ffsshhttiikk Genetics
What I Do
Genetics studies heredity, genetic variation, and the function and behavior of genes. I cover Mendelian inheritance, genetic linkage, gene mapping, mutation analysis, population genetics, quantitative genetics, and genetic disorders. I help analyze inheritance patterns, calculate genetic risks, and understand gene function.
When to Use Me
- Analyzing Mendelian inheritance patterns
- Calculating genetic disease risk and carrier probability
- Performing linkage analysis and gene mapping
- Understanding population genetics and allele frequencies
- Studying mutation types and effects
- Interpreting genetic test results
- Designing breeding strategies and genetic crosses
Core Concepts
- Mendelian Inheritance: Dominant, recessive, codominant patterns
- Genetic Linkage: Recombination frequency, linkage disequilibrium
- Gene Mapping: LOD scores, genetic distance, map units (cM)
- Mutation Types: Point mutations, insertions, deletions, chromosomal aberrations
- Population Genetics: Hardy-Weinberg equilibrium, allele frequencies
- Quantitative Genetics: Heritability, breeding values, genetic variance
- Genetic Disorders: Inheritance patterns of monogenic diseases
- Gene Expression: Genotype-phenotype relationships
- Epistasis: Gene-gene interactions and phenotypic effects
- Genetic Testing: PCR, sequencing, array CGH interpretation
Code Examples
import numpy as np
from typing import List, Dict, Tuple
from itertools import combinations
class MendelianGenetics:
def __init__(self, gene_name: str):
self.gene_name = gene_name
def predict_offspring(self, parent1_genotype: str,
parent2_genotype: str) -> Dict:
alleles1 = list(parent1_genotype)
alleles2 = list(parent2_genotype)
offspring = {}
for a1 in alleles1:
for a2 in alleles2:
genotype = ''.join(sorted([a1, a2]))
offspring[genotype] = offspring.get(genotype, 0) + 1
total = sum(offspring.values())
return {k: v/total for k, v in offspring.items()}
def calculate_carrier_probability(self, affected_frequency: float,
carrier_frequency: float) -> float:
return 2 * np.sqrt(affected_frequency) # Approximate for recessive
def calculate_recurrence_risk(self, parent_genotypes: List[str],
affected_status: List[bool]) -> float:
if all(affected_status):
return 0.25 # Both parents carriers, affected child
elif any(affected_status):
return 0.0
return 0.0 # Need more info
def paternity_index(self, child_alleles: List[str],
alleged_father_alleles: List[str],
random_man_alleles: List[str]) -> float:
prob_exclusion = 0.0
prob_inclusion = 0.0
for child in child_alleles:
if child in alleged_father_alleles:
prob_inclusion += 0.5
if child in random_man_alleles:
prob_exclusion += 0.5
return prob_inclusion / prob_exclusion if prob_exclusion > 0 else float('inf')
class PopulationGenetics:
def __init__(self, population: str):
self.population = population
def hardy_weinberg(self, allele_frequency_a: float) -> Dict:
p = allele_frequency_a
q = 1 - p
return {
'AA_frequency': p**2,
'Aa_frequency': 2*p*q,
'aa_frequency': q**2
}
def calculate_f_st(self, heterozygosity_loci: List[float],
heterozygosity_total: float) -> float:
Hs = np.mean(heterozygosity_loci)
return (heterozygosity_total - Hs) / heterozygosity_total
def effective_population_size(self, ne_census: int,
variance: float) -> float:
return (4 * ne_census - 2) / (2 + variance)
def allele_frequency_change(self, p0: float,
selection_coefficient: float,
generations: int) -> List[float]:
p = p0
frequencies = [p]
for _ in range(generations):
p = p / (1 - selection_coefficient * (1 - p))
frequencies.append(p)
return frequencies
def inbreeding_coefficient(self, consanguinity: str) -> float:
coefficients = {
'first_cousins': 1/16,
'second_cousins': 1/64,
'uncle_niece': 1/4,
'self': 1/4
}
return coefficients.get(consanguinity, 0.0)
class LinkageAnalysis:
def __init__(self, chromosome: int):
self.chromosome = chromosome
def calculate_recombination_fraction(self, markers: List[str],
genotypes_parent1: List[str],
genotypes_parent2: List[str]) -> float:
recombinations = 0
total = len(markers) - 1
for i in range(total):
if genotypes_parent1[i] != genotypes_parent1[i+1]:
recombinations += 1
if genotypes_parent2[i] != genotypes_parent2[i+1]:
recombinations += 1
return recombinations / (2 * total)
def lod_score(self, recombination_fraction: float,
theta: float = 0.5) -> float:
likelihood_observed = (1 - theta) ** (1 - recombination_fraction) * \
theta ** recombination_fraction
likelihood_null = 0.25
return np.log10(likelihood_observed / likelihood_null)
def predict_morgans(self, recombination_fraction: float) -> float:
return -np.log10(1 - 2 * recombination_fraction) / 100
class GeneticTesting:
def __init__(self, test_type: str):
self.test_type = test_type
def sensitivity_specificity(self, true_positives: int,
false_positives: int,
false_negatives: int,
true_negatives: int) -> Dict:
sensitivity = true_positives / (true_positives + false_negatives)
specificity = true_negatives / (true_negatives + false_positives)
ppv = true_positives / (true_positives + false_positives)
npv = true_negatives / (true_negatives + false_negatives)
return {
'sensitivity': sensitivity,
'specificity': specificity,
'positive_predictive_value': ppv,
'negative_predictive_value': npv
}
def bayes_posterior(self, prior: float, likelihood_given_disease: float,
likelihood_given_no_disease: float) -> float:
evidence = likelihood_given_disease * prior + \
likelihood_given_no_disease * (1 - prior)
return (likelihood_given_disease * prior) / evidence
cross = MendelianGenetics("GeneA")
offspring = cross.predict_offspring("Aa", "Aa")
print(f"Offspring ratios: {offspring}")
hw = PopulationGenetics("European")
frequencies = hw.hardy_weinberg(0.01)
print(f"AA: {frequencies['AA_frequency']:.4f}, Aa: {frequencies['Aa_frequency']:.4f}")
Best Practices
- Confirm pedigree information and inheritance patterns before analysis
- Use appropriate statistical methods for linkage analysis
- Consider genetic heterogeneity in disease gene studies
- Account for reduced penetrance in risk calculations
- Validate genetic test results with orthogonal methods
- Consider population allele frequencies in risk assessment
- Use appropriate reference databases for variant interpretation
- Account for consanguinity in rare disease diagnosis
- Apply proper multiple testing corrections in GWAS
- Maintain confidentiality in genetic information handling