Classification & Risk Stratification Prediction

Classification & Risk Stratification Prediction is available for cases created using Connected Insights v5.1+.

Overview

If the case disease is Acute Myeloid Leukemia or a subtype, Classification & Risk Stratification Prediction is provided on the Overview Tab.

APL with PML::RARA fusion prediction with decision tree

Classification and risk stratification predictions are based on WHO 2022 and ELN 2022 acute myeloid leukemia guidelines, respectively, focusing on Acute myeloid leukemia with defining genetic abnormalities.

Select a box to review how the evaluation was performed. For more information, refer to Decision Trees below.

Reporting

The report interpretation summary can be generated from the prediction results by clicking Report.

Generated interpretation summary text

Decision Trees

All variants described below must pass secondary analysis filters (VCF Filter = PASS).


APL with PML::RARA fusion

Classification

  • Blast count % ≥ 10

  • History of cytotoxic therapy exposure = No

  • Any of the following:

    • Detection of PML::RARA fusion in the Variants Tab

    • Detection of t(15;17)(q24;q21) in the User Determined Karyotype

If the above is met, the classification is predicted to be APL with PML::RARA fusion.

Risk Stratification

  • Detection of TP53 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Somatic origin (origin = somatic or unknown)

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • VAF ≥ 0.10 (10%)

If the above is met, the risk stratification is predicted to be Adverse. If not, then Intermediate.


AML with RUNX1::RUNX1T1 fusion

Classification

  • Blast count % ≥ 10

  • History of cytotoxic therapy exposure = No

  • Any of the following:

    • Detection of RUNX1::RUNX1T1 fusion in the Variants Tab

    • Detection of t(8;21)(q21.3;q22.1) in the User Determined Karyotype

The guideline specifies an outdated band 8q22 for RUNX1T1. It is now 8q21.3.

If the above is met, the classification is predicted to be AML with RUNX1::RUNX1T1 fusion.

Risk Stratification

  • Detection of TP53 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Somatic origin (origin = somatic or unknown)

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • VAF ≥ 0.10 (10%)

If the above is met, the risk stratification is predicted to be Adverse. If not, then Favorable.


AML with CBFB::MYH11 fusion

Classification

  • Blast count % ≥ 10

  • History of cytotoxic therapy exposure = No

  • Any of the following:

    • Detection of CBFB::MYH11 fusion in the Variants Tab

    • Detection of inv(16)(p13.1q22.1) in the User Determined Karyotype

    • Detection of t(16;16)(p13.1;q22.1) in the User Determined Karyotype

If the above is met, the classification is predicted to be AML with CBFB::MYH11 fusion.

Risk Stratification

  • Detection of TP53 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Somatic origin (origin = somatic or unknown)

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • VAF ≥ 0.10 (10%)

If the above is met, the risk stratification is predicted to be Adverse. If not, then Favorable.


AML with DEK::NUP214 fusion

Classification

  • Blast count % ≥ 10

  • History of cytotoxic therapy exposure = No

  • Any of the following:

    • Detection of DEK::NUP214 fusion in the Variants Tab

    • Detection of t(6;9)(p22.3;q34.1) in the User Determined Karyotype

If the above is met, the classification is predicted to be AML with DEK::NUP214 fusion.

Risk Stratification

Adverse


AML with RBM15::MRTFA fusion

Classification

  • Blast count % ≥ 10

  • History of cytotoxic therapy exposure = No

  • Any of the following:

    • Detection of RBM15::MRTFA fusion in the Variants Tab

    • Detection of t(1;22)(p13.3;q13.1) in the User Determined Karyotype

If the above is met, the classification is predicted to be AML with RBM15::MRTFA fusion.

Risk Stratification

  • Detection of TP53 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Somatic origin (origin = somatic or unknown)

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • VAF ≥ 0.10 (10%)

If the above is met, the risk stratification is predicted to be Adverse. If not, then Intermediate.


