SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to best use my lab data to check my alignment?? lg36 Bioinformatics 1 06-04-2012 05:41 AM
Quality check and analysis of Illumina NGS data subuhikhan General 1 02-29-2012 02:23 PM
Quality Check for Illumina Sequencing Santosh Illumina/Solexa 1 06-30-2011 07:35 AM
Check coverage from RNA-seq data??? ritzriya RNA Sequencing 15 02-17-2011 03:16 AM
how to check the quality of RNASEQ data repinementer Bioinformatics 1 05-18-2010 10:09 PM

Reply
 
Thread Tools
Old 03-21-2013, 12:37 PM   #1
kjaja
Member
 
Location: NY

Join Date: Aug 2011
Posts: 55
Default gender check using sequencing data

Hi All,

I have exome sequencing data from siblings and would like to confirm their gender and relationship using genetics to make sure they are in fact siblings. I also want to confirm that the gender information is correct. Are there tools out there that can do this using exome seq data?

Thanks,
kjaja is offline   Reply With Quote
Old 03-21-2013, 12:58 PM   #2
vivek_
PhD Student
 
Location: Denmark

Join Date: Jul 2012
Posts: 164
Default

To verify pedigree this post might help:

http://cphg.virginia.edu/quinlan/?p=300

To check gender, may be you could check the number of aligned reads to Y chromsome?
vivek_ is offline   Reply With Quote
Old 03-21-2013, 01:02 PM   #3
jgibbons1
Senior Member
 
Location: Worcester, MA

Join Date: Oct 2009
Posts: 133
Default

I would second that -- map reads against a panel of Y-chromosome genes/exons.
jgibbons1 is offline   Reply With Quote
Old 03-21-2013, 01:58 PM   #4
xied75
Senior Member
 
Location: Oxford

Join Date: Feb 2012
Posts: 129
Default

But I have pure female reads that can map a lot Y?
xied75 is offline   Reply With Quote
Old 03-22-2013, 02:36 AM   #5
LiLin
Member
 
Location: China

Join Date: May 2011
Posts: 15
Default

The average sequencing depth of chrY and chrX
LiLin is offline   Reply With Quote
Old 03-22-2013, 05:42 AM   #6
balaji
Junior Member
 
Location: Europe

Join Date: Feb 2011
Posts: 9
Default

in plink there is an option to check sex using X chr, I hope you are looking for this..
plink --bfile data --impute-sex --make-bed --out newfile
balaji is offline   Reply With Quote
Old 03-22-2013, 07:39 PM   #7
husamia
Member
 
Location: cinci

Join Date: Apr 2010
Posts: 66
Default

I also use the average depth of X and Y
husamia is offline   Reply With Quote
Old 12-04-2013, 01:39 AM   #8
bw.
Member
 
Location: San Francisco, CA

Join Date: Mar 2012
Posts: 21
Default Testing sex determination with CCLE samples

I've tried using [num reads mapped to chrX] / [num reads mapped to chrY]
to determine sex in some CCLE exome-seq samples. The ratios turned out to be:

Quote:
9.4 -- s1
304.6 -- s2
272.9 -- s3
168.3 -- s4
220.6 -- s5
297.8 -- s6
226.1 -- s7
257.1 -- s8
241.9 -- s9
287.0 -- s10
278.6 -- s11
260.3 -- s12
9.7 -- s13
8.7 -- s14
261.2 -- s15
279.3 -- s16
9.0 -- s17
8.5 -- s18
260.7 -- s19
297.4 -- s20
8.7 -- s21
261.8 -- s22
189.0 -- s23
147.4 -- s24
291.2 -- s25
So it looks like the difference is pretty wide -
[num reads mapped to chrX] / [num reads mapped to chrY] is < 10 for all male samples and > 100 for all female samples.

Still, I'm not sure whether these thresholds are stable across exome-seq kits, gene panels, etc. I wonder if there's a more robust way to determine sex.

Last edited by bw.; 02-13-2014 at 10:07 AM.
bw. is offline   Reply With Quote
Old 02-12-2014, 02:38 AM   #9
oyvindbusk
Member
 
Location: Norway

Join Date: Jan 2011
Posts: 14
Default

How about using % heterozygosity on X (without the pseudoautosomal regions (X:60000-2699520 and X:154931043-155260560). In our lab, male = < 30 % and female = > 50 %.
oyvindbusk is offline   Reply With Quote
Old 02-12-2014, 01:30 PM   #10
swbarnes2
Senior Member
 
Location: San Diego

Join Date: May 2008
Posts: 912
Default

Gender = biological sex + culture. You don't care about people's gender, you care about their sex. (And even the biology is not black and white 100% of the time)
swbarnes2 is offline   Reply With Quote
Old 02-12-2014, 08:55 PM   #11
bw.
Member
 
Location: San Francisco, CA

Join Date: Mar 2012
Posts: 21
Default

@swbarnes2 cool. never realized there was a difference.

@oyvindbusk thanks, I also tried this and ended up with similar thresholds (male < 40% and female > 50%). I didn't try to filter out pseudoautosomal regions since their coordinates differ across species and assembly versions (based on PAR coordinates at:
http://www.ncbi.nlm.nih.gov/projects...bly/grc/mouse/
http://www.ncbi.nlm.nih.gov/projects...bly/grc/human/
).


Looking at 322 CCLE samples, 233 were called Male, 73 Female, and 10 Unknown (which is >= 40% and <= 50%). Out of the 233 Male, only 5 would have been called differently with your thresholds. I will see if I can check the thresholds against a different approach. Also, a lot of the CCLE cells have copy number amplifications / deletions, so these results might be skewed by that.

Here is the distribution of nHet / nHomo for chrX in CCLE samples (I used this instead of nHet/(nHet+nHomo)). The 2 vertical blue lines are equivalent to 40% and 50% thresholds, and the 30% threshold is the red line.


Last edited by bw.; 02-12-2014 at 10:48 PM.
bw. is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:49 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO