ArticleAmerican journal of human genetics2014
Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants.
Article in American journal of human genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
41 citing papers in PubMed, 65 citations in OpenAlex.
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- Sequence-to-expression approach to identify etiological non-coding DNA variations in P53 and cMYC-driven diseases.Human molecular genetics · 2024Article
- The functional impact of rare variation across the regulatory cascade.Cell genomics · 2023Article
- Deleterious Mutations and the Rare Allele Burden on Rice Gene Expression.Molecular biology and evolution · 2022Article
- Integration of rare expression outlier-associated variants improves polygenic risk prediction.American journal of human genetics · 2022Article
- Gender-related differentially expressed genes in pancreatic cancer: possible culprits or accomplices?Frontiers in genetics · 2022Article
- Genetic Ancestry Inference and Its Application for the Genetic Mapping of Human Diseases.International journal of molecular sciences · 2021Review
- Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics.Nature genetics · 2021Article
- How Machine Learning and Statistical Models Advance Molecular Diagnostics of Rare Disorders Via Analysis of RNA Sequencing Data.Frontiers in molecular biosciences · 2021Review
- Article
- Transcriptomic signatures across human tissues identify functional rare genetic variation.Science (New York, N.Y.) · 2020Article
- Predicting target genes of non-coding regulatory variants with IRT.Bioinformatics (Oxford, England) · 2020Article
- Convolutional neural network model to predict causal risk factors that share complex regulatory features.Nucleic acids research · 2019Article
- Assessment of kinship detection using RNA-seq data.Nucleic acids research · 2019Article
- ORE identifies extreme expression effects enriched for rare variants.Bioinformatics (Oxford, England) · 2019Article
- Family-Based Quantitative Trait Meta-Analysis Implicates Rare Noncoding Variants in DENND1A in Polycystic Ovary Syndrome.The Journal of clinical endocrinology and metabolism · 2019Article
- Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding.Nature communications · 2019Article
- Article
- OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data.American journal of human genetics · 2018Article
- Rare Variants in theDrug metabolism and disposition: the biological fate of chemicals · 2018Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
Recent and rapid human population growth has led to an excess of rare genetic variants that are expected to contribute to an individual's genetic burden of disease risk. To date, much of the focus has been on rare protein-coding variants, for which potential impact can be estimated from the genetic code, but determining the impact of rare noncoding variants has been more challenging. To improve our understanding of such variants, we combined high-quality genome sequencing and RNA sequencing data from a 17-individual, three-generation family to contrast expression quantitative trait loci (eQTLs) and splicing quantitative trait loci (sQTLs) within this family to eQTLs and sQTLs within a population sample. Using this design, we found that eQTLs and sQTLs with large effects in the family were enriched with rare regulatory and splicing variants (minor allele frequency < 0.01). They were also more likely to influence essential genes and genes involved in complex disease. In addition, we tested the capacity of diverse noncoding annotation to predict the impact of rare noncoding variants. We found that distance to the transcription start site, evolutionary constraint, and epigenetic annotation were considerably more informative for predicting the impact of rare variants than for predicting the impact of common variants. These results highlight that rare noncoding variants are important contributors to individual gene-expression profiles and further demonstrate a significant capability for genomic annotation to predict the impact of rare noncoding variants.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.