AML with BCR::ABL1 fusion

Classification

  • Blast count % ≥ 20

  • History of cytotoxic therapy exposure = No

  • Any of the following:

    • Detection of BCR::ABL1 fusion in the Variants Tab

    • Detection of t(9;22)(q34.1;q11.2) in the User Determined Karyotype

If the above is met, the classification is predicted to be AML with BCR::ABL1 fusion.

Risk Stratification

Adverse


AML with KMT2A rearrangement

Classification

  • Blast count % ≥ 10

  • History of cytotoxic therapy exposure = No

  • Detection of KMT2A structural variant in the Variants Tab

If the above is met, the classification is predicted to be AML with KMT2A rearrangement.

Risk Stratification

  • Detection of TP53 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Somatic origin (origin = somatic or unknown)

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • VAF ≥ 0.10 (10%)

If the above is met, the risk stratification is predicted to be Adverse. If not, then continue below.

  • Any of the following:

    • Detection of MLLT3::KMT2A in the Variants Tab

    • Detection of t(9;11)(p21.3;q23.3) in the User Determined Karyotype

    • Detection of KMT2A partial tandem duplication in the Variants Tab

If the above is met, the risk stratification is predicted to be Intermediate. If not, then Adverse.


AML with MECOM rearrangement

Classification

  • Blast count % ≥ 10

  • History of cytotoxic therapy exposure = No

  • Any of the following:

    • Detection of MECOM structural variant in the Variants Tab

    • Detection of inv(3)(q21.3q26.2) in the User Determined Karyotype

    • Detection of t(3;3)(q21;q26) in the User Determined Karyotype

    • Detection of t(3;21)(q26.2;q22) in the User Determined Karyotype

    • Detection of t(3;12)(q26.2;p13) in the User Determined Karyotype

If the above is met, the classification is predicted to be AML with MECOM rearragement.

Risk Stratification

Adverse


AML with NUP98 rearrangement

Classification

  • Blast count % ≥ 10

  • History of cytotoxic therapy exposure = No

  • Any of the following:

    • Detection of NUP98 structural variant in the Variants Tab

    • Detection of t(5;11)(q35.2;p15.4) in the User Determined Karyotype

    • Detection of t(11;12)(p15.4;p13.3) in the User Determined Karyotype

If the above is met, the classification is predicted to be AML with NUP98 rearrangement.

Risk Stratification

  • Detection of TP53 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Somatic origin (origin = somatic or unknown)

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • VAF ≥ 0.10 (10%)

If the above is met, the risk stratification is predicted to be Adverse. If not, then Intermediate.


AML with NPM1 mutation

Classification

  • Blast count % ≥ 10

  • History of cytotoxic therapy exposure = No

  • Detection of NPM1 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

If the above is met, the classification is predicted to be AML with NPM1 mutation.

Risk Stratification

  • Any of the following:

    • Detection of TP53 variant in the Variants Tab with the following characteristics:

      • Small variant

      • Somatic origin (origin = somatic or unknown)

      • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

      • VAF ≥ 0.10 (10%)

    • Detection of DEK::NUP214 fusion in the Variants Tab

    • Detection of t(6;9)(p22.3;q34.1) in the User Determined Karyotype

    • Detection of KMT2A structural variant without MLLT3 fusion partner in the Variants Tab

    • Detection of BCR::ABL1 fusion in the Variants Tab

    • Detection of t(9;22)(q34.1;q11.2) in the User Determined Karyotype

    • Detection of KAT6A::CREBBP fusion in the Variants Tab

    • Detection of t(8;16)(p11.2;p13.3) in the User Determined Karyotype

    • Detection of MECOM structural variant in the Variants Tab

    • Detection of inv(3)(q21.3q26.2) in the User Determined Karyotype

    • Detection of t(3;3)(q21;q26) in the User Determined Karyotype

    • Detection of t(3;21)(q26.2;q22) in the User Determined Karyotype

    • Detection of t(3;12)(q26.2;p13) in the User Determined Karyotype

    • Detection of monosomy 5 in the User Determined Karyotype or Variants Tab

    • Detection of 5q deletion in the User Determined Karyotype, or Variants Tab with length ≥ 5 Mbp

