The Genetic of Earwax Wet earwax is a

The Genetic of Earwax • Wet earwax is a dominant allele! – Petrakis et. al (1967) Science 158, p 1992

World wild distribution of earwax types Open: dry type Dark: wet type Yoshiura (2006) Nat. Genetics

Earwax type linked to a disease? • Japanese Case Report: – A Paroxysmal kinesigenic choreoathetosis, (PKC, 陣發性運動障礙性疾病) patient who told that six people in her family also had choreoathetosis, and that those with the disease had wet earwax. – Wet earwax is rare in Japan and PKC is rare, too! – The cause of PKC is still unknown but seem linked to chromosome 16 near centremere • Swoboda, et al. Neurology 2000; 50: 224 -30.

Genetic marker typing LOD > 3 : evidence of linkage

Recombination rate Genotype A B (n 1) a b (n 2) A b (n 3) A B (n 4) Total Experiment 1 17 14 8 11 50 Experiment 2 34 28 16 22 100 總樣品數 互換率 θ 範圍 [0, 0. 5] 當 θ = 0 代表完全連鎖 當 θ = 0. 5 代表不連鎖

LOD score • logarithm (base 10) of odds • Developed by Newton E. Morton • NR: non recombination; R: recombination • LOD score > 3. 0: evidence for linkage. (A score of 3. 0 means the likelihood of observing the given pedigree if the two loci are not linked is less than 1 in 1000). • LOD score < -2. 0: evidence to exclude linkage

108 people: 64 wet earwax; 54 dry earwax

More detail study • More microsatellite markers • Use SNP study • 37 SNPs used • rs 17822931 in ABCC 1 exon 4 (538 G A, G 180 R) • rs 6500380 in LONPL intron 12 (A G) • ss 49784070 in LONPL intron 14 (A G)

SNP • Single nucleotide polymorphism (SNP, pronounced snip) • Within a population, SNPs can be assigned a minor allele frequency (>1%) • may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions between genes • synonymous or nonsynonymous • Missense or nonsense

How to find out new SNP? • Sequencing • SSCP (single strand conformation polymorphism)

How to determine SNP types? • SNP array

• Next Generation Screening® microarray with 25, 000 features

Genotyping of three SNPs • • Dry earwax (63/64): AA-AA-AA Dry earwax (1/64): GA-GA-GA Wet earwax (6/54): GG-GG-GG Wet earwax (33/54): GA-GA-GA Wet earwax (15/54): AA-AA-AA Only two haplotypes in Japan; Phenotype - genotype inconsistency

Do more case study • • • New series of 126 cases Dry type (87/88): AA homozygotes Wet type (38/38) GA or GG Only rs 17822931 is nonsynonymous Dry type is recessive

What happened to 1/88? • • A allele to dry type, G allele to wet type One exception is dry type with GA allele Sequence the gene of ABCC 11 G allele had a 27 -bp deletion (3939 -3965) in exon 29

What is the function ABCC 11? • Multidrug resistance-associated protein 8 (MRP 8) Rs 17822931 G 180 R

Effect of SNP rs 17822931 • Dry type: A allele G 180 R: Low activity in c. GMP transport Low lipophiles secretion

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