Coming soon
Genetics & Genomics
Read a genome and know what the variants mean.
The complete course
- modules
- 63
- topics
- 700
- min lessons
- 15
45%
of the global disease burden could be addressed with science conceivable today.
What you'll be able to do.
Solve crosses, pedigrees and linkage maps
Stage 1 · Foundations of Inheritance
Predict what a mutation will do
Stage 2 · Mutation & Variation
Assess coverage and variant-call quality
Stage 4 · Genomic Technologies
Interpret GWAS hits and polygenic scores
Stage 5 · Population & Quantitative Genetics
Classify variants on the five-tier scale
Stage 6 · Functional & Clinical Genomics
Design a genetic study that holds up
Stage 7 · Practicum & Research Project
Seven stages.One steady climb.
Mendel's peas on day one. A patient's genome by the end.
63modules
in 7 stages
700topics
≈ 11 per module
≈175hours
of 15-minute lessons
≈23months
≈11months
≈6months
to finish the whole course
- 1
Foundations of Inheritance
How traits pass from parent to child
12 modules · 133 topics · ≈ 33 hr
- 2
Mutation & Variation
Where variation comes from
9 modules · 100 topics · ≈ 25 hr
- 3
Genome Architecture & Regulation
Structure, switches and epigenetics
7 modules · 74 topics · ≈ 19 hr
- 4
Genomic Technologies
The tools that read DNA
5 modules · 60 topics · ≈ 15 hr
- 5
Population & Quantitative Genetics
Genes across whole populations
12 modules · 133 topics · ≈ 33 hr
- 6
Functional & Clinical Genomics
From genome to function and clinic
14 modules · 158 topics · ≈ 40 hr
- 7
Practicum & Research Project
Problem sets, then a study design
4 modules · 42 topics · ≈ 11 hr
Months
04812160246801234
MonthsFinish · ≈ 23 months · ≈ 11 months · ≈ 6 months
Hours and months are estimates: one 15-minute lesson per topic, every day.
Every module.Every topic.
Stage 1
Foundations of Inheritance
How traits pass from parent to child
12 modules · 133 topics
1Foundations of Genetic Reasoning10 topics
- Genetics and Genomics as Complementary Fields
- Heredity, Variation, and Biological Continuity
- Genetic Questions at Organism, Family, Population, and Genome Scales
- Genotype, Phenotype, and the Environment
- Transmission Genetics and Molecular Genetic Evidence
- Observational and Experimental Approaches to Inheritance
- Genetic Models, Predictions, and Falsifiable Hypotheses
- Association, Mechanism, and Causation in Genetics
- Levels of Evidence in Genetic Explanations
- Scope and Limitations of Genetic Determinism
2Genes, Alleles, and Genotypes12 topics
- Genes as Functional and Hereditary Units
- Loci, Alleles, and Allelic Diversity
- Genotypes and Genotype Notation
- Homozygosity, Heterozygosity, and Hemizygosity
- Haploid, Diploid, and Polyploid Genomes
- Homologous Chromosomes and Sister Chromatids
- Haplotypes and Diplotypes
- Cis and Trans Configurations of Variants
- Reference Alleles and Alternative Alleles
- Wild-Type, Mutant, and Ancestral Alleles
- Germline Genomes and Somatic Genomes
- Genetic Background and the Meaning of an Allelic Effect
3Probability and Statistical Reasoning in Genetics11 topics
- Probability Rules for Genetic Events
- Independent and Conditional Probabilities
- Bayes' Theorem in Inheritance Problems
- Binomial Models for Offspring Outcomes
- Multinomial Models for Genetic Crosses
- Expected Ratios and Sampling Variation
- Confidence Intervals for Genetic Proportions
- Goodness-of-Fit Tests for Segregation Models
- Likelihoods and Comparison of Genetic Hypotheses
- Statistical Significance and Biological Effect Size
- Independence, Pseudoreplication, and the Unit of Observation
4Chromosomes, Meiosis, and Genetic Transmission12 topics
- Chromosome Structure Relevant to Inheritance
- Chromosome Number, Ploidy, and DNA Content
- Centromeres, Telomeres, and Chromosome Identity
- Homolog Pairing and Meiotic Segregation
- Crossing Over and Chiasma Formation
- Sister Chromatid Cohesion and Segregation Fidelity
- Reductional and Equational Divisions
- Independent Assortment and Chromosome Combinations
- Gamete Formation and Transmission of Alleles
- Meiotic Recombination and Gene Conversion
- Transmission Distortion and Meiotic Drive
- Connecting Chromosome Behavior to Genetic Ratios
5Mendelian Inheritance and Genetic Crosses10 topics
- Mendel's Experimental Logic
- Monohybrid Crosses and the Law of Segregation
- Dihybrid Crosses and Independent Assortment
- Punnett Squares and Branching Probability Methods
- Testcrosses and Inference of Unknown Genotypes
- Backcrosses and Recovery of Parental Genotypes
- Reciprocal Crosses and Parent-Specific Effects
- Multilocus Crosses with Independently Assorting Genes
- Lethal Genotypes and Modified Segregation Ratios
- Distinguishing Biological Deviations from Sampling Error
6Allelic Relationships and Dominance9 topics
- Complete Dominance and Recessivity
- Incomplete Dominance and Intermediate Phenotypes
- Codominance and Simultaneous Allelic Expression
- Multiple Alleles at a Single Locus
- Dominance as a Relationship Between Alleles
- Trait and Measurement Dependence of Dominance
- Overdominance and Heterozygote Phenotypes
- Dominance Relationships Across an Allelic Series
- Distinguishing Dominance from Allele Frequency and Fitness
7Gene Interactions and Genetic Pathway Analysis11 topics
- Interactions Between Alleles and Between Loci
