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Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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Best Practice for Clinical Somatic Variant Interpretation and Reporting.

Jeffrey Schubert¹, Jinhua Wu¹, Marilyn M Li²

¹Division of Genomic Diagnostics, Department of Pathology & Laboratory Medicine, The Children's Hospital of Philadelphia, 3615 Civic Center boulevard, 706 ARC, Philadelphia, PA 19104, USA.

Clinics in Laboratory Medicine

|September 23, 2022

Summary

Standardizing cancer variant classification is crucial as tumor sequencing grows. Adopting established guidelines ensures accurate identification and assessment of clinically relevant somatic variants for better patient care.

Keywords:

Clinical impact Reporting criteria Somatic variant classification Variant oncogenicity

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Area of Science:

Oncology
Genomics
Molecular Pathology

Background:

The clinical significance of cancer genomics is increasingly recognized, driving the expansion of tumor sequencing.
A need exists for standardized approaches to classify and name somatic variants in cancer research and diagnostics.

Purpose of the Study:

To emphasize the importance of adopting established guidelines for classifying cancer-related somatic variants.
To advocate for a standardized nomenclature system for somatic variants in clinical practice.

Main Methods:

Review and adoption of guidelines from the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists.
Implementation of robust bioinformatics pipelines for variant identification.
Thorough data analysis for variant assessment.

Main Results:

Standardized classification systems are essential for the growing field of cancer genomics.
Adoption of guidelines facilitates reproducible identification of clinically relevant variants.
Bioinformatics and data analysis are key to assessing variant impact.

Conclusions:

Laboratory professionals must adopt existing guidelines to standardize somatic variant classification.
A unified system for nomenclature and classification is vital for advancing cancer genomics.
Efficient and reproducible identification of clinically relevant variants requires robust bioinformatics and data analysis.