4.6 Article

The Power of Single-Cell RNA Sequencing in eQTL Discovery

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Biochemical Research Methods

Comprehensive evaluation of noise reduction methods for single-cell RNA sequencing data

Shih-Kai Chu et al.

Summary: This study assessed the performance of 28 scRNA-seq noise reduction procedures in 55 scenarios, considering multiple biological and technical factors. It provided a comprehensive guideline for selecting suitable noise reduction procedures in different scenarios and highlighted the need for developing metrics to assess batch correction on imperceptible cell-type mixing.

BRIEFINGS IN BIOINFORMATICS (2022)

Article Genetics & Heredity

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

Julie Jerber et al.

Summary: The study utilized an efficient multiplexing strategy to differentiate 215 human induced pluripotent stem cell (iPSC) lines towards a midbrain neural fate, and used single-cell RNA sequencing to profile over 1 million cells across three differentiation time points. It revealed eQTL characteristics in neuronal development and identified a portion of eQTL that colocalize with known neurological trait risk loci.

NATURE GENETICS (2021)

Article Multidisciplinary Sciences

Genetic ancestry effects on the response to viral infection are pervasive but cell type specific

Haley E. Randolph et al.

Summary: Humans vary in susceptibility to infectious diseases due to differences in immune response. This study found differences in the immune response to influenza infection in peripheral blood mononuclear cells of males of European and African ancestry, with European ancestry associated with increased type I interferon pathway activity and predictive of reduced viral titers. Genes associated with genetic ancestry are enriched among genes correlated with COVID-19 disease severity, suggesting the early immune response plays a role in ancestry-related differences in viral infection outcomes.

SCIENCE (2021)

Article Multidisciplinary Sciences

scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies

Katharina T. Schmid et al.

Summary: The authors present a statistical framework for informed multi-sample experimental design in scRNASeq data to reduce unnecessary costs and maximize data utility. The study shows that shallow sequencing of high numbers of cells leads to higher overall power than deep sequencing of fewer cells. The model is implemented as an R package and accessible as a web tool.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

powerEQTL: an R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis

Xianjun Dong et al.

Summary: Genome-wide association studies have identified numerous genetic loci for common diseases, but understanding the causality of these variants remains a challenge. eQTL analysis is a powerful tool in addressing this issue, but determining the sample size required to detect genetic variants associated with gene expression is a common challenge, especially in single-cell RNAseq studies.

BIOINFORMATICS (2021)

Article Biology

Whole-organism eQTL mapping at cellular resolution with single-cell sequencing

Eyal Ben-David et al.

Summary: Researchers developed a novel approach in the nematode Caenorhabditis elegans to map eQTLs at cellular resolution in a single experiment, revealing cell-type-specific trans eQTL hotspots that affect core pathways. Additionally, they found single-cell-specific eQTL effects in the nervous system, including an eQTL with opposite effects in two individual neurons, demonstrating that eQTL effects can be specific down to the level of single cells.
Article Biochemistry & Molecular Biology

Integrated analysis of multimodal single-cell data

Yuhan Hao et al.

Summary: The study introduces a weighted-nearest neighbor analysis framework to learn the relative utility of each data type in each cell, enabling integrative analysis of multiple modalities. Applied to a CITE-seq dataset, the method constructs a multimodal reference atlas of the circulating immune system and successfully identifies and validates previously unreported lymphoid subpopulations.
Article Biotechnology & Applied Microbiology

Optimizing expression quantitative trait locus mapping workflows for single-cell studies

Anna S. E. Cuomo et al.

Summary: We evaluate the role of different normalization and aggregation strategies, covariate adjustment techniques, and multiple testing correction methods to establish best practice guidelines in single-cell eQTL mapping. Our recommendations for future single-cell eQTL studies can yield up to twice as many eQTL discoveries as default approaches ported from bulk studies.

GENOME BIOLOGY (2021)

Article Biotechnology & Applied Microbiology

Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells

Drew Neavin et al.

Summary: This study performed single cell RNA-sequencing on 64,018 fibroblasts from 79 donors to map expression quantitative trait loci (eQTLs) at the level of individual cell types, showing that the majority of eQTLs in fibroblasts are specific to an individual cell subtype. By generating single cell RNA-sequencing data on 19,967 iPSCs from 31 reprogrammed donor lines, highly cell type-specific eQTLs were identified in iPSCs, and it was found that eQTLs in fibroblasts almost entirely disappeared during reprogramming.

GENOME BIOLOGY (2021)

Article Multidisciplinary Sciences

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Anna S. E. Cuomo et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Benchmarking of cell type deconvolution pipelines for transcriptomics data

Francisco Avila Cobos et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis

Igor Mandric et al.

NATURE COMMUNICATIONS (2020)

Article Biotechnology & Applied Microbiology

Determining cell type abundance and expression from bulk tissues with digital cytometry

Aaron M. Newman et al.

NATURE BIOTECHNOLOGY (2019)

Article Multidisciplinary Sciences

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

Yingxin Lin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Genetics & Heredity

Discovery and characterization of variance QTLs in human induced pluripotent stem cells

Abhishek K. Sarkar et al.

PLOS GENETICS (2019)

Article Biochemistry & Molecular Biology

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

Molly Gasperini et al.

Article Multidisciplinary Sciences

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

Xuran Wang et al.

NATURE COMMUNICATIONS (2019)

Article Biotechnology & Applied Microbiology

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

Hyun Min Kang et al.

NATURE BIOTECHNOLOGY (2018)

Article Genetics & Heredity

Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs

Monique G. P. van der Wijst et al.

NATURE GENETICS (2018)

Article Genetics & Heredity

Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci

Boxiang Liu et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2018)

Article Multidisciplinary Sciences

RNA velocity of single cells

Gioele La Manno et al.

NATURE (2018)

Article Genetics & Heredity

Identification of context-dependent expression quantitative trait loci in whole blood

Dania V. Zhernakova et al.

NATURE GENETICS (2017)

Article Multidisciplinary Sciences

Common genetic variation drives molecular heterogeneity in human iPSCs

Helena Kilpinen et al.

NATURE (2017)

Article Multidisciplinary Sciences

Genetic effects on gene expression across human tissues

Francois Aguet et al.

NATURE (2017)

Article Biology

The Human Cell Atlas

Aviv Regev et al.

Article Cell Biology

A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project

Latarsha J. Carithers et al.

BIOPRESERVATION AND BIOBANKING (2015)

Article Biochemical Research Methods

Robust enumeration of cell subsets from tissue expression profiles

Aaron M. Newman et al.

NATURE METHODS (2015)

Article Cell Biology

A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project

Latarsha J. Carithers et al.

BIOPRESERVATION AND BIOBANKING (2015)

Article Biochemical Research Methods

Digital sorting of complex tissues for cell type-specific gene expression profiles

Yi Zhong et al.

BMC BIOINFORMATICS (2013)

Article Biotechnology & Applied Microbiology

Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments

Quin F. Wills et al.

NATURE BIOTECHNOLOGY (2013)

Article Biochemical Research Methods

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

Simone Picelli et al.

NATURE METHODS (2013)

Review Biology

Expression quantitative trait loci: present and future

Alexandra C. Nica et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2013)

Article Multidisciplinary Sciences

Selection at Linked Sites Shapes Heritable Phenotypic Variation in C. elegans

Matthew V. Rockman et al.

SCIENCE (2010)

Article Biochemical Research Methods

mRNA-Seq whole-transcriptome analysis of a single cell

Fuchou Tang et al.

NATURE METHODS (2009)