- Complementary Gene Action
- Recessive and Dominant Epistasis
- Duplicate and Redundant Gene Functions
- Suppressor and Enhancer Interactions
- Synthetic Lethality and Synthetic Sickness
- Additive and Nonadditive Genetic Effects
- Double-Mutant Analysis and Pathway Ordering
- Conditional Interpretation of Epistasis Experiments
- Pleiotropy and Multiple Phenotypic Outputs
- Distinguishing Genetic Interactions from Physical Interactions
8Pedigrees and Inheritance Patterns12 topics
- Pedigree Symbols and Family Data Structure
- Autosomal Dominant Inheritance
- Autosomal Recessive Inheritance
- X-Linked Recessive Inheritance
- X-Linked Dominant Inheritance
- Y-Linked and Mitochondrial Transmission Patterns
- Carrier Inference and Conditional Genotype Probabilities
- Consanguinity and Shared Ancestral Alleles
- Incomplete Family Information and Uncertain Phenotypes
- De Novo Variants in Apparently Sporadic Cases
- Ascertainment Bias in Family Studies
- Comparing Alternative Explanations for a Pedigree
9Sex Determination and Sex-Linked Inheritance11 topics
- Chromosomal and Genetic Sex-Determination Systems
- XY, ZW, and Haplodiploid Inheritance Systems
- Sex-Linked and Sex-Influenced Traits
- Sex-Limited Expression of Autosomal Traits
- Pseudoautosomal Regions and Recombination
- X-Chromosome Inactivation and Cellular Mosaicism
- Skewed X Inactivation and Phenotypic Effects
- Escape from X Inactivation
- Dosage Compensation Across Model Organisms
- Y-Chromosome Variation and Transmission
- Sex-Chromosome Evolution and Gene Content
10Penetrance, Expressivity, and Phenotypic Variation10 topics
- Complete and Incomplete Penetrance
- Variable Expressivity Within Families
- Age-Dependent Penetrance and Onset
- Sex-Dependent Effects of Genetic Variants
- Modifier Genes and Genetic Background Effects
- Environmental Modification of Genetic Phenotypes
- Phenocopies and Alternative Causes of Similar Traits
- Genetic Heterogeneity and Phenotypic Heterogeneity
- Stochastic Variation and Developmental Context
- Thresholds, Measurement Choices, and Phenotype Classification
11Linkage and Classical Genetic Mapping13 topics
- Linked Genes and Departures from Independent Assortment
- Coupling and Repulsion Phases
- Recombination Frequency and Genetic Distance
- Two-Point Testcross Mapping
- Three-Point Crosses and Gene Order
- Double Crossovers and Undetected Recombination
- Crossover Interference and Coefficients of Coincidence
- Mapping Functions and Their Assumptions
- Tetrad Analysis in Genetic Mapping
- Ordered Tetrads and Centromere Mapping
- Sex-Specific and Region-Specific Recombination Rates
- Genetic Maps and Physical Maps
- Family Linkage Evidence and LOD Scores
12Mitochondrial and Plastid Genetics12 topics
- Nuclear and Extranuclear Inheritance
- Mitochondrial Genome Organization
- Plastid Genome Organization
- Maternal, Paternal, and Biparental Organelle Transmission
- Homoplasmy and Heteroplasmy
- Replicative Segregation of Organelle Genomes
- Mitochondrial Genetic Bottlenecks
- Tissue-Specific Heteroplasmy and Threshold Effects
- Nuclear-Organelle Genetic Interactions
- Organelle Recombination and Genome Rearrangements
- Nuclear Insertions of Organelle DNA and Interpretation Pitfalls
- Distinguishing Cytoplasmic Inheritance from Maternal Effects
Stage 2
Mutation & Variation
Where variation comes from
9 modules · 100 topics
13Mutation Origins and Mutation Rates12 topics
- Mutation as a Source of New Genetic Variation
- Spontaneous and Induced Mutations
- Replication Errors and Mutational Outcomes
- DNA Damage, Repair Defects, and Mutation Spectra
- Transition and Transversion Mutations
- Sequence Context and Mutation Hotspots
- Germline and Somatic Mutation Processes
- Mutation Rate, Mutation Frequency, and Variant Frequency
- Per-Base, Per-Generation, and Per-Cell-Division Rates
- Parental Age Effects on De Novo Variation
- Fluctuation Tests and the Timing of Mutations
- Selection and Detection Bias in Mutation Measurements
14Sequence Variants and Functional Consequences13 topics
- Single-Nucleotide Variants and Small Insertions or Deletions
- Synonymous and Missense Variants
- Nonsense Variants and Premature Termination Codons
- Frameshift and In-Frame Coding Variants
- Start-Loss, Stop-Loss, and Translation-Initiation Effects
- Canonical Splice-Site and Splice-Region Variants
- Deep Intronic Variants and Cryptic Splicing
- Promoter, Enhancer, and Untranslated-Region Variants
- RNA Stability and Transcript-Level Consequences
- Nonsense-Mediated Decay in Variant Interpretation
- Transcript Dependence of Predicted Consequences
- Molecular Consequence Versus Phenotypic Effect
- Neutral, Deleterious, and Beneficial Effects in Context
15Repeat Expansions and Unstable Alleles10 topics
- Tandem Repeats and Repeat-Length Variation
- Microsatellites and Minisatellites
- Germline and Somatic Repeat Instability
- Coding and Noncoding Repeat Expansions
- Anticipation and Intergenerational Changes in Phenotype
- Repeat-Length Thresholds and Intermediate Alleles
- Parent-of-Origin Effects in Repeat Expansion Disorders
- Repeat Interruptions and Allele Stability
- Toxic RNA, Altered Proteins, and Silencing as Genetic Mechanisms
- Assay Limitations in Detecting Expanded Repeats
16Structural Variation and Gene Dosage12 topics
