Pedigree
Multi-generation genetic inheritance charts for clinical genetics. Affected/carrier/presymptomatic status fills, proband arrow markers, consanguinity. Standardized human pedigree nomenclature.
遗传学 pedigree chart 标准——追踪特定性状/疾病在家族中的遗传模式。
References:
- Bennett, R.L. et al. (1995). Recommendations for standardized human pedigree nomenclature. Am J Hum Genet, 56(3), 745-752.
- Bennett, R.L. et al. (2008). Standardized human pedigree nomenclature: Update and assessment. J Genet Couns, 17(5), 424-433.
- Bennett, R.L. (2022). The evolving pedigree: Updating to reflect modern family structures, sex, and gender. J Genet Couns, 31(6), 1267-1275. ← 最新标准
- NSGC (National Society of Genetic Counselors) pedigree standardization committee
1. Key Differences from Genogram
| 方面 | Genogram | Pedigree Chart |
|---|---|---|
| 主要用途 | 家庭关系 + 医疗 + 心理 + 社工评估 | 纯遗传追踪（单一或少量 trait） |
| Condition 表示 | 多条件 fill patterns (22 categories) | 只有 affected/carrier/unaffected (1-3 traits) |
| 关系质量 | 有（emotional relationships 34 types） | 无（只有 mated/not mated） |
| 代标记 | 无 | Roman numeral (I, II, III...) |
| 个体标记 | 名字 + birth year | Generation-number (II-3) + optional name |
| Proband | 无（有 Index Person） | 有（箭头指向 index case，P 标记） |
| Consultand | 无 | 有（箭头 + C 标记） |
| Consanguinity | 可选标注 | 关键信息（双线，必须标注） |
| Sex vs Gender | 传统 binary | Bennett 2022: sex ≠ gender，diamond for unknown/DSD |
| 关系表示 | 详细（divorce, separation, cohabitation） | 简化（mated line, no longer together, consanguinity） |
2. Individual Symbols
2.1 Core Shapes (Bennett 2022 Updated)
| Symbol | Shape | 含义 | DSL |
|---|---|---|---|
| □ | Square | AMAB (Assigned Male at Birth) | [male] or [amab] |
| ○ | Circle | AFAB (Assigned Female at Birth) | [female] or [afab] |
| ◇ | Diamond | UAAB (Unknown/Ambiguous at Birth) / DSD / Non-disclosed | [unknown] or [uaab] |
Bennett 2022 重要更新：
- Square/Circle 现在正式代表 assigned sex at birth，不是 gender identity
- Diamond 用于：sex unknown, differences of sex development (DSD/intersex), non-disclosed, or still in utero (sex unknown)
- Gender identity 如果与 assigned sex 不同，用 label 标注（不改变 shape）
- 例：transgender woman (AMAB) → square shape + "TW" label or gender annotation
2.2 Affected Status
| Status | Fill Pattern | SVG | DSL |
|---|---|---|---|
| Unaffected | Empty (white fill) | fill: white | (default) |
| Affected (single trait) | Full fill (black/dark) | fill: #333 | [affected] |
| Carrier (autosomal) | Half-filled (left half, vertical divide) | <clipPath> left half | [carrier] |
| Carrier (X-linked female) | Dot in center | Small <circle> inside | [carrier-x] |
| Obligate carrier | Dot in center | Small filled <circle> inside | [obligate-carrier] |
| Asymptomatic/presymptomatic | Vertical line through shape | <line> through center | [presymptomatic] |
| Multiple traits | Quadrant fill (like genogram) | See below | [affected: trait1 + trait2] |
多 trait pedigree（最多 4 traits）：
# Legend defines what each quadrant means
pedigree "Breast/Ovarian Cancer Family"
legend: trait1 = "Breast cancer" (fill: quad-tl)
legend: trait2 = "Ovarian cancer" (fill: quad-tr)
legend: trait3 = "Prostate cancer" (fill: quad-bl)
I-1 [male, affected: trait3] # bottom-left quadrant filled
I-2 [female, affected: trait1] # top-left quadrant filled
