Transcriptome analysis provides critical answers to the “variants of uncertain significance” conundrum

MRSD: A quantitative approach for assessing suitability of RNA-seq in the investigation of mis-splicing in Mendelian disease

(2022) Charlie F. Rowlands et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Identification of a Novel Five-Gene Signature as a Prognostic and Diagnostic Biomarker in Colorectal Cancers

(2022) Souvik Ghatak et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Role of whole exome sequencing for unidentified genetic syndromes

(2021) Shagun Aggarwal   CURRENT OPINION IN OBSTETRICS & GYNECOLOGY

Comprehensive characterisation of intronic mis-splicing mutations in human cancers

(2021) Hyunchul Jung et al.   ONCOGENE

Detection of aberrant splicing events in RNA-seq data using FRASER

(2021) Christian Mertes et al.   Nature Communications

Targeted splice sequencing reveals RNA toxicity and therapeutic response in myotonic dystrophy

(2021) Matthew K Tanner et al.   NUCLEIC ACIDS RESEARCH

SChLAP1 promotes prostate cancer development through interacting with EZH2 to mediate promoter methylation modification of multiple miRNAs of chromosome 5 with a DNMT3a-feedback loop

(2021) Kai Huang et al.   Cell Death & Disease

Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases

(2021) Xinye Qian et al.   Frontiers in Genetics

Spectrum of splicing variants in disease genes and the ability of RNA analysis to reduce uncertainty in clinical interpretation

(2021) Rebecca Truty et al.   AMERICAN JOURNAL OF HUMAN GENETICS

MicroRNA Biomarkers of High-Grade Cervical Intraepithelial Neoplasia in Liquid Biopsy

(2021) Rhafaela L. Causin et al.   Biomed Research International

Computational comparison of common event-based differential splicing tools: practical considerations for laboratory researchers

(2021) Ittai B. Muller et al.   BMC BIOINFORMATICS

Increase in diagnostic yield achieved for 174 whole-exome sequencing cases reanalyzed 1 to 2 years after initial analysis

(2021) Yingdi Liu et al.   CLINICA CHIMICA ACTA

An Overview of the Role of Long Non-Coding RNAs in Human Choriocarcinoma

(2021) Riccardo Di Fiore et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Urinary Exosomal CA9 mRNA as a Novel Liquid Biopsy for Molecular Diagnosis of Bladder Cancer

(2021) Jin Wen et al.   International Journal of Nanomedicine

miREV: An Online Database and Tool to Uncover Potential Reference RNAs and Biomarkers in Small-RNA Sequencing Data Sets from Extracellular Vesicles Enriched Samples

(2021) Alex Hildebrandt et al.   JOURNAL OF MOLECULAR BIOLOGY

Single-molecule amplification-free multiplexed detection of circulating microRNA cancer biomarkers from serum

(2021) Shenglin Cai et al.   Nature Communications

Improved methods for RNAseq-based alternative splicing analysis

(2021) Rebecca F. Halperin et al.   Scientific Reports

Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes

(2021) Zishan Wang et al.   Genome Medicine

Rare variants regulate expression of nearby individual genes in multiple tissues

(2021) Jiajin Li et al.   PLoS Genetics

Interpretable prioritization of splice variants in diagnostic next-generation sequencing

(2021) Daniel Danis et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants

(2021) Adam M. Bournazos et al.   GENETICS IN MEDICINE

The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics

(2021) Ming Tang et al.   Nature Communications

Lethal variants in humans: lessons learned from a large molecular autopsy cohort

(2021) Hanan E. Shamseldin et al.   Genome Medicine

Circulating miRNAs as Potential Biomarkers for Celiac Disease Development

(2021) Ineke L. Tan et al.   Frontiers in Immunology

Pathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq

(2021) R. Koster et al.   npj Genomic Medicine

Diagnosing Cornelia de Lange syndrome and related neurodevelopmental disorders using RNA sequencing

(2020) Stefan Rentas et al.   GENETICS IN MEDICINE

Blood RNA analysis can increase clinical diagnostic rate and resolve variants of uncertain significance

(2020) Htoo A. Wai et al.   GENETICS IN MEDICINE

Cis- and trans-regulations of pre-mRNA splicing by RNA editing enzymes influence cancer development