- Deletions, Duplications, Inversions, and Translocations
- Copy-Number Variants and Copy-Neutral Rearrangements
- Segmental Duplications and Recurrent Rearrangement Regions
- Nonallelic Homologous Recombination
- Replication-Based and End-Joining Rearrangement Mechanisms
- Breakpoint Position and Disruption of Gene Function
- Gene Dosage and Dosage-Sensitive Regions
- Regulatory Rewiring and Position Effects
- Fusion Genes and Novel Genomic Junctions
- Complex Structural Variants
- Structural Variant Haplotype and Inheritance Context
- Distinguishing Variant Size from Biological Impact
17Chromosome Abnormalities and Their Inheritance11 topics
- Aneuploidy and Changes in Chromosome Number
- Nondisjunction in Meiosis I and Meiosis II
- Postzygotic Chromosome Segregation Errors
- Monosomy, Trisomy, and Chromosomal Dosage
- Polyploidy and Whole-Genome Duplication
- Autopolyploid and Allopolyploid Inheritance
- Balanced and Unbalanced Chromosome Rearrangements
- Reciprocal and Robertsonian Translocations
- Inversions and Recombinant Chromosome Outcomes
- Chromosome Segregation in Rearrangement Carriers
- Cytogenetic Findings and Their Inheritance Implications
18Mosaicism, Chimerism, and Somatic Variation10 topics
- Genetic Mosaicism and Postzygotic Variant Origin
- Somatic, Germline, and Gonosomal Mosaicism
- Chimerism and Genetically Distinct Cell Origins
- Developmental Timing and Variant Distribution
- Variant Allele Fraction and Cellular Composition
- Tissue Sampling and Undetected Mosaicism
- Clonal Expansion and Somatic Selection
- Mosaic Copy-Number and Chromosome Changes
- Parental Mosaicism and Recurrence Considerations
- Lineage Relationships Inferred from Shared Somatic Variants
19Allelic Series and Inference of Gene Function11 topics
- Null, Hypomorphic, and Hypermorphic Alleles
- Neomorphic Alleles and Novel Gene Activities
- Loss-of-Function and Gain-of-Function Mechanisms
- Haploinsufficiency and Dosage Sensitivity
- Dominant-Negative Effects and Antimorphic Alleles
- Conditional and Temperature-Sensitive Alleles
- Allelic Strength and Phenotypic Severity
- Complementation Tests and Complementation Groups
- Intragenic Complementation and Interpretive Exceptions
- Genetic Rescue and Specificity of Functional Evidence
- Redundancy, Compensation, and Apparently Silent Phenotypes
20Genetic Screens and Genetic Evidence11 topics
- Forward and Reverse Genetic Reasoning
- Phenotype-First and Gene-First Study Designs
- Selection Screens and Observation-Based Screens
- Primary Hits and Independent Confirmation
- Recessive and Dominant Screening Strategies
- Modifier Screens and Genetic Interaction Discovery
- Saturation, Coverage, and Undetected Gene Functions
- Essential Genes and Conditional Phenotype Assessment
- Background Mutations and Confounding Alleles
- Independent Alleles and Orthogonal Functional Evidence
- Interpreting Perturbation Results Without Overstating Causality
21Model Systems and Experimental Genetic Designs10 topics
- Choosing Model Systems for Genetic Questions
- Haploid and Diploid Models in Genetic Analysis
- Yeast Tetrads and Eukaryotic Inheritance Studies
- Bacterial Recombination as a Genetic Mapping System
- Phage Crosses and Fine-Structure Genetic Analysis
- Drosophila Crosses and Chromosome-Based Genetic Tools
- Nematode and Vertebrate Models of Gene Function
- Plant Genetics and the Analysis of Polyploid Traits
- Human Families and Natural Genetic Variation
- Conservation and Limits of Cross-Species Genetic Inference
Stage 3
Genome Architecture & Regulation
Structure, switches and epigenetics
7 modules · 74 topics
22Genome Architecture and Organization12 topics
- Genome Size and Gene Number
- Coding and Noncoding Genome Fractions
- Unique, Repetitive, and Low-Complexity Sequences
- Gene Density and Regional Genome Composition
- Introns, Exons, and Intergenic Regions
- Gene Clusters and Distributed Gene Families
- Segmental Duplications and Pseudogenes
- Centromeric, Telomeric, and Subtelomeric Regions
- Sex Chromosomes and Organelle Genomes in Genome Surveys
- Genome Compartmentalization and Functional Constraints
- Genome Size Variation Across Lineages
- The C-Value Paradox and Limits of Genome Complexity Measures
23Gene Models, Transcripts, and Functional Annotation11 topics
- Gene Boundaries and Alternative Definitions of a Gene
- Protein-Coding and Noncoding Gene Models
- Transcript Isoforms and Alternative Exon Usage
- Alternative Promoters and Transcript Ends
- Overlapping Genes and Antisense Transcripts
- Readthrough Transcripts and Complex Locus Structure
- Processed and Unprocessed Pseudogenes
- Evidence Supporting a Gene Annotation
- Predicted Functions and Experimentally Supported Functions
- Tissue-Specific Transcript Relevance
- Annotation Uncertainty and Changes Between Releases
24Mobile Elements and Genome Restructuring9 topics
- Transposable Elements as Components of Genomes
- DNA Transposons and Retrotransposons
- Autonomous and Nonautonomous Elements
- Endogenous Retroviral Sequences
- Insertional Variation and Gene Disruption
- Mobile Elements as Sources of Regulatory Sequences
- Host Suppression and Heritable Element Activity
- Recombination Between Repetitive Elements
- Evolutionary Consequences of Transposable Element Expansion
25Epigenetic Variation and Inheritance10 topics
