Haematological Malignancies Flashcards
What is the required blast count for a diagnosis of AML (without genetic information)
20% myeloid blasts in the bone marrow
Whats rearrangements are diagnostic of AML regardless of the blast count?
t(8;21)(q22;q22) - RUNX1-RUNX1T1
inv(16)(p13;q22) / t(16;16)(p13.1;q22) - CBFB-MYH11
t(15;17)(q24;q21) - PML-RARA
What genes should be tested molecularly for all AML cases?
NPM1, FLT3 and CEBPA in cases with normal/intermediate risk cytogenetics
What gene should be tested for in core finding factor AML?
KIT
What genetic changes are associated with a favourable prognosis in AML?
t(8;21)(q22;q22.1) - RUNX1-RUNX1T1
inv(16)(p13;q22) / t(16;16)(p13;q22) - CBFB-MYH111
Muatetd NPM1 without FLT3-ITD or FLT3-ITD(low)
Biallelic mutated CEBPA
What genetic changes are associated with an intermediate prognosis in AML?
Mutated NPM1 with FLT3-ITD(high)
WT NPM1 without FLT3-ITD or FLT3-ITD(low)
t(9;11)(p21.3;q23.3) MLLT3-KMT2A
Cytogenetic abnormalites not classified as favourable/adverse
What genetic changes are associated with an adverse prognosis in AML?
t(6;9)(p23;q34.2) - DEK-NUP214 t(v11q23.3)KMT2A rearranged t(9;22)(q34.1;q11.2) - BCR-ABL1 inv(3)(q21.3;q26.2) or t(3;3)(q21.3;q26.2) - GATA2-MECOM (EVI1) -5 or del(5q) -7 -17 or abnormal 17p Complex or monosomal karyotype WT NPM1 and FLT3-ITD(high) Mutated RUNX1 Mutated ASXL1 Mutated TP53
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 call type needs to be >20% in the bone marrow/blood for a diagnosis of ALL
Lymphoblasts
What genetic changes are associated with a favourable prognosis in B-ALL?
High hyperdiploidy (>50 chromosomes) t(12;21)(p12;q22) - ETV6-RUNX1 t(5;14)(q31.1;q32.3) - IL3-IGH DUX4 rearranged NUTM1 rearrangements
What genetic changes are associated with an adverse prognosis in B-ALL?
t(9;22)(q34;q11) - BCR-ABL1 (Improved with TKI treatment)
Near haploid ALL (24-30) chromosomes
Low haploid ALL (31-39) chromosomes
KMT2A rearrangements
t(1;19) - TCF3-PBX1 fusion (improved with modern chemo)
TCF3-HLF - Extremely poor
Philadelphia like ALL (Expression profile similar to BCR-ABL1, CRLF2 rearrangement, ABL 1 class rearrangements, ETV6-NTRK, EPOR, IL7)
iAMP21 (>=5 copies of RUNX1)
IKZF1 rearrangements
What are the genetic alterations frequently associated with T-ALL?
NOTCH1 mutations (60% of cases)
FBXW7 (8-30%) - Presence of NOTCH1 and FBXW7 associated with a good prognosis
CDKN2A/B (50-80%)
JAK1 - (10-20% adults, rare in children) - Poor prognosis
PTEN (25-35%)
RAS (5-10%)
WT1 (10%)
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 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 is the most commonly identified marker in Follicular Lymphoma?
t(14;18) - BCL2/IGH fusion (90% of cases)
What is del(1p36) associated with when seen in follicular lymphoma?
FL with a diffuse pattern, lack of t(14;18) and a good prognosis
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 are the most common rearrangements in mucosa associated lymphoid tissues (MALT) lymphoma and associated clinical significance?
t(11;18) - API2-MALT1 frequently seen in gastric &pulmonary MALT lymphomas - locally advanced disease and resistance to antibiotic treatments
t(1;14) - Overexpression of BCL10 frequently seen in MALT of skin, lung and stomach - locally advanced disease and resistance to antibiotic treatments
t(14;18) - deregulation of MALT frequently seen in liver, skin, ocular and salivary gland MALT - unknown significance
t(3;4) - upregulation of FOXP1 frequently seen in thyroid, ocular and skin - unknown significance
What rearrangement is mantle cell lymphoma associated with?
t(11;14) - IGH/CCND1
What can be tested for if the t(11;14) - IGH/CCND1 rearrangement is not present in a suspected mantle cell lymphoma?
CCND2 & CCND3 may be overexpressed
SOX11 overexpression is seen in nearly all cases of MCL regardless of CCND1 expression
Mutations in what gene are associated with a very poor prognosis in mantle cell lymphoma?
TP53
What is the marker of high grade B-cell lymphoma?
Double/Triple hit of MYC and BCL2 and/or BCL6 rearrangements - poor prognosis
What rearrangement is typically seen in Burkitt Lymphoma ?
MYC gene rearrangement
t(8;14) - 80% of cases
t(2;8) or t(8;22) in the remaining 20%
What marker is associated with Burkitt-like lymphoma
11q deletion
What non genetic markers are used in the diagnosis of Multiple Myeloma?
Monoclonal protein quantification
Bone marrow eval - >=10% bone marrow plasma cells
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 six entities of myelodysplatic syndromes (MDS)?
- MDS with single lineage dysplastia (MDS-SLD)
- MDS with ring sideroblasts (MDS-RS)
- MDS with multilineage dysplasia (MDS-MLD)
- MDS with excess blasts (MDS-EB)
- MDS with isolated del(5q) +/- one other abnormality apart from -7/del(7q)
- MDS unclassifiable (MDS-U)
Mutations in which gene are considered diagnostic of MDS-RS and under what conditions?
SRSF2
- lacks excess blasts or isolated del(5q)
What is the prognostic impact of del(5q) in MDS?
Good prognosis (if seen isolated or one other abnormality which is not -7/del(7q))
What is the prognostic impact of -7/del(7q)in MDS?
Poor prognosis
What are the subtypes of Myelodysplastic/Myeloproliferative (MDS/MPN) neoplasms?
- Chronic myelomonocytic leukaemia (CMML)
- Atypical chronic myeloid leukaemia (aCML)
- BCR-ABL1 negative
- Juvenile myelomonocytic leukaemia (JMML)
- MDS/MPN with ring sideroblasts and thrombocytosis
- MDS/MPN unclassifiable (MDS/MPN-U)
Mutations in which genes are frequently identified in CMML?
TET2, SRSF2, ASXL1, RUNX1, NRAS and CBL
What is aCML phenotypically similar to and what molecular markers can be used to help distinguish between them?
aCML is phenotypically similar to the chronic neutrophilic leukaemia (CNL) of MPN.
- Copy number neutral loss of heterozygosity is found in 6-41% of MDS/MPN
- CSF3R mutations are strongly associated with CNL but is also present in <10% of aCML.
Mutations in which genes are seen frequently in JMML?
PTPN11 (40-50%), NRAS (15-20%), KRAS (10-15%), CBL(15-18%) and NF1 (10-15%)
How does the occurrence of an SRSF2 variant impact diagnosis in MDS/MPN-RT-T
Up tp 60% of MDS/MPN-RT-T cases have an SRSF2 variant. Unlike when identified in MDS, the occurrence of a SRSF2 variant does not change the required number of ring sideroblasts for diagnosis
In MDS, mutations in which genes are associated with a poor prognosis (Tier I)
TP53 (also associated with complex karyotypes) RUNX1 NRAS EZH2 ETV6 ASXL1
What Tier II level genes have been associated with a poor prognosis in MDS?
DNMT3A U2AF1 SRSF2 CBL PRPF8 SETBP1 KRAS
Mutations in which gene(s) are associated with a favorable prognosis in MDS?
SRSF2
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 theCALR 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.
Mutations in which genes are associated with a poor prognosis in PV?
ASXL1, SRSF2, IDH1/2, RUNX1
JAK2 exon 12 mutations in PV are associated with what clinical features compare to JAK2 V617F?
Young age, increased mean haemoglobin, lower white blood cell and platelet counts.
Both have a similar rate of thrombocytosis.
Mutations in which genes are associated with a poor prognosis in ET?
TP53, SH2B3, IDH2, U2AF1, SRSF2, SF3B1, EZH2, RUNX1
What is the significance of a CALR variant in ET?
Low risk of thromocytosis compared to JAK2 mutated ET
No difference in OS or transformation compared to JAK2 mutated
Mutations in which genes have clinical significance in in PMF and what is the significance?
