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There are several companies (most notably 23andMe) providing SNP genotyping for individuals claiming that there is no sense for individual in obtaining full genome sequence since only small part of it could be interpreted.

While this agrees with my understanding of the subject, I wonder whether there could be any use to perform full sequence of one's genome for means of personal health care?

The only effect I recall which affects individual's health and could not be caught by SNP genotyping is DNA methylation, but complete sequencing procedure does not detect it either, as far as I know.

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  • $\begingroup$ Our group does Whole Exome Sequencing. While not as exhaustive as whole genome sequencing, it does offer more coverage than SNP genotyping and can provide more useful data. $\endgroup$
    – jp89
    Commented May 10, 2012 at 23:28
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    $\begingroup$ Not my field, but I guess most DNA methylation and other epigenetic modifications would be organ specific. I wonder if a buccal swab could give useful information in this context. $\endgroup$
    – Gianpaolo R
    Commented May 11, 2012 at 8:54
  • $\begingroup$ If that were true, why do scientific projects bother with sequencing then? It’s way more expensive, and in general most labs don’t have money to waste. $\endgroup$
    – Konrad Rudolph
    Commented May 11, 2012 at 9:52
  • $\begingroup$ Sequencing gives the researcher data on rare or private mutations that are not on the genotyping arrays. $\endgroup$
    – Larry_Parnell
    Commented May 11, 2012 at 13:52

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This difference would have the greatest impact on treatment for cancer, in which a treatment protocol is based on genes deleted, amplified, altered in the tumor vs the reference genome for that patient.

In terms of health risks based on SNP genotypes, the data are far from complete. Sure, some level of risk can be assigned to a variant (SNP), say at certain markers within the FTO gene and risk of obesity. However, the complete list of risk alleles for this and numerous other complex traits is not fully described. Furthermore, the impact of environmental factors (EF), or lifestyle choices, on those genetic variants is only beginning to gain wider attention. For example, a risk allele may not show itself as risk until the EF, such as amount of physical activity or percent energy from dietary polyunsaturated fat, passes a certain threshold. Such gene-environment interactions are thought to contribute to the variance in traits (phenotypes), but to what degree is not known.

Added in edit 15 May 2012: Epistasis, or gene-gene interactions, also are important but far from being cataloged for humans. A situation could arise where one allele elevates risk for a certain condition, but compensatory alleles elsewhere in the genome decrease that risk. We don't know the full extent of epistasis in humans.

Thus, in terms of personal healthcare outside of something like cancer and monogenetic disorders, there may be little that is gained from genotyping or complete genome sequencing, little that is compared to other advice you already know. I carry risk alleles for certain conditions, but there is not really any advice one can give me that is specific for those alleles that I have, where that advice is different than or goes beyond general advice health care providers already have dispensed.

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Genotyping only tests for SNPs in predetermined locations. If you have SNPs in other places in your genome, genotyping won't tell you that, but whole genome sequencing will (by comparing your genome to a reference genome available at NCBI). Also, there are other variants such as copy number variations, repeats, insertions and deletions that genotyping can not capture, but all of those can contribute to disease.

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  • $\begingroup$ Genotyping can tell you more information than just SNP, for instance you could easily amplify a region of a gene for sequencing to determine if there are more serious errors. $\endgroup$
    – user560
    Commented Jan 5, 2013 at 16:18

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