- Genetic and Epigenetic Sources of Phenotypic Variation
- DNA Methylation as a Genomic Feature
- Chromatin States and Heritable Expression Differences
- Mitotic Maintenance of Epigenetic States
- Epigenetic Reprogramming Across Generations
- Epialleles and Metastable Epialleles
- Genetic Control of Epigenetic Variation
- Paramutation and Non-Mendelian Allelic Interactions
- Intergenerational and Transgenerational Effects
- Evidence Standards for Transgenerational Epigenetic Inheritance
26Imprinting, Parent-of-Origin Effects, and Uniparental Disomy10 topics
- Genomic Imprinting and Parent-Specific Allelic Expression
- Imprinting Control Regions and Imprinted Domains
- Establishment, Maintenance, and Resetting of Imprints
- Sequence Variants and Epimutations at Imprinted Loci
- Uniparental Disomy and Its Origins
- Heterodisomy, Isodisomy, and Mixed Patterns
- Uniparental Disomy and Recessive Allele Unmasking
- Maternal-Effect Genes and Maternal Genotype Effects
- Distinguishing Imprinting from Cytoplasmic Inheritance
- Integrating Pedigree, Dosage, and Methylation Evidence
27Regulatory Variation and Gene Expression Genetics12 topics
- Cis-Regulatory and Trans-Regulatory Variation
- Promoter and Enhancer Alleles
- Tissue-Specific and Developmental Regulatory Effects
- Expression Quantitative Trait Loci
- Splicing Quantitative Trait Loci
- Allele-Specific Expression and Allelic Imbalance
- Allele-Specific Chromatin and Methylation Effects
- Context-Dependent Regulatory Variants
- Local and Distant Regulation of Transcript Abundance
- Regulatory Buffering and Genetic Compensation
- Correlated Expression and Shared Genetic Regulation
- Distinguishing Regulatory Association from Direct Regulation
28Developmental Genetics and Genetic Networks10 topics
- Genetic Dissection of Developmental Phenotypes
- Maternal and Zygotic Genetic Contributions
- Patterning Mutants and Positional Identity
- Homeotic Genes and Changes in Developmental Fate
- Heterochronic Mutations and Developmental Timing
- Cell-Autonomous and Non-Cell-Autonomous Genetic Effects
- Mosaic Analysis and Lineage-Restricted Phenotypes
- Genetic Redundancy and Developmental Robustness
- Dosage Sensitivity in Developmental Networks
- Conserved Developmental Genes and Species-Specific Outcomes
Stage 4
Genomic Technologies
The tools that read DNA
5 modules · 60 topics
29Genetic Assays and the Evidence They Provide12 topics
- Matching Genetic Questions to Measurement Strategies
- Karyotyping and Chromosome-Scale Observations
- Fluorescence In Situ Hybridization and Locus-Level Evidence
- PCR-Based Genotyping and Allele Discrimination
- Fragment-Length Analysis and Repeat Alleles
- Quantitative and Digital Measurements of DNA Copy Number
- SNP Arrays and Genome-Wide Genotyping
- Comparative Genomic Hybridization and Copy-Number Detection
- Methylation Assays and Imprinting Evidence
- RNA Measurements as Evidence of Variant Effects
- Analytical Sensitivity, Specificity, and Detection Limits
- Orthogonal Confirmation and Assay-Dependent Blind Spots
30DNA Sequencing and Genome-Wide Variant Discovery12 topics
- Chain-Termination Sequencing and Targeted Sequence Evidence
- Massively Parallel Sequencing Principles
- Short-Read and Long-Read Sequencing Tradeoffs
- Targeted Panels, Exomes, and Whole Genomes
- Read Depth, Breadth of Coverage, and Sampling Variation
- Base Accuracy and Variant-Level Confidence
- Paired Reads and Evidence of Genomic Rearrangements
- Read-Based and Family-Based Haplotype Phasing
- Detection of Small Variants and Structural Variants
- Difficult Regions, Repeats, and Highly Similar Sequences
- Sample Mixtures, Contamination, and Sequencing Artifacts
- Discovery Sensitivity Across Different Variant Classes
31Reference Genomes, Assemblies, and Pangenomes11 topics
- Reference Genomes as Coordinate Frameworks
- Reference Sequences and Population Diversity
- Genome Assemblies, Contigs, and Scaffolds
- Assembly Continuity, Completeness, and Accuracy
- Gaps, Collapsed Repeats, and Duplicated Assembly Regions
- Haploid Representations and Phased Diploid Assemblies
- Telomere-to-Telomere Genome Representation
- Alternative Haplotypes and Structurally Variable Loci
- Pangenomes and Multiple-Genome Reference Models
- Reference Bias in Variant Detection and Interpretation
- Comparing Results Across Genome Builds
32Variant Representation, Annotation, and Genomic Resources12 topics
- Genomic, Transcript, and Protein Coordinates
- Reference Sequence Identifiers and Versioning
- Standardized Sequence Variant Descriptions
- Strand Orientation and Allele Representation
- Equivalent Representations of Insertions and Deletions
- Multiallelic Sites and Complex Variant Descriptions
- Genotype, Allele Count, and Allele Frequency Records
- Functional Annotations and Their Evidence Sources
- Population Variation Databases and Sampling Context
- Clinical Variant Archives and Conflicting Submissions
- Genome Browsers as Tools for Inspecting Genomic Context
- Resource Provenance, Update Dates, and Interpretation Limits
33Genomic Study Design and Statistical Evidence13 topics
- Defining a Genetic Question and Primary Outcome
- Phenotype Definitions and Measurement Reliability
- Cohort, Case-Control, Family, and Trio Designs
- Sampling Frames and Ascertainment Bias
