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Poster De Conférence Année : 2017

Effects of filtration on imputation in clusterised variants

Résumé

The standards based on the same principles of fi ltration are commonly used for genome-wide association studies and imputations. To investigate the eff ect of imputation with and without pre-fi ltration of SNP followed by post-fi ltration on the variants imputed at a conservative and less stringent threshold, we categorised them in diff erent classes. We used 1,031 individuals from diverse ethnicities and compared also their allele frequencies with the 1,089 NCBI recorded individuals, within a 2Mb of chr20 dbSNPB37.p13, after curation of the variants database. Only the markers removed during quality control (QC) and absent from the reference genome were not imputed, with shapeit 2 and impute 2 . Hence, to maintain genotyped variants the pre-fi ltration could be less stringent, but no signifi cant diff erences in that number was observed between the imputation prior and after pre-fi ltration of SNP. High correlation between frequencies minor alleles generated after imputation were found between both conditions. We didn’t fi nd any signifi cative diff erences between the frequencies, except within the range of very rare and rare variants . However, the magnitude of those diff erences were small and became non signifi cative under the hypothesis testing their true mean diff erences m = 1.85E-05. There was a slight loss of information after QC. The presence of low quality genotyped variants prior to imputation did not impair neither their imputation quality that showed maximum, nor the imputation of the remaining good quality SNP. When an indel and polymorphism were present at the same locus, there was dual imputation. Variants with no repository names, with position for sole identifi er produced unreliable maf. Null allele were detected in NCBI database, by comparison with the imputed variants, and vice et versa, NCBI showed records while many null alleles would be imputed. We also considered as unreliable, SNP with null allele frequencies in both the imputed results and the NCBI dbSNP B37.p13, having very poor quality scores. An addition of 0.5 in the post-fi ltration imputation score stringency from 0.3 to 0.8 lead to a decrease in the number of SNV < 0.01 maf by 1.8 fold, in both conditions with and without prior QC fi ltration, and by a 2.5 fold in the number of SNV < 0.001 maf and lowered by half the number of very rare variants (< 5E-04). With an average maf > 0.01, a standard threshold, showed a mean score > 0.8 whether QC was performed or not.
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Dates et versions

cea-04564140 , version 1 (11-06-2024)

Identifiants

  • HAL Id : cea-04564140 , version 1

Citer

C. M. Charon, R. Allodji, J.F. Deleuze. Effects of filtration on imputation in clusterised variants. ASHG 2017 - American Society of Human Genetics 67th Annual Meeting 2017, Oct 2017, Orlando, United States. The American Society of Human Genetics, American Society of Human Genetics 67th Annual Meeting, pp.1444W. ⟨cea-04564140⟩
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