WORKSHOP 1 | Fundamentals of Variant Filtering in the Genome

Pre-Workshop Expectations from Participants

Participation with a personal computer is expected.

Variant Interpretation Workshop Format

• Presentation
• Gennext Demo
• Hands-on training

PART 1: THEORETICAL PRESENTATION

Basic Concepts & Terminology

• Variant types (SNV, InDel, CNV)
• Germline vs Somatic variants
• VCF format and NGS data

Variant Filtering Strategy

• Filtering pyramid
• Frequency, quality, and functional impact filters
• Mendelian disease and cancer approaches

Tools & Databases

• In-silico tools (CADD, SIFT, PolyPhen-2)
• ClinVar, gnomAD, OMIM
• ACMG/AMP classification criteria

PART 2: GENNEXT DEMO

Germline Analysis

• Platform introduction
• Filtering and ACMG assessment

Learning Objectives

• Understanding the variant filtering logic
• Familiarity with the Gennext platform
• Applying ACMG criteria