Myeloid Malignancies Mutation and Copy Number Variation Panel by Next Generation Sequencing

Content Review: August 2023 Last Update:

For more information on ARUP’s AML panels, which include some of the genes in this panel specific to AML, refer to the Acute Myeloid Leukemia Mutation Panel by Next Generation Sequencing and Rapid Acute Myeloid Leukemia Targeted Therapy Mutation Panel Test Fact Sheets.

For more information on ARUP’s genomic microarray test offerings in oncology, refer to the Cytogenomic Microarray - Oncology Test Fact Sheet.

Myeloid malignancies are clonal disorders of hematopoietic stem and progenitor cells that include myelodysplastic syndromes (MDSs), myeloproliferative neoplasms (MPNs), myelodysplastic/myeloproliferative neoplasms (MDS/MPNs), acute myeloid leukemia (AML), and others. Recent studies have identified recurrently mutated genes with diagnostic, prognostic, and therapeutic impact in myeloid malignancies. The presence of certain variants may inform clinical management.

ARUP’s Myeloid Malignancies Mutation and Copy Number Variation Panel by Next Generation Sequencing (3016621) uses massively parallel sequencing (MPS; also known as next generation sequencing [NGS]) to detect molecular changes (single nucleotide variants [SNVs], small insertions and deletions), copy number variants (CNVs) for the targeted genes, and terminal copy number-neutral loss of heterozygosity (CN-LOH). Myeloid Malignancies Mutation Panel by Next Generation Sequencing (2011117) uses massively parallel sequencing to detect molecular changes including SNVs and small insertions and deletions but does not detect CNVs or CN-LOH. Because these panels overlap, they should not be concurrently ordered. If both panels are ordered on the same specimen, 2011117 will be canceled.

These tests are more cost-effective than multiple single gene tests for the detection of somatic variants in myeloid malignancies and can be used to complement the morphologic and cytogenetic workup of myeloid malignancies.

Disease Overview

Diagnostic, Prognostic, and Treatment Issues

  • Targets in this panel are relevant across the spectrum of myeloid malignancies.
  • Identification of one or more clonal genetic abnormalities, variants, or patterns of variants may aid in establishing the diagnosis and classification, prognosis, and clinical management of myeloid malignancies.

Genetics

Genes Tested

ANKRD26, ASXL1, ASXL2, BCOR, BCORL1, BRAF, CALR, CBL, CBLB, CEBPA, CSF3R, CUX1, DDX41, DNMT1, DNMT3A, ELANE, ETNK1, ETV6, EZH2, FBXW7, FLT3, GATA1, GATA2, GNAS, HNRNPK, IDH1, IDH2, IL7R, JAK1, JAK2, JAK3, KDM6A, KIT, KMT2A, KRAS, LUC7L2, MPL, NOTCH1, NPM1, NRAS, NSD1, PHF6, PIGA, PPM1D, PRPF40B, PRPF8, PTPN11, RAD21, RUNX1, SAMD9, SAMD9L, SETBP1, SF3B1, SH2B3, SMC1A, SMC3, SRSF2, STAG2, STAT3, STAT5B, SUZ12, TET2, TP53, U2AF1, U2AF2, UBA1, WT1, ZRSR2

For some genes, one or more exons of the preferred transcript are not covered by sequencing for the indicated gene. Refer to the Genes Tested table below for full list of targeted regions and exclusions.

Test Interpretation

Results

  • Variant classifications:
    • Tier 1: Molecular mutations, CNVs, and CN-LOH with known clinical significance in hematologic malignancies
    • Tier 2: Variants of unknown clinical significance in hematologic malignancies
    • Clinical significance in hematologic malignancies will be described, if known.

Reported Variants

  Myeloid Malignancies Mutation and Copy Number Variation Panel by Next Generation Sequencing (3016621) Myeloid Malignancies Mutation Panel by Next Generation Sequencing (2011117)

Reported

Sequence variants in the preferred transcript

CNVs (gains or losses) in the targeted genes

Likely acquired terminal CN-LOH

CNVs ≥5 Mb in any gene

Losses in TBL1XR1, CD200, IKZF1, CDKN2A, ASMTL, ERG, ARID2, ATM

Gains in MYC

Losses between FIP1LI and PDGFRA that result in a potential fusion

Any CN-LOH involving TP53, JAK2, and CBL

Sequence variants in the preferred transcript

Not reported

Benign or likely benign variants

Likely germline or interstitial CN-LOH

Due to the complexity of analysis, CNVs may not be reported in instances of stem cell transplants that present with mixed chimerism, increased genomic complexity (>4 CNVs), and complex aneuploidies (eg, hyper- or hypodiploidy)

