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Main Report Templates

This section describes the main report templates used to present data analysis results. Some of these templates may have been added to your profile by an administrator during registration in the System.

This section also serves as a repository of ready-to-use report templates: you can download template files and import them into the System manually. If a required template is not available in your profile, you can contact your administrator or add it as described below.

ACMG Secondary Findings Report#

The report includes the variants discovered in the sample, which are located in the genes from the Secondary Findings (SF) list of American College of Medical Genetics and Genomics (ACMG). For these genes, specific mutations are known to be causative of disorders with defined phenotypes that are clinically actionable by an accepted intervention. The ACMG recommends that pathogenic or likely pathogenic variants detected in any of these genes should be reported as they are of medical relevance and could be used in the future to inform clinical treatment. A detailed description of the report is provided in the corresponding section.

Report Generation Conditions#

The report can be generated if the following conditions are met:

  • The sample is uploaded in one of the supported formats (FASTQ, VCF, etc.)
  • The sample may be either normal (non-tumor) or tumor. The ability to generate the report depends on the template settings: the sample types to which it applies and the mutation origin.
  • The sample analysis has been successfully completed (all stages have the status "Complete").
  • The SNVs/Indels annotation stage has been successfully completed.
  • The report template is active.
  • The report template was added to the system before the sample processing was completed.

The report can be generated from any type of genetic test (NGS or DNA microarray); however, its completeness depends on the test type and data format:

  • Whole genome (WGS) and whole exome (WES) sequencing data in FASTQ format contain the most comprehensive information for this report.
  • Complete information is preserved in WGS and WES data in VCF format, provided that reference homozygotes are included in the VCF file.
  • VCF files generated from NGS data without reference homozygotes contain an acceptable but not exhaustive amount of information. They do not guarantee the absence of SNVs in the human genome, even if such variants are not listed in the report.
  • Targeted panel sequencing allows high-quality analysis of specific gene regions, entire genes, or selected gene sets. If variants are present in the analyzed regions, they are highly likely to be detected and included in the report. However, genes from the ACMG SF list that are not included in the panel will not be analyzed.
  • DNA microarray data (typically in TXT or VCF format) can also be used to generate an ACMG SF report. However, this testing approach allows detection of only a very limited subset of potential variants in the genes of interest. Therefore, the absence of variants in the report does not guarantee the absence of genomic alterations.

Adding a Report Template#

You can add the ACMG secondary findings report template in one of the following ways:

  • Import a ready-made template from the example below;
  • Create a template manually.

Importing a Report Template#

Report template parameters may vary depending on your data and research objectives. Below is an example template suitable for identifying secondary findings among germline variants in samples of any type (normal and tumor) using default settings.

After importing the template, you can modify any of its parameters or create a customized version with settings appropriate for your needs.

Example report template: ACMG SF

You can download the file using the link above and import it into the system as described here.

Creating a Report Template#

To create a report template manually, follow these steps:

  1. On the "Report templates" page, click to open the template creation page.

  2. Fill in the main fields:

  • Name (example): ACMG SF
  • Applicable to samples: Any / Normal / Tumor - select the appropriate option depending on which sample types the report should apply to. If unsure, it is recommended to select "Any".
  • Active: yes

  1. Click to save the template.

  2. Add the block "SNVs/Indels in ACMG SF genes" to the template. If necessary, you can modify the block parameters or add it with default settings by clicking . A detailed description of the block fields is available in the corresponding section.

Report on Polygenic Traits#

The block displays results of polygenic trait prediction. Polygenic traits are characteristics that result from the combined action of many different genes, each contributing a small effect to the overall trait score. The selection of polygenic traits to display in the report is determined in the report template block. A detailed description of the report is provided in the corresponding section.

Report Generation Conditions#

The report can be generated if the following conditions are met:

  • The normal sample (non-tumor) is uploaded in one of the supported formats (FASTQ, VCF, etc.)
  • The sample analysis has been successfully completed (all stages have the status "Complete").
  • The "Polygenic risk scores calculation" task of the "Genomic predictions" analysis stage has been successfully completed.
  • The report template is active.
  • The report template was added to the system before the sample processing was completed.

Polygenic traits can be calculated only using whole genome sequencing (WGS) data or whole genome genotyping data obtained from DNA microarrays. For WGS, the data must be provided in FASTQ format or in VCF format including reference homozygotes.

Adding a Report Template#

You can add the Polygenic Traits report template in one of the following ways:

  • Import a ready-made template from the example below;
  • Create a template manually.

