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1. Full Text The Ensembl Variant Effect Predictor
by McLaren, William and Gil, Laurent and Hunt, Sarah E and Riat, Harpreet Singh and Ritchie, Graham R.S and Thormann, Anja and Flicek, Paul and Cunningham, Fiona
Genome Biology, ISSN 1474-7596, 06/2016, Volume 17, Issue 1
The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding... 
NGS | SNP | Genome | Variant annotation | DATABASE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ANNOTATION | SEQUENCE | GENETICS & HEREDITY | CONSEQUENCES | MUTATIONS | COMPLEX TRAITS | GENCODE | SINGLE NUCLEOTIDE POLYMORPHISMS | Haplotypes | Disease | Genomics | Genes | Genomes | Patients | Consortia | Interfaces | Proteins | Annotations | Mutation | Bioinformatics | Cancer
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2. Full Text Distinguishing Variant Pathogenicity from Genetic Diagnosis: How to Know Whether a Variant Causes a Condition
by Biesecker, Leslie G and Nussbaum, Robert L and Rehm, Heidi L
JAMA - Journal of the American Medical Association, ISSN 0098-7484, 11/2018, Volume 320, Issue 18, pp. 1929 - 1930
The article discusses how genome sequencing and exome sequencing are increasingly being used in clinical settings when a genetic basis for disease is... 
MEDICINE, GENERAL & INTERNAL | GENOME | Genetic Variation | Genetic Testing | Humans | Genetic Diseases, Inborn - genetics | Genetic Diseases, Inborn - diagnosis | Sequence Analysis, DNA | Whole Exome Sequencing | Usage | Genetic screening | Exome sequencing | Pathogenicity | Pathogens | Genetic variance | Patient care planning | Genomes | Diagnostic systems | Genetic testing | Medical diagnosis | Gene sequencing
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3. Full Text A systematic analysis of disease-associated variants in the 3′ regulatory regions of human protein-coding genes II: the importance of mRNA secondary structure in assessing the functionality of 3′ UTR variants
by Chen, Jian-Min and Férec, Claude and Cooper, David N
Human Genetics, ISSN 0340-6717, 10/2006, Volume 120, Issue 3, pp. 301 - 333
In an attempt both to catalogue 3′ regulatory region (3′ RR)-mediated disease and to improve our understanding of the structure and function of the 3′ RR, we... 
THYMIDYLATE-SYNTHASE GENE | 3' UNTRANSLATED REGION | BREAST-CANCER RISK | AU-RICH ELEMENTS | UPSTREAM SEQUENCE ELEMENT | GENETICS & HEREDITY | ACUTE MYOCARDIAL-INFARCTION | PROHIBITIN 3'-UNTRANSLATED REGION | E-CADHERIN GENE | SINGLE NUCLEOTIDE POLYMORPHISMS | ENDOTHELIAL GROWTH-FACTOR | Humans | Regulatory Sequences, Nucleic Acid | 3' Untranslated Regions - classification | Genetic Diseases, Inborn - genetics | 3' Untranslated Regions - genetics | Models, Molecular | Molecular Sequence Data | Open Reading Frames - genetics | Base Composition | Base Sequence | RNA, Messenger - chemistry | Polymorphism, Single Nucleotide | 3' Untranslated Regions - physiology | Nucleic Acid Conformation
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4. Full Text Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST‐Indel)
by Douville, Christopher and Masica, David L and Stenson, Peter D and Cooper, David N and Gygax, Derek M and Kim, Rick and Ryan, Michael and Karchin, Rachel
Human Mutation, ISSN 1059-7794, 01/2016, Volume 37, Issue 1, pp. 28 - 35
ABSTRACT Insertion/deletion variants (indels) alter protein sequence and length, yet are highly prevalent in healthy populations, presenting a challenge to... 
bioinformatics pathogenicity predictor | meta‐predictor | insertion deletion variant | in‐frame frameshift | indel | In-frame frameshift | Meta-predictor | Bioinformatics pathogenicity predictor | Indel | Insertion deletion variant | DISEASE GENES | meta-predictor | in-frame frameshift | PREDICTION | NUCLEOTIDE | BIOINFORMATICS | DATABASE | GENOMES | SEQUENCE | MUTATION | GENETICS & HEREDITY | CONSEQUENCES | Computational Biology - methods | Reproducibility of Results | Algorithms | Datasets as Topic | Humans | Models, Genetic | Software | Mutation, Missense | INDEL Mutation | Web Browser | Proteins | Genetics | Mutation | Pathogenesis | Bioinformatics | Informatics
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5. Full Text Regulatory Single‐Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants
by Peterson, Thomas A and Mort, Matthew and Cooper, David N and Radivojac, Predrag and Kann, Maricel G and Mooney, Sean D
Human Mutation, ISSN 1059-7794, 11/2016, Volume 37, Issue 11, pp. 1137 - 1143
ABSTRACT In silico methods for detecting functionally relevant genetic variants are important for identifying genetic markers of human inherited disease. Much... 
