Artificial Intelligence (AI) Calculator for “Polymorphism (SNP) calculator”

Polymorphism (SNP) calculators quantify genetic variation at single nucleotide positions. These tools enable precise analysis of SNP data for research and clinical applications.

This article explores SNP calculator functionalities, key formulas, practical tables, and real-world examples for expert-level understanding.

Example Numeric Prompts for Polymorphism (SNP) Calculator

• Calculate allele frequency for SNP rs12345 with genotype counts: AA=50, AG=30, GG=20
• Determine Hardy-Weinberg equilibrium p-value for SNP with observed genotypes: CC=40, CT=45, TT=15
• Compute minor allele frequency (MAF) for SNP rs67890 with allele counts: C=120, T=80
• Estimate linkage disequilibrium (D’) between SNP1 and SNP2 with haplotype frequencies: AB=0.3, Ab=0.2, aB=0.1, ab=0.4

Comprehensive Tables of Common Values for Polymorphism (SNP) Calculations

Essential Formulas for Polymorphism (SNP) Calculations

1. Allele Frequency Calculation

Allele frequency is the proportion of a specific allele among all alleles in the population.

• p: Frequency of allele A
• q: Frequency of allele B (alternate allele)
• N_AA: Number of individuals homozygous for allele A
• N_AB: Number of heterozygous individuals
• N_total: Total number of individuals genotyped

Allele frequencies must sum to 1 (p + q = 1).

2. Genotype Frequency

Genotype frequency is the proportion of each genotype in the population.

• f_AA: Frequency of homozygous genotype AA
• f_AB: Frequency of heterozygous genotype AB
• f_BB: Frequency of homozygous genotype BB

3. Minor Allele Frequency (MAF)

MAF is the frequency of the less common allele in the population.

MAF is critical for filtering SNPs in genome-wide association studies (GWAS).

4. Hardy-Weinberg Equilibrium (HWE) Test

HWE tests whether observed genotype frequencies deviate from expected frequencies under random mating.

Chi-square test statistic:

• Degrees of freedom = 1 for biallelic SNPs
• p-value > 0.05 indicates no significant deviation from HWE

5. Linkage Disequilibrium (LD) Measures

LD quantifies non-random association of alleles at two loci.

• P_AB: Frequency of haplotype AB
• p_A, p_B: Allele frequencies at loci A and B
• D_max: Maximum possible value of D given allele frequencies
• D’: Normalized LD measure ranging from -1 to 1
• r²: Correlation coefficient between loci, ranges 0 to 1

Real-World Application Examples of Polymorphism (SNP) Calculator

Example 1: Calculating Allele Frequencies and MAF from Genotype Counts

Suppose a study genotyped 100 individuals for SNP rs1801133 with the following genotype counts:

• CC (homozygous reference): 40
• CT (heterozygous): 45
• TT (homozygous alternate): 15

Step 1: Calculate total alleles:

Total individuals = 100

Total alleles = 2 × 100 = 200

Step 2: Calculate allele counts:

• Number of C alleles = (2 × 40) + 45 = 80 + 45 = 125
• Number of T alleles = (2 × 15) + 45 = 30 + 45 = 75

Step 3: Calculate allele frequencies:

Step 4: Determine MAF:

This indicates the T allele is the minor allele with frequency 37.5%.

Example 2: Testing Hardy-Weinberg Equilibrium for SNP Genotypes

Using the same genotype counts from Example 1:

• CC = 40
• CT = 45
• TT = 15

Step 1: Calculate allele frequencies (already done):

p = 0.625 (C), q = 0.375 (T)

Step 2: Calculate expected genotype frequencies under HWE:

Step 3: Calculate expected genotype counts:

• Expected CC = 0.3906 × 100 = 39.06
• Expected CT = 0.4688 × 100 = 46.88
• Expected TT = 0.1406 × 100 = 14.06

Step 4: Compute chi-square statistic:

Step 5: Determine p-value:

With 1 degree of freedom, χ² = 0.1609 corresponds to p > 0.05 (using chi-square tables or software).

Interpretation: No significant deviation from HWE; genotype distribution is consistent with random mating.

Additional Technical Insights on SNP Calculations

Polymorphism calculators often integrate multiple statistical tests and data normalization steps to ensure accuracy. For example, quality control filters remove SNPs with low call rates or extreme deviations from HWE, which may indicate genotyping errors.

Advanced calculators also compute linkage disequilibrium metrics such as D’ and r² to assess haplotype structure, which is critical for fine-mapping genetic associations. These metrics require phased haplotype data or inferred haplotypes from genotype data using algorithms like EM (Expectation-Maximization).

Moreover, SNP calculators may incorporate population stratification adjustments to avoid confounding in association studies. This involves principal component analysis (PCA) or mixed models to correct for ancestry differences.

References and Authoritative Resources

• NCBI dbSNP Database – Comprehensive SNP repository
• Genome.gov Genetic Variation Fact Sheet – Overview of genetic polymorphisms
• Hardy-Weinberg Equilibrium Testing in Genetic Studies – Detailed methodology
• Linkage Disequilibrium and Its Applications – Review article on LD metrics