Importing a Report Template#

The report template defines the list of polygenic traits to display in the report. Below is an example template that includes all available polygenic traits. After importing the template, you can modify traits selection or create a customized version with a list of traits appropriate for your needs.

Example report template: Polygenic Traits

You can download the file using the link above and import it into the system as described here.

Creating a Report Template#

To create a report template manually, follow these steps:

  1. On the "Report templates" page, click to open the template creation page.

  2. Fill in the main fields:

  • Name (example): Polygenic Traits
  • Applicable to samples: Normal
  • Active: yes

  1. Click to save the template.

  2. Add the block "Polygenic traits" to the template.

  3. Select the traits to display in the report.

  4. Click to add the block.

Pharmacogenetic Report#

The report presents the results of pharmacogenetic testing, which makes it possible to account for the patient's hereditary characteristics when prescribing medications. Genetic variants can affect the effectiveness and safety of therapy by increasing, reducing, or completely eliminating the response to treatment, or by raising the risk of adverse drug reactions. A detailed description of the report is provided in the corresponding section.

Report Generation Conditions#

The report can be generated if the following conditions are met:

  • The normal sample (non-tumor) is uploaded in one of the supported formats (FASTQ, VCF, etc.)
  • The sample analysis has been successfully completed (all stages have the status "Complete").
  • The "Calculation of pharmacogenetic" task of the "Genomic predictions" analysis stage has been successfully completed.
  • The report template is active.
  • The report template was added to the system before the sample processing was completed.

As a rule, conclusions regarding the efficacy or contraindications of specific medications can be made (with varying degrees of confidence) based on most types of genetic testing (such as NGS or DNA microarrays), with the exception of targeted panel sequencing. In the case of targeted panel sequencing, the feasibility of generating the report depends on the panel design. If the panel includes the required genes, the report can be generated; otherwise, it cannot. Some targeted panels are specifically designed for this type of report.

The most comprehensive report can be generated using whole genome sequencing (WGS) or whole exome sequencing (WES) data. The data should be provided in FASTQ format or in VCF format including reference homozygotes. If WGS or WES data are provided in VCF format without reference homozygotes, reports cannot be generated for many medications. DNA microarray data (typically provided in TXT or VCF format and including reference homozygotes) are also suitable for generating reports for many, though not all, medications.

Adding a Report Template#

You can add the Pharmacogenetic report template in one of the following ways:

  • Import a ready-made template from the example below;
  • Create a template manually.

Importing a Report Template#

Download the template file (Pharmacogenetic) and import it as described here.

Creating a Report Template#

To create a report template manually, follow these steps:

  1. On the "Report templates" page, click to open the template creation page.

  2. Fill in the main fields:

  • Name (example): Pharmacogenetic
  • Applicable to samples: Normal
  • Active: yes

  1. Click to save the template.

  2. Add the block "Pharmacogenetic" to the template.

  3. Specify a block name (equivalent to a section title in a report).

  4. Click to add the block.

Ancestry Report#

The report presents the results of a genetic ancestry analysis. Ancestry inference is performed using ADMIXTURE and the Human Genome Diversity Project reference genotypic panel, constructed based on the GRCh38 human genome assembly and comprising data from 929 individuals from 54 populations. A detailed description of the report is provided in the corresponding section.

Report Generation Conditions#

The report can be generated if the following conditions are met:

  • The normal sample (non-tumor) is uploaded in one of the supported formats (FASTQ, VCF, etc.)
  • The sample analysis has been successfully completed (all stages have the status "Complete").
  • The "Ancestry analysis" task of the "Genomic predictions" analysis stage has been successfully completed.
  • The report template is active.
  • The report template was added to the system before the sample processing was completed.

For reliable ancestry analysis based on NGS sequencing or DNA microarray results, the data must include reference homozygotes. Whole genome sequencing (WGS) data in FASTQ format or in VCF format including reference homozygotes are best suited for this analysis. DNA microarray data (typically provided in TXT or VCF format and including reference homozygotes) are also highly suitable. Whole exome sequencing (WES) data can also be used, although with lower resolution and accuracy. In this case, the data must likewise be provided in FASTQ format or in VCF format including reference homozygotes. Targeted panel sequencing data are generally not suitable for ancestry analysis, except in the case of mitochondrial DNA genotyping or Y chromosome genotyping. Mitochondrial DNA is inherited from the mother by both sons and daughters and can therefore be used to determine maternal lineage. The Y chromosome is inherited from father to son and can be used to determine paternal lineage.