- Sample Size, Statistical Power, and Detectable Effects
- Relatedness and Nonindependent Observations
- Batch Effects and Technical Confounding
- Population Stratification as a Study Design Problem
- Multiple Testing and False Discovery Control
- Effect Estimates, Confidence Intervals, and Uncertainty
- Discovery, Replication, and External Validation
- Winner's Curse and Selective Reporting
- Preregistration and Transparent Analysis Decisions
Stage 5
Population & Quantitative Genetics
Genes across whole populations
12 modules · 133 topics
34Population Variation and Hardy-Weinberg Equilibrium10 topics
- Allele Frequencies and Genotype Frequencies
- Estimating Frequencies from Population Samples
- Heterozygosity and Genetic Diversity
- Hardy-Weinberg Proportions
- Assumptions Behind Hardy-Weinberg Equilibrium
- Multiallelic Loci and Equilibrium Expectations
- Sex-Linked Loci and Frequency Dynamics
- Departures from Equilibrium and Alternative Explanations
- Inbreeding Coefficients and Heterozygote Deficits
- Using Equilibrium Tests Without Overinterpreting Them
35Mutation, Selection, Drift, and Migration12 topics
- Mutation as an Input to Allele Frequency Change
- Relative Fitness and Selection Coefficients
- Directional, Purifying, and Balancing Selection
- Dominance and the Response of Alleles to Selection
- Mutation-Selection Balance
- Heterozygote Advantage and Stable Polymorphism
- Frequency-Dependent Selection
- Genetic Drift and Stochastic Allele Trajectories
- Fixation and Loss of Alleles
- Gene Flow and Migration-Selection Balance
- Bottlenecks and Founder Effects
- Interactions Between Evolutionary Forces
36Effective Population Size and Demographic History11 topics
- Census Size and Effective Population Size
- Reproductive Variance and Unequal Genetic Contributions
- Sex Ratios and Effective Population Size
- Fluctuating Population Sizes Across Generations
- Inbreeding Effective Size and Variance Effective Size
- Coalescence and Shared Ancestral Lineages
- Site Frequency Spectra and Demographic Signals
- Population Growth, Decline, and Historical Bottlenecks
- Recombination and Variation in Local Genealogies
- Distinguishing Demographic Signals from Selection Signals
- Model Dependence and Uncertainty in Demographic Inference
37Population Structure, Relatedness, and Genetic Ancestry12 topics
- Within-Population and Between-Population Variation
- Genetic Differentiation and Fixation Indices
- Identity by State and Identity by Descent
- Kinship, Relatedness, and Shared Genomic Segments
- Runs of Homozygosity and Parental Relatedness
- Isolation by Distance and Geographic Structure
- Admixture and Local Ancestry
- Reference Populations and Ancestry Estimates
- Continuous Variation and the Limits of Discrete Clusters
- Genetic Ancestry, Genealogical Ancestry, and Social Identity
- Sampling Representation and Population Descriptors
- Uncertainty and Appropriate Uses of Ancestry Inference
38Linkage Disequilibrium and Population Haplotypes11 topics
- Linkage and Linkage Disequilibrium as Distinct Concepts
- Two-Locus Haplotype Frequencies
- Measures of Linkage Disequilibrium
- Recombination and Decay of Allelic Associations
- Population History and Linkage Disequilibrium Patterns
- Selection, Admixture, and Long-Range Associations
- Haplotype Blocks and Recombination Hotspots
- Tagging Variants and Indirect Association Signals
- Statistical Phasing as an Inference Problem
- Genotype Imputation and Reference Panel Dependence
- Population Differences in Haplotype Structure
39Quantitative Traits and Genetic Variance12 topics
- Continuous Traits and Polygenic Inheritance
- Genotypic Values and Average Allelic Effects
- Additive Genetic Variance
- Dominance Variance and Interaction Variance
- Environmental Variance and Residual Variation
- Phenotypic Variance Decomposition and Its Assumptions
- Allele Frequency Dependence of Genetic Variance
- Genetic Covariance Between Traits
- Pleiotropy, Linkage, and Genetic Correlation
- Liability-Threshold Models for Binary Traits
- Rare and Common Alleles in Quantitative Trait Architecture
- Scale Dependence of Genetic Effects
40Heritability and Family-Based Quantitative Designs11 topics
- Broad-Sense and Narrow-Sense Heritability
- Parent-Offspring Resemblance
- Sibling and Extended-Family Comparisons
- Twin Studies and Their Assumptions
- Adoption Studies and Environmental Separation
- Shared and Nonshared Environmental Effects
- SNP-Based Heritability and Captured Genetic Variation
- Missing Heritability and Unmeasured Sources of Variation
- Population and Environment Dependence of Heritability
- Why Heritability Does Not Measure Immutability
- Limits of Inferring Between-Group Causes from Within-Group Heritability
41Gene-Environment Interplay9 topics
- Gene-Environment Interaction and Effect Modification
- Reaction Norms and Genotype-Specific Responses
- Crossover and Noncrossover Interactions
- Gene-Environment Correlation
- Environmental Exposure Measurement and Misclassification
- Longitudinal Phenotypes and Changing Genetic Effects
- Shared Family Environments and Confounding
- Interaction Tests, Statistical Scale, and Power
- Replication and Interpretation of Interaction Findings
42Quantitative Trait Locus Mapping10 topics
- Experimental Populations for QTL Mapping
