Question: Linkage With Whole Exome Data
gravatar for Biomed
9.6 years ago by
Bethesda, MD, USA
Biomed4.6k wrote:

Is it possible to do linkage analysis using whole exome data only (i.e. without using micro array data)? I would like to use whole exome sequence from small pedigrees (i.e children and parents) and be able to perform linkage analysis. I am mainly interested in defining haploblocks, homozygosity mapping, linkage regions detection etc. Would PLINK be an option for this ?

exome linkage • 6.8k views
ADD COMMENTlink modified 9.0 years ago by glyamamoto0 • written 9.6 years ago by Biomed4.6k

I am interested in where you are headed with this. Could you please expand your question?

ADD REPLYlink written 9.6 years ago by Zach Stednick650

I think the point of confusion is that biomed means "SNP microarray", not "expression microarray". Unless the intent is to do eQTL analysis using RNA-seq, in which case you should look at Johnathan Pritchard's recent papers.

ADD REPLYlink written 9.1 years ago by David Quigley11k

AFAIK, you don't need microarray data for linkage analysis. Are you looking at genetic linkage analysis or visualization of LD blocks ? You may use tools like PLINK, MapMaker or Haploview.

ADD REPLYlink written 9.6 years ago by Khader Shameer18k

linkage between exons? I don't understand the question.

ADD REPLYlink written 9.6 years ago by Giovanni M Dall'Olio26k

the question is not about linkage between exons but performing linkage analysis using whole exome data

ADD REPLYlink written 9.6 years ago by Biomed4.6k

I persume you referring to variants or (SNPs) found from exome sequencing. Be careful as adding 10-15% error rate may not be tolerated for linkage. My problem with exome data is you have to use good quality data so not to loose your linkage power.

ADD REPLYlink written 5.8 years ago by ammar.husami0
gravatar for Hanif Khalak
9.6 years ago by
Hanif Khalak1.2k
Doha, QA
Hanif Khalak1.2k wrote:

We're also thinking of using exome data to map loci - the idea seems reasonable:

  1. sequence exomes
  2. map both existing and new SNPs and corresponding genotypes across all samples
  3. construct custom genetic map file of markers from (2)
  4. format genotype data as a matrix similar to that obtained from microarrays (e.g PED file)
  5. run standard linkage / homozygosity mapping tool (Allegro, GeneHunter, etc)

PLINK does find ROHs (regions of homozygosity) but doesn't seem to do standard linkage. This paper describes how PLINK does "population-based linkage" based on analysis of shared IBS segments.

ADD COMMENTlink modified 9.1 years ago • written 9.6 years ago by Hanif Khalak1.2k
gravatar for glyamamoto
7.4 years ago by
glyamamoto0 wrote:

I have found this article and website interesting...

Will try it out and compare with our snpArray linkage in 4 patients (2 families)

ADD COMMENTlink written 7.4 years ago by glyamamoto0
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