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Identification of Influential Variants in Significant Aggregate Rare Variant Tests

By Rachel Z. Blumhagen, David A. Schwartz, Carl D. Langefeld, Tasha E. Fingerlin

Posted 03 Oct 2020
bioRxiv DOI: 10.1101/2020.10.01.322644

Introduction Studies that examine the role of rare variants in both simple and complex disease are increasingly common. Though the usual approach of testing rare variants in aggregate sets is more powerful than testing individual variants, it is of interest to identify the variants that are plausible drivers of the association. We present a novel method for prioritization of rare variants after a significant aggregate test by quantifying the influence of the variant on the aggregate test of association. Methods In addition to providing a measure used to rank variants, we use outlier detection methods to present the computationally efficient Rare Variant Influential Filtering Tool (RIFT) to identify a subset of variants that influence the disease association. We evaluated several outlier detection methods that vary based on the underlying variance measure: interquartile range (Tukey fences), median absolute deviation and standard deviation. We performed 1000 simulations for 50 regions of size 3kb and compared the true and false positive rates. We compared RIFT using the Inner Tukey to two existing methods: adaptive combination of p-values (ADA) and a Bayesian hierarchical model (BeviMed). Finally, we applied this method to data from our targeted resequencing study in idiopathic pulmonary fibrosis (IPF). Results All outlier detection methods observed higher sensitivity to detect uncommon variants (0.001 < MAF > 0.03) compared to very rare variants (MAF < 0.001). For uncommon variants, RIFT had a lower median false positive rate compared to the ADA. ADA and RIFT had significantly higher true positive rates than that observed for BeviMed. When applied to two regions found previously associated with IPF including 100 rare variants, we identified six polymorphisms with the greatest evidence for influencing the association with IPF. Discussion In summary, RIFT has a high true positive rate while maintaining a low false positive rate for identifying polymorphisms influencing rare variant association tests. This work provides an approach to obtain greater resolution of the rare variant signals within significant aggregate sets; this information can provide an objective measure to prioritize variants for follow-up experimental studies and insight into the biological pathways involved. ### Competing Interest Statement Dr. Schwartz reports personal fees from Eleven P15, Inc., outside the submitted work; In addition, Dr. Schwartz has a patent Compositions and Methods of Treating or Preventing Fibrotic Diseases pending, a patent Biomarkers for the diagnosis and treatment of fibrotic lung disease pending, and a patent Methods and Compositions for Risk Prediction, Diagnosis, Prognosis, and Treatment of Pulmonary Disorders issued. Dr. Fingerlin reports consulting fees from Eleven P15, Inc., outside the submitted work and a patent Methods and Compositions for Risk Prediction, Diagnosis, Prognosis, and Treatment of Pulmonary Disorders issued. All remaining authors besides Dr. Schwartz and Dr. Fingerlin declare no competing interest.

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