Molecular
Nomenclature
Technical standards and guidelines
Integrative Genomics Viewer
NGS bioinformatics and file types
Analysis of constitutional/ germline sequence variants
Guidelines
Online variant interpretation tool
Using the gnomAD database
Analysis of somatic/acquired sequence variants
Guidelines
Introduction to cancer variant databases and knowledge-bases (Coming Soon!)
Nomenclature
Human Genome Variation Society (HGVS) Nomenclature
- HGVS Nomenclature is an internationally-recognized standard for the description of variants
- The website is free to use and provides recommendations for variant description including examples, organized by category (DNA, RNA, protein) and variant type.
Technical standards and guidelines
ACMG Technical Standards for Clinical Genetics Laboratories (2021 revision)
- Voluntary standards that establish criteria for clinical labs to provide accurate and reliable testing
- Seven sections, including personnel and general lab policies
- Clinical Molecular Genetics (section G)
- Includes guidelines for sequencing as well as other non-sequencing based tests, as well as assay validation, quality control, interpretation and reporting
Integrative Genomics Viewer (IGV)
How to use Integrative Genomics Viewer (IGV)
NGS Bioinformatics File Types
Introduction to NGS Bioinformatics and File Types
Guidelines
Richards et al. 2015 (PMID: 25741868)
Recommendations from the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) for the interpretation of sequence variants.
Online Variant Interpretation Tool
Genetic Variant Interpretation Tool (University of Maryland)
- Freely available online tool for variant classification based on the ACMG/AMP guidelines
- Allows you to select the applicable evidence categories (PVS1, PM2, etc.) and provides the variant classification
Using the gnomAD database
This document provides some background about the Genome Aggregation Database (gnomAD) including sources of gnomAD data, and some points to consider when using different versions of gnomAD.
Analysis of somatic/acquired sequence variants
Guidelines
Li et al. 2017 (PMID: 27993330)
Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists
Coming Soon! Introduction to cancer variant databases and knowledgebases
Data and information obtained from the Cancer Genomics Consortium (CGC) and the Geneticist Toolkit are provided as an educational resource only; they should not be used as a stand-alone resource for clinical decision making or reporting, as they may contain errors or omissions. Review of the data by an appropriately trained medical professional is required for clinical reporting. Some of these resource pages may include links to content created by commercial entities and/or which require a fee for service; the inclusion of such material is meant for educational purposes only and does not represent an endorsement of these entities by the CGC.
The CGC and all participating entities make no representation or warranty, express or implied, including without limitation any warranties of merchantability or fitness for a particular purpose or warranties as to the identity or ownership of data or information, the quality, accuracy or completeness of data or information, or that the use of such data or information will not infringe any patent, intellectual property or proprietary rights of any party. The CGC shall not be liable for any claim for any and all loss, harm, illness or other damage or injury arising from access to or use of data or information howsoever caused, including without limitation, any direct, indirect, incidental, exemplary, special or consequential damages, even if advised of the possibility of such damages. The data and information obtained from the Geneticist Toolkit shall not be used as a substitute for the user's skills, expertise and experience.