    • Detection of monosomy 7 in the User Determined Karyotype or Variants Tab

    • Detection of monosomy 17 in the User Determined Karyotype or Variants Tab

    • Detection of 17p deletion in the User Determined Karyotype, or Variants Tab with length ≥ 5 Mbp

    • Detection of complex karyotype in the User Determined Karyotype or Variants Tab

    • Detection of monosomal karyotype in the User Determined Karyotype or Variants Tab

If the above is met, the risk stratification is predicted to be Adverse. If not, then continue below.

  • Detection of FLT3 internal tandem duplication in the Variants Tab

If the above is met, the risk stratification is predicted to be Intermediate. If not, then Favorable.


AML with CEBPA mutation

Classification

  • None of the classifications above should be met.

  • Blast count % ≥ 20

  • History of cytotoxic therapy exposure = No

  • Any of the following:

    • Detection of 2 CEBPA variants in the Variants Tab with the following characteristics:

      • Small variant

      • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • Detection of CEBPA variant in the Variants Tab with the following characteristics:

      • Small variant

      • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

      • Located in the bZIP domain

If the above is met, the classification is predicted to be AML with CEBPA mutation.

Risk Stratification

  • Detection of TP53 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Somatic origin (origin = somatic or unknown)

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • VAF ≥ 0.10 (10%)

If the above is met, the risk stratification is predicted to be Adverse. If not, then continue below.

  • Detection of CEBPA variant in the Variants Tab with the following characteristics:

    • Small variant

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • In-frame (not a frameshift variant)

If the above is met, the risk stratification is predicted to be Favorable. If not, then Intermediate.


AML with other defined genetic alterations

Classification

  • None of the classifications above should be met.

  • Blast count % ≥ 20

  • History of cytotoxic therapy exposure = No

  • Any of the following:

    • Detection of CBFA2T3::GLIS2 fusion in the Variants Tab

    • Detection of inv(16)(p13q24) in the User Determined Karyotype

    • Detection of KAT6A::CREBBP fusion in the Variants Tab

    • Detection of t(8;16)(p11.2;p13.3) in the User Determined Karyotype

    • Detection of FUS::ERG fusion in the Variants Tab

    • Detection of t(16;21)(p11;q22) in the User Determined Karyotype

    • Detection of MNX1::ETV6 fusion in the Variants Tab

    • Detection of t(7;12)(q36;p13) in the User Determined Karyotype

    • Detection of NPM1::MLF1 fusion in the Variants Tab

    • Detection of t(3;5)(q25;q35) in the User Determined Karyotype

If the above is met, the classification is predicted to be AML with other defined genetic alterations.

Risk Stratification

  • Detection of TP53 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Somatic origin (origin = somatic or unknown)

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • VAF ≥ 0.10 (10%)

If the above is met, the risk stratification is predicted to be Adverse. If not, then continue below.

  • Any of the following:

    • Detection of KAT6A::CREBBP fusion in the Variants Tab

    • Detection of t(8;16)(p11.2;p13.3) in the User Determined Karyotype

If the above is met, the risk stratification is predicted to be Adverse. If not, then Intermediate.


Classification

  • None of the classifications above should be met.

