In Need Of Help With Family Genetics Research Project

Question

[jwells21]

I am an undergraduate biochemistry student and have recently embarked upon a family genetics research project to investigate the underlying genetics of a hereditary health condition which segregates in my family in an autosomal dominant pattern. The underlying gene(s) responsible for this health condition have not been conclusively identified, although there appear to be quite a few published studies which have identified a number of candidate genes and chromosome regions which may be involved. Several family members who share the phenotype have volunteered to have their DNA genotyped by the 23andMe company. I would like to use the data to identify chromosome regions which are shared by family members who are affected by the condition, and then compare the results with the published literature to see if any of these regions have an established association with the condition. Basically, I would like to do a miniature linkage study. 23andMe has built-in software which can be used to identify the chromosome regions shared by two individuals, but not several individuals.

My question is: Is there any software available, preferentially open-source, which can read the SNP raw data file (.txt format) for the purposes I have in mind? I am aware of Haploview, but this program only accepts certain file-types as inputs. Any other suggestions, resources, or other sources of information which may be of help would be greatly appreciated! (Please note that I am only a humble beginner and have no experience with bioinformatics software).

[munch]

23andMe uses OmniExpress+ from Illumina. First of all, you are sure that 23andMe will provide the raw file?

Edit: Ok, they are providing the raw data.

Answer 1

[DG]

We use a program called Homozygosity Haplotype (HH) to identify putatively shared regions in family members when the condition is suspected of being dominant. However it takes a bit of know-how to get the proper Illumina annotation files for the specific chip-type you are using and to convert in to the right call format (AB call format instead of raw genotypes).

You can also use PLINK, or other linkage programs to do this, you will need to provide pedigree information and specify mode of inheritance, how penetrant you believe the variant to be, etc. As well as do LD pruning of SNPs so you are only looking at SNPs not in linkage with each other. None of these will be that straightforward to do but if you read some of the published papers doing linkage analysis it will give you a better idea of some of the programs and program settings you need to use and experiment with.

You may also want to look at researchers in your University who conduct this sort of work, they may be willing/able to provide some guidance. Although this may require doing an ethics approval, getting informed consent, etc.

Answer 2

[munch]

If you want to use R (http://www.r-project.org/) you can use the crlmm package (http://www.bioconductor.org/packages/2.12/bioc/vignettes/crlmm/inst/doc/AffyGW.pdf) to process the datasets. I think this will also work for the OmniExpress+ Chip type. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329223/

You can also take a look here: http://www.23andyou.com/3rdparty

and here: What is the best program to determine structural variation (CNV) for Illumina Omniexpress data?