Somatic Structural Alterations in Childhood Leukemia Can Be Backtracked in Neonatal Dried Blood Spots by Use of Whole-Genome Sequencing and Digital PCR

Recurrent chromosomal rearrangements generating fusion genes in childhood acute lymphoblastic leukemia (ALL)1 provide a precise DNA fingerprint of the leukemic clone that can be used to investigate disease progression (1, 2). Previous studies on archived neonatal dried blood spots (DBSs) using conventional nested PCR or real-time quantitative reverse transcription PCR (RT-qPCR) have shown that most recurrent leukemic subgroups with chromosomal aberrations arise in utero (3). Here, we report a chip-based digital PCR (dPCR) approach that targets patient-specific somatic chromosomal rearrangements to detect and quantify both leukemic and preleukemic clones in diagnostic bone marrow samples and in DBSs. We performed whole-genome sequencing (WGS) (4) in 5 singletons and 1 monozygotic twin pair with childhood ALL of age 1 month to 4 years to pinpoint the sequence composition at breakpoints in the diagnostic bone marrow: 2 t(12;21)(p13;q22), 2 dic(9;20)(p13;q11), 1 lysine methyltransferase 2A ( KMT2A )2 rearrangement, t(10;11)(q25;q23), and 2 t(11;12;21)(q23;p13;q22) (Table 1). We retrieved 5 pieces (3 mm in diameter) from archived neonatal DBSs of the patients and, as control, from DBSs that were located next to the patients' DBSs from the Swedish National PKU (Phenylketonuria) Register at the Karolinska University Hospital. The study was approved by the ethics board at Karolinska Institutet and informed consent from parents was obtained according to the Declaration of Helsinki. We extracted genomic DNA from DBSs using QIAamp DNA …