Publications

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)
doi:10.1089/cmb.2014.0029

 

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)
doi:10.1101/023754

 

Papers citing RTG

 

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

 

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)
doi:10.1073/pnas.1607187113

 

Expanding the genotypic spectrum of CCBE1 mutations in Hennekam syndrome
Crawford, Joanna, et al., American Journal of Medical Genetics (2016)
doi:10.1002/ajmg.a.37803

 

Whole exome sequencing in patients with white matter abnormalities
Vanderver, Adeline, et al., Annals of Neurology (2016)
doi:10.1002/ana.24650

 

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)
doi:10.1371/journal.pgen.1005963

 

Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition
Littlejohn, Mathew D. et al., Nature Scientific Reports (2016)
doi:10.1038/srep25376

 

Health and population effects of rare gene knockouts in adult humans with related parents
Narasimhan, Vagheesh et al., Science (2016)
doi:10.1126/science.aac8624

 

Medical implications of technical accuracy in genome sequencing
Goldfeder, Rachel et al., Genome Medicine (2016)
doi:10.1186/s13073-016-0269-0

 

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing
Zheng, Grace et al., Nature Biotechnology (2016)
doi:10.1038/nbt.3432

 

Introduction to the analysis of next generation sequencing data and its application to venous thromboembolism
Cunha, Marisa et al., Thrombosis and Haemostasis (2016)
doi:10.1160/TH15-05-0411

 

Comparison of genetic variants in matched samples using thesaurus annotation
Konopka, Tomasz et al., Bioinformatics (2015)
doi:10.1093/bioinformatics/btv654

 

Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III
Thiffault, Isabelle et al., Nature Communications (2015)
doi:10.1038/ncomms8623

 

Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes
Shringarpure, SS et al., PLoS One (2015)
doi:10.1371/journal.pone.0129277

 

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)
doi:10.1016/j.ajhg.2015.02.012

 

Achieving high-sensitivity for clinical applications using augmented exome sequencing
Patwardhan, Anil et al., Genome Medicine (2015)
doi:10.1186/s13073-015-0197-4

 

Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease
Michail, Sonia et al., FEMS Microbiology Ecology (2015)
doi:10.1093/femsec/fiu002

 

Achieving high-sensitivity for clinical applications using augmented exome sequencing
Patwardhan, Anil et al., Genome Medicine (2015)
doi:0.1186/s13073-015-0197-4

 

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)
doi:10.1136/jmedgenet-2014-102798

 

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)
doi:10.1186/1471-2164-15-1155

 

Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle
Littlejohn, Mathew D. et al., Nature Communications (2014)
doi:10.1038/ncomms6861

 

Metagenomic analysis of double-stranded DNA viruses in healthy adults
Wylie, Kristine M. et al., BMC Biology (2014)
doi:10.1186/s12915-014-0071-7

 

Mutations in the voltage-gated potassium channel KCNH1 cause Temple-Baraitser syndrome and syndromic epilepsy
Simons, Cas et al., Nature Genetics (2014)
doi:10.1038/ng.3153

 

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)
doi:10.1093/jpids/piu090

 

Clinical pertinence metric enables hypothesis-independent genome-phenome analysis for neurologic diagnosis
Segal, Michael M. et al., Journal of Child Neurology (2014)
doi:10.1177/0883073814545884

 

Expression variants of the lipogenic AGPAT6 gene affect diverse milk composition phenotypes in Bos taurus
Littlejohn, Mathew D. et al., PLOS One (2014)
doi:10.1371/journal.pone.0085757

 

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
Abubucker, Sahar et al., PLOS Computational Biology (2012)
doi:10.1371/journal.pcbi.1002358

 

Emerging view of the human virome
Wylie, Kristine M. et al., Translational Research (2012)
doi:10.1016/j.trsl.2012.03.006

 

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing
Reumers, Joke et al., Nature Biotechnology (2012)
doi:10.1038/nbt.2053