Clinical bioinformatics encompasses generating raw sequence data from the machine
through identifying reportable variants.
Keywords
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References
- Confirming variants in next-generation sequencing panel testing by sanger sequencing.J Mol Diagn. 2015; 17: 456-461
- Detecting copy number variation via next generation technology.Curr Genet Med Rep. 2016; 4: 74-85
- HGVS recommendations for the description of sequence variants: 2016 update.Hum Mutat. 2016; 37: 564-569
- Analysis of protein-coding genetic variation in 60,706 humans.Nature. 2016; 536: 285-291
- A global reference for human genetic variation.Nature. 2015; 526: 68-74
gnomAD browser. Available at: http://gnomad.broadinstitute.org/. Accessed April 16, 2018.
- MutationTaster evaluates disease-causing potential of sequence alterations.Nat Methods. 2010; 7: 575-576
- Predicting the functional impact of protein mutations: application to cancer genomics.Nucleic Acids Res. 2011; 39: e118
- Predicting functional effect of human missense mutations using PolyPhen-2.Curr Protoc Hum Genet. 2013; Chapter 7: Unit7.20
- REVEL: an ensemble method for predicting the pathogenicity of rare missense variants.Am J Hum Genet. 2016; 99: 877-885
- ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.Nucleic Acids Res. 2010; 38: e164
- The ensemble variant effect predictor.Genome Biol. 2016; 17: 122
- 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
- Oncotator: cancer variant annotation tool.Hum Mutat. 2015; 36: E2423-E2429
- WGSA: an annotation pipeline for human genome sequencing studies.J Med Genet. 2016; 53: 111-112
- Evaluating the clinical validity of gene-disease associations: an evidence-based framework developed by the clinical genome resource.Am J Hum Genet. 2017; 100: 895-906
- A framework for the interpretation of de novo mutation in human disease.Nat Genet. 2014; 46: 944-950
- Genic intolerance to functional variation and the interpretation of personal genomes.PLoS Genet. 2013; 9: e1003709
- ClinVar: improving access to variant interpretations and supporting evidence.Nucleic Acids Res. 2017; 46: D1062-D1067
- Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the association for molecular pathology, American Society of Clinical Oncology, and College of American Pathologists.J Mol Diagn. 2017; 19: 4-23
- Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.Genet Med. 2015; 17: 405-424
- Standards for clinical grade genomic databases.Arch Pathol Lab Med. 2015; 139: 1400-1412
- Standards and guidelines for validating next-generation sequencing bioinformatics pipelines: a joint recommendation of the association for molecular pathology and the College of American Pathologists.J Mol Diagn. 2018; 20: 4-27
- College of American Pathologists’ laboratory standards for next-generation sequencing clinical tests.Arch Pathol Lab Med. 2015; 139 (Available at:) (Accessed April 16, 2018): 481-493
College of American Pathologists (CAP). Accreditation checklists. Available at: http://www.cap.org/web/home/lab/accreditation/accreditation-checklists. Accessed April 16, 2018.
- Extensive sequencing of seven human genomes to characterize benchmark reference materials.Sci Data. 2016; 3: 160025
- A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree.Genome Res. 2017; 27: 157-164
- Characterization of 137 genomic DNA reference materials for 28 pharmacogenetic genes: a GeT-RM collaborative project.J Mol Diagn. 2016; 18: 109-123
Genetic Testing Reference Materials Coordination Program (GeT-RM) - Home. Available at: https://wwwn.cdc.gov/clia/Resources/GetRM/. Accessed April 16, 2018.
- A model study of in silico proficiency testing for clinical next-generation sequencing.Arch Pathol Lab Med. 2016; 140: 1085-1091
- In silico proficiency testing for clinical next-generation sequencing.J Mol Diagn. 2017; 19: 35-42
- A comparison of tools for the simulation of genomic next-generation sequencing data.Nat Rev Genet. 2016; 17: 459-469
- Creating a universal SNP and small indel variant caller with deep neural networks.bioRxiv. 2016; https://doi.org/10.1101/092890
- CrossMap: a versatile tool for coordinate conversion between genome assemblies.Bioinformatics. 2014; 30: 1006-1007
Lift genome annotations. Available at: http://genome.ucsc.edu/cgi-bin/hgLiftOver. Accessed April 17, 2018.
Coordinate remapping service: NCBI. Available at: https://www.ncbi.nlm.nih.gov/genome/tools/remap. Accessed April 17, 2018.
ga4gh. ga4gh/benchmarking-tools. GitHub. Available at: https://github.com/ga4gh/benchmarking-tools. Accessed April 16, 2018.
- Navigating highly homologous genes in a molecular diagnostic setting: a resource for clinical next-generation sequencing.Genet Med. 2016; 18: 1282-1289
- Sanger confirmation is required to achieve optimal sensitivity and specificity in next-generation sequencing panel testing.J Mol Diagn. 2016; 18: 923-932
- Systematic evaluation of sanger validation of next-generation sequencing variants.Clin Chem. 2016; 62: 647-654
- Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory.Genet Med. 2014; 16: 510-515
- Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics. 2009; 25: 1754-1760
- Fast and accurate long-read alignment with Burrows-Wheeler transform.Bioinformatics. 2010; 26: 589-595
NovoAlign | Novocraft. Available at: http://www.novocraft.com/products/novoalign/. Accessed April 16, 2018.
- A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.Bioinformatics. 2011; 27: 2987-2993
- The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.Genome Res. 2010; 20: 1297-1303
- Scaling accurate genetic variant discovery to tens of thousands of samples.BioRxiv. 2017; https://doi.org/10.1101/201178
Erik Garrison, Gabor Marth. Haplotype-based variant detection from short-read sequencing. arXiv, 2012; 1207.3907
- a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.Bioinformatics. 2009; 25: 2865-2871
- BreakDancer: identification of genomic structural variation from paired-end read mapping.Curr Protoc Bioinformatics. 2014; 45: 15.6.1-15.6.11
- Large multiallelic copy number variations in humans.Nat Genet. 2015; 47: 296-303
- Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.Bioinformatics. 2016; 32: 1220-1222
- Using XHMM software to detect copy number variation in whole-exome sequencing data.Curr Protoc Hum Genet. 2014; 81: 7.23.1-21
- VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data.Genet Med. 2016; 18: 712-719
- BEDTools: the Swiss-army tool for genome feature analysis.Curr Protoc Bioinformatics. 2014; 47: 11.12.1-34
- Comparing variant call files for performance benchmarking of next-generation sequencing variant calling pipelines.bioRxiv. 2015; https://doi.org/10.1101/023754
Babraham Bioinformatics - FastQC a quality control tool for high throughput sequence data. Available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed April 16, 2018.
- Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data.Am J Hum Genet. 2012; 91: 839-848
Picard Tools - By Broad Institute. Available at: https://broadinstitute.github.io/picard/. Accessed April 16, 2018.
- A general framework for estimating the relative pathogenicity of human genetic variants.Nat Genet. 2014; 46: 310-315
- DANN: a deep learning approach for annotating the pathogenicity of genetic variants.Bioinformatics. 2014; 31: 761-763
Article info
Footnotes
This article originally appeared in Advances in Molecular Pathology, Volume 1, 2018.
Disclosure: The authors have nothing to disclose.
Identification
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