exomes - trios - extra sibling?

[Elsie]

Hi, I've got several families (trios, looking for denovos) where another sibling has also been sequenced. Can anyone suggest some good options for using these extra individuals?
thanks.

[Bukowski]

Hi, I've got several families (trios, looking for denovos) where another sibling has also been sequenced. Can anyone suggest some good options for using these extra individuals?
thanks.

We're rarely looking for de novo's in that situation if we have larger families, but in this case I'd be using the extra sib as a subtractive screen (if unaffected) or looking for the same de novo in both (if affected).

Seeing as there are so few de novo mutations (certainly in exomes which is what we generally do) this may not be entirely cost effective. But when you have a suspected recessive in a consanguineous family and you have either another affected or unaffected sib it can really reduce the search space.

[AJERYC]

You can use the extra genotyped individual to add information. For example you can use kggseq with a recessive study option:

java -jar ./kggseq.jar --buildver hg19 --vcf-file path/to/file1 --ped-file path/to/file2 --genotype-filter 1

Filter out variants for which their genotypes are not consistent with the assumption of disease inheritance pattern.

Functions and applicable models for each code of '--genotype-filter'options are listed below:
Code Function Applicable model
1 Exclude variants at which affected subjects have heterozygous genotypes. Recessive

[mamons]

Hello,

I've written a small program for annotating inheritance patterns in arbitrary pedigrees, it might be of some help.

Check out https://github.com/moonso/genmod

Good luck!