- The table given below shows the Lod score values of three different pairs of genes studied for assessing if they are linked pairs:
| Gene Pair ‘1’ | Gene Pair ‘2’ | Gene Pair ‘3’ | |
| Lod Score | 1 | 2 | 3 |
The following conclusions were made from the data given above:
A. For gene pair 1 the probability of the genes being linked is 10 times more likely than them assorting independently.
B. For gene pair 2, theLod score 2 indicates that the probability of the genes being linked is twice more likely than assorting independently.
C. The genes of pair1 and 2, can both be considered as linked, while the genes of pair 3 exhibits independent assortment.
D. The genes of pair 3 can be considered as linked.
Which one of the following options represents statement(s) that is/are correct?
(1) A and C (2) B and D
(3) A and D (4) A and B
LOD Score Interpretation for Linked Genes
Introduction:
LOD score interpretation for linked genes is a common conceptual problem in CSIR NET and other genetics exams, because it directly tests understanding of how linkage evidence is quantified on a logarithmic odds scale. In this question, three gene pairs have LOD scores of 1, 2 and 3, and the task is to decide which verbal statements about odds of linkage and “linked vs independent assortment” status are correct. Correctly answering requires converting LOD scores into odds ratios and applying the usual decision thresholds for linkage significance.
Concept: What a LOD Score Means
A LOD score (Z) is defined as the base‑10 logarithm of the likelihood ratio of the data under the hypothesis of linkage versus no linkage, i.e.
Z = log10(Llinked / Lindependent)
Therefore, a LOD score of X means the observed data are 10X times more likely if the loci are linked than if they assort independently.
Common interpretive thresholds are:
- Z ≥ 3: Strong, statistically significant evidence for linkage (about 1000:1 odds in favor of linkage).
- −2 ≤ Z < 3: Inconclusive evidence; data are not strong enough to claim linkage or to rule it out definitively.
Evaluating Each Gene Pair
| Gene Pair | LOD Score (Z) | Odds for Linkage |
|---|---|---|
| 1 | 1 | 10:1 |
| 2 | 2 | 100:1 |
| 3 | 3 | 1000:1 |
LOD 3 crosses the standard significance threshold for declaring genes as linked.
Option A Analysis
Statement A: For gene pair 1 the probability of the genes being linked is 10 times more likely than them assorting independently.
LOD = 1 means the likelihood ratio Llinked/Lindependent = 101 = 10. This exactly matches the verbal description “10 times more likely,” so statement A correctly interprets the odds corresponding to LOD 1.
Conclusion for A: Statement A is correct.
Option B Analysis
Statement B: For gene pair 2, the LOD score 2 indicates that the probability of the genes being linked is twice more likely than assorting independently.
LOD = 2 means the data are 102 = 100 times more likely under linkage than under independent assortment, not “2 times more likely.” The phrase “twice more likely” implies an odds ratio of about 2:1, which corresponds to a LOD close to log10(2) ≈ 0.3, not 2.
Conclusion for B: Statement B is incorrect, because it misunderstands the logarithmic nature of the LOD scale.
Option C Analysis
Statement C: The genes of pair 1 and 2 can both be considered as linked, while the genes of pair 3 exhibit independent assortment.
A conventional cutoff for declaring significant linkage is LOD ≥ 3, corresponding to about 1000:1 odds in favor of linkage. LOD scores of 1 and 2 (gene pairs 1 and 2) provide some evidence for linkage (10:1 and 100:1 odds, respectively) but are typically treated as suggestive or inconclusive, not definitively linked. LOD 3 (gene pair 3) meets the usual threshold for significant linkage and does not indicate independent assortment; instead, it is the strongest candidate for being considered a linked pair among the three.
Conclusion for C: Statement C is incorrect on both counts: it prematurely labels pairs 1 and 2 as definitively linked, and it wrongly says pair 3 is independently assorting.
Option D Analysis
Statement D: The genes of pair 3 can be considered as linked.
With LOD = 3, the odds in favor of linkage are 1000:1, and this value is widely accepted as the threshold for significant evidence of linkage in classical linkage analysis. Therefore, it is appropriate to “consider gene pair 3 as linked” under standard criteria.
Conclusion for D: Statement D is correct.
Final Option Choice
Correct statements: A and D.
Incorrect statements: B and C.
Final Answer: Option (3) A and D.
