DRAGEN Array Methylation QC Cloud v1.0.0 Release Notes

RELEASE DATE

May 2024

RELEASE HIGHLIGHTS

• Adjustable thresholds to determine pass/fail status

• Data summary plots for a quick visual check of each analysis batch

• Determining detection p-value, beta-values, and m-values from each methylation sample

• Deployment on BaseSpace™ Sequence Hub user interface for easy analysis kickoff

NEW FEATURES IN DETAIL

• Adjustable thresholds for 21 built in controls, p-value detection, proportion probes passing, and offset correction within BaseSpace Sequence Hub to customize for user’s study needs

  • Thresholds are used to assign pass (1) or fail (0) status to each sample

    • Failed metrics can be highlighted for easy viewing

  • Pinpoint areas of failure including bisulfite conversion, staining, hybridization, etc. to identify assay steps in need of troubleshooting

  • Quantitative values for each control removing ambiguity with manual interpretation

• Data summary plots with information on passing p-value detection and principal component analysis of beta values

• Provides detection p-value, beta-values and m-values for each CG site per sample to use in downstream analysis

KNOWN ISSUES

• Analysis may fail for the 80-100 sample size range when using large (>900K probes) arrays. If encountering this issue users are recommended to increase sample size as a workaround. The issue does not affect sample sizes strictly greater than 100.

KNOWN LIMITATIONS

• Standard thresholds may not be applicable for all discontinued, semi-custom or custom BeadChips and IDATs originating from NextSeq550

• Built-in controls may not be available on all discontinued, semi-custom or custom BeadChips