Importing Variants

Start new analysis #

A new analysis can be initiated by clicking on the “Start New Analysis” button, which will guide the process of importing variants. This feature entails importing VCF files and associated clinical and general details regarding the subject of the analysis.

Select Start New Analysis

Select Start New Analysis

Protocol #

In the first stage of the analysis, the user will be required to select the protocol. A protocol is a template for analysis which includes predefined filters, the list of required and associated samples and the report template. The protocols are categorized into Germline, Somatic, and Health Screening.

Specify the Protocol for the analysis

Each category includes a set of default protocols representing the most common cases of NGS analysis. These include:

  • Germline
    • Single Sample Analysis – The single sample workflow is used to analyze affected germline samples that do not have maternal or paternal associated VCF files.
    • Trio Analysis– The trio workflow utilizes inheritance models to analyze rare Mendelian mutations using mother, father, and proband samples.
    • Single Sample SNV/SV – This template is used to analyze affected germline samples for single nucleotide polymorphisms and structural variations.
    • CNV Only Analysis– The CNV workflow is used to detect large structural variations that are composed of a specific file format. This format requires: chr, start, end, effect, score, copy number.
    • Mitochondria Analysis– This is used specifically for the analysis of mitochondrial variants.
  • Somatic
    • Tumor Only Analysis – This template is used to analyze tumor-only samples without a paired normal/germline sample.
    • Tumor Normal Analysis – This template is commonly used to analyze somatic samples together with their germline counterparts.
    • Cancer Screening– This template is used to detect the presence of somatic mutations that are not isolated from tumor tissue.
  • Health Screening
    • Carrier Screening– This template is used for the analysis of mutations that could be passed as an inherited genetic condition to offspring.

Subject #

Geneyx Analysis was designed as a subject-centric platform. As such, each analysis contains a single main sample with the option to be accompanied by several associated samples (for example: the parents in a trio case or the matched germline in a tumor biopsy case).

In this section of the wizard, users can enter general details regarding the subject of the analysis. These details will be available throughout the analysis process for reference, and automatically included in the generated report.

Defining patient details in the Subject window for New Subject

For new subjects, the following information can be entered:

  • SUBJECT ID (required) – A unique identifier for your subject. Commonly it would be the patient identifier in your EMR or LIMS system, but it can be any identifier you choose.
  • NAME (optional) – The name of your subject
  • DATE OF BIRTH (optional) – The date of birth of your subject
  • GENDER (optional) – Male / Female. Leave blank for unknown / unspecified
  • CONSANGUINITY (optional) – Commonly used to specify parental consanguinity in cases of rare disease analysis
  • POPULATION TYPE (optional) – Population, people or ethnic groups

You can also select an existing subject if one has already been created.

Defining patient details in the Subject window for Existing Subjects

Samples #

In the Samples section you can either upload a new sample by clicking on Select Sample next to the relevant sample or select an existing pre-loaded sample for the analysis. When a new VCF is uploaded into the system, the user can then define additional parameters. These include:

  • Serial Number: Specify a unique identifier for this analysis. A default value is automatically generated but can be replaced with your own identifier (for example, ID of the case in your system)
  • Sequencing Machine:  The machine used to automate the DNA sequencing process
  • Enrichment Kit: Defines the target capture regions. User can also implement their own BED files
  • Genome Build: The reference genome assembly build used for alignment and mapping
  • Taken Date: Date sample was obtained
  • Sequence Date: Date sample was sequenced
  • Received Date: Date sequencing data was received
  • Sequencing Target: NGS data type
  • Sample Source: Method DNA was collected
  • Notes: Any additional comments
Upload Sample and define general information

Note: If existing samples were selected, the import will use the enrichment kit that was defined on initial import. To change, you can delete the current annotation, then use the edit option to the right of the sample name to change the enrichment kit and then re-annotate.

Clinical Information #

The Clinical Information section is used to incorporate additional context about the analysis and subject. Here the user can set the phenotype terms that will be used to score and rank candidate variants during the analysis stage. Information entered here will be available during the analysis stage for reference.

Enter Clinical Information

The following information can be entered:

  • Serial Number (required): Specify a unique identifier for this analysis. A default value is automatically generated but can be replaced with your own identifier (for example, ID of the case in your system)
  • Name (optional): The protocol used for the analysis
  • Owner (Doctor) (optional): The name of the referring clinician
  • Description (optional): Free text to describe the clinical aspects of the case
  • Disease frequency (required): Expected frequency of this disease occurring in the population. This will be applied in the filter to reduce the number of variants that are observed above the defined threshold.
  • Phenotypes (optional): Any biological term (phenotype) that will be used to score and rank the candidate variants. Multiple phenotypes can be entered using the Advanced option and for compound terms to be recognized properly, users will need to use quotations around the term. For example, a compound term such as Developmental Delay should be entered as “Developmental Delay” to ensure the entire term is used. Once the phenotypes are entered, select Keywords. This will then show which terms are highly specific, which reflects how many genes are associated with the given condition.

Clicking on ‘Save’ in the last section of the wizard will enter this new analysis to your account and will redirect you to the Analysis Summary page.

Analysis summary window

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