## 2 Materials and Methods
### ONT Library Preparation and Sequencing on the GridION Instrument  
Two distinct libraries were prepared for comparative analysis in this study. (i) WGS Baseline Library: Approximately 1 \(\upmu\)g of untreated native genomic DNA (gDNA) served as the input for standard library preparation. This library represents the baseline genomic material sequenced via WGS. (ii) Adaptive Sampling (AS) Library: Approximately 1 \(\upmu\)g of gDNA that had been previously treated with Pvull-HF (as described in Section 2.4) served as the input for this library. This library was subjected to targeted enrichment via adaptive sampling during sequencing. Each DNA sample was prepared independently for Oxford Nanopore Technologies (ONT) (Oxford, UK) sequencing on R9.4.1 flow cells using the Ligation Sequencing Kit (SQK-LSK109, ONT). Library preparation commenced with DNA  
Figure 3: Fragment analysis of HAdMSCs on Qsep-100 Bio-Fragment Analyzer. (**A**) Native DNA isolated from HAdMSCs. (**B**) DNA from HAdMSCs after treatment with Pvull-HF. (**C**) Library prepared with Ligation Sequencing Kit SQK-LSK109 for whole genome sequencing of HAdMSCs. (**D**) Library prepared from HAdMSCs after Pvull-HF digestion for adaptive sampling.  
repair and end-preparation. In a 0.2 mL PCR tube, 48 \(\upmu\)L containing 1 \(\upmu\)g of input DNA was mixed with 1 \(\upmu\)D DNA control sample (CS, provided with kit), 3.5 \(\upmu\)L. NEBNext FFPE DNA Repair Buffer (New England Biolabs [NEB]), 2 \(\upmu\)L NEBNext FFPE DNA Repair Mix (NEB), 3.5 \(\upmu\)L NEBNext Ultra II End-prep Reaction Buffer (NEB), and 3 \(\upmu\)L NEBNext Ultra II End-prep Enzyme Mix (NEB). The reaction was incubated at 20 \({}^{\circ}\)C for 5 min, followed by 65 \({}^{\circ}\)C for 5 min. The reaction mixture was purified using AMPure XP beads (Beckman Coulter, Singapore). Subsequently, 1 \(\upmu\)L of the purified, repaired, and end-prepped DNA was quantified using a Qubit fluorometer (Invitrogen, Waltham, MA, USA) to confirm DNA recovery before proceeding.  
For adapter ligation, the remaining purified DNA (\(\sim\)60 \(\upmu\)L) was transferred to a 1.5 mL tube and mixed with 25 \(\upmu\)L Ligation Buffer (LNB, kit component), 10 \(\upmu\)L NEBNext Quick T4 DNA Ligase (NEB), and 5 \(\upmu\)L Adapter Mix (AMX, kit component). This ligation mixture was incubated at room temperature (approximately 20-25 \({}^{\circ}\)C) for 10 min. The adapter-ligated DNA was then purified using AMPure XP beads, utilizing the Short Fragment Buffer (SFB, kit component) during the wash steps as per the manufacturer's protocol to ensure retention of all fragments for both libraries. Finally, the purified library DNA was eluted in 15 \(\upmu\)L Elution Buffer (EB, kit component). The final adapter-ligated libraries were quantified using a Qubit fluorometer, and their size distribution and quality were assessed using a Qsep100 instrument (BiOptic Inc., Taiwan, China) before proceeding to flow cell loading. As there is no requirement in the Ligation Sequencing Kit SQK-LSK109 (ONT, Oxford, UK) for fragment analysis prior library loading, no such has been performed and an average fragment length of 4 kB was taken considering the initial fragment analysis after digestion with PvuII-HF. Library with an approximate concentration of 50 fmol was loaded onto the flow cell.