analysis of Homozygosity mapping

Question

[samarpana.chakraborty]

Dear all

I am working on a consanguinous family indicating autosomal recessive inheritance. I have performed exome sequencing on 6 embers and identified variants based on the same model. i also used the same .vcf file to do homozygosity mapping using the tool - "homozygosity mapper". It gives a homozygosity plot with chromosome number on x-axis and (n x ma>) score on y axis (where n = 0.6, 0.7, 0.8, 0.9, 1.0). I am not able to understand the significance of Y axis.

Can anyone help me with that? What does m.a. mean? The technical documentation of the tool does not address this question properly. Please tell me how the score is calculated and how the cut off is decided? I have attached the image of the plot for reference.

Please help me with this. I really need to understand.

[Devon Ryan]

The image is missing. You tried to copy and paste it in, but that won't work. Upload the image somewhere and then link to it.

[samarpana.chakraborty]

I am really sorry for the trouble.

I hope you can access it from google drive link.

https://drive.google.com/file/d/0BxfnAjfSW9CzeHJ3WnhkaXBFZUk/edit?usp=sharing

[Devon Ryan]

I've updated your post to include the image.

[samarpana.chakraborty]

Thank you very much for your efforts. But now the Y-axis is not showing anymore in the image. So I guess people will have to follow the link.

[Devon Ryan]

Note the scroll bar at the bottom below this post :) Anyway, I changed the HTML to make the image not the original size.

[samarpana.chakraborty]

Oh.. yes.. I missed the scroll bar.. Apologies again.. Its my first post here so I am still getting well-versed with the site. :)

Answer 1

[Alex Paciorkowski]

This looks like a standard plot of homozygosity score (Y axis) against genomic region (X axis). The authors of the tool don't seem to indicate what "m.a." means, even in their documentation:

http://www.homozygositymapper.org/HomozygosityMapper/documentation.html#analysis

But their discussion on that page makes it fairly clear that the larger the value is on the Y axis, the greater the homozygosity score, and depending on your parameters, the bars marked in red are "most interesting".

Maybe the authors say more in their publication: http://www.ncbi.nlm.nih.gov/pubmed/19465395

[samarpana.chakraborty]

Alex, yes I read their documentation before and the graph in itself is clear. But I was just wondering how it is calculated and the significance of m.a. They have not mentioned about it in their publication too.

I found many articles using this tool but unfortunately none of them mention about it as well.

Anyway thank you for trying.

[Alex Paciorkowski]

Then I would try emailing the authors.