Pedigree MCP Server

Installation

Add to your MCP client configuration (e.g., Claude Desktop):

{
  "mcpServers": {
    "pedigree": {
      "command": "npx",
      "args": ["pedigree-mcp"],
      "env": {}
    }
  }
}

Build from Source

If you prefer to build from source:

git clone https://github.com/zzgael/pedigree-mcp.git
cd pedigree-mcp
npm install
npm run build

Then use in your MCP client configuration:

{
  "mcpServers": {
    "pedigree": {
      "command": "node",
      "args": ["/absolute/path/to/pedigree-mcp/dist/index.js"],
      "env": {}
    }
  }
}

Features

Bennett 2008 Standard Compliance

This implementation follows the NSGC Standardized Human Pedigree Nomenclature:

| Symbol | Description | Property | |--------|-------------|----------| | Square | Male | sex: "M" | | Circle | Female | sex: "F" | | Diamond | Unknown sex | sex: "U" | | Filled shape | Affected individual | conditions: [...] | | Diagonal line | Deceased | status: 1 | | Arrow (lower-left) | Proband | proband: true | | Double arrow (lower-left) | Consultand (person seeking counseling) | consultand: true | | Brackets [ ] | Adopted | noparents: true | | Double line | Consanguinity | Auto-detected from shared ancestors | | Text on double line | Consanguinity degree | consanguinity_degree: "1st cousins" | | Horizontal bar | MZ (identical) twins | mztwin: "group_id" | | Diagonal lines | DZ (fraternal) twins | dztwin: "group_id" | | Dot in center | Carrier status | carrier: true | | Outlined dot | Obligate carrier (inferred) | obligate_carrier: true | | "P" inside symbol | Pregnancy | pregnant: true | | "P" + weeks label | Pregnancy duration | pregnant: true, terminated_age: 12 | | Small triangle | Early pregnancy loss (<20 weeks) | terminated: true, terminated_age: 8 | | Large triangle | Stillbirth (≥20 weeks) | terminated: true, terminated_age: 24 | | "EP" below symbol | Ectopic pregnancy | ectopic: true | | Crossed lines (X) | Infertility | infertility: true | | Hash marks on line | Divorced/separated | divorced: true | | Line through offspring | No children by choice | no_children_by_choice: true | | "A" in upper right | Ashkenazi ancestry | ashkenazi: 1 | | "*" in upper left | Genetic anticipation | anticipation: true | | "d. XXy" label | Age at death (auto-calculated) | yob: 1950, yod: 2020, status: 1 | | Arrow + "OUT" label | Adopted OUT (placed for adoption) | adoption_type: "out" | | Dashed brackets | Foster placement (temporary) | adoption_type: "foster" | | Roman numerals I, II, III | Birth order in sibling group | birth_order: 1 (displays as "I") | | "E" marker (blue) | ART - Egg donor conception | art_type: "egg_donor" | | "S" marker (blue) | ART - Sperm donor conception | art_type: "sperm_donor" | | "Em" marker (blue) | ART - Embryo donor conception | art_type: "embryo_donor" | | "GC" marker (blue) | ART - Gestational carrier (surrogate) | art_type: "surrogate" | | "SAB" label | Pregnancy outcome - Spontaneous abortion | pregnancy_outcome: "miscarriage" | | "TOP" label | Pregnancy outcome - Termination of pregnancy | pregnancy_outcome: "induced_termination" | | "SB" label | Pregnancy outcome - Stillbirth | pregnancy_outcome: "stillbirth" | | "Het" label (green) | Gene copy number - Heterozygous | gene_copy_number: "heterozygous" | | "Hom" label (green) | Gene copy number - Homozygous | gene_copy_number: "homozygous" | | "CH" label (green) | Gene copy number - Compound heterozygous | gene_copy_number: "compound_heterozygous" | | Dashed partnership line | Unmarried/common-law partnership | relationship_type: "unmarried" |

Conditions (Bennett Standard - FREE TEXT)

Per Bennett 2008 standard, conditions are documented using free text. Simply provide a conditions array with any disease/condition name:

{
  "conditions": [
    { "name": "Breast cancer", "age": 42 },
    { "name": "Ovarian cancer", "age": 55 }
  ]
}

Examples:

• { "name": "Huntington's disease", "age": 45 }
• { "name": "Type 2 diabetes" } (no age = affected status only)
• { "name": "Cystic fibrosis" }
• { "name": "Hereditary hemochromatosis", "age": 38 }

Colors are auto-assigned from a palette based on unique condition names. Multiple conditions show as quadrants (male) or pie slices (female).

Genetic Testing Results

Supports any gene - use pattern {gene}_gene_test:

{
  "brca1_gene_test": { "type": "T", "result": "P" },
  "htt_gene_test": { "type": "T", "result": "P" },
  "apoe_gene_test": { "type": "S", "result": "N" }
}

Gene test result codes:

• type: T (tested), S (screening), - (unknown)
• result: P (positive), N (negative), - (unknown/VUS)

Labels appear as: BRCA1+ (positive), HTT- (negative)

Tools

get_pedigree_documentation

Returns comprehensive documentation about the pedigree data format. Always call this first before generating a pedigree.

generate_pedigree

Generates a family pedigree tree in PNG or SVG format.