IDH1/2, SRSF2, TP53, U2AF1 Q157 (Inferior OS compared to U1AF1 S34 or unmutated), U2AF1, DNMT3A and CBL - Poor prognosis (Inferior OS/Inferior risk of leukaemic transformation)
Combined CALR and ASXL1
Longest OS - CALR(+)/ASXL1(-)
Intermediate OS - CALR(+)/ASXL1(+)
Shortest Survival CALR(-)/ASXL1(+)
What diagnostic testing should be carried out for MPNs?
PMF and ET - JAK2, CALR, MPL
PV - JAK2 V167F and JAK2 exon 12
What gene rearrangements are associated with B-cell and T-cell clonality
B-cell - IGH
Tcell - TCR
What is the demographic of AML and what is incidence linked to?
AML can occur at any age but is more prevalent later in life with the incidence increasing in correlation with age.
By what mechanisms can AML occur?
AML can arise de novo or can be secondary to underlying myeloproliferative neoplasms or myelodysplastic syndromes.
Diagnosis and classification requires a multidisciplinary diagnostic approach . What forms of testing are required?
Cytomorphology
Immunophenotyping
Cytogenetics
molecular Genetics
What are the 11 AML subtypes as classified by WHO
- AML with t(8;21)(q22;q22.1) RUNX1-RUNX1T1
- AML with inv(16)(p13.1;q22) or t(16;16)(p13.1;q22) CBFB-MYH11
- Acute promyelocytic leukaemia with t(15;17) (q24;q21) PML-RARA
- AML with t(9;11)(p21.3;q23.3) KMT2A-MLLT3
- AML with t(6;9)(p23;q34.1) DEK-NUP214
- AML with inv(3)(q21.3;q26.2) or t(3;3;)(q21.3;q26.2) GATA2, MECOM
- AML (megakaryoblastic) with t(1;2)(p13..3;q13.1) RBM15-MKL1
- Provision entity - AML with BCR-ABL1 t(9;22)(q34;q11)
- Provision Entity - AML with mutated NPM1
- Provision entity - AML with biallelic CEBPA
- Provisional entity - AML with mutated RUNX1
What are the genetic abnormalities which can be used to diagnosis AML regardless of blast count?
t(8;21)(q22;q22.1) - RUNX1-RUNX1T1
inv(16)(q13.1;q22) - CBFB-MYH11
t(15;17)(q24;q21) - PML-RARA
What is required for a classification of AML with myelodysplastic changes?
A diagnosis can be made if the AML exhibits MDS like features and includes
i) history of MDS or MDS/MPN
ii) MDS related cytogenetic abnormalities
iii) multilineage dysplasia
According to the European LeukaemiaNet AML guidance, which genetic abnormalities are associated with a favourable prognosis?
t(8;21)(q22.1;q22) - RUNX1-RUNX1T1
inv(16)(q13;q22) or t(16;16)(q13;q22) CBFB-MYH11
NPM1 mutated with no FLT3-ITD or FLT3-ITD (low)
Biallelic mutated CEBPA
According to the European LeukaemiaNet guidance, what genetic abnormalities are associated with an intermediate prognosis?
Mutated NPM1 with FLT3-ITD high
Wild type NPM1 without FLT3-ITD or with FLT3-ITD(low) (no other adverse genetic changes)
t(9;11)(q21.3;q23.3) - MLLT3-KMT2A
Cytogenetic abnormalities not classified as favourable or adverse
According to the Europen LeukaemiaNet guidance, which genetic abnormalities in AML are associated with a poor prognosis?
inv(3)(q21.3;q26.2) or t(3;3)(q21.3;q26.2) GATA2, MECOM t(6;9)(q23;q34.1) DEK-NUP214 t(v;11q23.3) KMT2A rearranged t(9;22)(q34.1;q11.2) BCR-ABL1 -5 or del(5q) -7 -17/abn(17p) (TP53)
What targeted treatment is available for AML and with which genetic aberration is it associated?
Midostaurin is recommended by NICE for the treatment of newly diagnosed FLT3-mutation positive AML. Midostaurin is a multi target kinase inhibitor
What are the recommended genetic biomarkers which can be used for MRD analysis in AML?
RUNX1-RUNX1T1
PML-RARA (APL)
CBFB-MYH11
What type of inherited disorder is associated with MDS and what genes are typically involved?
Bone marrow failure syndromes
Genes - RUNX1, ANKRD26, DDX41, ETV6, GATA2 and SRP7
