,1,2 AML,3–5 chronic lymphocytic leukemia,4,6 diffuse large B-cell lymphoma,7,8 acute lymphoblastic leukemia (ALL),9 and several others.10–14 Acquisition of new chromosomal abnormalities over the course of the disease (clonal evolution) is also associated with unfavorable prognosis in these conditions.

The oligonucleotide-single nucleotide–polymorphism (oligo-SNP) array is a genome-wide DNA assay that detects deletions and duplications at high resolution as well as allelic imbalance. Oligo-SNP is complementary to CC analysis (ie, karyotyping) and fluorescence in situ hybridization (FISH). CC and oligo-SNP testing are better suited for detecting unknown abnormalities than FISH, which is limited to probing specific chromosomal regions. Oligo-SNP array is especially useful when karyotyping fails (eg, when there is no or insufficient growth in cell culture).

Oligo-SNP resolution for detecting unbalanced genomic abnormalities is greater than that of CC analysis; however, oligo-SNP testing cannot detect any balanced rearrangements such as translocations and inversions. Oligo-SNP complements CC by defining cryptic lesions and genomic complexity, while CC detects balanced events and overall karyotype architecture. CC or FISH should be used to detect balanced abnormalities that have diagnostic or prognostic significance. Both FISH and oligo-SNP testing can detect cryptic dosage genomic alterations not identified by karyotyping.9,15

By detecting genomic gains and losses throughout the genome, the Chromosomal Microarray, Hematologic Malignancy, ClariSure® Oligo-SNP (test code 90961) is well suited to detect and characterize genomic complexity characteristic of leukemia, lymphoma, MDS, or MPN. This genomic complexity can be used to stratify risk associated with malignancies such as high-grade B-cell lymphoma with 11q aberration, ALL with masked hypodiploidy, and allelic state of TP53 mutation (monoallelic vs biallelic).3,8,13,16,17 Furthermore, the test can be used to monitor increases in the number of genomic imbalances over time that are associated with disease progression.9

Individuals suitable for testing

  • Individuals suspected of having leukemia, lymphoma, MDS, or MPN especially after normal or failed CC and/or negative FISH results
  • Patients with leukemia, lymphoma, MDS, or MPN who are being evaluated for disease progression

Method

  • DNA extraction from cultured cells, blood, or bone marrow and digestion by restriction enzymes
  • Polymerase chain reaction (PCR) amplification of digested DNA
  • Hybridization of amplified products to oligo-SNP microarray
  • ˜750,000 SNP probes designed to detect copy number neutral events, eg, loss of heterozygosity (LOH) and copy number variations (CNVs)
  • ˜1.9 million copy number probes to detect CNVs
  • Microarray analysis: resolution set at >50 kb for copy number loss, >200 kb for copy number gain, and 10 Mb for segments of homozygosity
  • Results reported by a board-certified geneticist: International System for Human Cytogenomic Nomenclature (ISCN)18 description of any genomic abnormality detected and clinical interpretation (CNVs known to have no phenotypic consequence not reported)

Interpretive information

In general, an increased number of unbalanced genomic abnormalities is associated with disease progression and unfavorable prognosis (ie, reduced survival). For patient-specific interpretive information, refer to the test report. Test reports will incorporate published clinical correlation data when available. Test results should be interpreted in conjunction with clinical and laboratory findings that may include CC and/or FISH test results.

Oligo-SNP testing does not detect balanced polyploidy, balanced rearrangements, low-level mosaicism, or dosage abnormalities that are not represented in the array. Also, false-negative results may occur when a low percentage of abnormal cells are in the specimen. Thus, negative results do not completely rule out the possibility of dosage genomic alterations.

Additional assistance in interpretation of results is available from our genomic science specialists by calling 1.866.GENE.INFO (1.866.436.3463).

