RTG Publications


The following paper describes the underpinnings of the RTG products, and is a good citation for use in your own publications:

Joint Variant and De Novo Mutation Identification in Pedigrees from High-Throughput Sequencing Data
John G. Cleary, Ross Braithwaite, Kurt Gaastra, Brian S. Hilbush, Stuart Inglis, Sean A. Irvine, Alan Jackson, Richard Littin, Sahar Nohzadeh-Malakshah, Mehul Rathod, David Ware, Len Trigg, and Francisco De La Vega
Journal of Computational Biology (2014)


The following manuscript describes the representation-agnostic variant comparison algorithm used in vcfeval:

Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines
John G. Cleary, Ross Braithwaite, Kurt Gaastra, Brian S Hilbush, Stuart Inglis, Sean A Irvine, Alan Jackson, Richard Littin, Mehul Rathod, David Ware, Justin M. Zook, Len Trigg, Francisco M. M. De La Vega
BioRxiv (2015)


The following publications have been co-authored with RTG:

Reproducible integration of multiple sequencing datasets to form high-confidence SNP, indel, and reference calls for five human genome reference materials
Zook, J. et al., BioRxiv (2018)


Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes
Krusche, P. et al., BioRxiv (2018)


Papers citing RTG


The following is a sampling of publications citing RTG or where RTG has been used during the research:



Mutations in SZT2 result in early‐onset epileptic encephalopathy and leukoencephalopathy
Pizzino, A., Whitehead, M., Sabet Rasekh, P. et al., The American Journal of Medical Genetics (2018)


Patient-iPSC-Derived Kidney Organoids Show Functional Validation of a Ciliopathic Renal Phenotype and Reveal Underlying Pathogenetic Mechanisms
Forbes, Thomas A. et al., The American Journal of Human Genetics (2018)


A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
Xu, Chang. et al., Computational and Structural Biotechnology Journal (2018)


A robust targeted sequencing approach for low input and variable quality DNA from clinical samples
So, Austin P. et al., npj Genomic Medicine (2018)


Compound heterozygous mutations in glycyl-tRNA synthetase (GARS) cause mitochondrial respiratory chain dysfunction
Nafisinia, Michael. et al., PLoS One (2017)


Early somatic mosaicism is a rare cause of long-QT syndrome
Priest, James R. et al., Proceedings of the National Academy of Sciences of the United States of America (2016)


Expanding the genotypic spectrum of CCBE1 mutations in Hennekam syndrome
Crawford, Joanna, et al., American Journal of Medical Genetics (2016)


Whole exome sequencing in patients with white matter abnormalities
Vanderver, Adeline, et al., Annals of Neurology (2016)


De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects
Priest, James R. et al., PLOS Genetics (2016)


Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition
Littlejohn, Mathew D. et al., Nature Scientific Reports (2016)


Health and population effects of rare gene knockouts in adult humans with related parents
Narasimhan, Vagheesh et al., Science (2016)


Medical implications of technical accuracy in genome sequencing
Goldfeder, Rachel et al., Genome Medicine (2016)


Haplotyping germline and cancer genomes with high-throughput linked-read sequencing
Zheng, Grace et al., Nature Biotechnology (2016)


Introduction to the analysis of next generation sequencing data and its application to venous thromboembolism
Cunha, Marisa et al., Thrombosis and Haemostasis (2016)


Comparison of genetic variants in matched samples using thesaurus annotation
Konopka, Tomasz et al., Bioinformatics (2015)


Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III
Thiffault, Isabelle et al., Nature Communications (2015)


Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes
Shringarpure, SS et al., PLoS One (2015)


Loss-of-function alanyl-tRNA synthetase mutations cause an autosomal-recessive early-onset epileptic encephalopathy with persistent myelination defect
Simons, Cas et al., American Journal of Human Genetics (2015)


Achieving high-sensitivity for clinical applications using augmented exome sequencing
Patwardhan, Anil et al., Genome Medicine (2015)


Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease
Michail, Sonia et al., FEMS Microbiology Ecology (2015)


Achieving high-sensitivity for clinical applications using augmented exome sequencing
Patwardhan, Anil et al., Genome Medicine (2015)


Whole exome sequencing in family trios reveals de novo mutations in PURA as a cause of severe neurodevelopmental delay and learning disability
Simons, Cas et al., Journal of Medical Genetics (2014)


Exome sequencing and genome-wide copy number variant mapping reveal novel associations with sensorineural hereditary hearing loss
Haraksingh, Rajini R. et al., BMC Genomics (2014)


Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle
Littlejohn, Mathew D. et al., Nature Communications (2014)


Metagenomic analysis of double-stranded DNA viruses in healthy adults
Wylie, Kristine M. et al., BMC Biology (2014)


Mutations in the voltage-gated potassium channel KCNH1 cause Temple-Baraitser syndrome and syndromic epilepsy
Simons, Cas et al., Nature Genetics (2014)


Emergence of Rotavirus G12P[8] in St. Louis During the 2012–2013 Rotavirus Season
Wylie, Kristine M. et al., Journal of the Pediatric Infectious Diseases Society (2014)


Clinical pertinence metric enables hypothesis-independent genome-phenome analysis for neurologic diagnosis
Segal, Michael M. et al., Journal of Child Neurology (2014)


Expression variants of the lipogenic AGPAT6 gene affect diverse milk composition phenotypes in Bos taurus
Littlejohn, Mathew D. et al., PLOS One (2014)


Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
Abubucker, Sahar et al., PLOS Computational Biology (2012)


Emerging view of the human virome
Wylie, Kristine M. et al., Translational Research (2012)


Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing
Reumers, Joke et al., Nature Biotechnology (2012)