Adding a Report Template#

You can add the Ancestry report template in one of the following ways:

  • Import a ready-made template from the example below;
  • Create a template manually.

Importing a Report Template#

Download the template file (Ancestry Report) and import it as described here.

Creating a Report Template#

To create a report template manually, follow these steps:

  1. On the "Report templates" page, click to open the template creation page.

  2. Fill in the main fields:

  • Name (example): Ancestry Report
  • Applicable to samples: Normal
  • Active: yes

  1. Click to save the template.

  2. Add the block "Ancestry" to the template.

  3. Specify a block name (equivalent to a section title in a report). If necessary, the probability threshold for populations can be adjusted (see the corresponding section for details).

  4. Click to add the block.

Onco-Genetic Testing Report#

The report contains onco-relevant variants discovered in the sample and included to the report by the user, and clinical guidelines corresponding to these variants. A detailed description of the report is provided in the corresponding section.

Report Generation Conditions#

The report can be generated if the following conditions are met:

  • The sample is uploaded in one of the supported formats (FASTQ, VCF, etc.)
  • The sample may be either normal (non-tumor) or tumor. The ability to generate the report depends on the sample types to which it applies.
  • The sample analysis has been successfully completed (all stages have the status "Complete").
  • The SNVs/Indels annotation stage has been successfully completed.
  • The report template is active.
  • The report template was added to the system before the sample processing was completed.

Adding a Report Template#

You can add the Onco-genetic testing report template in one of the following ways:

  • Import a ready-made template from the example below;
  • Create a template manually.

Importing a Report Template#

Download the template file (Onco-Genetic Testing Report) and import it as described here. This template is suitable for generating an onco-genetic testing report for both normal and tumor samples.

Creating a Report Template#

To create a report template manually, follow these steps:

  1. On the "Report templates" page, click to open the template creation page.

  2. Fill in the main fields:

  • Name (example): Onco-Genetic Testing Report
  • Applicable to samples: Any / Normal / Tumor - select the appropriate option depending on which sample types the report should apply to. If unsure, it is recommended to select "Any".
  • Active: yes

  1. Click to save the template.

  2. Add the block "Onco: Onco relevant SNVs/Indels selected by user for reports" to the template. Specify a block name (equivalent to a section title in a report). Click .

  3. Add the block "Onco: Clinical Guidelines for onco relevant SNVs/Indels selected by user for reports" to the template. Specify a block name (equivalent to a section title in a report). Click

CNV Report#

The report presents the results of the analysis of the patient sample or samples in order to detect changes in the number of copies of chromosomes. The template affects Sample CNV Report and Patient CNV Report (for all patient samples) generation.

Report Generation Conditions#

The report can be generated if the following conditions are met:

  • The normal sample (non-tumor) is uploaded in FASTQ or BAM format.
  • The sample analysis has been successfully completed (all stages have the status "Complete"). If the analysis fails, then a corresponding message is displayed in the patient report, and the sample report is not built.
  • The "Copy number variations discovery" stage has successfully completed. If the stage fails, then a corresponding message is displayed in the patient report, and the sample report is not built. If the stage is turned off, then the report for the sample will not be built, and the sample will not be mentioned in the report for the patient. If the stage is turned off for all patient samples, then the report for the patient will not be built.
  • The report template is active.
  • The report template was added to the system before the sample processing was completed.

Add CNV Report template#

To add CNV Report template to the system, you can either import it or create it yourself.

Import CNV Report template#

Download the template file (CNV Report) and import it as described here.

Create CNV Report template#

To create a template yourself, follow these steps:

  1. On the Report templates page, click on to open the page for a report template adding.

  2. On the page that opens, fill in the following fields:

  • Name: CNV Report
  • Applicable to samples: Normal
  • Active: yes
  • Report title:
REPORT ON THE RESULTS OF THE ANALYSIS OF SEQUENCING DATA IN ORDER TO DETECT CHANGES IN THE NUMBER OF COPIES OF CHROMOSOMES

  1. Click on to save the template.

  2. Add all the blocks listed below to the template. The list of blocks is given in the order in which they appear in the template. If there are no clarifications after the block name, then the block generated by default is used.

