Possible discrepancy between Manhattan plot and Lead SNP
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Musalula Sinkala
Mar 2, 2023, 2:55:15 AM3/2/23
to FUMA GWAS users
Hi,
I am writing to share with you some concerning observations I made while analyzing FUMA Job ID 233376. Upon review of the results, I noticed that the significant SNPs (p-value < 5e-8) located on Chromosome 20 in the GWAS summary statistics were not showing up among the independent SNPs or Index SNP in the FUMA results. In fact, the FUMA analysis reported no significant SNPs located on chromosome 20, which contradicts the 54 SNPs that achieved genome-wide significance (p-value < 5e-8) that I counted on chromosome 22.
I have attached four screenshots that provide a visual representation of these inconsistencies. I would appreciate it if you could help me understand what might be causing these discrepancies, as I am concerned that I may have missed something important in my analysis.
Thank you for your assistance in this matter. I look forward to your response.
Best regards
I am writing to share with you some concerning observations I made while analyzing FUMA Job ID 233376. Upon review of the results, I noticed that the significant SNPs (p-value < 5e-8) located on Chromosome 20 in the GWAS summary statistics were not showing up among the independent SNPs or Index SNP in the FUMA results. In fact, the FUMA analysis reported no significant SNPs located on chromosome 20, which contradicts the 54 SNPs that achieved genome-wide significance (p-value < 5e-8) that I counted on chromosome 22.
I have attached four screenshots that provide a visual representation of these inconsistencies. I would appreciate it if you could help me understand what might be causing these discrepancies, as I am concerned that I may have missed something important in my analysis.
Thank you for your assistance in this matter. I look forward to your response.
Best regards
Marijn Schipper
Mar 2, 2023, 3:53:26 AM3/2/23
to FUMA GWAS users
Hi Musalula,
Thank you for reaching out. As most of the positions are denoted in scientific notation I can only look up the top two SNPs for which I can see the genomic position.
In order to make loci we need LD information to see where the LD block in which your SNPs are located ends. We use the 1000G reference panel for this.
This also means that we have to drop variants which are not part of the 1000G reference panel.
These top two SNPs are not part of the 1000G european reference panel which you selected.
From the job title you submitted I deduce that your sample might be from an African population.
These top two SNPs are part of the AFR reference panel, which would therefore allow FUMA to create this locus.
Please let me know if this solves your problem, or if you have any further questions.
Cheers,
Marijn
Thank you for reaching out. As most of the positions are denoted in scientific notation I can only look up the top two SNPs for which I can see the genomic position.
In order to make loci we need LD information to see where the LD block in which your SNPs are located ends. We use the 1000G reference panel for this.
This also means that we have to drop variants which are not part of the 1000G reference panel.
These top two SNPs are not part of the 1000G european reference panel which you selected.
From the job title you submitted I deduce that your sample might be from an African population.
These top two SNPs are part of the AFR reference panel, which would therefore allow FUMA to create this locus.
Please let me know if this solves your problem, or if you have any further questions.
Cheers,
Marijn
Op donderdag 2 maart 2023 om 08:55:15 UTC+1 schreef Musalula Sinkala:
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