Comprehensive guide for selecting appropriate tissues based on trait biology.

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## GTEx v8 Available Tissues (54 Total)

### Cardiovascular System

- **Artery\_Coronary** - Coronary artery disease, atherosclerosis
- **Artery\_Aorta** - Aortic aneurysm, arterial stiffness
- **Artery\_Tibial** - Peripheral artery disease
- **Heart\_Atrial\_Appendage** - Atrial fibrillation
- **Heart\_Left\_Ventricle** - Heart failure, cardiomyopathy

### Metabolic Tissues

- **Liver** - Lipid metabolism, T2D, NAFLD
- **Pancreas** - Diabetes, insulin secretion
- **Adipose\_Subcutaneous** - Obesity, metabolic syndrome
- **Adipose\_Visceral\_Omentum** - Central obesity, insulin resistance
- **Muscle\_Skeletal** - Insulin sensitivity, exercise response

### Brain and Nervous System

- **Brain\_Cortex** - Cognitive function, neurodegeneration
- **Brain\_Cerebellum** - Motor control, ataxia
- **Brain\_Hippocampus** - Memory, Alzheimer's disease
- **Brain\_Substantia\_nigra** - Parkinson's disease
- **Brain\_Anterior\_cingulate\_cortex\_BA24** - Psychiatric disorders
- **Brain\_Putamen\_basal\_ganglia** - Movement disorders
- **Brain\_Nucleus\_accumbens\_basal\_ganglia** - Reward, addiction
- **Nerve\_Tibial** - Peripheral neuropathy

### Immune System

- **Whole\_Blood** - Autoimmune, infection, hematologic traits
- **Spleen** - Immune response
- **Cells\_EBV-transformed\_lymphocytes** - Immune cell function

### Respiratory

- **Lung** - Asthma, COPD, pulmonary fibrosis

### Gastrointestinal

- **Colon\_Sigmoid** - Colorectal cancer, IBD
- **Colon\_Transverse** - IBD, colon cancer
- **Small\_Intestine\_Terminal\_Ileum** - Crohn's disease
- **Esophagus\_Mucosa** - Barrett's esophagus, GERD
- **Esophagus\_Muscularis** - Esophageal motility
- **Stomach** - Gastric cancer, ulcers

### Renal

- **Kidney\_Cortex** - Chronic kidney disease, glomerular function
- **Kidney\_Medulla** - Renal tubular function

### Reproductive

- **Testis** - Male infertility, testosterone
- **Ovary** - PCOS, ovarian cancer
- **Prostate** - Prostate cancer, BPH
- **Uterus** - Endometriosis, fibroids
- **Vagina** - Reproductive tract disorders
- **Breast\_Mammary\_Tissue** - Breast cancer

### Endocrine

- **Thyroid** - Thyroid function, autoimmune thyroid disease
- **Pituitary** - Hormone regulation
- **Adrenal\_Gland** - Cortisol, stress response

### Skin

- **Skin\_Sun\_Exposed\_Lower\_leg** - Melanoma, skin aging
- **Skin\_Not\_Sun\_Exposed\_Suprapubic** - Dermatologic disorders

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## Trait-to-Tissue Mapping

### Cardiovascular Diseases

| Trait | Primary Tissues | Secondary Tissues |
| --- | --- | --- |
| Coronary artery disease | Artery\_Coronary, Artery\_Aorta | Heart\_Left\_Ventricle, Liver, Whole\_Blood |
| Atrial fibrillation | Heart\_Atrial\_Appendage | Heart\_Left\_Ventricle, Whole\_Blood |
| Hypertension | Artery\_Aorta, Artery\_Tibial | Kidney\_Cortex, Adrenal\_Gland |
| Heart failure | Heart\_Left\_Ventricle | Heart\_Atrial\_Appendage, Liver |

### Metabolic Disorders

| Trait | Primary Tissues | Secondary Tissues |
| --- | --- | --- |
| Type 2 diabetes | Pancreas, Liver | Adipose\_Visceral, Muscle\_Skeletal |
| Obesity | Adipose\_Subcutaneous, Adipose\_Visceral | Hypothalamus, Liver |
| Hyperlipidemia | Liver | Adipose, Small\_Intestine |
| NAFLD | Liver | Adipose\_Visceral, Pancreas |

### Neurological Disorders

| Trait | Primary Tissues | Secondary Tissues |
| --- | --- | --- |
| Alzheimer's disease | Brain\_Hippocampus, Brain\_Cortex | Brain\_Frontal\_Cortex |
| Parkinson's disease | Brain\_Substantia\_nigra | Brain\_Putamen |
| Schizophrenia | Brain\_Cortex, Brain\_Hippocampus | Brain\_Anterior\_cingulate |
| Depression | Brain\_Anterior\_cingulate | Brain\_Hippocampus |

### Autoimmune Diseases

| Trait | Primary Tissues | Secondary Tissues |
| --- | --- | --- |
| Rheumatoid arthritis | Whole\_Blood, EBV\_lymphocytes | Spleen |
| Crohn's disease | Small\_Intestine, Colon\_Transverse | Whole\_Blood |
| Ulcerative colitis | Colon\_Sigmoid, Colon\_Transverse | Whole\_Blood |
| Multiple sclerosis | Brain\_Cortex, Brain\_Cerebellum | Whole\_Blood |

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## Data-Driven Tissue Selection with LDSC

For rigorous studies, use LDSC partitioned heritability to identify tissues statistically enriched for trait heritability.

**See gwas-heritability-ldsc workflow** for:
- Running LDSC tissue enrichment analysis
- Statistical evidence for tissue relevance
- Unbiased tissue recommendations

**When to use LDSC-based selection:**
- Novel traits with uncertain tissue relevance
- Comprehensive analyses requiring statistical rigor
- Publishing results (reviewers expect statistical justification)

**When biology-based selection is acceptable:**
- Well-studied traits with clear tissue relevance (e.g., CAD → Artery)
- Exploratory hypothesis generation
- Time/resource constraints

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## TCGA Cancer Tissues

For cancer GWAS, use TCGA expression references:
- **BRCA**: Breast invasive carcinoma
- **LUAD**: Lung adenocarcinoma
- **COAD**: Colon adenocarcinoma
- **PRAD**: Prostate adenocarcinoma
- **THCA**: Thyroid carcinoma
- (+ 28 more cancer types)

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## How Many Tissues to Analyze?

**Conservative (3-5 tissues)**:
- Disease-specific tissues only
- Reduces multiple testing burden
- Faster runtime

**Moderate (5-10 tissues)**:
- Primary + secondary tissues
- Balance between discovery and specificity
- Recommended for most studies

**Comprehensive (S-MultiXcan, all 54 tissues)**:
- Maximum discovery power
- Cross-tissue meta-analysis
- Good for polygenic traits affecting multiple systems

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**Last Updated:** 2026-01-28