Mosaic Overview

Mosaic is a comprehensive genomic data management and analysis platform for clinical and research teams. It brings a case's data, the team's discussion of that case, and the tools needed to analyze it together in one place, so that the work of reaching a genetic diagnosis is collaborative, organized, and reproducible.

This Overview introduces what Mosaic does and the core concepts you will meet throughout the rest of the documentation. If you are signing in for the first time, start with Getting Started.

What Mosaic Is For

Clinical genomic diagnostics requires a multidisciplinary collaborative effort. Mosaic is built for the teams who do that work — clinicians, genetic counselors, laboratory scientists, bioinformaticians, and researchers — and for the reality that a single case passes through many hands. Rather than spreading a case across spreadsheets, email threads, file shares, and separate analysis tools, Mosaic keeps the data, the conversation, and the results in a single shared workspace.

Team-based genomic diagnostics

Mosaic provides tools to enable clinical and research teams to collaborate on the management of patient populations, data analytics, and variant analysis. All case discussions can be easily managed and organised by content. Conversations on a patient's clinical presentation or on specific genetic variants do not need to be lost across email threads or slide shows, but can be easily shared with the whole team in a single central location - tied directly to the underlying genomic data.

From Cases to Cohorts

Mosaic uses Projects to store data on individual cases, for example a family trio (proband, mother and father) with sequencing data or a singleton (proband only). Collections of Projects allow cohorts of patients to be managed, edited, and variants analysed at the cohort/population level. The same tools work at both levels: what you do for one case in a project, you can do across an entire cohort in a collection.

Data Reanalysis

Automated reanalysis methods ensure that updating resources can be immediately leveraged to identify changes that may be relevant for the diagnosis of cases. Mosaic has a robust notification and tasks system where clinical team members receive notifications indicating the need to review updated variant evidence or add phenotype information to a case, for example. This ensures that cases which are undiagnosed today can be revisited automatically when the evidence changes — without anyone having to remember to re-run it.

All Experts in One Place

Clinical genomic diagnostics requires a multidisciplinary collaborative effort. Having data, communication, and results in one place streamlines the process of achieving diagnosis for patients living with genetic conditions.

Core Concepts

The rest of this documentation refers to some key concepts repeatedly. Here's quick summary to help you understand them up front.

Projects are the basic unit of organization — typically one case (a single patient, a family trio, or any group you choose). A project holds that case's samples, phenotypes, variants, documents, data files, and conversations. See Projects.

Collections are essentially groups of projects that can be managed and analyzed together. A collection lets you compare attributes and query variants across every case/project it contains. Project can belong to more than one collection. See Collections.

Samples are the individuals within a project — for example a proband, parent or sibling. Information specific to a person, such as affected status, sex or sequencing depth, are stored as sample attributes.

Attributes are structured pieces of information. Project attributes describe the case/project as a whole (for example, diagnostic status); sample attributes describe an individual sample. Recording information as attributes — rather than free text — is what makes it possible to compare and chart data across a whole cohort. See Project Attributes.

HPO terms capture a patient's phenotype using the standardized vocabulary of the Human Phenotype Ontology, which Mosaic uses to relate clinical features to candidate genes and to prioritize variants. See HPO Terms.

MONDO terms are similar to HPO terms but use the standardized MONDO disease ontology. This helps teams clarify specific genetic diagnoses and reconcile sometimes unclear or disparate sets of HPO terms See MONDO terms.

Variants are the genetic findings for a case. Mosaic's variant analysis tools let you view, annotate, filter, discuss, and track variants for one case or across a cohort. See Variants.

Templates are special projects that define a standard set of attributes, conversations, and dashboard layout, applied automatically when projects are created so that every case in a program starts out with consistent views. See Templates.

Conversations are discussion threads attached to a project, a collection, or a specific variant, keeping the team's reasoning beside the data it concerns. You can tag specific users in your comments using the @ symbol. See Communication.

Tasks are outstanding items — required information to complete, or variants flagged for review — that give the team a shared, trackable to-do list. See Tasks.

How This Documentation Is Organized

The documentation broadly moves from organizing data to analyzing it:

• Getting set up — Getting Started and the FAQs.
• Organizing your data — Projects, Collections, Templates, Policies, and Creating Projects and Collections.
• Describing your data — Project Attributes, Sample Attributes, and Communication.
• Analyzing your data — Variants, Genes, Tasks, Analytics and Charts, and ClinVar Reanalysis.
• Automating your work — the API.

Mosaic also integrates a set of Client Applications — including genome browsers — for visualizing data in detail.

Tip: You do not have to read the documentation in order. If you have a specific goal in mind — analyzing a case's variants, setting up a new cohort, or configuring reanalysis — jump to the relevant section and follow its cross-references.