The AML-MDS Panel (IAD245850_243), request code P042, exists of 348 amplicons and is in silico covering 100% of submitted areas (all coding regions (exons)) and is able to analyze variants in 31 genes related to AML.

Indicated exons (Table 1) include flanking intronic regions based on 10 base exon padding. For some genes only a hotspot location is covered. See Table 1 and 2 for detailed coverage information about these aberrant regions.

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Design AML-MDS Panel

Indicated exons include flanking intronic regions based on 10 base exon padding. For some genes only a hotspot location is covered. See table 2 for detailed coverage information.

Table 1. Design AML-MDS panel

Gene

Chromosome

Transcript

Exon

ASXL1

Chr20

NM_015338.6

1, 2, 4-13

BCOR

ChrX

NM_001123385.2

2-15 (full)

CALR

Chr19

NM_004343.4

9

CBL

Chr11

NM_005188.3

8-9

CEBPA

Chr19

NM_004364.4

1

CSF3R

Chr1

NM_000760.4

12-17

DDX41

Chr5

NM_016222.4

1-17 (full)

DHX34

Chr19

NM_014681.6

2-17 (full)

DNMT3A

Chr2

NM_022552.4

2-23 (full)

ETNK1

Chr12

NM_018638.4

3

ETV6

Chr12

NM_001987.5

1-8 (full)

EZH2

Chr7

NM_004456.5

2-20 (full)

FLT3

Chr13

NM_004119.3

13,14,15,16,20,21

GATA2

Chr3

NM_032638.5

2-6 (full)

IDH1

Chr2

NM_005896.3

4

IDH2

Chr15

NM_002168.3

4

JAK2

Chr9

NM_004972.4

12 and 14

KIT

Chr4

NM_000222.3

8-19

KRAS

Chr12

NM_033360.3

2-5 (full)

KRAS

Chr12

NM_004985.5

alt 5

MPL

Chr1

NM_005373.3

3,4,6,10,12

NPM1

Chr5

NM_002520.6

11

NRAS

Chr1

NM_002524.5

2-3

RUNX1

Chr21

NM_001754.4

2-9 (full)

SETBP1

Chr18

NM_015559.2

4 (hotspot)

SF3B1

Chr2

NM_012433.4

12-24

SRSF2

Chr17

NM_003016.4

1

STAG2

ChrX

NM_001042749.2

3-35 (full)

TET2

Chr4

NM_001127208.2

3-11 (full)

TP53

Chr17

NM_000546.5

2-11 (full)

TP53β

Chr17

NM_001126114.2

alt 10

TP53γ

Chr17

NM_001126113.2

alt 10

U2AF1

Chr21

NM_006758.2

2, 6

ZRSR2

ChrX

NM_005089.3

1-11 (full)

Table 2. Aberrant covered regions AML-MDS panel

Gene

Exon

Coding DNA region

SETBP1

4

c.2477-c.2760

Coverage of the NGS AML-MDS Panel

Coverage is the number of times a base is sequenced. The deeper the coverage of each base the greater the reliability and sensitivity of the sequencing assay. The minimum depth of coverage required for detection of somatic variants with the AML-MDS AmpliSeq Panel is 500X. The percentage of Target Base coverage (%Base500x) is the percentage of target bases in a panel that is covered at least 500 times.

The percentage of target bases that is covered at least 500 times (%Base500x) is at least 99% at 2.200.000 Mapped Reads. With this acceptance criteria two regions failed to yield >500 times coverage, specific locations are listed in Table 3.  One amplicon covering exon 1 in ASXL1 failed to reach >500 times coverage. A region in the middle of exon 1 of CEBPA also did not reach >500 times coverage. This does not concern the bZIP domain of CEBPA, which is used for the AML risk classification. The bZIP domain is covered >500 times. In the regions of ASXL1 and CEBPA that are covered <500 times, germline variants will be called, but for somatic variants the coverage might be too low.

Table 3. Information amplicons AML-MDS panel that fail to reach >500 times coverage

 

GRCh37/hg19 coordinates

 

 

 

Chr

Start

End

Gene

Number of bases

Exon

Chr20

30946569

30946645

ASXL1

77

1

Chr19

33792690

33793122

CEBPA

433

1

Since May 2024 the AML-MDS panel is in use. Until this time the previous version of the AML panel has been used. The specifications of this AML panel can be downloaded here.

Design AML Fusion Transcript Panel

The AML-Fusion Transcript Panel (IAD84643) is able to detect fusion transcripts BCR::ABL1, CBFB::MYH11, PML::RARA and RUNX1::RUNX1T1 (AML1::ETO).
Fusion of genes may result in the usage of different donor and/or acceptor exons. Consequently, the corresponding fusion gene transcripts will have different exon compositions. In Table 4, a summation is listed with the number of fusion forms that are detected by the AML Fusion Transcript Panel.

Table 4. Overview fusion transcripts in AML Fusion Transcript Panel

Fusion Gene

Transcript Variants

BCR::ABL1

18

CBFB::MYH11

11

PML::RARA

5

RUNX1::RUNX1T1

5

Reporting: addition hematological malignancies variants

This test does not distinguish between somatic and germ line alterations in analyzed gene regions, particularly when variant allele frequencies (VAF) are near 50% or 100%. If nucleotide alterations in genes associated with germ line mutation syndromes are present and there is also a strong clinical suspicion or family history of malignant disease predisposition, appropriate genetic counselling may be indicated.

Variants detected between 5% and 10% Variant Allele Frequency may indicate subclonal tumor populations. However the clinical significance of these findings may not always be distinct. It is demonstrated that in blood DNA samples from individuals with advancing age and who do not have a hematologic neoplasm, a low incidence of gene variants that are associated with myeloid neoplasms can be detected. This phenomenon of clonal hematopoiesis of indeterminate potential (CHIP) may not be clearly distinguishable from tumor-associated mutations, especially if detected as a sole abnormality (Steensma et al).

Correlation with clinical, histopathologic and additional laboratory findings is required for final interpretation of the results. The final interpretation of results for clinical management of the patient is the responsibility of the managing physician.

Read more about reporting in the background information