(2020) Sze Jing Tang et al.   Nature Communications

Integrative comparison of the genomic and transcriptomic landscape between prostate cancer patients of predominantly African or European genetic ancestry

(2020) Jiao Yuan et al.   PLoS Genetics

LeafCutterMD: an algorithm for outlier splicing detection in rare diseases

(2020) Garrett Jenkinson et al.   BIOINFORMATICS

X-linked diseases: susceptible females

(2020) Barbara R. Migeon   GENETICS IN MEDICINE

Ancestry-specific hereditary cancer panel yields: Moving toward more personalized risk assessment

(2020) Maegan E. Roberts et al.   Journal of Genetic Counseling

Comprehensive genetic sequence and copy number analysis for Charcot-Marie-Tooth disease in a Canadian cohort of 2517 patients

(2020) Michael Volodarsky et al.   JOURNAL OF MEDICAL GENETICS

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Clinical impact of splicing in neurodevelopmental disorders

(2020) Stephan J. Sanders et al.   Genome Medicine

Changing Technologies of RNA Sequencing and Their Applications in Clinical Oncology

(2020) Ye Wang et al.   Frontiers in Oncology

The Clinical Application of RNA Sequencing in Genetic Diagnosis of Mendelian Disorders

(2020) Sarah L. Stenton et al.   CLINICS IN LABORATORY MEDICINE

Racial and Ethnic Disparities in Genetic Testing at a Hereditary Breast and Ovarian Cancer Center

(2020) Eloise Chapman-Davis et al.   JOURNAL OF GENERAL INTERNAL MEDICINE

Leveraging genetic ancestry to study health disparities

(2020) Ken Batai et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

Genome sequencing increases diagnostic yield in clinically diagnosed Alagille syndrome patients with previously negative test results

(2020) Ramakrishnan Rajagopalan et al.   GENETICS IN MEDICINE

Improving Genetic Testing in Hereditary Cancer by RNA Analysis

(2020) Paula Rofes et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing

(2020) David R. Murdock et al.   JOURNAL OF CLINICAL INVESTIGATION

Clinical significance and potential molecular mechanism of miRNA-222-3p in metastatic prostate cancer

(2020) Yu Sun et al.   Bioengineered

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

New Attempts to Define and Clarify Lupus

(2019) Marta E. Alarcón-Riquelme   Current Rheumatology Reports

Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis

(2019) Lin Shao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Genetic Testing Identifies Germline Pathogenic MSH2 Tandem Duplications in Lynch Syndrome Patients

(2019) Blair R. Conner et al.   GASTROENTEROLOGY

Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease

(2019) Hernan D. Gonorazky et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Liquid Biopsy beyond Circulating Tumor Cells and Cell-Free DNA

(2019) Susana Junqueira-Neto et al.   ACTA CYTOLOGICA

Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification

(2019) Michael T. Parsons et al.   HUMAN MUTATION

Recent advances in understanding the molecular genetic basis of mitochondrial disease

(2019) Kyle Thompson et al.   JOURNAL OF INHERITED METABOLIC DISEASE

SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation

(2019) Nathan Ungerleider et al.   BMC BIOINFORMATICS

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts

(2019) Laure Frésard et al.   NATURE MEDICINE

Integrative multi-omic analysis identifies new drivers and pathways in molecularly distinct subtypes of ALS

(2019) Giovanna Morello et al.   Scientific Reports

Non-coding RNAs as biomarkers in liquid biopsies with a special emphasis on extracellular vesicles in urological malignancies

(2019) Philip Zeuschner et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Inequities in multi-gene hereditary cancer testing: lower diagnostic yield and higher VUS rate in individuals who identify as Hispanic, African or Asian and Pacific Islander as compared to European

(2019) Mesaki K. Ndugga-Kabuye et al.   Familial Cancer

Diagnostic utility of transcriptome sequencing for rare Mendelian diseases

(2019) Hane Lee et al.   GENETICS IN MEDICINE

Is there a duty to reinterpret genetic data? The ethical dimensions

(2019) Paul S. Appelbaum et al.   GENETICS IN MEDICINE

Utilizing RNA and outlier analysis to identify an intronic splice‐altering variant in AP4S1 in a sibling pair with progressive spastic paraplegia

