Haematological Malignancies Flashcards
What is the requisite blast count for a diagnosis of AML?
> 20%
What rearrangements are diagnostic of AML regardless of blast %?
t(8;21)(q22;q22) RUNX1-RUNX1T1
inv(16)(p13;q22) or t(16;16)(p13;q22) CBFB-MYH11
t(15;17)(q24;q21) PML-RARA (acute promyelocytic lekaemia)
What are the WHO sub-classifications for AML with recurrent genetic abnormalities?
- AML with t(8;21)(q22;q22) RUNX1-RUNX1T1 (Good)
- AML with inv(16)(p13;q22) or t(16;16)(p13;q22) CBFB-MYH11 (Good)
- AML with t(15;17)(q24;q21) PML-RARA (APL)
- AML with t(9;11)(p21;q23) MLLT3-KMT2A (Int)
- AML with t(6;9)(p23;q34) DEK-NUP214 (Poor)
- AML with inv(3)(q21;q26) or t(3;3)(q21;q26) GATA2,MECOM (Poor)
- AML with t(1;22) RBM15-MKL1 (megakaryoblastic)
- AML with mutated NPM1 (Good)
- AML with biallelic CEBPA mut (Good)
- (Prov) AML with t(9;22)( q34;q11) BCR-ABL1
- (Prov) AML with RUNX1 mut
What are the favourable prognostic marks in AML?
t(8;21)(q22;q22) RUNX1-RUNX1T1
inv(16)(p13;q22) / t(16;16)(p13,q22) CBFB-MYH11
Mutated NPM1 without FLT3-ITD or FLT3-ITD low
Biallelic CEBPA mutations
What cytogenetic abnormalities are associated with AML with myelodysplasia?
- 7 / del(7q)
- 17 / abn(17p)
- 13 / del(13q)
- KMT2A rearrangement (not t(9;11)(p21;q23) MLLT3-KMT2A)
- isochromosome X
- PDGFRB rearrangements
What are the intermediate prognostic markers in AML?
Mutated NPM1 with FLT3-ITD high
WT NPM1 with no FLT3-ITD or FLT3-ITD high
t(9;11)(p21;q23) MLL3T-KMT2A
Cytogenetic rearrangements otherwise not classifiable
What are the poor prognostic markers in AML?
-5 / del(5q)
-7
-17 / abn(17p)
Complex / Monosomal Karyotype
t(6;9)(p23;q34) DEK-NUP214
inv(3)(q21;q26) or t(3;3)(q21;q26) GATA2,MECOM
KMT2A rearrangements
BCL-ABL1 t(9;22)(p34;q11)
WT NPM1 with FLT3-ITD high
TP53, RUNX1, ASXL1 mutations *without favourable marker
What are the WHO subtypes for B-ALL?
B-ALL with t(9;22)(q34;q11) BCR-ABL1 (Poor)
B-ALL with KMT2A rearranged (Poor)
B-ALL with High Hyperdiploidy (Good)
B-ALL with Low Hyperdiploidy (Poor)
B-ALL with t(12;21)(p13;q22) ETV6-RUNX1 (Good)
B-ALL with t(5;14)(q31;q32) IL3-IGH (Good)
B-ALL with t(1;19)(q23;p13) TCF3-PBX1 (Standard)
B-ALL with BCR-ABL1 like (Poor)
B-ALL with iAMP21 (Poor)
In B-ALL how many chromosomes are required to be considered High, Near Haploid and Low ALL?
High - >=50
Near Haploid - 24-30
Low - 31-39
What is the most frequent abnormality identified in paediatric B-ALL?
ETV6-RUNX1 t(12;21)(p13;q22)
Why is it important to identify the fusion partner of TCF in B-ALL?
The prognosis is different depending on the partner
What is the TCF3 rearrangement with the poorest prognosis?
TCF3-HLF
What is iAMP21 in B-ALL and how is it identified?
iAMP21 is a grossly abnormal copy of chromosome 21 comprising multiple regions of gain, amplification, inversion and deletion
It can be defined as >= 5 copies of RUNX1 and can be detected by FISH, arrays or MLPA
What genetic abnormalities are associated with a good prognosis in B-ALL?
High hyperdipolidy
ETV6-RUNX1 t(12;21)(p12;q22)
IL3-IGH t(5;14)(p31;q32)
What genetic abnormalities are associated with a poor prognosis in B-ALL?