II-3 [female, affected: trait1+trait2] # top-left + top-right filled2.3 Life Status Symbols
| Status | Visual | SVG | DSL |
|---|---|---|---|
| Alive | Normal shape | Default rendering | (default) |
| Deceased | Diagonal slash through shape (/) | Single <line> top-right to bottom-left | [deceased] |
| Stillborn (SB) | Small shape + SB text | 60% scale + label "SB" | [stillborn] |
| Pregnancy (P) | Diamond (sex unknown) or shape with P | shape + "P" label | [pregnancy] |
| Spontaneous abortion (SAB) | Small triangle | <polygon> 15×15 | [sab] |
| Induced abortion (TAB) | Small triangle with horizontal line | <polygon> + <line> | [tab] |
| Ectopic pregnancy (ECT) | Small triangle + ECT label | <polygon> + text | [ectopic] |
| Affected SAB | Filled small triangle | <polygon> filled | [sab, affected] |
Bennett 2022 注意：
- Deceased 标记从传统的 "X through shape" 更新为 "diagonal slash (/)"，与 genogram 的 X 标记不同
- 这是 pedigree 与 genogram 的重要视觉区别
2.4 Special Markers
| Marker | Symbol | 位置 | DSL |
|---|---|---|---|
| Proband | Arrow (↗) pointing to shape + "P" | 左下方 | [proband] |
| Consultand | Arrow (↗) pointing to shape + "C" | 左下方 | [consultand] |
| Evaluated | "E" above or inside shape | 上方 | [evaluated] |
| No offspring by choice | Crossed out drop line | Couple line 下方 | [no-children] |
| Infertility | Crossed out drop line + "∞" | Couple line 下方 | [infertile] |
| Adopted in | Brackets around shape | [ shape ] | [adopted-in] |
| Adopted out | Brackets around shape, dashed line to parents | [ shape ] + dashed line | [adopted-out] |
2.5 Assisted Reproduction (Bennett 2022)
Bennett 2022 增加了辅助生殖的标准符号，这在现代临床中越来越重要：
| Type | Symbol | DSL |
|---|---|---|
| Donor egg | "D" on connecting line from egg donor | [donor-egg] |
| Donor sperm | "D" on connecting line from sperm donor | [donor-sperm] |
| Donor embryo | "D" on connecting lines from both donors | [donor-embryo] |
| Surrogacy (gestational) | "S" label on surrogate, dashed line to child | [surrogate] |
| IVF | "IVF" label on couple line | couple line 标注 |
3. Relationship Lines (Pedigree-Specific)
Pedigree 的关系线比 genogram 简单得多——没有 emotional relationships，只有遗传学相关的结构线。
3.1 Partnership Lines
| Type | Line Style | DSL | 含义 |
|---|---|---|---|
| Mated (together) | Single horizontal solid line | A -- B | 有后代的配偶 |
| Mated (no longer together) | Single line + single slash | A -/- B | 分开（不区分 divorce/separation） |
| Consanguinity | Double horizontal line | A == B | 近亲婚配（遗传学关键！） |
| Relationship line (no offspring) | Single horizontal dashed | A ~ B | 配偶但无后代 |
3.2 Parent-Child Lines
| Type | Line | DSL |
|---|---|---|
| Biological | Solid vertical | (default) |
| Adopted in | Dashed vertical + brackets on child | [adopted-in] |
| Adopted out | Dashed vertical + brackets, line goes to new parents | [adopted-out] |
| Identical twins | V-shape (meet at single point) | [twin-mz] (monozygotic) |
| Fraternal twins | Inverted-V with horizontal bar | [twin-dz] (dizygotic) |
| Twins (unknown zygosity) | Inverted-V, question mark on bar | [twin-unknown] |
| Triplets+ | 3+ lines from point/bar | [triplet-mz] etc. |
4. Generation and Individual Labeling
4.1 Generation Labels
- 左侧显示 Roman numeral（I, II, III, IV...）
- I = 最年长的一代
- 对齐到该代的中心 Y 坐标
- Font: bold, 14px, class="schematex-generation-label"
4.2 Individual Labels
- 每代内从左到右编号：1, 2, 3...
