l*********s
发帖数: 5409 | 1 are they related? My teacher asked me to present a paper on GWAS, hopefully
some bullren on this board could share some insight, thanks. | s*****0
发帖数: 357 | 2 Not quite sure the "connection" you are referring to, but here are my 2cents
, hopefully they will be helpful.
GWAS tests a huge number of SNPs. To control the global significance at
level of 0.05, usually the local significance is calculated through
Bonferroni correction. For example, for a million SNPs to be tested, the
local significance will be set at magnitude of 1e-7. However, not all SNPs
are independent. LD would be observed from nearby SNPs on the same
chromosome, which means the Bonferroni correction appears to be too
stringent and the local significance should be relaxed. Otherwise, the
chance of false negative might dramatically increase.
If several SNPs in a gene have moderate to strong LD with each other and all
show certain levels of association with disease or drug response, that gene
could be of particular interest and is worth further exploration.
hopefully
【在 l*********s 的大作中提到】
: are they related? My teacher asked me to present a paper on GWAS, hopefully
: some bullren on this board could share some insight, thanks.
| r*****l
发帖数: 457 | 3 LD is the non random association between two loci. If one site is your marker and
the other is the causal variance and these two sites are in high LD. Then
you can declare this marker is associated with the phenotype.
hopefully
【在 l*********s 的大作中提到】
: are they related? My teacher asked me to present a paper on GWAS, hopefully
: some bullren on this board could share some insight, thanks.
| o********r
发帖数: 775 | 4 LD is the basic for GWAS. Essentially the disease loci won't be typed
directly. However, usually there will be typed SNPs on an array that are
physically close to the disease loci and in strong LD. You can think those
typed SNPs in strong LD as surrogate markers for disease loci. | l*********s
发帖数: 5409 | 5 thank you for such detailed explanation.
2cents
【在 s*****0 的大作中提到】
: Not quite sure the "connection" you are referring to, but here are my 2cents
: , hopefully they will be helpful.
: GWAS tests a huge number of SNPs. To control the global significance at
: level of 0.05, usually the local significance is calculated through
: Bonferroni correction. For example, for a million SNPs to be tested, the
: local significance will be set at magnitude of 1e-7. However, not all SNPs
: are independent. LD would be observed from nearby SNPs on the same
: chromosome, which means the Bonferroni correction appears to be too
: stringent and the local significance should be relaxed. Otherwise, the
: chance of false negative might dramatically increase.
| l*********s
发帖数: 5409 | 6 thank you for such detailed explanation.
2cents
【在 s*****0 的大作中提到】
: Not quite sure the "connection" you are referring to, but here are my 2cents
: , hopefully they will be helpful.
: GWAS tests a huge number of SNPs. To control the global significance at
: level of 0.05, usually the local significance is calculated through
: Bonferroni correction. For example, for a million SNPs to be tested, the
: local significance will be set at magnitude of 1e-7. However, not all SNPs
: are independent. LD would be observed from nearby SNPs on the same
: chromosome, which means the Bonferroni correction appears to be too
: stringent and the local significance should be relaxed. Otherwise, the
: chance of false negative might dramatically increase.
|
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