20.06.16 Genetic of ALL

Question 1

What is ALL

Answer 1

• Acute lymphoblastic leukemia
• Neoplastic disease characterised by clonal expansion of leukemic cells (B or T cells) in bone marrow (BM), lymph nodes, thymus, or spleen.

Question 2

Review of adult ALL

Answer 2

-0.9-1.6 in 100,000
6% of adult leukemias.
-Clinical features: fever, fatigue, bone/joint pain, headache, weight loss, swollen lymph nodes, hepato/ splenomegaly, anaemia, busing, infections
-B cell= 75%
-T cell= 25%

Question 3

Common genetic abnormalities in adult B-cell ALL

Answer 3

• t(9;22)(q34;q11) BCR-ABL1 Ph chromosome. In 25-30% cases
• t(4;11)(q21;q23) KMT2A-AFF1. 10% cases (also in T-cell ALL).
• Ploidy (7% cases) with 5 or more abnormalities.

Question 4

Diagnostic testing strategies- Cytogenetics and FISH

Answer 4

• Cytogenetic abnormalities seen in 70% of B-ALL and 50-70% of T-ALL
• Disadvantages= normal marrow outgrowing leukemic clones, apoptosis of leukemic cells, high failure rate, poor quality metaphases, cryptic/subtle rearrangements
• Minimum of 2 cultures set up, one with an incubation time of <24 hours to minimise effect of apoptosis.
• As BCR-ABL1, ETV6-RUNX1, iAMP21 and KMT2A (MLL) rearrangements are thought to be mutually exclusive, if one abnormality is detected it is not mandatory to exclude others
• If there is normal/failed result, ALL BPGs suggest additional FISH to detect hidden hyper/hypodiploidy

Question 5

Diagnostic testing strategies- molecular testing

Answer 5

• No mandatory molecular tests in ALL BPGs.
• Multiplex RT-PCR used for common fusion transcripts. Can be used for MRD monitoring.
• qPCR/ flow cytometry used for clonality testing and MRD monitoring
• Microarrays/MLPA: Frequent deletions in genes involving B cell development (IKZF1, PAX5, EBF1)
• NGS: offers prognostic information.

Question 6

Follow up testing in ALL

Answer 6

• Chromosome analysis in remission is not mandatory
• Interphase FISH is helpful in cases with low numbers of poor quality ALL metaphases.
• MRD is best monitored by molecular means (qPCR) vs flow cytometry
• At relapse, cytogenetic analysis may identify karyotype evolution of secondary malignancy.

Question 7

Review of childhood ALL

Answer 7

• 25% of pediatric cancer.
• 75% of childhood leukemias
• 3-4 in 100,000
• Symptoms: bruising/bleeding due to thrombocytopenia, pallor, fatigue, infection. Leukemic infiltration of liver, spleen and lymph nodes
• B cell= 85%
• T cell= 15%

Question 8

Common genetic abnormalities in childhood B-cell ALL

Answer 8

• t(4;11)(q21;q23) KMT2A-AFF1. 40-50%
• t(9;11)(q22;q23) KMT2A-MLLT3. 10%
• t(11;19)(q23;p13.3) KMT2A-MLLT1. 10%
• t(12;21) ETV6-RUNX1. 25%
• t(9;22)(q34;q11) BCR-ABL1. 2-4% of cases
• High hyperdiploidy (51-65 chromosomes). 25-30%
• IGH rearrangements in 8% cases.
• Near haploidy, low/high hypodiploidy is rare. Could be missed by G-banding

Question 9

Common genetic abnormalities in childhood T-cell ALL

Answer 9

• Recurring rearrangements in regulatory elements of TCR (T cell receptor) loci with transcription factors or homeobox genes.e.g. TLX1-TRA in 7% cases
• SIL-TAL1 (1p32 deletion) in 30% cases