Mission Bio's MRD Pipeline allows customers to process single-cell MRD DNA + Protein sequencing data generated on the Tapestri Platform.
Table of Contents
MRD single or multiplexed sample analysis
NOTE: Mission Bio’s single cell MRD (scMRD) analysis pipeline has been replaced with Tapestri Single cell Clonal Insights Software. Please refer to this article to start the runs and analyze data from the new software.
MRD-AML Output Files
MRD pipeline outputs the following files:
MRD single or multiplexed sample analysis
- <prefix>.report.html - HTML report for the DNA+Protein pipeline
- <prefix>--fastp.html - QC HTML report for DNA data
- <prefix>-fastp.html - QC HTML report for Protein data
- <prefix>.cells.bam - BAM file with reads for the called cells
- <prefix>.cells.bam.csi - BAM index file
- {patient_name}.html - MRD HTML report file with details on somatic variants, clonal architecture, protein differential expression and other details. For multiplexed runs, one file is produced for each sample.
- {patient_name}.h5 - This is the final per-sample h5 file and contains filtered variants, clone assignments, normalized CNV and protein data in addition to the contents of a regular h5 file as described in this article. This file can be used for time-course analysis.
Time course analysis reports
- <prefix>.html - Time course analysis HTML report file with details on somatic variants, clonal architecture, protein differential expression, and other details stratified by timepoint. Additionally displays changes in mutational profiles and protein expression across time points.
To download any output file, click the download icon to the left of the File Name.
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The first 5 files are produced by the DNA+Protein pipeline, for more information on these files refer to this article. The last two files are MRD specific, and for multiplexed runs there will be one of each of these files per multiplexed sample.
MRD-AML Report Overview
To download the MRD Run Report, go to the Output Files tab and download the mrd/{patient_name}.html file. Plots and tables in the report are interactive.
Summary
The Summary page displays the following information:
- Mutant clones detected
- Mutant cells detected
- Total cells
- Time points for time course reports
- Clone Barchart: A bar chart that shows the number of cells per clone.
- Somatic variant heatmap per clone
- Protein expression heatmap per clone
- Fishplot for time course reports
- Clones table: A table with sample name (for time course), clone name, the number of cells in clone, mutations and protein differential expression per clone.
- Variants table: A table with the sample name (for time course), variant ID, gene, protein change, coding impact, cells mutated % and various other metrics.
Details
The Details page displays the following information:
- Phylogenetic tree: A visualization showing the order in which the mutations were acquired and how they co-occur.
- Protein UMAP: A UMAP plot showing the protein expression colored by either Protein, sample, clone or genotype.
- Protein expression correlation: A plot showing the correlation in expression for two proteins.
- Protein expression change over time: A time course analysis only plot showing the change in protein expression over a period of time.
- Copy number analysis: Two plots providing a way to visualize copy number profiles for each clone grouped by either chromosome or gene.
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Sample
- Run ID
- Sample ID
- DNA panel name
- DNA panel size
- Reference genome
- Secondary analysis pipeline version
- scMRD pipeline version
- Date analyzed
QC
- Germline variant / multiplexing diagnostic plot: A plot providing a visual representation of germline variant information to help confirm and diagnose sample identity issues.
- Heatmap of somatic variants(raw genotypes): A heatmap showing raw genotype for the somatic variants per cell.
- Heatmap of protein expression: A heatmap showing the normalized protein expression per cell.
Help
The Help page contains a glossary of key words used in the report and a description of every table and plot contained in the report.