(2019) Carmel G. McCullough et al.   HUMAN MUTATION

Germline variants in cancer genes in high-risk non-BRCA patients from Puerto Rico

(2019) Julie Dutil et al.   Scientific Reports

RNA-Seq Perspectives to Improve Clinical Diagnosis

(2019) Guillermo Marco-Puche et al.   Frontiers in Genetics

Systematic evaluation of differential splicing tools for RNA-seq studies

(2019) Arfa Mehmood et al.   BRIEFINGS IN BIOINFORMATICS

Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium whole genome sequences improves imputation quality and detection of rare variant associations in admixed African and Hispanic/Latino populations

(2019) Madeline H. Kowalski et al.   PLoS Genetics

The Expanding Landscape of Alternative Splicing Variation in Human Populations

(2018) Eddie Park et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Response to Biesecker and Harrison

(2018) C Sue Richards et al.   GENETICS IN MEDICINE

Lack Of Diversity In Genomic Databases Is A Barrier To Translating Precision Medicine Research Into Practice

(2018) Latrice G. Landry et al.   HEALTH AFFAIRS

The Role of Long Non-Coding RNAs in Hepatocarcinogenesis

(2018) Manuela Lanzafame et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Splicing mutations in human genetic disorders: examples, detection, and confirmation

(2018) Abramowicz Anna et al.   JOURNAL OF APPLIED GENETICS

“Transcriptomics”: molecular diagnosis of inborn errors of metabolism via RNA-sequencing

(2018) Laura S. Kremer et al.   JOURNAL OF INHERITED METABOLIC DISEASE

Prospective Study of Cancer Genetic Variants: Variation in Rate of Reclassification by Ancestry

(2018) Thomas P Slavin et al.   JNCI-Journal of the National Cancer Institute

Massive mining of publicly available RNA-seq data from human and mouse

(2018) Alexander Lachmann et al.   Nature Communications

Review of recent efforts to discover biomarkers for early detection, monitoring, prognosis, and prediction of treatment responses of patients with gastric cancer

(2018) Koichi Sawaki et al.   Expert Review of Gastroenterology & Hepatology

The Challenges and Opportunities in the Clinical Application of Noncoding RNAs: The Road Map for miRNAs and piRNAs in Cancer Diagnostics and Prognostics

(2018) Preethi Krishnan et al.   International Journal of Genomics

Prospective Study of Cancer Genetic Variants: Variation in Rate of Reclassification by Ancestry

(2018) Thomas P Slavin et al.   JNCI-Journal of the National Cancer Institute

Added Value of Whole-Exome and Transcriptome Sequencing for Clinical Molecular Screenings of Advanced Cancer Patients With Solid Tumors

(2018) Florence Koeppel et al.   CANCER JOURNAL

Promoting guideline-based cancer genetic risk assessment for hereditary breast and ovarian cancer in ethnically and geographically diverse cancer survivors: Rationale and design of a 3-arm randomized controlled trial

(2018) Anita Y. Kinney et al.   Contemporary Clinical Trials

RNA variant identification discrepancy among splice-aware alignment algorithms

(2018) Ji Hyung Hong et al.   PLoS One

Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach

(2018) Yi Zhang et al.   BMC GENOMICS

Skewed X-inactivation is common in the general female population

(2018) Ekaterina Shvetsova et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Deep intronic mutations and human disease

(2017) Rita Vaz-Drago et al.   HUMAN GENETICS

Complexities of Variant Classification in Clinical Hereditary Cancer Genetic Testing

(2017) Erin Mundt et al.   JOURNAL OF CLINICAL ONCOLOGY

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer

(2017) Marilyn M. Li et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

The impact of rare variation on gene expression across tissues

(2017) Xin Li et al.   NATURE

ClinVar Is a Critical Resource to Advance Variant Interpretation

(2017) Heidi L. Rehm et al.   ONCOLOGIST

Improving genetic diagnosis in Mendelian disease with transcriptome sequencing

(2017) Beryl B. Cummings et al.   Science Translational Medicine

Annotating pathogenic non-coding variants in genic regions

(2017) Sahar Gelfman et al.   Nature Communications

UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq

(2017) Zhifu Sun et al.   Scientific Reports

The effect of phenotypic outliers and non-normality on rare-variant association testing

