Beyond FISH, SNVs and indels – improved resolution of translocation detection using NGS

Contributors

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

Introduction

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 activity^1,2. 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.