Difference between revisions of "Project:Alcohol Flush Genotyping"
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== Genetics == | == Genetics == | ||
=== ''ALDH2'' === | === ''ALDH2'' === | ||
| − | ''ALDH2'' is a ~43 kb gene on chromosome 12 consisting of 13 exons and encodes the ALDH2 enzyme found in the mitochondria, it has two alleles ''ALDH2*1'' and ''ALDH2*2''. The [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs671 rs671 SNP] ([ | + | ''ALDH2'' is a ~43 kb gene on chromosome 12 consisting of 13 exons and encodes the ALDH2 enzyme found in the mitochondria, it has two alleles ''ALDH2*1'' and ''ALDH2*2''. The [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs671 rs671 SNP] ([[#rs671 FASTA sequence|FASTA]]), in which a guanine in the ancestral ''ALDH2*1'' is substituted for an adenine in ''ALDH2*2'' is responsible for these two alleles. The G -> A substitution in ''ALDH2*2'' causes the amino acid lysine to be expressed instead of glutamate and causes an inactive ALDH2 enzyme to be expressed. ''ALDH2*2'' is considered nearly dominant as heterozygous individuals have almost no detectable ALDH2 activity in the liver and people who carry two copies of the ''ALDH2*2'' allele have no detectable activity. |
The inactivity of the ALDH2 enzyme in individuals with at least one ''ALDH2*2'' allele causes acetaldehyde levels in the blood to increase after the imbibing of alcohol to a level high enough to cause a flushing reaction and possibly nausea or increased heart rate. | The inactivity of the ALDH2 enzyme in individuals with at least one ''ALDH2*2'' allele causes acetaldehyde levels in the blood to increase after the imbibing of alcohol to a level high enough to cause a flushing reaction and possibly nausea or increased heart rate. | ||
| − | ''ALDH2*2'' is relatively common in people of Chinese, Japanese, and Korean descent but is essentially absent in people of European or African descent and is strongly associated with a drastic reduction in the likelihood of an individual becoming alcohol dependent. | + | ''ALDH2*2'' is relatively common in people of Chinese, Japanese, and Korean descent but is essentially absent in people of European or African descent and is strongly associated with a drastic reduction in the likelihood of an individual becoming alcohol dependent. |
=== Other Relevant Genes === | === Other Relevant Genes === | ||
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GAGAGACTTC AGGGGGCGGA GCGGAGAGGA AAAGCTTCTA GTAAGAATCT TTTCAGATTT | GAGAGACTTC AGGGGGCGGA GCGGAGAGGA AAAGCTTCTA GTAAGAATCT TTTCAGATTT | ||
TCACCAGGCG CGGTGGCTTT | TCACCAGGCG CGGTGGCTTT | ||
| + | |||
| + | === Tetra-primers === | ||
| + | Suggested primers for tetra=primer PCR from [http://primer1.soton.ac.uk/primer1.html tetra-primer designer]: | ||
| + | |||
| + | Forward inner primer (A allele): Melting temperature | ||
| + | 474 GGCGAGTACGGGCTGCAGGCATACAATA 501 74 | ||
| + | |||
| + | Reverse inner primer (G allele): | ||
| + | 530 AGCAGGTCCCACACTCACAGTTTTCACGTC 501 74 | ||
| + | |||
| + | Forward outer primer (5' - 3'): | ||
| + | 238 GCAACTCCAGCCTGGGCAACAGAGAAA 264 74 | ||
| + | |||
| + | Reverse outer primer (5' - 3'): | ||
| + | 669 GTCCTGAACTTCCAGCAGGCCCTGAGTC 642 74 | ||
| + | |||
| + | Product size for A allele: 197 | ||
| + | Product size for G allele: 293 | ||
| + | Product size of two outer primers: 432 | ||
== Links == | == Links == | ||
Latest revision as of 23:19, 21 October 2013
Overview
The main pathway of ethanol metabolism in humans consists of two critical reactions that occur in the liver. First the ethanol is oxidised to acetaldehyde (a toxic substance) by alcohol dehydrogenases (ALDHs). Second, the acetaldehyde is further oxidised to acetate (ethanoic acid) by aldehyde dehydrogenases (ALDHs).
Several SNP based alleles exist for many of the ADH and ALDH genes, each of which alters the kinetic activity of the enzymes encoded by each gene. Among these alleles, the ALDH2*2 allele of the of the ALDH2 is commonly found in people of Chinese, Japanese, and Korean descent and is associated with alcohol flush.
Genetics
ALDH2
ALDH2 is a ~43 kb gene on chromosome 12 consisting of 13 exons and encodes the ALDH2 enzyme found in the mitochondria, it has two alleles ALDH2*1 and ALDH2*2. The rs671 SNP (FASTA), in which a guanine in the ancestral ALDH2*1 is substituted for an adenine in ALDH2*2 is responsible for these two alleles. The G -> A substitution in ALDH2*2 causes the amino acid lysine to be expressed instead of glutamate and causes an inactive ALDH2 enzyme to be expressed. ALDH2*2 is considered nearly dominant as heterozygous individuals have almost no detectable ALDH2 activity in the liver and people who carry two copies of the ALDH2*2 allele have no detectable activity.
