homozygous and heterozygos

[asankaf]

Can anybody pls tell me what is homozygous indel/snp and heterozygous indel/snp?

[ECO]

This page should help you tremendously:

http://en.wikipedia.org/wiki/Zygosity

[asankaf]

thanks for the link.
As I understood Heterozygous means having 2 different alleles.
But how do you explain the Heterozygous indel/snp?
Is Heterozygous snp is the change in single nueclietide in a one allele or two allelies?
Lets say allele1 and allele2 are Heterozygous?
how do you explain the Heterozygous snp on those 2 allelies?

[asankaf]

indel detection

what is indel detection for plymorphism discovery and indel detection for mutation discovery?
can anybody tell me the difference between those two?

[ECO]

An "allele" does not have zygosity...so it cannot be either hetero- or homozygous. An allele is defined as one of potentially many possibilities at a given location in a genome (a "locus").

A "locus" can be heterozygous or homozygous (among other things), meaning it either has two different alleles, or exactly the same two alleles.

Common SNP terminology is somewhat confusing...based on the acronym one would expect it to refer to a given allele at a specific position, and sometimes it does. However, "SNP" is more often used to refer to a specific base (the "locus") that has multiple possible alleles (for example, a A or a G).

So a heterozygous indel would be one copy of the specific lesion (an insertion or a deletion), the other strand lacking that particular insertion or deletion.

Hopefully that helps, if I didn't understand your question, let me know.

[ECO]

Asankaf...Let's try to have one question thread at a time, when they are so closely related. I'll do my best to help you, but please try to fully explain your questions.

Merging this into your original thread.

[asankaf]

ok.thanks and my apologies to miss use of thread topics.

[Sharmistha]

Can anyone set me an example to understand how to differentiate homozygous SNP from heterozygous SNP? If an indel can be categorised for the same, please explain that as well. I am very curious.

[ECO]

Hi dude,

If u need more details about this then please visit this below webs, from these links u can get answer about your difficulty,

www. sanger.ac.uk/ humgen/exoseq/analysis.shtml
www. ncbi.nlm.nih.gov/ pmc/articles/PMC1458964/

Any reason you intentionally broke the links?

edit: Ah...it's because you're a sneaky spammer. Nice try with the articles you chose though. Bye!

[Michael.James.Clark]

Can anyone set me an example to understand how to differentiate homozygous SNP from heterozygous SNP? If an indel can be categorised for the same, please explain that as well. I am very curious.

Explanation by example:

SNPs

Heterozygous:

GCTA
GCCA


Homozygous:

GCTA
GCTA


Indels

Heterozygous:

GCTA
GC*A

Homozygous:

GC*A
GC*A

Hope that helps.

[Sharmistha]

Thanks a lot for all the illustrations and explanations. But, one quick concept on the same once again.
When an alignment is done with respect to a reference genome, in such case how do you signify the respective indels and SNPs(viz.,hmozygous and heterozygous) since in such case only when the difference lies of a single nucleotide from the query against a reference genome will be signified as SNP right, so how you check out the homozygous SNPs in such condition?. In short w.r.t. the context of alignment how do I specify what kind of SNP I have? if someone can cite with examples will be good.

Regards,
Sharmistha

[ntremblay]

Hi,

you'll generally have a look at your sequencing data (ie. trace diagram) to see if the snp is homo/heterogenous.

See: http://www.sanger.ac.uk/Teams/Team76/gfx/trace.gif

In the first line, you see only a C being called.
In the second line, you can see a C and a T overlapping, thus revealing that this snp is heterozygous at this location for this person.
The third line shows only a T.

Hope thats help,

[Cramsmith]

So can anyone explain the significance between and homozygous snp vs heterozygous snp?

[dpryan]

So can anyone explain the significance between and homozygous snp vs heterozygous snp?

It might have been best for you to have started a new thread. In short, have a look at the wikipedia article. You can also have a look at the articles on genetic dominance and recessiveness, if that's what your underlying question is. If those don't answer your question, you should be a bit more specific.

[Cramsmith]

It might have been best for you to have started a new thread. In short, have a look at the wikipedia article. You can also have a look at the articles on genetic dominance and recessiveness, if that's what your underlying question is. If those don't answer your question, you should be a bit more specific.

Thanks for the reply and sorry for the vague question. I think I have figured out what I need to know but let ask again for clarity.

So I saw in reference to some performance data on the IonTarget Seq Exome, the poster presented and ASHG, by LT. So they had a metric on the poster Ts:Tv, I did not at first get it, but now I believe it to be just a measure of perfomance, i.e. that you captured appropriate fractions of the exome and the predicted ration of Ts:Tv is present.

Is that correct in thinking that it is just a q.c. score to see how your seq exp. performed.