Additional file 1 of Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling

Additional file 1: Table S1. Summary of probes on EPICv2, divided by probe type and Infinium design type. Table S2. Details of nv probes and their matched variant within the COSMIC census database. Table S3. Summary of control probes on EPICv2. Table S4. Discrepant probes between Illumina manifest and script to recompute sequence from Illumina manifest 'Forward sequence' and 'IlmnID'. Table S5. Summary of number of probes per a) exact-replicate, b) location-replicate and c) sequence-only-replicate probe set. Table S6. Examples of a) exact-replicate, b) location-replicate and c) sequence-only-replicate probe sets. Table S7. Lists of IlmnIDs for probes that have different types of replicate. Table S8. Lists of IlmnIDs for probes that have different types of replicate, grouped by probe set. Table S9. Matches between EPICv2 probes and probes on older versions of the microarray based on 1) probe name, 2) target location (hg38) and 3) probe sequence of sesame manifests. Table S10. Number of replicate probes within older arrays (excluding control probes). Table S11. Number and percentage of sites targeted on each chromosome for each probe category. Table S12. Distribution of probes relative to different genomic features. Table S13. Details of samples profiled on EPICv2. Table S14. Number of probes with detection p-value >0.05 per sample. Table S15. Probes with no BLAT hits. Table S16. BLAT hit locations for probes that do not map to their target location in the Illumina manifest. Table S17. Results of competitive evaluation of location replicates