CSN and CAVA: Variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting

Genome Medicine

Volumn 7, Issue 1, 2015, Pages

  Münz, Márton ^a   Ruark, Elise ^b   Renwick, Anthony ^b   Ramsay, Emma ^b   Clarke, Matthew ^b   Mahamdallie, Shazia ^b   Cloke, Victoria ^b   Seal, Sheila ^b   Strydom, Ann ^b   Lunter, Gerton ^a   Rahman, Nazneen ^b,c  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b INSTITUTE OF CANCER RESEARCH   (United Kingdom)

^c INSTITUTE OF CANCER RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; CLINICAL ANNOTATION OF VARIANTS; CLINICAL SEQUENCING NOMENCLATURE; EXOME; GENE MUTATION; GENE NOMENCLATURE; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; INDEL MUTATION; INTERMETHOD COMPARISON; NEXT GENERATION SEQUENCING; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; SANGER SEQUENCING; SEQUENCE ANALYSIS; TUMOR SUPPRESSOR GENE; BIOLOGY; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; MUTATION; PROCEDURES;

BRCA1 PROTEIN; BRCA1 PROTEIN, HUMAN; BRCA2 PROTEIN; BRCA2 PROTEIN, HUMAN;

BRCA1 PROTEIN; BRCA2 PROTEIN; COMPUTATIONAL BIOLOGY; EXOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR SEQUENCE ANNOTATION; MUTATION; SEQUENCE ANALYSIS, DNA;

EID: 84940200842     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-015-0195-6     Document Type: Article

References (27)

1. Green ED, Guyer MS, Manolio TA, Peterson JL. Charting a course for genomic medicine from base pairs to bedside. Nature. 2011;470:204-13.
2. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29:308-11.
3. dbSNP information for rs80357713. http://www.ncbi.nlm.nih.gov/SNP/ .
4. den Dunnen JT, Antonarakis SE. Nomenclature for the description of human sequence variations. Hum Genet. 2001;109:121-4.
5. Wildeman M, van Ophuizen E, den dunnen JT, Taschner PE. Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker. Hum. Mutat. 2008; 29, 6-13; Mutalyzer. http://mutalyzer.nl/ .
6. Counsyl. HGVS variant name parsing and generation. https://github.com/counsyl/hgvs .
7. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics. 2010;26:2069-70.
8. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38, e164.
9. Cingolani P, Platts A, Wangle L, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6:80-92.
10. The NCBI handbook [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2002 Oct. Chapter 18, The Reference Sequence (RefSeq) Project. http://www.ncbi.nlm.nih.gov/books/NBK21091/ .
11. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004;431:931-45.
12. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27:2156-8.
13. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078-9.
14. SAMtools. http://www.htslib.org/.
15. Rahman N. Realizing the promise of cancer predisposition genes. Nature. 2014;505:302-8.
16. Rahman N. Mainstreaming genetic testing of cancer predisposition genes. Clin Med. 2014;14:436-9.
17. The Institute of Cancer Research, London. Mainstreaming Cancer Genetics Programme. http://mcgprogramme.com
18. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, et al. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 2005;6:R44.
19. Münz M, Ruark E, Rahman N, Lunter G. CAVA: Clinical Annotation of Variants. http://www.icr.ac.uk/cava .
20. Exome Aggregation Consortium (ExAC), Cambridge, MA http://exac.broadinstitute.org ) Accessed December 2014.
21. Access Committee for CLS Cohorts: 1958 Birth Cohort. http://www2.le.ac.uk/projects/birthcohort .
22. Lunter G, Goodson M. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 2011;21:936-9.
23. Picard. http://broadinstitute.github.io/picard/ .
24. Rimmer A, Phan H, Mathieson I, Iqbal Z, Twigg SR, Wilkie AO, et al. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nat Genet. 2014;46:912.
25. European Genome-phenome Archive: Exome sequencing of 1000 population control samples from the UK 1958 birth cohort. https://www.ebi.ac.uk/ega/studies/EGAS00001000971 .
26. TGLclinical. http://www.tglclinical.com/ .
27. Illumina. TruSight Cancer: targeting genes previously linked to a predisposition towards cancer. http://www.illumina.com/products/trusight_cancer.html .