  • Blast count % ≥ 20

  • History of cytotoxic therapy exposure = No

  • Any of the following:

    • History of myelodysplastic syndrome = Yes

    • Both of the following:

      • History of myelodysplastic syndrome = Yes

      • History of myeloproliferative neoplasm = Yes

    • Detection of complex karyotype in the User Determined Karyotype or Variants Tab

    • Detection of 5q deletion in the User Determined Karyotype, or Variants Tab with length ≥ 5 Mbp

    • Detection of monosomy 7 in the User Determined Karyotype or Variants Tab

    • Detection of 11q deletion in the User Determined Karyotype, or Variants Tab with length ≥ 5 Mbp

    • Detection of 12p deletion in the User Determined Karyotype, or Variants Tab with length ≥ 5 Mbp

    • Detection of monosomy 13 in the User Determined Karyotype or Variants Tab

    • Detection of 17p deletion in the User Determined Karyotype, or Variants Tab with length ≥ 5 Mbp

    • Detection of isochromosome 17q in the User Determined Karyotype

    • Detection of idic(X)(q13) in the User Determined Karyotype

    • Detection of ASXL1 variant in the Variants Tab with the following characteristics:

      • Small variant

      • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • Detection of BCOR variant in the Variants Tab with the following characteristics:

      • Small variant

      • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • Detection of EZH2 variant in the Variants Tab with the following characteristics:

      • Small variant

      • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • Detection of SF3B1 variant in the Variants Tab with the following characteristics:

      • Small variant

      • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • Detection of SRSF2 variant in the Variants Tab with the following characteristics:

      • Small variant

      • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • Detection of STAG2 variant in the Variants Tab with the following characteristics:

      • Small variant

      • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • Detection of U2AF1 variant in the Variants Tab with the following characteristics:

      • Small variant

      • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • Detection of ZRSR2 variant in the Variants Tab with the following characteristics:

      • Small variant

      • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

If the above is met, the classification is predicted to be AML, myelodysplasia-related.

Risk Stratification

Any of the following:

  • Detection of TP53 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Somatic origin (origin = somatic or unknown)

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

    • VAF ≥ 0.10 (10%)

  • Detection of monosomy 5 in the User Determined Karyotype or Variants Tab

  • Detection of 5q deletion in the User Determined Karyotype, or Variants Tab with length ≥ 5 Mbp

  • Detection of monosomy 7 in the User Determined Karyotype or Variants Tab

  • Detection of monosomy 17 in the User Determined Karyotype or Variants Tab

  • Detection of 17p deletion in the User Determined Karyotype, or Variants Tab with length ≥ 5 Mbp

  • Detection of complex karyotype in the User Determined Karyotype or Variants Tab

  • Detection of monosomal karyotype in the User Determined Karyotype or Variants Tab

  • Detection of ASXL1 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

  • Detection of BCOR variant in the Variants Tab with the following characteristics:

    • Small variant

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

  • Detection of EZH2 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

  • Detection of SF3B1 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

  • Detection of SRSF2 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

  • Detection of STAG2 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

  • Detection of U2AF1 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

  • Detection of ZRSR2 variant in the Variants Tab with the following characteristics:

    • Small variant

    • Oncogenic or likely oncogenic (as indicated by a knowledge base biological classification or oncogenicity prediction)

If the above is met, the risk stratification is predicted to be Adverse. If not, then Intermediate.


Definitions

Complex Karyotype

According to WHO/ISCN: ≥ 3 abnormalities, where abnormalities are counted as follows:

  • Only clonal abnormalities are counted; abnormalities present in only 1 metaphase are ignored.

  • Numerical gains and losses, simple and complex balanced translocations, unbalanced aberrations involving one chromosome, as well as multiplication of a complete chromosome set are counted as one abnormality.

  • Unbalanced aberrations involving two or more chromosomes, tetrasomy of same chromosome, triplication or quadruplication, as well as isoderivative chromosomes, are counted as 2 abnormalities.

  • Constitutional abnormalities are not counted.

  • In case of multiple clones (subclones or independent clones), chromosome abnormalities in each clone/subclone are counted separately and the number of chromosomal abnormalities is defined by the clone with the highest abnormalities.

  • For composite karyotypes, clonal chromosomal aberrations are counted in metaphases with the highest number of abnormalities.

Monosomal Karyotype

According to ELN: Presence of two or more distinct monosomies (excluding loss of X or Y), or one single autosomal monosomy in combination with at least one structural chromosome abnormality.

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