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Lyudmila Georgieva, Ezam Uddin, Aysel Heckel, Jacqueline Chan, James Reid, Jolyon Holdstock, David Cook and Graham Speight



Karyotyping, FISH, RT-PCR and microarrays are currently considered to be the gold standard techniques for structural variant discovery and detection. However, there is a desire to combine analysis of large structural alterations such as translocations alongside smaller mutations such as SNVs and indels. With development of newer technologies such as NGS for DNA- and RNA-sequencing, simultaneous discovery of multiple mutation types is now possible, enabling development of more comprehensive assays.

Chronic myeloid leukaemia (CML) is a myeloproliferative neoplasm with incidence of 1 to 2 per 100,000 and constitutes 15-20 % of adult leukaemias1. CML is characterised by the Philadelphia chromosome (Ph), resulting from the t(9;22)(q34;q11) balanced reciprocal translocation. The translocation generates the BCR-ABL1 fusion gene encoding the BCR-ABL1 protein with constitutive kinase and oncogenic activity1,2. The breakpoints in the ABL1 gene lie in 90 kb long intron 1, upstream of the ABL1 tyrosine kinase domains encoded in exons 2 to 11. The breakpoints within BCR are mapped to a 3.1 kb area spanning exons 13 to 15, the major breakpoint cluster region (M-bcr), found in 90% of CML and 20 to 30% of cases with Ph-positive B-cell acute lymphoblastic leukaemia (Ph+ B-ALL)3.

In this study, we tested the capability of a SureSeq myPanel™ NGS Custom Cancer Panel to detect known t(9;22)(q34;q11) translocations.

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