Near haploid Low hypodiploid BCR-ABL1 t(9;22)(q34;q11) KMT2A rearrangements t(?;11) TCF-HLF TCF-PBX1 t(1;19) BCR-ABL1 like expression profiles (CRLF2 rearrangement 50% of cases) iAMP21 IKZF1 rearrangements
What are the most common rearrangements identified in T-ALL?
Rearrangements involving the T-cell recetor genes
35% of cases have a rearrangement at a TCR locus - TRA (14q11), TRB (7q34-35), TRG (7p15) and TRD (14q11)
Mutations in what genes are associated with a good prognosis in T-ALL?
NOTCH1 and FBXW7
Mutations in what gene are associated with a poor prognosis in T-ALL?
JAK1
What rearrangement is present in 90% of patients with follicular lymphoma (FL)?
t(14;18))(q32;q21) IGH-BCL2
Follicular lymphoma without a t(14;18))(q32;q21) rearrangement is seen with what features?
1p36 deletion and uniform CD23 expression
What rearrangement is seen in large B-cell lymphoma and how is it tested for?
IRF4 rearrangements
Seen as strong expression of IRF4/MUM1 on IHC
Should be managed as if DLBCL
What are the common rearrangements identified in MALT lymphoma and what are the associated prognostic significance?
t(11;18) API2-MALT1 - Associated with locally advanced disease
t(1;14) IGH-BCL10 - Associated with locally advanced disease
t(14;18) IGH-MALT1 - No known significance
t(4;14) FOXP1-IGH - No known significance
What rearrangement is mantle cell lymphoma characterised by?
Reciprocal translocation t(11;14)(q13;q32) CCND1-IGH
What is the prognostic significance of TP53 variants in Mantle Cell Lymphoma?
Worse prognosis in patients treated with conventional therapy including haematopoietic stem cell transplant.
High grade B-cell lymphomas are a sub type of Diffuse Large B-cell lymphoma with a particularly poor prognosis. What genetic alterations are associated with these?
Double/Triple hit that harbour MYC and BCL2 and/or BCL6 translocations
What rearrangements are characteristic of Burkitt Lymphoma?
MYC gene rearrangement
t(8;14)(q24;q32) MYC-IGH is most common (80%)
t(2;8)(p11;q24) IGK-MYC and t(8;22) are most common in the remaining cases
What is the most reliable method of detecting MYC rearrangements in Burkitt lymphoma?
FISH breakapart probe
Burkitt like lymphoma is a similar more aggressive form of B-cell lymphoma with immunophenotypic/molecular features to Burkitt but does not have an MYC rearrangement. What genetic abnormality characterises these?
Dysregulation of 11q
MYC translocations can be seen in DLBCL as well as Burkitts lymphoma. Lymphomas with features of both and cannot be diagnosed either way have what prognosis?
Poor prognosis.
Why can clonality testing be used in all lymphoproliferations?
A key feature of lymphocytes is that they have rearranged antigen receptor genes which are unique for each lymphocyte
What happens during the rearrangement process in the immunoglobulin (Ig) or T-cell receptor (TCR) genes?
Step wise rearrangement of the variable (V), Diversity (D) and Joining (J) gene segments. During the rearrangement process, nucelotides are deleted and randomly inserted at joining sites resulting in an enormous diversity of antigen receptors.
What is the difference in clonality between reactive and malignant lymphoproliferations?
In clonality testing, reactive lymphoproliferations will be polyclonal and malignant will be monoclonal.
What is the most commonly used method for clonality testing?
PCR based testing using the BIOMED developed standards. Consensus primers have been established for the Ig and TCR genes.
What are the T cell receptor gene locations called, where are they located and in which order are they rearranged during recombination?
TRA (14q11), TRB (7q35), TRD (14q11, sandwiched between the TRA V & J domains) and TRG (7p15-p14)
Order - TRD, TRG, TRB and finally TRA
What are the Ig gene locations which are rearranged in B-Cell lmphoproliferations and in which order do they occur?
IGH (heavy chains) and IGK and IGL (light chains)
Order - IGH followed by IGK, if a functional rearrangement isn’t achieved IGL then rearranges
What are the poor prognosis markers in CLL?
Umutated IGHV region (>98% germline homology))
Del(11q23) / ATM deletion
Del(17p13) / TP53 deletion / TP53 mutation
IGH rearrangements (14q32)
Mutated NOTCH1
Mutated SF3B1
What are the good/intermediate prognosis markers in CLL?
