Question about genotype and +/- strands

[leontp587]

I prefer to avoid complementary mutations (if possible) due to ambiguity around genotyping. Without surrounding sequence you can't tell what strand a variant comes from, which can lead to a great deal of confusion.

This is a particular issue when validating your variant information. I've had a few cases where a sequenom service provider has used a strand for genotyping that is the opposite from what HapMap, Illumina, or Affymetrix used. For non-complementary variants this is an easy and obvious fix, but it's much trickier when you have C/G or A/T variants.

Thank you everyone for your answers. It's much clearer now.

I definitely agree it's more challenging about complementary mutations, hopefully eventually there will be a widely followed consensus on how to genotype, because certainly it makes biological sense to have C/G or A/T variants.

[gringer]

I prefer to avoid complementary mutations (if possible) due to ambiguity around genotyping. Without surrounding sequence you can't tell what strand a variant comes from, which can lead to a great deal of confusion.

This is a particular issue when validating your variant information. I've had a few cases where a sequenom service provider has used a strand for genotyping that is the opposite from what HapMap, Illumina, or Affymetrix used. For non-complementary variants this is an easy and obvious fix, but it's much trickier when you have C/G or A/T variants.

[Brian Bushnell]

Genotype refers to the allele on the plus strand regardless of whether a gene is read from the plus or minus strand. And yes, your understanding of risk is correct.

[leontp587]

Hi everyone,

I'm new to bioinformatics and have a basic question.

On Snepedia, Rs1333049 (http://snpedia.com/index.php/Rs1333049) has the following genotype vs clinical effect information:
Chromosome: 9
Orientation: plus

Geno: Summary
(C;C): 1.9x increased risk for CAD
(C;G): 1.5x increased risk for CAD
(G;G): normal

Does this mean that a person with a plus strand of C and minus strand of G on one chromosome 9 and the same on the other homologous chromosome 9, he/she will have 1.9x risk of CAD? And, if the plus strand was G and the minus strand was C on both chromosomes, then the risk is normal?

This is probably a very basic question. I just wanted to ask to see if I understand genotypes and plus/minus strands correctly.

Thanks!