- 完整标识：
II-3= 第二代第 3 个人 - 显示在 shape 下方
- Proband 和 consultand 额外有箭头标记
4.3 Legend (Required for Multi-Trait Pedigrees)
- Pedigree 图必须包含 legend，解释 fill pattern 的含义
- Legend 通常放在右下角或图表底部
- Legend 内容：每个 trait 对应的 fill pattern + color
5. Layout Rules
与 genogram 共享大部分布局逻辑（generation alignment, male-left, children ordering），区别：
5.1 Pedigree-Specific Layout
- Generation label 列： 左侧留出 40px 列宽显示 Roman numeral
- Individual numbering： Shape 下方显示 "II-3" 格式的标识
- No emotional lines： 不需要 emotional relationship routing
- Consanguinity emphasis： 双线要明显可见，因为这是遗传学的关键信息
- Proband arrow： 从左下 45° 指向 proband shape，长度 20px
- Legend box： 右下角或底部，包含 trait 说明
5.2 Spacing (Pedigree-Specific Adjustments)
| Parameter | Default | 与 Genogram 差异 |
|---|---|---|
| Left margin (for gen labels) | 50px | Genogram 无此需求 |
| Node width | 40px | 同 |
| Node height | 40px | 同 |
| Generation spacing | 100px | 略小于 genogram (120px)，因为无 emotional lines |
| Sibling spacing | 50px | 略小于 genogram (60px) |
| Legend box width | 150px | Genogram 无此需求 |
| Legend box height | auto (based on traits) | — |
6. DSL Grammar (Pedigree — Expanded)
document = header legend_def* statement*
header = "pedigree" quoted_string? NEWLINE
legend_def = "legend:" IDENTIFIER "=" quoted_string legend_fill? NEWLINE
legend_fill = "(" "fill:" FILL_SPEC ")"
FILL_SPEC = "full" | "quad-tl" | "quad-tr" | "quad-bl" | "quad-br"
| "half-left" | "half-right" | "striped" | "dotted"
statement = comment | individual_def | couple_def
individual_def = ID properties? NEWLINE
properties = "[" property ("," property)* "]"
property = sex_prop | status_prop | genetic_prop | special_prop | kv_prop
sex_prop = "male" | "female" | "unknown" | "amab" | "afab" | "uaab"
status_prop = "deceased" | "stillborn" | "pregnancy"
| "sab" | "tab" | "ectopic"
genetic_prop = "affected" | "carrier" | "carrier-x" | "obligate-carrier"
| "presymptomatic" | "unaffected"
| "affected:" trait_list
trait_list = IDENTIFIER ("+" IDENTIFIER)*
special_prop = "proband" | "consultand" | "evaluated"
| "adopted-in" | "adopted-out"
| "donor-egg" | "donor-sperm" | "donor-embryo" | "surrogate"
| "no-children" | "infertile"
| "twin-mz" | "twin-dz" | "twin-unknown"
| "triplet-mz" | "triplet-dz"
couple_def = ID couple_op ID couple_label? NEWLINE (INDENT child+ DEDENT)?
couple_op = "--" | "==" | "-/-" | "~"
couple_label = "[" kv_prop "]"
child = individual_def
comment = "#" [^\n]* NEWLINE
ID = /[a-zA-Z][a-zA-Z0-9_-]*/
IDENTIFIER = /[a-zA-Z][a-zA-Z0-9_-]*/
VALUE = /[^\],\n]+/
quoted_string = '"' /[^"]*/ '"'
INDENT = increase in leading whitespace (2+ spaces)
DEDENT = decrease in leading whitespace
NEWLINE = /\n/7. Test Cases
Case 1: Autosomal Recessive (Cystic Fibrosis)
pedigree "Cystic Fibrosis Family"
I-1 [male, carrier]
I-2 [female, carrier]
I-1 -- I-2
II-1 [male, unaffected]
II-2 [female, carrier]
II-3 [male, affected, proband]
II-4 [female, unaffected]验证：I-1/I-2 half-filled (carrier)，II-3 full-filled + proband arrow，左侧有 "I" "II" 标记。
Case 2: Consanguinity
pedigree "Consanguineous Marriage"
I-1 [male, carrier]
I-2 [female, unaffected]
I-1 -- I-2
II-1 [male, carrier]
II-2 [female, unaffected]
I-3 [male, unaffected]
I-4 [female, carrier]
I-3 -- I-4
II-3 [female, carrier]
II-1 == II-3
III-1 [male, affected, proband]验证：II-1 和 II-3 之间是双线（consanguinity），III-1 full-filled + proband arrow。
Case 3: X-Linked Recessive (Hemophilia)