The inactivity of the ALDH2 enzyme in individuals with at least one ALDH2*2 allele causes acetaldehyde levels in the blood to increase after the imbibing of alcohol to a level high enough to cause a flushing reaction and possibly nausea or increased heart rate.
ALDH2*2 is relatively common in people of Chinese, Japanese, and Korean descent but is essentially absent in people of European or African descent and is strongly associated with a drastic reduction in the likelihood of an individual becoming alcohol dependent.
Other Relevant Genes
ADH Genes
A small region of chromosome 4 contains all seven ADH genes found in humans, ADH1A, ADH1B, ADH1C, ADH4, ADH5, ADH6, and ADH7. The various ADH enzymes that are encoded by these genes are dimers. The ADH1A, ADH1B, and ADH1C genes are closely related to each other but each produces a different subunit that form either homodimers or heterodimers (to give a total of 9 possible ADH1 enzymes).
2 SNPs in the ADH1B gene give rise to three commonly found alleles: ADH1B*1, ADH1B*2 (common in Asians), ADH1B*3 (found mainly in people of African descent). The ADH1B*2 allele results in an enzyme with a 70- to 80-fold higher turnover rate than that produced by the ADH1B*1 allele and is associated with a lower risk of alcoholism.
SNP genotyping
Tetra-primer ARMS-PCR
Requires the design of 2 primer pairs. See this PDF
rs671 FASTA sequence
FASTA >gnl|dbSNP|rs671|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=138 AGGCATAGTG GCACATACTT GTTATCTTAA CTACTTGGGA GGCTGAGGCA GGAGGATCAC TGAAGACCAG GAGTTGGAGA CCAGCCTGGG TAACATAATC AGACCCTGTC TCTTAAAAAA AAATTTATTG CCAGGCGTGG TTGCACGTGC TGGTAGTCCA GCTACTCAGG AAGCTGAGGC AGGAGAATCT CTTGAACCCC AGATGTGGAG GTTGCAACGA GCCAAGATCA TGCCATGGCA ACTCCAGCCT GGGCAACAGA GAAAGATTCT ATCTCAAAAA AAAAAATTTT TTTTTAAGTT AAAAATAAAA TAAAGACTTT GGGGCAATAC AGGGGGTCCT GGGAGTGTAA CCCATAACCC CCAAGAGTGA TTTCTGCAAT CTCGTTTCAA ATTACAGGGT CAACTGCTAT GATGTGTTTG GAGCCCAGTC ACCCTTTGGT GGCTACAAGA TGTCGGGGAG TGGCCGGGAG TTGGGCGAGT ACGGGCTGCA GGCATACACT R AAGTGAAAAC TGTGAGTGTG GGACCTGCTG GGGGCTCAGG GCCTGTTGGG GCTTGAGGGT CTGCTGGTGG CTCGGAGCCT GCTGGGGGAT TGGGGTCTGT TGGGGGCTCG GGGCCTGCCA GAGGTTCAGG ACCTGCCGGG GACTCAGGGC CTGCTGGAAG TTCAGGACCT GCTGGGGATC AGGGCCTGCC AGGGATTTAG GGTCTGCTGG GCGGGCCACC TTTTGGCCTC TCCCTCATGC TTGAGGCCAT CAGTGTTTCC TACTAATTTC CCATTTTAAG CCTGAGAAGT GACAAGAGAG GGTAAAGACC CAGCCTCTGC TCTGTCCCAT GAGAAATACT GAGGGACGTG CCCCCATCAG GCCTATGCGG TCATTTGCTG GGCTTCGTTA TACGCCAAGG CCTGTAGGCC TGAGAAGAGG GAGAGACTTC AGGGGGCGGA GCGGAGAGGA AAAGCTTCTA GTAAGAATCT TTTCAGATTT TCACCAGGCG CGGTGGCTTT
Tetra-primers
Suggested primers for tetra=primer PCR from tetra-primer designer:
Forward inner primer (A allele): Melting temperature 474 GGCGAGTACGGGCTGCAGGCATACAATA 501 74 Reverse inner primer (G allele): 530 AGCAGGTCCCACACTCACAGTTTTCACGTC 501 74 Forward outer primer (5' - 3'): 238 GCAACTCCAGCCTGGGCAACAGAGAAA 264 74 Reverse outer primer (5' - 3'): 669 GTCCTGAACTTCCAGCAGGCCCTGAGTC 642 74 Product size for A allele: 197 Product size for G allele: 293 Product size of two outer primers: 432
Links
An efficient procedure for genotyping single nucleotide polymorphisms