Dear Sir, Thanks for this video and surely waiting for the next! Like previous videos, please also show here online downloaded BeadChip data links (usually originated from company/laboratory) so that we can practice following your classes using PLINK, R or others.
Hi, in between there is a video that summarizes data sources for free livestock data, and soon there will be also a video that gives links to freely available human genotype data.
Hi, sorry for the late answer. If you consider a 3GB mammalian genome and let's say 700K evenly spaced SNPs, then there is an average distance between two SNPs about 4.2kb. From this reason this is the minimal resolution in the BEST case scenario, but realistically it is definitely more. So the detection on a below-kb level is definitely not possible.
Dear professor, is it possible to detect triallelic SNP in bead-chip? What will happen if a SNP is A/G in the manifest file, but in our sample it's a different allele?
Hi, There are no triallelic SNPs on the bead-chips. If you are really sure that you have a different, non-missing SNP in your data file, it is likely that you have information from a different strand (Top, Forward, AB-coding). For these occassions it is really useful to have the final reports, so you can have the other one, if needed e.g. for merging.
Not sure if this is a proper reference, or if the author shares my views on this, but there is a paper called "Genome-wide association studies: the good, the bad and the ugly" :D pmc.ncbi.nlm.nih.gov/articles/PMC4952840/
If you have the "final report" for your data, and the values for B allele frequency and Log-R ratio, you can use these to dectect CNVs, also based on SNP data. See e.g. Figure 1 in our paper: gsejournal.biomedcentral.com/articles/10.1186/s12711-018-0414-x
I have a question: if we have a CG heterozygous (like I do have in my data), how will the scan differentiate both green signals and not misinterpret it as being homozygous? The illumina reference guide itself does now cite "fluorophore", not even once. And both there and in their videos, they only show biotin associated with C and G, which after will have a green signal, and DNP with A and T, with a red signal. How is it possible to differentiate CG or AT heterozygous?
Thank you for answering questions I did not even know I had. Excellent video!
Great vid!
thanks
Dear Sir, Thanks for this video and surely waiting for the next! Like previous videos, please also show here online downloaded BeadChip data links (usually originated from company/laboratory) so that we can practice following your classes using PLINK, R or others.
Thank you for your comment! Yes, this is the plan, as FinalReport data is not so straightforward to come by.
Hi, in between there is a video that summarizes data sources for free livestock data, and soon there will be also a video that gives links to freely available human genotype data.
This illustration initially confused me because the nucleotides look like antibodies
Yes, they look like antibodies, or something else than SNP genotyping illustration, but I hope the video cleared that one up :)
thank so much for this video. I have a question please : Could SNP array 700 K illumina detect indels on locus with size < 1 kb?
Hi, sorry for the late answer.
If you consider a 3GB mammalian genome and let's say 700K evenly spaced SNPs, then there is an average distance between two SNPs about 4.2kb. From this reason this is the minimal resolution in the BEST case scenario, but realistically it is definitely more. So the detection on a below-kb level is definitely not possible.
Dear professor, is it possible to detect triallelic SNP in bead-chip? What will happen if a SNP is A/G in the manifest file, but in our sample it's a different allele?
Hi, There are no triallelic SNPs on the bead-chips. If you are really sure that you have a different, non-missing SNP in your data file, it is likely that you have information from a different strand (Top, Forward, AB-coding). For these occassions it is really useful to have the final reports, so you can have the other one, if needed e.g. for merging.
I need to know the reference for "there are no ugly SNPs", nhaha
Not sure if this is a proper reference, or if the author shares my views on this, but there is a paper called "Genome-wide association studies: the good, the bad and the ugly" :D
pmc.ncbi.nlm.nih.gov/articles/PMC4952840/
Sir , how are the SNP chips used to detect copy number variation?
If you have the "final report" for your data, and the values for B allele frequency and Log-R ratio, you can use these to dectect CNVs, also based on SNP data. See e.g. Figure 1 in our paper: gsejournal.biomedcentral.com/articles/10.1186/s12711-018-0414-x
@@GenomicsBootCamp Thank you so much professor!
I have a question: if we have a CG heterozygous (like I do have in my data), how will the scan differentiate both green signals and not misinterpret it as being homozygous?
The illumina reference guide itself does now cite "fluorophore", not even once. And both there and in their videos, they only show biotin associated with C and G, which after will have a green signal, and DNP with A and T, with a red signal. How is it possible to differentiate CG or AT heterozygous?
Cool Channel!