LOD Score Calculator
Calculate LOD score (logarithm of odds) for linkage analysis between a genetic marker and a disease locus. LOD > 3 is strong evidence for linkage.
🧬 Genetics📐 Z(θ) = log10[L(θ) / L(0.5)]🧬 Biology
Number of recombinant offspring
Number of non-recombinant offspring
Please enter valid values.
Formula & Reference
| Variable | Symbol | Formula | Units |
|---|---|---|---|
| LOD Score Calculator | — | Z(θ) = log10[L(θ) / L(0.5)] | dimensionless |
Step-by-Step Examples
Example 1
Strong Linkage Signal
8 recombinants out of 50 offspring (theta ~ 0.16).
- L(0.16) = 0.16^8 x 0.84^42
- L(0.5) = 0.5^50
- Z(0.16) = log10[0.16^8 x 0.84^42 / 0.5^50]
- Calculates to Z > 3: strong evidence for linkage
✓ Z > 3 at theta ~ 0.15 (strong linkage)
Example 2
Weak Signal
4 recombinants out of 20.
- theta_estimate = 4/20 = 0.20
- Small sample: LOD may not reach 3
- Need more families for reliable linkage detection
✓ Small sample: LOD < 3 likely (insufficient power)
Example 3
Exclusion
Many recombinants: 48 out of 100.
- theta = 0.48, near 0.5
- Z(all theta) will be negative
- LOD < -2: exclude linkage in this region
✓ LOD < -2: evidence AGAINST linkage at this locus
Real-World Applications
Disease Gene Mapping
LOD score analysis identifies chromosomal regions harboring disease genes by tracking co-inheritance with markers.
Clinical Genetics
BRCA1 and hundreds of other disease genes were first mapped using LOD score linkage analysis.
Forensics
Paternity testing uses likelihood ratios related to LOD score methodology.
Statistical Genetics
LOD scores replaced chi-square in genetics because they can be summed across families and give explicit odds ratios.
Common Mistakes to Avoid
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LOD > 3 is conventional threshold
LOD = 3 means 1000:1 odds in favor of linkage. This threshold accounts for the multiple testing problem of testing all chromosomal locations.
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LOD < -2 excludes linkage
LOD < -2 is conventional threshold to exclude linkage. Means less than 1:100 odds favoring linkage at that theta.
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Sum LOD scores across families
One advantage of LOD scores: sum across independent families. Combined LOD > 3 even if individual families are uninformative.
Frequently Asked Questions
What is LOD score? ▾
LOD = log10 (Likelihood of linkage at recombination fraction theta / Likelihood of no linkage). LOD = log10[odds ratio]. LOD > 3 is accepted as significant evidence for linkage.
What is the significance threshold LOD = 3? ▾
LOD = 3 corresponds to 1000:1 odds in favor of linkage. Chosen to control false positive rate across all possible map positions tested (roughly equivalent to p < 0.001 corrected for multiple testing).
What is parametric vs non-parametric linkage? ▾
Parametric LOD: requires known inheritance model (dominant, recessive). Non-parametric (NPL, allele sharing): does not require genetic model. Used when mode of inheritance is unknown.
How has linkage analysis been replaced? ▾
For common variants: GWAS using millions of SNPs. For rare disease genes: exome/genome sequencing within families. LOD score linkage analysis still useful for rare diseases in large families.
What is multipoint linkage? ▾
Uses multiple markers simultaneously (rather than one marker at a time) to increase power. Implemented in LINKAGE, MENDEL, and other software packages.