pedigree "Hemophilia A"
I-1 [male, unaffected]
I-2 [female, carrier-x]
I-1 -- I-2
II-1 [male, affected]
II-2 [female, carrier-x]
II-3 [male, unaffected]
II-4 [female, unaffected]
II-2 -- II-5 [male, unaffected]
III-1 [male, affected]
III-2 [female, carrier-x]
III-3 [male, unaffected]验证：carrier-x females 有 center dot，affected males full-filled。
Case 4: Multi-Trait Pedigree
pedigree "Cancer Family Syndrome"
legend: breast = "Breast cancer" (fill: quad-tl)
legend: ovarian = "Ovarian cancer" (fill: quad-tr)
legend: prostate = "Prostate cancer" (fill: quad-bl)
legend: colon = "Colon cancer" (fill: quad-br)
I-1 [male, affected: prostate, deceased]
I-2 [female, affected: breast, deceased]
I-1 -- I-2
II-1 [female, affected: breast+ovarian]
II-2 [male, unaffected]
II-3 [female, unaffected, evaluated]
II-1 -- II-4 [male, unaffected]
III-1 [female, unaffected, proband]
III-2 [male, unaffected]验证：legend box 显示 4 个 trait 对应的 quadrant fill，I-1 有 quad-bl filled，II-1 有 quad-tl + quad-tr filled，III-1 有 proband arrow。
Case 5: Modern Family (Bennett 2022 — Assisted Reproduction)
pedigree "Donor Conception"
I-1 [male]
I-2 [female]
I-1 -- I-2
II-1 [female]
donor [male, donor-sperm]
II-1 -- II-2 [male]
III-1 [female, proband]验证：donor-sperm 标注在 donor 到 child 的连接线上，donor node 可选显示。
Case 6: Pregnancy / Loss
pedigree "Reproductive History"
I-1 [male]
I-2 [female]
I-1 -- I-2
II-1 [male]
II-2 [female, sab]
II-3 [male, stillborn]
II-4 [female, pregnancy]
II-5 [female]验证：II-2 是小三角 (SAB)，II-3 是小 shape + SB label + deceased slash，II-4 是 diamond/shape with "P"。
Case 7: Large Pedigree (5 Generations)
pedigree "Huntington Disease"
I-1 [male, affected, deceased]
I-2 [female, deceased]
I-1 -- I-2
II-1 [male, affected, deceased]
II-2 [female, unaffected]
II-3 [male, unaffected, deceased]
II-1 -- II-4 [female, unaffected]
III-1 [female, affected]
III-2 [male, presymptomatic]
III-3 [female, unaffected]
III-1 -- III-4 [male, unaffected]
IV-1 [male, presymptomatic, proband]
IV-2 [female, unaffected]
III-3 -- III-5 [male, unaffected]
IV-3 [male, unaffected]
IV-4 [female, unaffected]
IV-1 -- IV-5 [female, unaffected]
V-1 [unknown, pregnancy]验证：5 代 Roman numeral 标记（I-V），presymptomatic 有 vertical line 标记，V-1 是 pregnancy diamond。
8. Implementation Priority
| Priority | Feature | Complexity |
|---|---|---|
| P0 (Phase 2.1) | Basic pedigree layout reusing genogram engine + Roman numeral labels + individual numbering | Medium |
| P0 | Affected/carrier/unaffected fill + proband arrow | Low |
| P1 | Consanguinity double line (already in genogram, but critical for pedigree) | Low |
| P1 | Deceased slash (/ not X), SAB/TAB/stillborn symbols | Medium |
| P1 | Legend box rendering | Medium |
| P2 | Multi-trait quadrant fill system | Medium |
| P2 | X-linked carrier dot | Low |
| P2 | Bennett 2022 sex/gender annotation | Low |
| P2 | Assisted reproduction symbols (donor, surrogate) | Medium |
| P3 | Presymptomatic vertical line marker | Low |
| P3 | Adopted in/out bracket notation | Low |
Ecomap
Family systems embedded in institutional, social, and cultural support networks. Radial layout with weighted connection strengths and directional energy flow arrows. Based on Hartman (1978).
Phylogenetic tree
Evolutionary trees with Newick/NHX input, clade coloring, bootstrap support values, proportional branch lengths. Indent-based DSL alternative also supported.