Genomic inbreeding | Introduction to genomics theory | Genomics101 (beginner-friendly)

[@eulacarrara]

Thank you for this brilliant explanation!

[@lucasf.c.y.dossoukpongan4684]

Thank you professor

[@fulingchen2543]

Really like your videos. They are very helpful to beginners. I would go on watch your other videos about LD and PLINK. But it would be great if you can share some knowledge about the computational models.

[@Rivendicato]

Fantastic explanation! Pretty much understood everything from start to finish. Thank you for the content. I have a question about stretches of ROH. How long can the smallest possible ROH be in terms of nucleotides? Is there a gold standard, like for example a minimum of 3 consecutive nucleotides? How does this factor in determining the genomic inbreeding coefficient?

[@GenomicsBootCamp]

Hi, Good question! The 3 consecutive nucleotides are way too short, as hit could easily happen by chance. So the question is, what is the shortest distance you are sure is not by chance. An other level of the question is, that in this video we deal with ROH based on SNP. i.e. we know there is many other nucleotides in between each SNP, which we assume are also all homozygous. For this reason one has to be careful with shorter ROH. It was shown that some ROH segments of 1 Mb were likely false positives, when determined by 50K chip, and then cross checked with HD chip gsejournal.biomedcentral.com/articles/10.1186/1297-9686-45-42

[@georgewanjala4605]

Wonderful, i get enlightened everyday i visit genomics boot camp. How would it be possible to differentiate IBD and IBS in the present population without using reference ancestors?

[@GenomicsBootCamp]

No, to my knowledge this is not possible.

[@christianfer84]

Great explanation!, thank you very much for the contribution. Where can I find information about the other methods to estimate inbreeding with genomic data?

[@matteosebastianelli5498]

Hi! Do you also have a tutorial on how to run these analysis in PLINK?

[@GenomicsBootCamp]

I do not have a video on this yet, but in PLINK you can do that using --homozyg option, and others for defining various parameters. (There are also other software for ROH.) www.cog-genomics.org/plink/1.9/ibd#homozyg