ArticleScientific reports2021
Impact of pre- and post-variant filtration strategies on imputation.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Genetics are not likely to offer clinically useful predictions for elevated liver enzyme levels in patients using low dose methotrexate.Seminars in arthritis and rheumatism · 2022Trial
- Frailty and abdominal wall hernias: a Mendelian randomization and retrospective study.Surgical endoscopy · 2026Article
- Causal association between sleep disorders and nephrolithiasis: a two-sample Mendelian randomization study.International urology and nephrology · 2026Article
- Causal Association Between Transferrin Saturation and Periodontitis: A Mendelian Randomization Study.Oral health & preventive dentistry · 2026Article
- Distinct gut microbiota profiles in acute vs. chronic sinusitis: potential biomarkers.European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery · 2025Article
- Exploring the causal association between circulating leukocyte count and IgA nephropathy based on two-sample Mendelian randomization: possible role of transitional B cells.Clinical and experimental nephrology · 2025Article
- Aggregating single nucleotide polymorphisms improves filtering for false-positive associations postimputation.G3 (Bethesda, Md.) · 2025Article
- Cohort profile update: the Korean Cancer Prevention Study-II (KCPS-II) biobank.Epidemiology and health · 2025Article
- Local Ancestry-Informed Candidate Pathway Analysis of Warfarin Stable Dose in Latino Populations.Clinical pharmacology and therapeutics · 2023Article
- A Pipeline for Phasing and Genotype Imputation on Mixed Human Data (Parents-Offspring Trios and Unrelated Subjects) by Reviewing Current Methods and Software.Life (Basel, Switzerland) · 2022Review
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Quality control (QC) methods for genome-wide association studies and fine mapping are commonly used for imputation, however they result in loss of many single nucleotide polymorphisms (SNPs). To investigate the consequences of filtration on imputation, we studied the direct effects on the number of markers, their allele frequencies, imputation quality scores and post-filtration events. We pre-phrased 1031 genotyped individuals from diverse ethnicities and compared the imputed variants to 1089 NCBI recorded individuals for additional validation. Without QC-based variant pre-filtration, we observed no impairment in the imputation of SNPs that failed QC whereas with pre-filtration there was an overall loss of information. Significant differences between frequencies with and without pre-filtration were found only in the range of very rare (5E-04-1E-03) and rare variants (1E-03-5E-03) (p < 1E-04). Increasing the post-filtration imputation quality score from 0.3 to 0.8 reduced the number of single nucleotide variants (SNVs) < 0.001 2.5 fold with or without QC pre-filtration and halved the number of very rare variants (5E-04). Thus, to maintain confidence and enough SNVs, we propose here a two-step filtering procedure which allows less stringent filtering prior to imputation and post-imputation in order to increase the number of very rare and rare variants compared to conservative filtration methods.
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