Isolated del(13q14) - Good
Trisomy 12 - Intermediate
Mutated MYD88 - Good
What genetic alterations are considered high risk in Multiple Myeloma?
TP53 mutations
IGH rearrangements
del(13q) on metaphase
Outline the clonal development of multiple myeloma
Normal Cells -> Primary Abnormalities - IGH rearrangements and/or Trisomy (hyperdipolid) establish clone -> MGUS -> Secondary Abnormalities - del(17p/TP53), 1qamp, t(4;14) - All high risk of progression -> Myeloma -> Secondary Abnormalities - del(17p/TP53), del(1p), MYC rearrangements - All high risk of progression -> Plasma Cell Leukaemia
What are the three subtypes of MPN?
Myelofibrosis (MF) Polycythemia Vera (PV) Essential Thrombocythemia (ET)
What of the MPN subtypes has the worst prognosis?
Myelofibrosis (MF)
What is the frequency of the JAK2 V617F variant in the MPN subtypes?
JAK2 V617F variants are identified in the majority of patients with PV (>90%) and in 60% of patients with MF or ET
What is the frequency of the MPL W515L/K variant in the MPN subtypes?
5-8% of patients with MF
1-4% of patients with ET
What is the frequency of the CALR exon 9 variant in the MPN subtypes and which types are more frequent in these?
20-25% of patients with ET and MF (accounts for 60-80% of JAK2 - patients)
Type 1 variants (52bp deletions) are more frequent in MF and Type 2 variants (5bp insertions) are more frequent in ET.
What diagnostic testing should be carried out for MPNs?
PMF and ET - JAK2, CALR, MPL
PV - JAK2 V167F and JAK2 exon 12
Which of the CALR, JAK2 and MPL variants in MPNs is associated with a good prognosis?
CALR
What configuration of CALR, JAK2 and MPL variants is associated with a poor prognosis?
Triple negative
What rearrangement is diagnostic for CML?
t(9;22)(q34.1;q11.2) - BCR-ABL1
What are the three phases of CML?
Chronic, Accelerated, Blast
What method is typically used to detect the BCR-ABL1 rearrangement in CML?
Qualitative Reverse Transcriptase (RT) PCR (Diagnosis)
Quantitative Reverse Transcriptase (RT) PCR (MRD)
What could cause a false negative when using routine BCR-ABL1 fusion analysis in CML?
Atypical breakpoint fusions occur in around 2-4% of CML patients
What type of treatment is used to target the BCR-ABL1 fusion in CML?
Tyrosine Kinase Inhibitors (TKIs) - imatiib, dasatinib and nilotinib
How is molecular response assessed in CML?
Assessed according to the international scale (IS) as the ratio of BCR-ABL1 transcripts to ABL1 transcripts or an accepted control transcript such as GUSB. Must be reported as BCR-ABL1 % on a log scale
What are the molecular response groups and corresponding % of transcripts in BCR-ABL1 monitoring in CML?
Cytogenetic Remission - BCR-ABL1 <1%
Major Molecular Response (MMR) / MR3 - BCR-ABL1 < 0.1%
MR4 - BCR-ABL1 <0.01% or udetectable with >10,000 ABL1 transcripts
MR - BCR-ABL1 <0.0032% or undetectable with >32,000 ABL1 transcripts
25% of CML patients will experience TKI resistance. What mechanisms can cause resistance?
Mutations in the kinase domain of BCR-ABL1
Reactivation of signalling pathways downstream of BCR-ABL1 (including MAPK, PI3K, SRC and JAK/STAT)
What molecular tests can be used for ALL?
- Reverse Transcriptase PCT (RT-PCR_ to identify common fusions, also identifies exact breakpoints for monitoring
- q-PCR/flow cytometry for clonality testing for IGH and TCR rearrangements - can be used for monitoring
- MLPA / SNP Array for detection of critical new targets in B-ALL
What are IRF4-MUM1 rearrangements associated with?
Large B cell lymphoma - poor prognosis & aggressive disease
What variant can be useful to distinguish Waldenström macroglobulinemia from other B-cell malignancies with overlapping phenotypes?
MYD88 L265P - Seen in ~90% of WM cases
What genes should be tested molecularly for AML cases?
NPM1, FLT3 and CEBPA in cases with normal/intermediate risk cytogenetics
