Frequency Data and SNP Analysis

Q1, Sample Band 6 response (8 marks), annotated

The difference in C-allele frequency between the island (0.30) and the mainland (0.07) is 0.30 − 0.07 = 0.23 (23 percentage points). [1, correct calculation]

The data show a clear trend: the C allele appears more common in the island sample than in the mainland sample, suggesting a higher frequency of the disease-linked allele in the island population. Using cautious language: in these sampled groups, the C allele occurs at roughly four times the frequency on the island compared with the mainland. [1, states trend with cautious language]

However, several limitations reduce the strength of the conclusion. First, the island sample is only 400 individuals from a single isolated village, this is a small, geographically specific sample that may not represent any broader population or ancestry group. Even if the frequency is accurately measured for this village, generalising it to "island populations" is not justified. [1, sample size / representativeness limitation 1]

Second, the data describe a single SNP. One marker alone cannot determine whether the overall disease risk, which may depend on many genetic and environmental factors, is genuinely higher. A higher frequency of one allele at one position is a frequency trend, not proof of elevated individual risk. The strength of the conclusion depends on how many markers were compared and whether the single SNP has been confirmed as the primary cause of the condition. [1, single-marker limitation]

Third, the mainland sample of 50,000 provides a much stronger frequency estimate, but it is collected from an urban metropolitan area with diverse ancestry, this may not be the most appropriate reference group for comparison with a small isolated village. A more useful comparison might involve several island and mainland populations sampled consistently. [1, bias / comparison group limitation]

To strengthen the claim, the team should compare multiple SNPs across the genome to check whether the elevated C frequency reflects a genuine disease-risk trend or a chance result at one locus; collect larger and more representative samples from the island and the mainland; and document actual disease incidence to see whether the frequency difference corresponds to a real difference in observed cases. [1, suggestions to strengthen]

The evaluative judgement is that the team's conclusion is moderate at best. The data support a trend, the C allele is more frequent in the island sample, but the jump from "allele more common" to "population at substantially higher risk" is too strong for a single SNP measured in one small, isolated sample. [1, evaluative rating with reasoning]

A defensible version of the conclusion would be: "In this sampled island village, the C allele occurs at a higher frequency (0.30) than in the sampled mainland group (0.07), suggesting a possible trend toward higher carrier frequency for this disease-linked allele. This finding warrants further investigation using multiple markers and larger representative samples before any population-wide risk claim can be justified." [1, defensible reformulation using lesson vocabulary]

Q2, Sample Band 6 response (7 marks), annotated

A SNP (single nucleotide polymorphism) is a one-base difference at a specific position in the DNA between individuals or populations. The frequency of an allele at a SNP is calculated as p = (2 × homozygotes + heterozygotes) ÷ (2 × total individuals), so a population of 100 people with 49 TT and 42 TC has p(T) = (98 + 42) ÷ 200 = 0.70. [1, definition + formula]

A single SNP gives one comparison between populations. A whole-genome SNP panel (thousands of SNPs) gives thousands of effectively independent comparisons, so the resolution of relatedness inference is dramatically higher with the panel. [1, resolution]

A single SNP is also vulnerable to single-locus forces: natural selection acting at one site (e.g. the lactase-persistence SNP near LCT) can drive the allele frequency from 0.06 in East Asian samples to 0.70 in Northern European samples without making the two populations distant overall. A whole-genome panel averages over these locus-specific signals, so it is much less likely to mislead about overall relatedness. [1, locus-level selection criterion]

Both approaches share the same sample-size and bias issues, they use the same individuals, but per-locus noise is much higher than panel-wide noise. A 0.05 frequency in a sample of 50 has a much larger margin of error than the same number averaged across thousands of loci. [1, sampling-error criterion]

For example, two populations might differ by 0.89 in the frequency of one SNP (0.05 vs 0.94) yet share 99.8% of their overall genome. The first number is per-locus; the second is genome-wide. Treating the two as the same would be the error the lesson warns against, drawing a sweeping identity (or non-identity) claim from a single marker. [1, worked numerical example interpreted]

One SNP is sometimes the right tool: e.g. clinical testing for a specific disease allele, where the question is "does this person carry this allele?", the relatedness question is not in play. A panel is the right tool when the question is overall relatedness, ancestry, or population structure. [1, appropriate context]

Neither approach is universally better, it depends on the question. The lesson's caution applies: the strength of a conclusion drawn from SNP data must be proportional to how many positions were compared, how many individuals were sampled, and how representative those samples are. [1, context-aware judgement linked to lesson framing]

Q3, Sample Band 6 response (6 marks)

The claim is partly correct but largely flawed. [1, judgement]

What is defensible: If 24 of 30 sampled individuals carry the trait, then 24 ÷ 30 = 80% is the correct observed frequency in the sample, this part is arithmetic and accurate. [1, concedes the defensible element]

What is wrong:

• "Exactly 80% of all individuals." A sample of 30 is small and may not be representative. 80% in the sample is a point estimate of the wider population, the true value may be quite different, and individual outcomes are not bound by it. A larger, representative sample is required before generalising. [1, refutes "exactly 80% of all"]
• "Must be due to natural selection." Allele frequencies change through several mechanisms: natural selection, genetic drift (especially powerful in small populations), mutation, and gene flow / migration. Concluding "natural selection" from a frequency change alone requires additional evidence, for example, evidence of differential survival or reproduction tied to the allele. [1, refutes "must be natural selection" using the lesson's misconceptions box]

Defensible reformulation: "In a sample of 30 individuals from Population X, 80% showed the trait. This is an observed sample frequency; the wider population frequency may differ, and a larger representative sample would give a more reliable estimate. A change in this frequency between generations could be caused by natural selection, but also by genetic drift, mutation or migration, additional evidence is required before attributing the change to any one mechanism." [1, uses precise lesson terminology and rewrites the claim defensibly]