VAF for CNVs with copy number >3

Benign or likely benign variants

CNVs

CN-LOH

Mb, megabases; VAF, variant allele fraction

Limitations

  • Variants may not be identified due to technical limitations in the presence of pseudogenes or in repetitive or homologous regions.
  • Not intended to detect minimal residual disease (MRD).
  • Interpretation may be impacted if the patient has had an undisclosed allogeneic bone marrow or stem cell transplant.
  • Does not distinguish between somatic and germline variants.
  • The Myeloid Malignancies Mutation and Copy Number Variation Panel by Next Generation Sequencing (3016621) does not replace conventional cytogenetic studies or genomic microarray in the workup of hematologic malignancies.
  • Neither panel detects the following types of variants:
    • Variants in regions that are not included in the preferred transcript for the targeted genes; refer to the Genes Tested table
    • RNA variants
    • Gene fusions, balanced translocations, and other structural variants

Limit of Detection

  • SNVs and variants <24 bp: 5% VAF
    • Variants >24 bp may be detected at limit of detection (LOD), but analytic sensitivity may be reduced.
  • CNVs (gains and losses): >2 Mb in approximately 30% of the sample
  • CN-LOH: >10 Mb in approximately 30% of the sample 
    • Some areas of the genome may have a reduced sensitivity for CNVs and CN-LOH at LOD.

Analytic Sensitivity

Variant Class Analytic Sensitivity (PPA)a Estimate (%) Analytic Sensitivity (PPA) 95% Credibility Regiona (%)

SNVs

96.9

95.1-98.1

Insertions/duplications (1-24 bp)

98.1

95.5-99.3

Insertions/duplications (>24 bp)

>99

92.9-100.0

Deletions (1-24 bp)

96.7

92.8-98.7

Deletions (>24 bp)

90

79.5-96.1

MNVs

97

93.0-99.0

FLT3 ITDs

>99

97.1-100.0

Copy number gains (>2 Mb)

91.8

86.7-95.3

Copy number losses (>2 Mb)

92.3

87.7-95.5

Copy number-neutral LOH (>10 Mb)

98.1

91.5-99.8

aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived.

bp, base pairs; ITDs, internal tandem duplications; MNVs, multinucleotide variants; PPA, positive percent agreement

Genes Tested

Gene Preferred Transcripta Excluded Exonsb

ANKRD26

NM_014915

—

ASXL1

NM_015338

—

ASXL2

NM_018263

—

BCOR

NM_001123385

—

BCORL1

NM_021946

—

BRAF

NM_004333

—

CALR

NM_004343

—

CBL

NM_005188

—

CBLB

NM_170662

—

CEBPA

NM_004364

—

CSF3R

NM_156039

—

CUX1

NM_181552

24

DDX41

NM_016222

—

DNMT1

NM_001130823

5

DNMT3A

NM_175629

—

ELANE

NM_001972

—

ETNK1

NM_018638

—

ETV6

NM_001987

—

EZH2

NM_004456

—

FBXW7

NM_033632

—

FLT3

NM_004119

—

GATA1

NM_002049

—

GATA2

NM_032638

—

GNAS

NM_000516

—

HNRNPK

NM_002140

—

IDH1

NM_005896

—

IDH2

NM_002168

—

IL7R

NM_002185

—

JAK1

NM_002227

—

JAK2

NM_004972

—

JAK3

NM_000215

—

KDM6A

NM_001291415

13

KIT

NM_000222

—

KMT2A

NM_001197104

—

KRAS

NM_004985

—

LUC7L2

NM_016019

—

MPL

NM_005373

—

NOTCH1

NM_017617

—

NPM1

NM_002520

1

NRAS

NM_002524

—

NSD1

NM_022455

—

PHF6

NM_001015877

—

PIGA

NM_002641

—

PPM1D

NM_003620

—

PRPF8

NM_006445

—

PRPF40B

NM_001031698

—

PTPN11

NM_002834

—

RAD21

NM_006265

—

RUNX1

NM_001754

—

SAMD9

NM_017654

—

SAMD9L

NM_152703

—

SETBP1

NM_015559

—

SF3B1

NM_012433

—

SH2B3

NM_005475

—

SMC1A

NM_006306

—

SMC3

NM_005445

—

SRSF2

NM_003016

—

STAG2

NM_001042749

—

STAT3

NM_139276

—

STAT5B

NM_012448

6-9

SUZ12

NM_015355

1-9

TET2

NM_001127208

—

TP53

NM_000546

—

U2AF1

NM_006758

—

U2AF2

NM_007279

—

UBA1

NM_003334

—

WT1

NM_024426

—

ZRSR2

NM_005089

—

aThis is the transcript number used for analyzing and reporting variants. The transcript version number may change periodically and thus is not listed here. The transcript with version number will be included on the patient's report if a variant is detected in the gene.

bNoncoding exons are not analyzed, except for regions containing known clinically relevant variants in the ANKRD26 5’UTR and NOTCH1 3’UTR. In addition, coding exons noted here are not sequenced due to technical limitations of the assay.