❓ What are Genomic Variants from omics (WGS/WES) data and what scientific concepts should you know for stress-free, organized and accurate 🧬 variant curation and classification? 🎯

💡 Concepts to know:

Genomic Variants Definition:

Differences in DNA sequences among human genomes, detected either in coding regions (via WES) or across the entire genome (via WGS) and central to understanding health-related traits and diseases | https://www.genome.gov/about-genomics/educational-resources/fact-sheets/human-genomic-variation

Variant Curation and Classification:

(I) Based on various criteria and the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) system:

1. Minor Allele Frequency (MAF) as per Genome Aggregation Database (gnomAD) | https://pubmed.ncbi.nlm.nih.gov/34889978/ , https://pubmed.ncbi.nlm.nih.gov/34859531/ , https://pubmed.ncbi.nlm.nih.gov/35856030

   • MAF < 0.000001 % => Hyper-rare
   • 0.001% < MAF < 0.1% => Ultra-rare
   • 0.1% ≤ MAF < 1% => Rare
   • 1% ≤ MAF < 5% => Low-frequency
   • MAF ≥ 5% => Common

2. Computational predictive tools | https://pubmed.ncbi.nlm.nih.gov/25741868/

   • Missense prediction
   • Splice site prediction
   • Nucleotide conservation prediction

3. Clinical Significance | https://pubmed.ncbi.nlm.nih.gov/25741868

   • Pathogenic (P)
   • Likely Pathogenic (LP)
   • Variant of Uncertain Significance (VUS)
   • Likely Benign (LB)
   • Benign (B)

4. Evidence Framework | https://pubmed.ncbi.nlm.nih.gov/25741868/

   • Criteria of pathogenicity
     • Very strong: PVS1
     • Strong: PS1, PS2, PS3, PS4
     • Moderate: PM1, PM2, PM3, PM4, PM5, PM6
     • Supporting: PP1, PP2, PP3, PP4, PP5
   • Benign
     • Stand-alone: BA1
     • Strong: BS1, BS2, BS3, BS4
     • Supporting: BP1, BP2, BP3, BP4, BP5, BP6, BP7

5. Disease-associated variant class | https://pubmed.ncbi.nlm.nih.gov/37982373/ , https://pubmed.ncbi.nlm.nih.gov/37234922/ Fig 4

   • Non-synonymous (Missense)
   • Synonymous
   • Splicing
   • UTR
   • Intronic
   • Regulatory

6. Disease-associated variant consequence | https://pubmed.ncbi.nlm.nih.gov/37982373/

   • Altered gene product level
   • Increased gene product level
   • Decreased gene product level
   • Absent gene product
   • Altered gene product sequence
   • Functionally normal

7. HPO (Human Phenotype Ontology) Mode of Inheritance | https://pubmed.ncbi.nlm.nih.gov/37982373/

   • Allelic Requirement | Mendelian Inheritance Term
     • monoallelic_autosomal | Autosomal Dominant (AD)
     • biallelic_autosomal | Autosomal Recessive (AR)
     • monoallelic_X_heterozygous | X-linked Dominant
     • monoallelic_X_hemizygous | X-linked Recessive
     • monoallelic_Y_hemizygous | Y-Linked
     • mitochondrial | Mitochondrial
     • monoallelic_PAR | PAR dominant
     • biallelic_PAR | PAR recessive
   • Non-Mendelian Inheritance
     • Digenic
     • Multigenic/Complex
   • Additional Context / Optional Terms
     • De novo (new)
     • Somatic mosaicism
     • Incomplete penetrance
     • Complete penetrance
     • Highly variable age of onset
     • Age-related onset
     • Imprinted: maternal or paternal
     • Repeat expansion
     • Requires heterozygosity
     • Sex-limited expression
     • Contiguous gene syndrome

8. Type of alteration | https://www.genome.gov/about-genomics/educational-resources/fact-sheets/human-genomic-variation

   • Single Nucleotide Variant (SNV)
   • Insertion (INS)
   • Deletion (DEL)
   • Copy Number Variant (CNV)

9. Cell type (origin) | https://pubmed.ncbi.nlm.nih.gov/32498674/

   • Germline (heritable)
   • Somatic
   • Shared

(II) Based on ABC system | https://pubmed.ncbi.nlm.nih.gov/33981013/ , https://pubmed.ncbi.nlm.nih.gov/38778080/

1. Step A: Functional grading (functional classes)

   • functional VUS (fVUS)
   • Normal function (NF)
   • Likely normal function (LNF)
   • Hypothetical functional effect (HFE)
   • Likely functional effect (LFE)
   • Functional effect (FE)

2. Step B: Clinical grading (clinical classes)

   • clinical VUS (cVUS)
   • Variant of potential interest (VOI)
   • Known or assumed risk factor variant
   • Pathogenic variant
   • Moderate penetrance pathogenic variant
   • High penetrance pathogenic variant

3. Combined A+B class

   • 0: Not reported
   • F: Not reported; gene is unrelated to the phenotype
   • E: Variant of potential interest (VOI)
   • D: Low penetrance and good candidate
   • C: Pathogenic: disease-associated variant
   • B: Pathogenic: disease-associated variant of moderate penetrance
   • A: Pathogenic: disease-associated variant of high penetrance
   • X: Secondary/incidental finding

4. Step C: Selection of standard variant comment based on combined class C

   • 0: Normal findings
   • F: Normal findings - No P/LP
   • F/E: Normal findings - No P variants related to the phenotype
   • E/D: Normal findings - No P variants to explain the phenotype
   • E/D: Genetic variant of potential interest
   • E/D: Heterozygosity for a recessive genetic variant of potential interest
   • D: Genetic variant that increases susceptibility for this phenotype
   • C/B/A: Disease-associated pathogenic variant
   • X: Genetic variant unrelated to the clinical question

📌 Tutorial

Refer tutorial here: https://github.com/gurpreet-bioinfo/vcf_concepts_analysis_visualization/tree/main to explore and interactively visualize a VCF file using free web-based tools, and hands-on with the above concepts.