How many SNPs are needed to perform haplotype analysis on close relatives?

[Masklin]

Hello!

I need to haplotype a patient, their mother, and three or four of the (deceased) father's (living) siblings, so that we can deduce where the patient's (mutant) haplotype came from. We suspect a de novo SNV, only the patient has symptoms.

Many years ago my group supposedly performed this type of haplotyping using 20 microsatellites (short tandem repeats) in a 1 Mbp window surrounding the SNV. STRs are very polymorphic which made the haplotyping possible (the haplotypes of 20 STRs were unique). For some reason we no longer have access to a lab that can perform this type of STR analysis, so I'm searching for alternatives. One alternative is a SNP array, its specifications suggest 300 SNPs per Mbp on average. Are 300 SNPs enough to perform this haplotyping on these ~5 individuals? I've no idea who to ask, so I ask here.

Alternatively, are there better ways entirely to do this sort of thing?

Big big thanks for any help!


Masklin

[GenomicSeq]

Hi Masklin!

Do you have a reference or link to the SNP array you were talking about using?

I haven't done haplotyping yet, but I know some companies like Illumina have calculators to determine what type of coverage you need for each type of experiment. That may not be useful here, but it could be worth a shot.

I used to know some good references for haplotyping, I just can't seem to find them now.

[Masklin]

Hello and thanks for replying!

The SNP array I was thinking of is the one CentoGene offers, here is a pdf describing it:

https://www.centogene.com/fileadmin/downloads/accreditations/products/genetic-testing/centoarray-product-sheet/centogene_centoarray_product_sheet_web_v1eng_20220530.pdf

There are other options though, but many of them seem to accept only purified DNA, rather than blood, and we don't have the facilities to extract the DNA here, locally. CentoGene does all that for you, but the price... is vast.

I'll see if I can find a calculator on Illumina's site, thanks!

[GenomicSeq]

Thanks for the link. Let me look more into this panel and I will get back to you.

Also, you said you didn't have the facilities to extract the DNA, but if you have access to a few things I think you might be able to make it work. Qiagen has a ton of kits that really only require a small centrifuge and some pipettes to extract genomic DNA from blood. There are also a lot of smaller biotech companies with cheap spin columns.

I remember I used Qiagen's PAXgene Blood tubes for DNA extractions once and it was super easy and didn't require much stuff. Although if you don't have access to a few pipettes and a small centrifuge then it still won't work.

[Masklin]

Hello again,

I asked my PI and apparently we have no lab equipment whatsoever, but he also said he's been thinking about starting a small lab, or a cooperation with an existing lab. I will urge him to realise this hypothetical, probably it will pay for itself in time...

[Shina]

The computer analysis of APOL1 and single nucleotide polymorphisms in chronic kidney disease (CDK). Any help anyone can provide me with will be really appreciated. Thank you very much, everyone