- F2, Backcross, and Recombinant Inbred Designs
- Segregating Markers and Quantitative Phenotypes
- Single-Marker and Interval Mapping Concepts
- Multiple QTL and Linked Effects
- Detection Thresholds and Mapping Resolution
- Epistatic QTL and Background Dependence
- Near-Isogenic Comparisons and QTL Validation
- From a QTL Interval to Candidate Genes
- Transferability of QTL Findings Across Genetic Backgrounds
43Genome-Wide Association Studies13 topics
- Common-Variant Association Study Logic
- Case-Control and Quantitative-Trait GWAS
- Additive, Dominant, and Recessive Association Models
- Genotype Quality and Phenotype Quality Requirements
- Ancestry, Relatedness, and Confounding Control
- Family-Based Association and Transmission Tests
- Rare-Variant Burden and Variance-Component Tests
- Genome-Wide Significance and Multiple Comparisons
- Association Plots and Calibration of Test Statistics
- Independent Signals and Conditional Associations
- Meta-Analysis and Cross-Cohort Heterogeneity
- Cross-Ancestry Studies and Generalizability
- Replication, Effect Inflation, and the Limits of Association
44Fine-Mapping and Causal Gene Prioritization11 topics
- From Associated Regions to Candidate Causal Variants
- Linkage Disequilibrium and Uncertain Signal Localization
- Statistical Fine-Mapping and Credible Sets
- Multiple Causal Variants Within a Locus
- Cross-Population Differences as Mapping Information
- Colocalization of Trait and Molecular Associations
- Regulatory Target Genes and Distal Variant Effects
- Coding Variants and Gene-Level Evidence
- Tissue and Cell-Type Relevance in Gene Prioritization
- Integrating Segregation, Association, and Functional Evidence
- Distinguishing Prioritization from Causal Demonstration
45Polygenic Scores and Genetic Prediction11 topics
- Polygenic Scores and Weighted Allelic Effects
- Discovery Data and Independent Evaluation Data
- Trait Prediction and Disease Risk Prediction
- Discrimination, Calibration, and Explained Variation
- Relative Risk and Absolute Risk
- Age, Environment, and Baseline Risk in Interpretation
- Population Transferability and Ancestry Representation
- Indirect Genetic Effects and Population-Level Associations
- Combining Genetic and Nongenetic Predictors
- Prediction Uncertainty at the Individual Level
- Statistical Performance and Practical Utility
Stage 6
Functional & Clinical Genomics
From genome to function and clinic
14 modules · 158 topics
46Comparative Genomics and Gene Family Evolution12 topics
- Homology, Orthology, and Paralogy
- Conserved Synteny and Genome Rearrangements
- Gene Duplication and Gene Loss
- Whole-Genome Duplication and Duplicate Gene Retention
- Subfunctionalization and Neofunctionalization
- Gene Family Expansion and Contraction
- Pseudogenization and Loss of Functional Constraint
- Comparative Analysis of Coding and Regulatory Regions
- Lineage-Specific Genes and Annotation Artifacts
- Horizontal Gene Transfer in Genome Evolution
- Species Trees, Gene Trees, and Discordant Histories
- Limits of Transferring Functional Annotations Across Species
47Molecular Evolution and Genomic Signatures of Selection12 topics
- Neutral and Nearly Neutral Models of Sequence Evolution
- Mutation, Substitution, and Evolutionary Rate
- Synonymous and Nonsynonymous Sequence Change
- Purifying Selection and Sequence Conservation
- Positive Selection and Accelerated Evolution
- Balancing Selection and Maintained Diversity
- Selective Sweeps and Linked Variation
- Background Selection and Reduced Local Diversity
- Molecular Clocks and Rate Heterogeneity
- Incomplete Lineage Sorting and Introgression
- Ancient DNA as Evidence of Genetic Change Through Time
- Demography, Technical Bias, and Alternative Explanations for Selection Signals
48Functional Genomics and Genome-Wide Regulatory Evidence12 topics
- Genome-Wide Measurements of Gene Activity
- Transcript Abundance and Differential Expression Evidence
- Chromatin Accessibility and Candidate Regulatory Regions
- Protein-DNA Occupancy and Regulatory Associations
- Methylation Landscapes and Genomic Context
- Chromatin Contact Maps and Regulatory Neighborhoods
- Interpreting Genome-Scale Perturbation Screens
- Reporter Assays and Endogenous Genomic Context
- Variant Effect Maps and Assay Calibration
- Cell-Type Specificity of Functional Evidence
- Orthogonal Assays and Convergent Support for Function
- Biochemical Activity, Biological Function, and Phenotypic Relevance
49Single-Cell and Spatial Genomics11 topics
- Bulk Measurements and Cellular Heterogeneity
- Single-Cell DNA Variation and Clonal Structure
- Single-Cell Transcriptomic and Epigenomic Readouts
- Joint Genotype and Cell-State Measurements
- Allelic Dropout and Sparse Observations
- Doublets, Ambient Signals, and Cell Assignment Errors
- Biological Replicates and Cell-Level Pseudoreplication
- Spatial Context and Tissue-Specific Genetic Effects
- Cell Composition as a Source of Apparent Genomic Differences
- Trajectory Inference and Its Relationship to Lineage Evidence
- Linking Cell-Specific Findings to Organism-Level Phenotypes
50Integrative Genomics and Molecular Trait Architecture10 topics
- Connecting DNA Variation to Intermediate Molecular Traits
- Transcript, Protein, and Metabolite Quantitative Trait Loci