(2016) Paul L Auer et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Accelerating Medicines Partnership: Alzheimer’s Disease (AMP-AD) Knowledge Portal Aids Alzheimer’s Drug Discovery through Open Data Sharing

(2016) Richard J. Hodes et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

Sequencing-based diagnostics for pediatric genetic diseases: progress and potential

(2016) Ahmad N. Abou Tayoun et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Noncoding RNA: Current Deep Sequencing Data Analysis Approaches and Challenges

(2016) Dario Veneziano et al.   HUMAN MUTATION

dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs

(2016) Xiaoming Liu et al.   HUMAN MUTATION

Therapeutic targeting of splicing in cancer

(2016) Stanley Chun-Wei Lee et al.   NATURE MEDICINE

Translating RNA sequencing into clinical diagnostics: opportunities and challenges

(2016) Sara A. Byron et al.   NATURE REVIEWS GENETICS

Whole Genome Sequencing Increases Molecular Diagnostic Yield Compared with Current Diagnostic Testing for Inherited Retinal Disease

(2016) Jamie M. Ellingford et al.   OPHTHALMOLOGY

Replication and Heritability of Prostate Cancer Risk Variants: Impact of Population-Specific Factors

(2015) V. Virlogeux et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

The PsychENCODE project

(2015) Schahram Akbarian et al.   NATURE NEUROSCIENCE

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

(2015) Hui Yang et al.   Nature Protocols

RNA mis-splicing in disease

(2015) Marina M. Scotti et al.   NATURE REVIEWS GENETICS

High-throughput long noncoding RNA profiling for diagnostic and prognostic markers in cancer: opportunities and challenges

(2015) Zhifu Sun   Epigenomics

siRNA Versus miRNA as Therapeutics for Gene Silencing

(2015) Jenny K W Lam et al.   Molecular Therapy-Nucleic Acids

Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing

(2014) Yaping Yang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Clinical Exome Sequencing for Genetic Identification of Rare Mendelian Disorders

(2014) Hane Lee et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

In silico prediction of splice-altering single nucleotide variants in the human genome

(2014) Xueqiu Jian et al.   NUCLEIC ACIDS RESEARCH

Alternative splicing in cancer: implications for biology and therapy

(2014) J Chen et al.   ONCOGENE

Characterization of X Chromosome Inactivation Using Integrated Analysis of Whole-Exome and mRNA Sequencing

(2014) Szabolcs Szelinger et al.   PLoS One

IsoSCM: improved and alternative 3′ UTR annotation using multiple change-point inference

(2014) Sol Shenker et al.   RNA

Alternative splicing of mutually exclusive exons—A review

(2013) Martin Pohl et al.   BIOSYSTEMS

Variants of uncertain significance inBRCAtesting: evaluation of surgical decisions, risk perception, and cancer distress

(2013) JO Culver et al.   CLINICAL GENETICS

Cancer Outlier Analysis Based on Mixture Modeling of Gene Expression Data

(2013) Keita Mori et al.   Computational and Mathematical Methods in Medicine

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts

(2012) Michael C. Ryan et al.   BIOINFORMATICS

BRCA2 Deep Intronic Mutation Causing Activation of a Cryptic Exon: Opening toward a New Preventive Therapeutic Strategy

(2012) O. Anczukow et al.   CLINICAL CANCER RESEARCH

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Allele-specific expression in the germline of patients with familial pancreatic cancer: An unbiased approach to cancer gene discovery

(2010) Aik Choon Tan et al.   CANCER BIOLOGY & THERAPY

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Genomic features defining exonic variants that modulate splicing

(2010) Adam Woolfe et al.   GENOME BIOLOGY

Nonsense-mediated mRNA decay (NMD) mechanisms

(2009) Saverio Brogna et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Assessing pathogenicity: overview of results from the IARC Unclassified Genetic Variants Working Group

(2008) Sean V. Tavtigian et al.   HUMAN MUTATION

Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results

(2008) Sharon E. Plon et al.   HUMAN MUTATION