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
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)
doi:10.1101/281006
Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes
Krusche, P. et al., BioRxiv (2018)
doi:10.1101/270157
Approaches to variant discovery for conifer transcriptome sequencing
Telfer, E. et al., PLOS One (2018)
doi:10.1371/journal.pone.0205835
Papers citing RTG
The following is a sampling of publications citing RTG or where RTG has been used during the research:
Benchmarking small-variant genotyping in polyploids
Cooke, D. et al., BioRxiv (2021)
doi:10.1101/2021.03.29.436766
Reducing Sanger confirmation testing through false positive prediction algorithms
Holt, J. et al., Genetics in Medicine (2021)
doi:10.1038/s41436-021-01148-3
Interplay between probe design and test performance: overlap between genomic regions of interest, capture regions and high quality reference calls influence performance of WES-based assays
Pranckeviciene, E. et al., Human Genetics (2021)
doi:10.1007/s00439-020-02201-y
Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly
Holley, G. et al., Genome Biology (2021)
doi:10.1186/s13059-020-02244-4
Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays
Krishnan, V. et al., BMC Bioinformatics (2021)
doi:10.1186/s12859-020-03934-3
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Cheng, H. et al., Nature Methods (2021)
doi:10.1038/s41592-020-01056-5
A Distributed Whole Genome Sequencing Benchmark Study
Corbett, R. et al., Frontiers in Genetics (2020)
doi:10.3389/fgene.2020.612515
Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit
Sirén, J. et al., BioRxiv (2020)
doi:10.1101/2020.12.04.412486
A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis
Shand, M. et al., Nature Communications (2020)
doi:10.1038/s42003-020-01460-9
Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study
Foox, J. et al., BioRxiv (2020)
doi:10.1101/2020.07.23.218602
Recurrent inversion toggling and great ape genome evolution
Porubsky, D. et al., Nature Genetics (2020)
doi:10.1038/s41588-020-0646-x
Fast and accurate genomic analyses using genome graphs
Rakocevic, G. et al., Nature Genetics (2019)
doi:10.1038/s41588-018-0316-4
Sequencing of human genomes with nanopore technology
Bowden, R. et al., Nature Communications (2019)
doi:10.1038/s41467-019-09637-5
Comparative Analysis for the Performance of Variant Calling Pipelines on Detecting the de novo Mutations in Humans
Liang, Y. et al., Frontiers in Pharmacology (2019)
doi:10.3389/fphar.2019.00358
Longshot: accurate variant calling in diploid genomes using single-molecule long read sequencing
Edge, P. et al., BioRxiv (2019)
doi:10.1101/564443
Highly-accurate long-read sequencing improves variant detection and assembly of a human genome
Wenger, A. et al., BioRxiv (2019)
doi:10.1101/519025
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)
doi:10.1002/ajmg.a.38717
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)
doi:10.1016/j.ajhg.2018.03.014
A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
Xu, Chang. et al., Computational and Structural Biotechnology Journal (2018)
doi:10.1016/j.csbj.2018.01.003
A robust targeted sequencing approach for low input and variable quality DNA from clinical samples
So, Austin P. et al., npj Genomic Medicine (2018)
doi:10.1038/s41525-017-0041-4
Compound heterozygous mutations in glycyl-tRNA synthetase (GARS) cause mitochondrial respiratory chain dysfunction
Nafisinia, Michael. et al., PLoS One (2017)
doi:10.1371/journal.pone.0178125
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