- Shared and Distinct Genetic Regulation Across Molecular Layers
- Tissue-Matched and Cross-Tissue Genomic Evidence
- Molecular Mediation and Competing Causal Explanations
- Concordant and Discordant Molecular Effects
- Environmental and Temporal Context in Multiomic Studies
- Missing Modalities and Unequal Measurement Sensitivity
- Evidence Integration Without Double Counting
- Designing Follow-Up Studies for Integrated Genomic Hypotheses
51Rare Disease and Mendelian Genomic Analysis12 topics
- Phenotype-First and Genotype-First Rare Disease Studies
- Structured Phenotyping and Candidate Disease Models
- Trio, Family, and Unrelated-Case Evidence
- De Novo, Recessive, and Dominant Variant Hypotheses
- Compound Heterozygosity and Phase Determination
- Runs of Homozygosity and Recessive Candidate Regions
- Copy-Number, Repeat, and Mitochondrial Explanations
- Reduced Penetrance and Apparently Unaffected Carriers
- Blended Phenotypes and Multiple Molecular Diagnoses
- Candidate Genes and Gene-Disease Evidence Gaps
- Negative Results, Residual Uncertainty, and Reanalysis
- Diagnostic Yield and the Influence of Ascertainment
52Gene-Disease Validity and Clinical Variant Interpretation13 topics
- Gene-Disease Relationships and Modes of Inheritance
- Gene-Disease Validity, Variant Pathogenicity, and Actionability
- Five-Tier Classification: Benign, Likely Benign, Uncertain Significance, Likely Pathogenic, and Pathogenic
- Population Frequency Evidence in Disease Context
- Segregation and De Novo Evidence
- Functional Assay Evidence and Clinical Relevance
- Computational Predictions and Their Evidentiary Limits
- Loss-of-Function Evidence and Disease Mechanism Compatibility
- Dosage Sensitivity and Structural Variant Interpretation
- Avoiding Double Counting of Dependent Evidence
- Variants of Uncertain Significance and Unresolved Evidence
- Conflicting Interpretations, Reclassification, and Evidence Updates
- Distinguishing Variant Classification from an Individual Diagnosis
53Genetic Epidemiology and Causal Inference10 topics
- Genetic Susceptibility and Multifactorial Disease Models
- Intermediate Phenotypes and Disease Endpoints
- Mendelian Randomization and Instrumental Variable Logic
- Relevance, Independence, and Exclusion Assumptions
- Horizontal and Vertical Pleiotropy
- Population Structure, Assortative Mating, and Family Effects
- Direction of Causation and Reverse-Causation Questions
- Sample Overlap, Selection Bias, and Weak Instruments
- Shared Genetic Signals and Alternative Causal Explanations
- Triangulation Across Family, Population, and Functional Studies
54Cancer Genomics and Somatic Evolution12 topics
- Germline Predisposition and Acquired Somatic Variation
- Oncogenes, Tumor Suppressor Genes, and Allelic Mechanisms
- Two-Hit Models and Loss of Heterozygosity
- Driver, Passenger, and Context-Dependent Mutations
- Somatic Copy-Number Changes and Genome Instability
- Mutational Signatures and Their Interpretation Limits
- Tumor Purity, Ploidy, and Variant Allele Fractions
- Clonal and Subclonal Genetic Architecture
- Branched Evolution and Intratumor Heterogeneity
- Longitudinal Genomic Change Under Selection
- Clonal Hematopoiesis and Nontumor Somatic Variation
- Distinguishing Somatic Evidence from Inherited Risk Evidence
55Immunogenetics and Complex Immune Loci10 topics
- Inherited Variation in Immune-System Genes
- HLA Allelic Diversity and Haplotype Structure
- Linkage Disequilibrium Across the MHC Region
- Highly Polymorphic Loci and Genotyping Ambiguity
- Germline Variation and Somatic Receptor Diversification
- Recombination and Mutation as Sources of Receptor Diversity
- Copy-Number Variation in Immune Gene Families
- Genetic Associations with Immune-Mediated Traits
- Balancing Selection and Immune-Locus Evolution
- Separating Inherited Genotypes from Acquired Receptor Repertoires
56Reproductive Genetics and Genomic Screening11 topics
- Carrier Status and Recessive Inheritance
- Carrier Screening Scope and Residual Risk
- Couple-Based Interpretation of Inheritance Models
- Prenatal Screening and Diagnostic Testing as Distinct Questions
- Cell-Free DNA Sources and Placental Contributions
- Mosaicism and Discordant Prenatal Findings
- Preimplantation Genetic Testing: Questions and Assay Limits
- Chromosome Findings and Reproductive Outcomes
- Newborn Screening and Genomic Screening Concepts
- Analytical Validity, Clinical Validity, and Clinical Utility
- Consent, Uncertainty, and Communication in Reproductive Testing
57Ecological and Conservation Genetics10 topics
- Genetic Diversity and Population Persistence
- Inbreeding Depression and Fitness Consequences
- Genetic Load and the Distribution of Deleterious Alleles
- Local Adaptation and Environmental Heterogeneity
- Neutral and Adaptive Genetic Variation
- Population Connectivity and Fragmentation
- Hybridization, Introgression, and Species Boundaries
- Genetic Rescue and Context-Dependent Outcomes
- Distinguishing Population Size from Genetic Viability
- Genomic Sampling and Conservation Decision Uncertainty
58Ethics, Society, and Genomic Data Governance12 topics
- Informed Consent for Genetic and Genomic Research
- Broad Consent, Reuse, and Future Research Questions
- Identifiability and Privacy of Genomic Data
- Familial Implications of Individual Genetic Findings
