Sp blood and cell culture dna isolation kit

OGM was performed for patient 1, harboring biallelic SVs. Ultra-high molecular weight DNA was extracted from 1.5 million lymphoblastoid cells using the SP Blood and Cell Culture DNA Isolation Kit according to the manufacturer’s instructions (Bionano Genomics) (Mantere et al, 2021 (link); Bruijn et al, 2022 (link)). DNA was labeled using a DLS Labeling Kit (Bionano Genomics). The labeled DNA was loaded on a Saphyr chip G2.3 and run on a Saphyr instrument (Bionano Genomics) for an output of 400 Gb. De novo assembly and variant annotation of the OGM data were conducted on Bionano Solve software version 3.7. We focused on FGF12 and visualized it on Bionano Access 1.7.1.1.

Optical genome mapping of control samples S3.1 to S3.4 was performed as described previously^{29 (link)}, with minor modifications. In brief, ultra-high molecular weight DNA was isolated from 650 ul peripheral blood (EDTA) using the SP Blood and Cell Culture DNA Isolation Kit according to manufacturers’ instructions (Bionano Genomics). Per sample, 750 ng of DNA was labeled with the DLS (Direct Label and Stain) DNA Labeling Kit (Bionano Genomics), and labeled DNA was imaged on the Saphyr System (Bionano Genomics) using ICS version 5.2. The annotated de novo assembly pipeline was executed with Bionano Solve software 3.6.1. Data of genome in a bottle sample NA12878^{28 (link)} is provided by courtesy of Bionano Genomics. Quality statistics of the samples are stated in Supplementary Table 5.

We extracted high-molecular-weight (HMW) DNA from PBMNC or BMMNC at initial diagnosis using the SP Blood and Cell Culture DNA Isolation Kit, according to the manufacturer’s guidelines (Bionano Genomics, San Diego, CA). In addition, HMW DNA was extracted from remission material or fibroblasts (if available) of the respective children as matching nontumor control. Labeling of HMW DNA was performed using the DLS DNA Labeling Kit (Bionano Genomics), according to the manufacturer’s protocol (Bionano Prep Direct Label and Stain [DLS] Protocol 30206). The labeled DNA was loaded on a Saphyr G2.3 chip and molecules were imaged using the Saphyr instrument (Gen 2, Bionano Genomics). Overall, we performed OGM on 60 matched tumor/non-tumor pairs (120 samples), and 1 sequential sample including tumor material from initial diagnosis and relapse in comparison to matched non-tumor material (ALL4). Refer to Suppl. Figure S2 for an overview of the applied OGM workflow.