References

  1. Shahjahani M, Hadad EH, Azizidoost S, et al. Complex karyotype in myelodysplastic syndromes: diagnostic procedure and prognostic susceptibility. Oncol Rev. 2018;13(1):389. doi:10.4081/oncol.2019.389
  2. National Comprehensive Cancer Network® Clinical Practice Guidelines in Oncology (NCCN Guidelines®). Myelodysplastic syndromes version1.2026. Published October 9, 2025. Accessed October 31, 2025. http://www.nccn.org
  3. Döhner H, Wei AH, Appelbaum FR, et al. Diagnosis and management of AML in adults: 2022 ELN Recommendations from an International Expert Panel. Blood. 2022;140(12):1345-1377. doi:10.1182/blood.2022016867
  4. Song J, Shao H. SNP array in hematopoietic neoplasms: a review. Microarrays. 2015;5(1):0001. doi:10.3390/microarrays5010001
  5. National Comprehensive Cancer Network® Clinical Practice Guidelines in Oncology (NCCN Guidelines®). Acute myeloid leukemia version2.2026. Published October 2, 2025. Accessed October 31, 2025. http://www.nccn.org
  6. Goergen E, Al-Sawaf O. The prognostic significance of genomic complexity in patients with CLL. Leuk Lymphoma. 2024;65(7):873-881. doi:10.1080/10428194.2024.2333448
  7. Ma C, Siddiqi IN, Xie Y, et al. Genomic complexity in diffuse large B-cell lymphoma is associated with p53 expression and inferior survival. Blood. 2014;124(21):3023. doi:10.1182/blood.v124.21.3023.3023
  8. Bernard E, Tuechler H, Greenberg PL, et al. Molecular international prognostic scoring system for myelodysplastic syndromes. NEJM Évid. 2022;1(7):EVIDoa2200008. doi:10.1056/evidoa2200008
  9. Simons A, Sikkema-Raddatz B, Leeuw N de, et al. Genome-wide arrays in routine diagnostics of hematological malignancies. Hum Mutat. 2012;33(6):941-948. doi:10.1002/humu.22057
  10. Sethi S, Epstein-Peterson Z, Kumar A, et al. Current knowledge in genetics, molecular diagnostic tools, and treatments for mantle cell lymphomas. Front Oncol. 2021;11:739441. doi:10.3389/fonc.2021.739441
  11. Shao L, Akkari Y, Cooley LD, et al. Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2021;23(10):1818-1829. doi:10.1038/s41436-021-01214-w
  12. Wang C, Tang J, Tong K, et al. Chromosomal microarray analysis versus noninvasive prenatal testing in fetuses with increased nuchal translucency. J Hum Genet. 2022;67(9):533-539. doi:10.1038/s10038-022-01041-0
  13. Kurz KS, Ott M, Kalmbach S, et al. Large B-cell lymphomas in the 5th Edition of the WHO-Classification of Haematolymphoid Neoplasms—updated classification and new concepts. Cancers. 2023;15(8):2285. doi:10.3390/cancers15082285
  14. Akkari Y, Baughn LB, Kim A, et al. Section E6.1–6.6 of the American College of Medical Genetics and Genomics (ACMG) Technical Laboratory Standards: cytogenomic studies of acquired chromosomal abnormalities in neoplastic blood, bone marrow, and lymph nodes. Genet Med. 2024;26(4):101054. doi:10.1016/j.gim.2023.101054
  15. Ptashkin RN, Ewalt MD, Jayakumaran G, et al. Enhanced clinical assessment of hematologic malignancies through routine paired tumor and normal sequencing. Nat Commun. 2023;14(1):6895. doi:10.1038/s41467-023-42585-9
  16. National Comprehensive Cancer Network® Clinical Practice Guidelines in Oncology (NCCN Guidelines®). B-cell lymphomas v3.2025. Published August 25, 2025. Accessed November 3, 2025. http://www.nccn.org
  17. Arber DA, Orazi A, Hasserjian RP, et al. International Consensus Classification of Myeloid Neoplasms and Acute Leukemias: integrating morphologic, clinical, and genomic data. Blood. 2022;140(11):1200-1228. doi:10.1182/blood.2022015850
  18. Shaffer LG, Slovak ML, Campbell LJ. ISCN 2009: An International System for Human Cytogenetic Nomenclature (2009). Karger; 2009.

Content reviewed 11/2025

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