- Consent and Assent in Research Involving Children
- Secondary Findings and Return-of-Results Policies
- Participant Preferences and the Right Not to Know
- Community Engagement and Data Sovereignty
- Representation, Equity, and Research Benefit Sharing
- Genetic Discrimination and Social Misuse of Genetic Claims
- Responsible Communication of Ancestry and Group Differences
- Controlled Access, Data Stewardship, and Accountability
59Reproducibility, Reporting, and Scientific Communication11 topics
- Recording Samples, Phenotypes, and Genetic Assumptions
- Tracking Genome Builds, Transcript Versions, and Annotation Sources
- Documenting Inclusion, Exclusion, and Quality Decisions
- Separating Exploratory and Confirmatory Findings
- Reporting Effect Sizes and Uncertainty
- Communicating Negative Results and Detection Limits
- Evaluating Database Assertions and Primary Evidence
- Reproducing Published Genetic Claims from Available Evidence
- Updating Interpretations as Evidence Changes
- Writing Clear Genetic and Genomic Research Reports
- Communicating Probabilistic Findings to Nonspecialist Audiences
Stage 7
Practicum & Research Project
Problem sets, then a study design
4 modules · 42 topics
60Classical Genetics Problem-Solving Practicum10 topics
- Inferring Genotypes from Segregation Data
- Comparing Mendelian and Modified Inheritance Models
- Solving Multigenerational Pedigree Problems
- Estimating Conditional Carrier Probabilities
- Building a Three-Point Genetic Map
- Interpreting Tetrad and Gene Conversion Data
- Analyzing Complementation and Suppressor Results
- Inferring Pathway Relationships from Double Mutants
- Distinguishing Maternal Effects, Imprinting, and Organelle Inheritance
- Explaining Mosaic and Variable-Penetrance Pedigrees
61Population and Quantitative Genetics Practicum10 topics
- Estimating Allele Frequencies and Sampling Uncertainty
- Evaluating Hardy-Weinberg Departures
- Comparing Drift, Selection, and Migration Scenarios
- Interpreting Founder Effects and Population Bottlenecks
- Analyzing Relatedness and Runs of Homozygosity
- Reading Linkage Disequilibrium and Haplotype Summaries
- Interpreting Heritability Estimates Across Study Designs
- Evaluating QTL and Association Study Results
- Assessing Confounding and Replication in GWAS
- Comparing Polygenic Score Calibration Across Populations
62Genomic Evidence Interpretation Practicum11 topics
- Choosing Assays for Different Genetic Hypotheses
- Interpreting Coverage Gaps and Difficult Genomic Regions
- Comparing Variant Consequences Across Transcript Models
- Evaluating Structural Variant and Repeat Expansion Evidence
- Interpreting Trio Findings and Compound Heterozygous Alleles
- Comparing Gene-Disease Validity and Variant-Level Evidence
- Assessing Functional Evidence for a Regulatory Variant
- Interpreting Single-Cell Genotypes and Clonal Relationships
- Explaining Tumor Variant Fractions Under Different Purity and Ploidy Models
- Critiquing an Integrated Genomic Causality Claim
- Preparing an Evidence Summary with Explicit Uncertainty
63Integrated Genetics and Genomics Research Project11 topics
- Formulating a Testable Genetic Research Question
- Defining the Organism, Population, and Phenotype
- Selecting an Inheritance or Genetic Architecture Model
- Choosing Suitable Data and Measurement Strategies
- Planning Sampling, Comparisons, and Statistical Power
- Identifying Confounders and Competing Explanations
- Integrating Transmission, Population, and Functional Evidence
- Evaluating Data Quality and Unresolved Genomic Regions
- Designing Independent Validation and Follow-Up Studies
- Addressing Consent, Representation, and Data Stewardship
- Presenting Conclusions, Limitations, and Reproducible Evidence
Fifteen minutes.Every day.
- 1
A lesson fits a lunch break
One idea at a time, in short slides. A whole lesson takes about fifteen minutes.
- 2
Practice with instant feedback
Questions sit inside the lesson. Answer one and see right away whether you got it.
- 3
A streak that brings you back
A lesson a day keeps the streak alive. Small, steady sessions carry you through.
- 1
A lesson fits a lunch break
One idea at a time, in short slides. A whole lesson takes about fifteen minutes.
- 2
Practice with instant feedback
Questions sit inside the lesson. Answer one and see right away whether you got it.
- 3
A streak that brings you back
A lesson a day keeps the streak alive. Small, steady sessions carry you through.
For people who work with DNA.
Biology grads heading into genomics
Future genetic counselors
Where you'll grow most
Classify variants on the five-tier scale
Stage 6 · Functional & Clinical GenomicsBioinformaticians who want the biology
Where this course leads.
The job this course is built around, and how people get into it.
Bioinformatics Analyst
Analyses DNA and RNA sequencing data to find what matters in a genome.
All future careersOn the job
- Run a sequencing analysis pipeline end to end
- Find and annotate variants that may cause disease
- Explain genomic results to biologists and clinicians
How people get in
Usually a degree in biology, bioinformatics or computer science, with programming skills.
Be first in line.
Early access for individuals, pilots for teams. Tell us who's learning.
enterprise@astratrainer.com