Reanalysis and Autopilot

Owned by Cyrielle Kint
Last updated: Apr 29, 2022 by Sara Haers
3 min read

With new genetic knowledge on rare diseases being published every day, it is possible that an undiagnosed patient might receive a diagnosis later on, based on this new information. As the annotation sources used by Moon are constantly updated, reanalysing your samples might thus yield additional diagnoses over time.

Manual reanalysis

The Reanalysis button at the top right of the Shortlist screen allows you to reanalyse a specific sample of interest, either with the original or updated patient information. Samples in which reanalysis yields new relevant findings or new variant classifications, are highlighted in green both in the sample overview screen and in the analysis screen. After manually checking the new results, these can be marked as reviewed.

Autopilot

Once the NGS data and patient info are provided, Moon can automatically reanalyse samples in the background without the need for manual intervention.

The Autopilot can only be configured by the account Admin, by using the Reanalysis & Autopilot menu at the top left of the screen. Through this same menu, non-Admin users are able to review the Reanalysis & Autopilot settings and the list of updated samples.

Once the Autopilot settings are saved (see below), Moon will check on a daily basis which samples are due for analysis and automatically start reanalysis of these samples with the latest VCF and patient info. Samples in which results change will be highlighted. Samples in which results remain the same will undergo a next rounds of reanalysis.

A list of all the samples that harbour updates after reanalysis (new variants and/or updated classifications) is displayed at the bottom of the Reanalysis & Autopilot screen. Once these samples have undergone manual review, they will disappear from the list.

If a variant is added to the KB from within a certain sample in Moon, the 'updated variants' label will not be displayed for that sample.

Reanalysis can also be automated through the API.

Reanalysis & Autopilot settings

Admins can define different settings using the Reanalysis & Autopilot page, including:

Both for manual reanalysis and the Autopilot (if active):

  • The “top n” variants in the Shortlist for which to compare updates during reanalysis. By default, Moon will highlight cases in which there are changes within the top 5 variants. Limiting the comparison to the top n variants will reduce the number of cases flagged for manual review, and increase the chance of relevant new findings in the updated cases.

  • Whether to also check for variant classification updates in the lab’s internal knowledge base (KB), Clinvar, or both, during reanalysis

ClinVar variants with ‘Conflicting interpretations’ are annotated with a single ClinVar classification in Moon. If at least 1 LP or P classification is present, this will be the annotated ClinVar classifiction. If there is no LP/P classification and there is at least 1 LB/B classification, this will be the annotated classification in Moon. Flagging cases for updated ClinVar classifications takes into account the annotated classifications by Moon.

For the Autopilot:

  • Which samples to regularly reanalyse

  • The time frame for automated reanalysis

  • Whether you would like the assigned scientist to receive an email notification for cases where results/classifications are different from the previous analysis

Time Machine

For each sample, you can review the results and reports for all analyses performed over time. Via the menu at the bottom of the Shortlist screen, an analysis of choice can be selected. Previous results are displayed similarly to results from new analyses. The patient info for previous analyses is displayed based on the info that was inputted in Moon at the time of that specific analysis.