What is a SNP?

A SNP is a single nucleotide polymorphism. The Human Genome actually has very little variation between individuals. It is estimated that for every 1000 base pairs of DNA, there is only 1base pair of DNA is different. But with 3.3 billion base pairs to consider, there is still a lot of variation to understand.

There are several types of genetic variation between humans-

• Insertions and deletions of repetitive DNA- including expansions of trinucleotide and dinucleotide repeats (e.g. Fragile X, Huntington's Disease)
• Smaller duplications and deletions of genes (e.g. alpha amylase, lactase)
• Point mutations that result in single base pair substitutions or deletions (Hemoglobin S sickle cell anemia, some types of Cyctic Fibrosis)

Each of these types of variation require different diagnotic tests. The earliest SNP diagnostics were RFLP tests- Restriction Fragment Length Polymorphisms.

However the Polymerase Chain Reaction or PCR is a common method used for SNP detection.

This is a review of PCR method written by Current Protocols in Molecular Biology

More on PCR:

PCR Song

MTHFR SNPS :

This is the DNA Standard we use on the gels

 

 

 

 

 

 

 

 

677 PCR Gel These are 1% Flash Gels from Lonza

1298 PCR Gel These are 1% Flash Gels from Lonza

677 1-6 These are Flash Gels

677 7-12 These are Flash Gels

1298 1-6 These are 1% Flash Gels from Lonza

1298 7-12 These are 1% Flash Gels from Lonza

677 Repeated gel These are 1% Flash Gels from Lonza

1298 Repeated Gel This is a 4-20% Acrylamide TBE Gradient Gel stained after running with ethidium Bromide.

In the group 1298 there were 6 of the AA and 6 of the AC.   2,5,6,7,11,12  were AA and the rest were AC (4 bands not 3).  The picture in the van der Puten article is OK at telling them apart, but our gel is a little compressed.   Don't foreget to label the markers.

677Hinf I digest Repeated Gel 2 This gel was run on a 2% Metaphor Agarose gel with the 100 bp Low Scale DNA ladder from Fisher Scientific. In the Group 677 there were 9 CC, 2 TT and 1 CT.  Person 12 was the CT.  The Frosst article has a pretty good comparison picture.

Frosst et al. 1995 This is the first reference to MTHFR 677 mutation

van der Put et al. 1998 This is the first reference to the MTHFR Mutation

Link to OMIM page for MTHFR allele variation

Grading Sheet for Lab Reports

Link to LabWrite

Excel Chart of MTHFR Data from Dr Murray

Word Chart of MTHFR Data from Dr. Murray

Athletic Performance SNP papers

Yang et al. 2003 1 gene paper

Li Ling 2 gene paper

Ahmetov et al.2008 5 gene paper

Mills Paper 2001

Athletic Performance SNP Gels

ACTN3 gel uncut

UCP2 Temperature Optimization Gel with gradient run Lower on left to higher on right. Gel was 2% Metafor Agarose in TBE

UCP3 Temperature Optimization Gel with gradient run lower on left to higher on right. Gel was 2% Metaphor Agarose in TBE

ACE uncut gel There is a large and a small fragment and heterozygotes. This gel was a 4-20% acrylamide gell. The ACE SNP is actually a SNP- it is an indel or insertion/deletion. An Alu repetitive element was inserted into an intron of the ACE gene. Alleles containing the insertion are called "I" alleles, and "D" alleles lack the repetitive element. There is competition in the PCR reaction leading to less product in the I band in the heterozygotes, because the smaller D allele could be amplified more efficiently than the I allele.

ACT3 This is a 3% metaphore agarose gel. Person 5 isn't on the gel however. R is the larger band and X is the smaller band.

Better complete ACTN3 Gel

UCP2 4-20% Acrylamide Gel Cut

ACAGCCAGC  Alanine uncut
ACAGTCAGC Valine cut

UCP3 gel 3% metaphor agarose Sma cuts the C (smalled band)and not the T. -55C/T

UCP3 gel with all samples 4% regular agarose