DIYgenomics citizen science research studies - MTHFR mutations and Vitamin B deficiency

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Maker Faire flyer describing the study

Study protocol

Results

SNPedia link

 

A. Background

As a proof of concept for DIYgenomics citizen science, this study seeks to replicate and extend existing studies to examine mutations in the MTHFR gene, investigate the potential corresponding phenotype, Vitamin B deficiency and higher homocysteine levels, and determine if vitamin supplementation or other remedies may improve the deficiency. Coordinating investigators: Melanie Swan, Raymond McCauley 

 

B. Methodology and Findings

Genotyping values are sought from citizen science participants. Participants that are homozygous and perhaps heterozygous for risk variants will be asked to take a blood test to assess B deficiency. Questionnaires are employed to ask participants about Vitamin B deficiency. Participants with Vitamin B deficiency may begin a vitamin supplementation program or other remedies which are self-tracked with additional blood tests after 3, 6 and 12 months.

 

1. Genotype data

SNPs 1&2: Gene mutation: MTHFR (Source: Wikipedia, NIH) Methylenetetrahydrofolate reductase (MTHFR) is an enzyme that in humans is encoded by the MTHFR gene.

• C677T SNP (Ala²²²Val): The MTHFR nucleotide at position 677 in the gene has two possibilities: C or T. C at position 677 (leading to an alanine at amino acid 222) is the normal allele. The 677T allele (leading to a valine substitution at amino acid 222) encodes a thermolabile enzyme with reduced activity. Individuals with two copies of 677C (677CC) have the "normal" or "wildtype" genotype. 677TT individuals (homozygous) are said to have mild MTHFR deficiency. 677CT individuals (heterozygotes) are almost the same as normal individuals because the normal MTHFR can make up for the thermolabile MTHFR. Population prevalence: About ten percent of the North American population are T-homozygous for this polymorphism. There is ethnic variability in the frequency of the T allele - frequency in Mediterranean/Hispanics > Caucasians > Africans/African-Americans). (Source: Wikipedia) 
• A1298C SNP (Glu⁴²⁹Ala): At nucleotide 1298 of the MTHFR, there are two possibilities: A or C. 1298A (leading to a Glu at amino acid 429) is the most common while 1298C (leading to an Ala substitution at amino acid 429) is less common. 1298AA is the "normal" homozygous, 1298AC the heterozygous, and 1298CC the homozygous for the "variant". In studies of human recombinant MTHFR, the protein encoded by 1298C cannot be distinguished from 1298A in terms of activity, thermolability, FAD release, or the protective effect of 5-methyl-THF.^[11] The C mutation does not appear to affect the MTHFR protein. It does not result in thermolabile MTHFR and does not appear to affect homocysteine levels.

 

SNP 3: Gene mutation: FUT2 (Source: Research Study 2 (below))

Women homozygous for the rs492602[G] allele had higher B12 levels.

 

	Chr/Locus	Gene	SNP	Platform	Location	Genotype values	Normal genotype(s)	Risk variant(s)	Research study
1	1p36.3	MTHFR:677C>T	rs1801133	D,23	11778965	CT	C, CT	TT	1,4
2	1p36.3	MTHFR:1298A>C	rs1801131	D,23,N	11777063	AC	AA, AC(?)	AC(?), CC	1
3	19q13.33	FUT2	rs492602	D		AG	AA, AG(?)	AG(?), GG	2

 

Research studies: 

1. Examining B12 Deficiency Associated With C677T Mutation on MTHFR Gene in Terms of Commonness and Endothelial Function (clinical study in progress (July 2008 - July 2010))

2. Hazra., A. et al. Common Variants of FUT2 are Associated with Plasma Vitamin B12 Levels, Nat Genet. 2008 Oct;40(10):1160-2. Epub 2008 Sep 7. (Nature Genetics paper, PubMed citation, Science Daily article)

3. Matteini, A.M. et al. Transcobalamin-II variants, decreased vitamin B12 availability and increased risk of frailty. J Nutr Health Aging. 2010 Jan;14(1):73-7. (Pubmed citation)

4. Hacques, P.F. et al. Relation between folate status, a common mutation in methylenetetrahydrofolate reductase, and plasma homocysteine concentrations. Circulation. 1996 Jan 1;93(1):7-9. (Pubmed citation)

5. Tanaka, T. et al. Genome-wide Association Study of Vitamin B6, Vitamin B12, Folate, and Homocysteine Blood Concentrations, The American Journal of Human Genetics. 2009 Apr 10;84:477-482. (Pubmed citation)

6. Zittan, E. et al. High frequency of vitamin B12 deficiency in asymptomatic individuals homozygous to MTHFR C677T mutation is associated with endothelial dysunction and homocysteinemia. Am J Physiol Heart Circ Physiol 2007 April 20;293:H860-H865. (Link to article)

Relevant Pathways:

1. One Carbon Metabolism (Simple Schematic, Wikipathways Schematic)

 

 

1.a. Data Collection: participant genotyping data (how to find and add your data)

Particpant	rs1801133 (D,23)	rs1801131 (D,23,N)	rs492602 (D)	Genotyping platform(s)	Study group	Date added	Questionnaire
Citizen Scientist 100	AG	GT		23andme-original edition	Heterozygous/heterozygous	2/5/10	Incomplete
Citizen Scientist 101
Citizen Scientist 102

 

2. Phenotype data: Vitamin B deficiency, Increased Homocysteine levels

Blood tests (US: LabCorp; Canada: LifeLabs)

• Homocysteine - Can indicate  
• Quest Diagnostics: Vitamin B12 Cobalamin/Cyanocobalamin Test (physician prescription required; reimbursable)
• DirectLabs: Vitamin B-12 or Vitamin B-12 and Folic Acid test (no physician prescription required; $59 or $98)

 

2.a. Data Collection: participant blood test data 

Participant	Study group	Blood test data	Blood test
Citizen Scientist 0	Heterozygous/heterozygous		DirectLabs Vit B12

 

3. Dietary supplementation

Regimen...

3.a. Data Collection

 

Custom vitamin supplement ordering (for blinding)

• Vitaganic

 

C. Conclusions and Significance