Parameters: | Parameter | Type | Default | Description | |-----------|------|---------|-------------| | dataset | Individual[] | required | Array of family members | | width | number | 800 | Image width in pixels | | height | number | 600 | Image height in pixels | | symbol_size | number | 35 | Node diameter in pixels | | background | string | #ffffff | Background color | | labels | string[] | ['age'] | Attributes to display | | format | 'png' \| 'svg' | 'png' | Output format: png (base64 image) or svg (XML text) |

Data Format

Individual Object

interface Individual {
  // Required
  name: string;           // Unique ID (max 7 chars)
  sex: "M" | "F" | "U";   // Male, Female, Unknown

  // Identity
  display_name?: string;  // Human-readable name for display (max 13 chars)
  top_level?: boolean;    // Founding individual (no parents)
  proband?: boolean;      // Index case

  // Relationships
  mother?: string;        // Mother's name (must exist in dataset)
  father?: string;        // Father's name (must exist in dataset)

  // Demographics
  age?: number;           // Current age
  yob?: number;           // Year of birth
  status?: number;        // 0 = alive, 1 = deceased

  // Twins (Bennett standard)
  mztwin?: string;        // MZ twin group ID (identical)
  dztwin?: string;        // DZ twin group ID (fraternal)

  // Special indicators (Bennett standard)
  carrier?: boolean;      // Carrier status (dot in center)
  pregnant?: boolean;     // Current pregnancy (P inside symbol)
  terminated?: boolean;   // Stillbirth/SAB (small triangle)
  divorced?: boolean;     // Divorced from partner (hash marks)
  noparents?: boolean;    // Adopted (brackets around symbol)

  // Conditions (Bennett standard - FREE TEXT)
  conditions?: Array<{
    name: string;         // Any condition: "Breast cancer", "Huntington's disease", etc.
    age?: number;         // Age at diagnosis/onset
  }>;

  // Genetic tests (pattern: {gene}_gene_test)
  brca1_gene_test?: { type: "-"|"S"|"T", result: "-"|"P"|"N" };
  brca2_gene_test?: { type: "-"|"S"|"T", result: "-"|"P"|"N" };
  // ... any gene test
}

Examples

📸 View All 21 Scenario Examples →

See the full gallery of standardized pedigree scenarios demonstrating Bennett 2008/2022 compliance, including gender diversity, twins, consanguinity, ART indicators, and complex multi-generation families.

Basic Three-Generation Pedigree

[
  {"name": "MGF", "sex": "M", "top_level": true},
  {"name": "MGM", "sex": "F", "top_level": true, "conditions": [{"name": "Breast cancer", "age": 55}]},
  {"name": "Mother", "sex": "F", "mother": "MGM", "father": "MGF", "conditions": [{"name": "Breast cancer", "age": 42}]},
  {"name": "Father", "sex": "M", "top_level": true},
  {"name": "Proband", "display_name": "Sarah", "sex": "F", "mother": "Mother", "father": "Father", "proband": true, "age": 25, "brca1_gene_test": {"type": "T", "result": "P"}}
]

Neurological Condition Pedigree

[
  {"name": "GF", "sex": "M", "top_level": true, "status": 1, "conditions": [{"name": "Huntington's disease", "age": 52}]},
  {"name": "GM", "sex": "F", "top_level": true},
  {"name": "Father", "sex": "M", "mother": "GM", "father": "GF", "conditions": [{"name": "Huntington's disease", "age": 48}]},
  {"name": "Mother", "sex": "F", "top_level": true},
  {"name": "Proband", "sex": "M", "mother": "Mother", "father": "Father", "proband": true, "age": 25, "carrier": true}
]

Twins Example

[
  {"name": "Dad", "sex": "M", "top_level": true},
  {"name": "Mom", "sex": "F", "top_level": true},
  {"name": "Twin1", "sex": "M", "mother": "Mom", "father": "Dad", "mztwin": "mz1"},
  {"name": "Twin2", "sex": "M", "mother": "Mom", "father": "Dad", "mztwin": "mz1"},
  {"name": "DZTwin1", "sex": "M", "mother": "Mom", "father": "Dad", "dztwin": "dz1"},
  {"name": "DZTwin2", "sex": "F", "mother": "Mom", "father": "Dad", "dztwin": "dz1"}
]

Complex Family with Bennett Features

[
  {"name": "GF", "sex": "M", "top_level": true, "status": 1},
  {"name": "GM", "sex": "F", "top_level": true, "carrier": true},
  {"name": "Father", "sex": "M", "mother": "GM", "father": "GF", "divorced": true},
  {"name": "Mother", "sex": "F", "top_level": true},
  {"name": "Child1", "sex": "F", "mother": "Mother", "father": "Father", "proband": true, "noparents": true},
  {"name": "Loss", "sex": "U", "mother": "Mother", "father": "Father", "terminated": true}
]

Development

# Install dependencies
npm install

# Run in development mode (watch)
npm run dev

# Run all tests
npm test

# Build for production
npm run build

# Type check
npx tsc --noEmit

Testing

• 159 tests total covering:
  • Validation (parent references, gender constraints)
  • SVG rendering (all symbol types, indicators)
  • Condition markers and multi-condition pie charts
  • Gene test formatting
  • Twin rendering (MZ with bar, DZ without)
  • Consanguinity detection
  • Bennett 2008 compliance (carrier, pregnancy, termination, divorced)
  • Edge cases (deep pedigrees, wide generations, half-siblings)

References

• Bennett et al. 2008 - Standardized Human Pedigree Nomenclature
• Bennett et al. 2022 - Sex and Gender Inclusivity Update
• Iowa Human Genetics - How to Draw a Pedigree

License

MIT License - see LICENSE