The template blocks#

  1. "Patient info". Display fields: Patient id, First name, Last name, Date of birth, Sex.
  2. "Sample info". Display fields: Sequencing type, Sample collection date.
  3. "Germline CNV: results".
  4. "Germline CNV: interpretation".
  5. "Disclaimer". Text:
# Technical constraints
Whole genome sequencing may be insufficiently sensitive for detecting aneuploidies and determining sex of a sample at a genome reading depth of less than 0.01 per one base pair (bp). Analytical sensitivity for all types of aneuploidies is available upon request or in the software documentation.
# Restrictions on the use of the Report
The information provided in this document is intended solely for internal professional use. The information cannot be used as a substitute for professional medical advice, diagnosis, treatment or care. The report can only be used in conjunction with all available clinical and laboratory data and should not be used in isolation from this data. The studies were carried out to the extent specified by the customer.
Additional information on this analysis can be obtained at {url} in the section "Bioinformatics report" or upon request from the company that provided this report.
  1. "Sign place".

Glioma report#

  • a clinical report on the characteristics of gliomas, based on tumor markers identified in the sample, and a base created on the basis of expert knowledge and published research on this topic;
  • suitable for presenting the results of the analysis of glioma samples in any file format.

Report Generation Conditions#

Glioma report is generated for the sample if the following conditions are met:

  1. The sample is uploaded as a tumor tissue sample.
  2. The sample analysis was successfully completed (that is, all stages of the analysis have the status "Complete").
  3. For a single tumor sample (tumor-only), at least one of the following stages was successfully completed: "Somatic SNVs/Indels annotation", "Germline SNVs/Indels annotation", or "Copy number variations discovery". If you have a set of tumor and corresponding non-tumor samples (tumor-normal), then it is necessary that the "Somatic SNVs/Indels annotation" stage was successfully completed for tumor sample, and "Germline SNVs/Indels annotation" stage was successfully completed for normal sample.
  4. The report template is active.
  5. The report template was created before the sample was processed.

Add Glioma Report template#

To add Glioma Report template to the system, you can either import it or create it yourself.

Import Glioma Report template#

Download the template file (Glioma report) and import it as described here.

Create Glioma Report template#

To create a template yourself, follow these steps:

  1. On the Report templates page, click on to open the page for a report template adding.

  2. On the page that opens, fill in the following fields:

  • Name: Glioma report
  • Applicable to samples: Tumor
  • Active: yes

  1. Click on to save the template.

  2. Add all the blocks listed below to the template. The list of blocks is given in the order in which they appear in the template. If there are no clarifications after the block name, then the block generated by default is used.

The template blocks#

  1. "Patient info".
  2. "Section".

Name:

SOMATIC MUTATIONS REPORT

Description:

Tumor specimen
  1. "Sample info".
  2. "Glioma: Tier I variants".
  3. "Glioma: Tier II variants".
  4. "Immunotherapy markers".
  5. "Glioma: Suggested diagnosis".
  6. "Glioma: Suggested drugs".
  7. "Glioma: Mutations details".
  8. "Glioma: Tier III variants".
  9. "Clinical trials".

Description:

List of ongoing clinical trials from <https://clinicaltrials.gov> found for Glioma

Phenotypes:

Glioma;Astrocytoma;Glioblastoma;Diffuse Intrinsic Pontine Glioma;Ependymoma;Glioma, Subependymal;Ganglioglioma;Gliosarcoma;Medulloblastoma;Oligodendroglioma;Optic Nerve Glioma
  1. "Glioma: Glioma genes panel details".
  2. "Section".

Name:

GERMLINE VARIANTS REPORT

Description:

Normal specimen
  1. "Control (normal) sample info".
  2. "Glioma: Germline pathogenic for gliomas".
  3. "SNVs/Indels in ACMG SF genes".
  4. "Glioma: Germline pathogenic for any other diseases".
  5. "Glioma: Germline glioma associated".
  6. "Section". Name:
REFERENCE LIST
  1. "Glioma: Literature".
  2. "Section". Name:
TECHNICAL LIMITATIONS
  1. "Disclaimer". Text:
# Limit of detection
The NGS method may be not sensitive enough for detection of SNVs and Indels with less than 5% and 10% variant allele frequency respectively.
# Analytical sensitivity
Analytical sensitivity for all variant classes is available upon request or through our website.
# Clinical disclaimer
 All content found in this report was provided for informational purposes only. It is not intended to substitute a professional medical advice, diagnosis, treatment or care. The report should be used with all available clinical and laboratory data and should not be used separately to diagnose a malignancy. Please contact your doctor or any other qualified professional to seek a medical advice. Never use this report to disregard a medical advice or delay contacting a qualified professional.