Allele-specific expression: applications in cancer and technical considerations

Allele-Specific QTL Fine Mapping with PLASMA

(2020) Austin T. Wang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The yin and yang of co-inhibitory receptors: toward anti-tumor immunity without autoimmunity

(2020) Alexandra Schnell et al.   CELL RESEARCH

Genomic basis for RNA alterations in cancer

(2020) Claudia Calabrese et al.   NATURE

Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci

(2020) Maria Gutierrez-Arcelus et al.   NATURE GENETICS

Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations

(2020) Pawel F. Przytycki et al.   Cell Systems

scHLAcount: allele-specific HLA expression from single-cell gene expression data

(2020) Charlotte A Darby et al.   BIOINFORMATICS

Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing

(2020) Charles Cole et al.   GENOME RESEARCH

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

(2020) Michael Hagemann-Jensen et al.   NATURE BIOTECHNOLOGY

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

(2020) Jiarui Ding et al.   NATURE BIOTECHNOLOGY

Demographic and genetic factors influence the abundance of infiltrating immune cells in human tissues

(2020) Andrew R. Marderstein et al.   Nature Communications

Transcriptomic signatures across human tissues identify functional rare genetic variation

(2020) Nicole M. Ferraro et al.   SCIENCE

Cell type–specific genetic regulation of gene expression across human tissues

(2020) Sarah Kim-Hellmuth et al.   SCIENCE

Expression estimation and eQTL mapping for HLA genes with a personalized pipeline

(2019) Vitor R. C. Aguiar et al.   PLoS Genetics

The Cancer-Associated Genetic Variant Rs3903072 Modulates Immune Cells in the Tumor Microenvironment

(2019) Yi Zhang et al.   Frontiers in Genetics

Standardization of Sequencing Coverage Depth in NGS: Recommendation for Detection of Clonal and Subclonal Mutations in Cancer Diagnostics

(2019) Anna Petrackova et al.   Frontiers in Oncology

Genetic regulatory variation in populations informs transcriptome analysis in rare disease

(2019) Pejman Mohammadi et al.   SCIENCE

A Bayesian mixture model for the analysis of allelic expression in single cells

(2019) Kwangbom Choi et al.   Nature Communications

Allelic Imbalance of Recurrently Mutated Genes in Acute Myeloid Leukaemia

(2019) Aarif M. N. Batcha et al.   Scientific Reports

Leveraging allelic imbalance to refine fine-mapping for eQTL studies

(2019) Jennifer Zou et al.   PLoS Genetics

Regulatory variants: from detection to predicting impact

(2018) Elena Rojano et al.   BRIEFINGS IN BIOINFORMATICS

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19

(2018) Junjie Tony Hua et al.   CELL

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data

(2018) Jean Fan et al.   GENOME RESEARCH

Identification of an enhancer region within the TP63/LEPREL1 locus containing genetic variants associated with bladder cancer risk

(2018) Aleksandra M. Dudek et al.   CELLULAR ONCOLOGY

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk

(2018) Stephane E. Castel et al.   NATURE GENETICS

Alternative transcript imbalance underlying breast cancer susceptibility in a family carrying PALB2 c.3201+5G>T

(2018) Laura Duran-Lozano et al.   BREAST CANCER RESEARCH AND TREATMENT

Widespread Selection for Oncogenic Mutant Allele Imbalance in Cancer

(2018) Craig M. Bielski et al.   CANCER CELL

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

(2018) Livnat Jerby-Arnon et al.   CELL

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

(2018) Moshe Sade-Feldman et al.   CELL

Screening of BRCA1/2 deep intronic regions by targeted gene sequencing identifies the first germline BRCA1 variant causing pseudoexon activation in a patient with breast/ovarian cancer

(2018) Gemma Montalban et al.   JOURNAL OF MEDICAL GENETICS

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

Germline genetic polymorphisms influence tumor gene expression and immune cell infiltration

(2018) Yoong Wearn Lim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive cellular heterogeneity of X inactivation revealed by single-cell allele-specific expression in human fibroblasts

(2018) Marco Garieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity

(2018) Weiwei Shi et al.   Cell Reports

A Genome-Wide Study of Allele-Specific Expression in Colorectal Cancer

(2018) Zhi Liu et al.   Frontiers in Genetics

Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia

(2017) Lili Wang et al.   GENOME RESEARCH

Landscape of X chromosome inactivation across human tissues

(2017) Taru Tukiainen et al.   NATURE

A common intronic variant of PARP1 confers melanoma risk and mediates melanocyte growth via regulation of MITF

(2017) Jiyeon Choi et al.   NATURE GENETICS

Allele-specific expression reveals interactions between genetic variation and environment

(2017) David A Knowles et al.   NATURE METHODS

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Allele-specific wild-type TP53 expression in the unaffected carrier parent of children with Li–Fraumeni syndrome

(2017) Jeffrey S. Buzby et al.   Cancer Genetics

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden

(2017) Zachary R. Chalmers et al.   Genome Medicine

Genome-Wide Association Study of Bladder Cancer in a Chinese Cohort Reveals a New Susceptibility Locus at 5q12.3

(2016) M. Wang et al.   CANCER RESEARCH

High-throughput allele-specific expression across 250 environmental conditions

(2016) Gregory A. Moyerbrailean et al.   GENOME RESEARCH

Rare variant phasing and haplotypic expression from RNA sequencing with phASER

(2016) Stephane E. Castel et al.   Nature Communications

Biased Allelic Expression in Human Primary Fibroblast Single Cells

(2015) Christelle Borel et al.   AMERICAN JOURNAL OF HUMAN GENETICS

WASP: allele-specific software for robust molecular quantitative trait locus discovery

(2015) Bryce van de Geijn et al.   NATURE METHODS

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

(2015) Jong Kyoung Kim et al.   Nature Communications

Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing

(2015) Maria Gutierrez-Arcelus et al.   PLoS Genetics

Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins

(2014) Alfonso Buil et al.   NATURE GENETICS

Defining a personal, allele-specific, and single-molecule long-read transcriptome

(2014) Hagen Tilgner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

(2013) Sebastian M. Waszak et al.   BIOINFORMATICS

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

(2013) H. Kilpinen et al.   SCIENCE

Integrating GWAS and Expression Data for Functional Characterization of Disease-Associated SNPs: An Application to Follicular Lymphoma

(2012) Lucia Conde et al.   AMERICAN JOURNAL OF HUMAN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels

(2012) Athma A. Pai et al.   PLoS Genetics

Monoallelic Expression Determines Oncogenic Progression and Outcome in Benign and Malignant Brain Tumors

(2011) E. J. Walker et al.   CANCER RESEARCH

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Upregulation of c-MYC in cis through a Large Chromatin Loop Linked to a Cancer Risk-Associated Single-Nucleotide Polymorphism in Colorectal Cancer Cells

(2010) J. B. Wright et al.   MOLECULAR AND CELLULAR BIOLOGY

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Genome-wide allele-specific analysis: insights into regulatory variation

(2010) Tomi Pastinen   NATURE REVIEWS GENETICS

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer

(2009) Mark M Pomerantz et al.   NATURE GENETICS