Labchip gx touch system

Germline DNA was extracted from buccal mucosa using the DNeasy Tissue Kit (Qiagen, USA) according to the manufacturer’s guidelines. CSF was collected and processed within 4 h. CSF-derived circulating cell-free DNA (cfDNA) was extracted with the QIAamp Circulating Nucleic Acid Kit (Qiagen). Then, the fragment length and quantity of cfDNA were assessed with the Qubit Fluorometer, Qubit dsDNA BR Assay Kit (Invitrogen, USA), and Labchip GX Touch system (PerkinElmer, Shanghai, China). All libraries were hybridized to custom-designed biotinylated oligonucleotide probes (IDT, Coralville, IA, USA) covering 413 genes. DNA sequencing was performed using the GeneSeq-2000 (Geneplus-Suzhou, Suzhou, China) with a read length of PE100 and depth of 500–1,000× (49 (link)), and 90 genes related to lymphoma were used for subsequent analysis (Supplementary Table S1).

A DNeasy Tissue Kit (Qiagen, USA) was used to extract DNA from the buccal mucosa (germline DNA) and tumor tissue (tumor DNA). Frozen CSF was first thawed, and then, a QIAamp Circulating Nucleic Acid Kit (Qiagen) was used to extract cfDNA from it. Next, we used a Qubit fluorometer, a Qubit dsDNA BR Assay Kit (Invitrogen, USA), and a LabChip GX Touch system (PerkinElmer, Shanghai, China) to estimate the DNA concentration and fragment length. After the ends were repaired, A-tailed and the adapters were ligated, double-stranded cfDNA fragments went on PCR cycles to generate enough fragments for hybridization to custom-designed biotinylated oligonucleotide probes (IDT, Coralville, IA, USA) covering 413 genes.

The total RNA from samples was extracted using Plant RNA MiniPrep Kit (Zymo Research, Irvine, CA, USA) with additional treatment with RNase-Free DNase Set (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions and protocols. Evaluation of the quantity and purity of RNA was performed on a Nanodrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA); integrity was assessed using LabChip GX Touch™ system (PerkinElmer, Waltham, MA, USA).
MACE libraries were constructed using the MACE kit (Zawada et al., 2014 (link)) according to the manual provided with the kit. Sequencing was performed on Illumina NextSeq 500 platform. PCR duplicates were removed automatically.
All raw data are available in NCBI SRA (PRJNA630059).