Molecular Diagnostics

  1. Bioinformatics and Data Analysis
    1. Sequence Data Processing
      1. Raw Data Handling
        1. FASTQ File Format
          1. Quality Score Encoding
            1. Read Structure
            2. Quality Control Assessment
              1. Per-Base Quality Scores
                1. Sequence Length Distribution
                  1. GC Content Analysis
                    1. Adapter Contamination
                  2. Sequence Alignment
                    1. Reference Genome Alignment
                      1. Alignment Algorithms
                        1. Mapping Quality Assessment
                          1. Handling Multi-Mapping Reads
                          2. File Formats
                            1. SAM Format
                              1. BAM Format
                                1. CRAM Format
                                2. Alignment Quality Control
                                  1. Coverage Analysis
                                    1. Insert Size Distribution
                                      1. Duplicate Read Identification
                                  2. Variant Detection and Analysis
                                    1. Variant Calling
                                      1. Single Nucleotide Variants
                                        1. Insertion and Deletion Variants
                                          1. Structural Variants
                                            1. Copy Number Variants
                                            2. Variant Filtering
                                              1. Quality-Based Filtering
                                                1. Population Frequency Filtering
                                                  1. Functional Impact Filtering
                                                  2. Variant Annotation
                                                    1. Functional Consequence Prediction
                                                      1. Population Frequency Databases
                                                        1. Clinical Significance Databases
                                                          1. Pathogenicity Prediction Tools
                                                          2. Variant Classification
                                                            1. ACMG Guidelines
                                                              1. Pathogenic Variants
                                                                1. Likely Pathogenic Variants
                                                                  1. Variants of Uncertain Significance
                                                                    1. Likely Benign Variants
                                                                      1. Benign Variants
                                                                  2. Gene Expression Analysis
                                                                    1. RNA-Seq Data Processing
                                                                      1. Read Alignment to Transcriptome
                                                                        1. Gene Expression Quantification
                                                                          1. Transcript Assembly
                                                                          2. Differential Expression Analysis
                                                                            1. Statistical Methods
                                                                              1. Multiple Testing Correction
                                                                                1. Fold Change Calculations
                                                                                2. Functional Analysis
                                                                                  1. Gene Ontology Analysis
                                                                                    1. Pathway Enrichment Analysis
                                                                                      1. Network Analysis
                                                                                    2. Data Management and Storage
                                                                                      1. Database Systems
                                                                                        1. Relational Databases
                                                                                          1. NoSQL Databases
                                                                                            1. Cloud Storage Solutions
                                                                                            2. Data Security and Privacy
                                                                                              1. Encryption Methods
                                                                                                1. Access Control
                                                                                                  1. Audit Trails
                                                                                                  2. Laboratory Information Management Systems
                                                                                                    1. Sample Tracking
                                                                                                      1. Result Reporting
                                                                                                        1. Quality Control Integration

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                                                                                                    2. Core Methodologies and Technologies

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                                                                                                    4. Clinical Applications of Molecular Diagnostics