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Protocols

RUNES specifications

Information


Unique identifier OMICS_33278
Name RUNES
Alternative name Rapid Understanding of Nucleotide variant Effect Software

Maintainer


This tool is not maintained anymore.

Publication for Rapid Understanding of Nucleotide variant Effect Software

RUNES citations

 (10)
library_books

The NSIGHT1 randomized controlled trial: rapid whole genome sequencing for accelerated etiologic diagnosis in critically ill infants

2018
PMCID: 5807510
PMID: 29449963
DOI: 10.1038/s41525-018-0045-8

[…] detected and genotyped with the Genome Analysis Tool Kit (v1.6-13. and v3.2-2).,,, Copy number variants and structural variants were not detected in WGS. Nucleotide variants were annotated with the Rapid Understanding of Nucleotide variant Effect Software (RUNES).,, – Variants were interpreted by board certified molecular geneticists using American College of Medical Genetics guidelines for path […]

library_books

Hypotonia and intellectual disability without dysmorphic features in a patient with PIGN related disease

2017
BMC Med Genet
PMCID: 5668960
PMID: 29096607
DOI: 10.1186/s12881-017-0481-9

[…] r a mean of 78× average coverage. Bidirectional sequence was assembled, aligned to reference gene sequences based on human genome build GRCh37/UCSC hg19, and analyzed using custom-developed software, RUNES and VIKING [], variants were filtered to 1% minor allele frequency in our variant database, then prioritized by the American College of Medical Genetics (ACMG) categorization [], OMIM identity a […]

library_books

Immunodeficiency Associated Lymphoid Hyperplasia As a Cause of Intussusception in a Case of Activated PI3K δ Syndrome

2017
PMCID: 5395656
PMID: 28469999
DOI: 10.3389/fped.2017.00071

[…] ctional sequence was assembled and aligned to reference sequence (GRCh37/UCSC hg19). Alignment and variant calling was performed as previously published (–). Briefly, using custom-developed software, RUNES and VIKING, variants were filtered to 1% minor allele frequency, then prioritized by the American College of Medical Genetics categorization (), OMIM (http://www.omim.org) identity, and phenotyp […]

library_books

Functional validation of novel compound heterozygous variants in B3GAT3 resulting in severe osteopenia and fractures: expanding the disease phenotype

2016
BMC Med Genet
PMCID: 5117547
PMID: 27871226
DOI: 10.1186/s12881-016-0344-9

[…] of 12.7 GB of data resulting in a mean 66× coverage. Gapped alignment to reference sequences (GRCh37.p5) was performed with GSNAP and the GATK and analysis completed using custom-developed software, RUNES and VIKING as previously reported [, ]. […]

call_split

Diagnostics of Primary Immunodeficiencies through Next Generation Sequencing

2016
Front Immunol
PMCID: 5098274
PMID: 27872624
DOI: 10.3389/fimmu.2016.00466
call_split See protocol

[…] inimum target coverage of 50×. For all samples, sequence was assembled, aligned to reference gene sequences based on human genome build GRCh37/UCSC hg19, and analyzed using custom-developed software, RUNES and VIKING ().Alignment, variant calling, and analysis were performed, as described previously (). In detail, variants were filtered by frequency and variant category (). Variant analysis was co […]

library_books

Clinical detection of deletion structural variants in whole genome sequences

2016
PMCID: 5685307
PMID: 29263817
DOI: 10.1038/npjgenmed.2016.26

[…] otide variants were detected and genotyped with the Genome Analysis Toolkit (GATK) v. 1.4 or 1.6, and yielded an average of 4.9 million nucleotide variants per sample (). Variants were annotated with RUNES, noncommercial CMH software (Children's Mercy Hospital, Kansas City, MO, USA)., WGS variant interpretations considered multiple sources of evidence, including variant attributes, the gene involv […]

Citations

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RUNES institution(s)
Center for Pediatric Genomic Medicine, Children’s Mercy Hospital, Kansas City, MO, USA; Department of Pediatrics, Children’s Mercy Hospital, Kansas City, MO, USA; Department of Pathology, Children’s Mercy Hospital, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, MO, USA; University of Kansas Medical Center, Kansas City, MO, USA; Illumina Inc., Chesterford Research Park, Little Chesterford, UK
RUNES funding source(s)
Supported by the Marion Merrell Dow Foundation, Children’s Mercy Hospital, and Illumina Inc.

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