SNPs and haplotypes rs384756(A>C)or(T>G)[0.670.33] Chromosome 1 AATGCCGATTCAGGGCTTAACG TTACGGCTAAGTCCCGAATTCG Chromosome 2 AATGCCGATTCCGGGCTTAACG TTACGGCTAAGGCCCGAATTCG SNP1(A/C) SNP2(G/T SNP3 (C/A) SNP4(T/C) AAcc GrTG ↓ccAA ← Chromosome H1 Tc H2 Haplotypes H3 H4
SNPs and haplotypes AATGCCGATTCAGGGCTTAACG TTACGGCTAAGTCCCGAATTCG AATGCCGATTCCGGGCTTAACG TTACGGCTAAGGCCCGAATTCG Chromosome 1 Chromosome 2 rs384756 (A > C) or (T > G) [0.67/0.33] SNP1 (A/C) SNP2 (G/T) SNP3 (C/A) SNP4 (T/C) A G C T H1 A T C T H2 C T A C H3 C G A T H4 Chromosome Haplotypes
Allele and genotype frequencies in populations: the Hardy-Wienberg equilibrium(HWE) PA population frequency of A-allele= p Pa= population frequency of a-allele = q a+ Pa=p+ q Sperm A-allele Sperm a-allele p q Egg A-allele AA aA Egg a-allele Aa aa q pg aa 2Aa aa p2+ 2pq g Assumptions: large population; no: new mutations, selection; migration
Allele and genotype frequencies in populations: the Hardy-Wienberg equilibrium (HWE) Let: PA = population frequency of A-allele = p Pa = population frequency of a-allele = q PA + Pa = p + q = 1 Sperm A-allele p Sperm a-allele q Egg A-allele p AA p2 aA qp Egg a-allele q Aa pq aa q2 AA 2Aa aa p2 + 2pq + q2 = 1 Assumptions: large population; no: new mutations, selection; migration
Incidence, Gene Frequency, and Heterozygote Frequency for Selected Autosomal Disorders in Different Populations Disorder Population Incidence Allele Frequency Heterozygote Frequency RECESSIVE q 2pq Sickle cell anemia(S/S genotype) U.S. African American 1 in 400 0.05 1in11 Hispanic American 1in40,000 0.005 1in101 ar-Antitrypsin deficiency Denmark 1in2000 0.022 1in22 (Z/Z genotype)t U.S. African American 1 in 100.000 1in125 Cystic fibrosis(all mutant alleles) U.S. white 1in2000 0.022 1in22 1in25,000 0.0063 Mexico 1in8500 0.011 1in47 Phenylketonuria(all mutant Scotland 1in5300 0.014 1in37 alleles)t Finland 1in200,000 0.002 1in250 Japan 1in109000 0.003 1in166 Tay-Sachs diseaset U.S. Ashkenazi Jewish 1 in 3900 0.016 1in32 U.S. non-Ashkenazi 1in112,000 0.003 1in170 Jewish DOMINANT 2pq+ q Familial hy percholesterolemia' Regions of Quebec, 1in122 0.004 Canada Kaner 1in70 0.007 South afr Myotonic dystrophy 1in25,000 0.00002 1in475 011