variant prediction | regulatory variant | RSVP | intergenic | variant predictor | ENCODE | Regulatory variant | Variant predictor | Intergenic | Variant prediction | VALIDATION | GENETIC-VARIANTS | IDENTIFICATION | ELEMENTS | HUMAN GENOME | POLYMORPHISMS | PROMOTERS | SEQUENCE | DISEASE | GENETICS & HEREDITY | SNPS | Computational Biology - methods | Genetic Predisposition to Disease | Computer Simulation | Humans | Polymorphism, Single Nucleotide | Genome, Human | Genomics - methods | Machine Learning | Genetic research | Genetic markers | Analysis | Genomics | Proteins | Genetic disorders | Mutation | Gene expression | Pathogenesis | intergenic variant
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6. Full Text The variant call format and VCFtools
by Danecek, Petr and Auton, Adam and Abecasis, Goncalo and Albers, Cornelis A and Banks, Eric and DePristo, Mark A and Handsaker, Robert E and Lunter, Gerton and Marth, Gabor T and Sherry, Stephen T and McVean, Gilean and Durbin, Richard and 1000 Genomes Project Anal Grp and 1000 Genomes Project Analysis Group
Bioinformatics, ISSN 1367-4803, 8/2011, Volume 27, Issue 15, pp. 2156 - 2158
The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with... 
BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Genetic Variation | Information Storage and Retrieval - methods | Humans | Alleles | Genotype | Software | Genome, Human | Genomics - methods | Applications Note
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7. Full Text The VAAST Variant Prioritizer (VVP): Ultrafast, easy to use whole genome variant prioritization tool
by Flygare, Steven and Hernandez, Edgar Javier and Phan, Lon and Moore, Barry and Li, Man and Fejes, Anthony and Hu, Hao and Eilbeck, Karen and Huff, Chad and Jorde, Lynn and G. Reese, Martin and Yandell, Mark
BMC Bioinformatics, ISSN 1471-2105, 02/2018, Volume 19, Issue 1, pp. 57 - 13
Background: Prioritization of sequence variants for diagnosis and discovery of Mendelian diseases is challenging, especially in large collections of whole... 
Variants of uncertain significance | Human genome | Variant prioritization | Genomics | GUIDELINES | BIOCHEMICAL RESEARCH METHODS | SEQUENCE VARIANTS | MODEL | IDENTIFICATION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DISEASE | MATHEMATICAL & COMPUTATIONAL BIOLOGY | FRAMEWORK | PROTEIN FUNCTION | ASSOCIATION | Usage | Analysis | Science | Research | Computational biology | Computer programs
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8. Full Text TREM2 Variants in Alzheimer's Disease
by Guerreiro, Rita and Wojtas, Aleksandra and Bras, Jose and Carrasquillo, Minerva and Rogaeva, Ekaterina and Majounie, Elisa and Cruchaga, Carlos and Sassi, Celeste and Kauwe, John S.K and Younkin, Steven and Hazrati, Lilinaz and Collinge, John and Pocock, Jennifer and Lashley, Tammaryn and Williams, Julie and Lambert, Jean-Charles and Amouyel, Philippe and Goate, Alison and Rademakers, Rosa and Morgan, Kevin and Powell, John and St. George-Hyslop, Peter and Singleton, Andrew and Hardy, John and Alzheimer Genetic Anal Grp and EADI Consortium and GERAD Consortium and UKBE Consortium and Alzheimer Genetic Analysis Group
The New England Journal of Medicine, ISSN 0028-4793, 01/2013, Volume 368, Issue 2, pp. 117 - 127
This study shows that variants in TREM2 are a rare cause of Alzheimer's disease and underscores the role of the microglial cell in the disease mechanism and as... 
COMMON VARIANTS | MEDICINE, GENERAL & INTERNAL | IDENTIFIES VARIANTS | GENE | MICROGLIA | FRAMEWORK | DNA-SEQUENCING DATA | MISSENSE MUTATIONS | GENOME-WIDE ASSOCIATION | TRANSGENIC MICE | CD2AP | Genome-Wide Association Study | Membrane Glycoproteins - metabolism | Mice, Inbred A | Humans | Risk Factors | Genotype | Genotyping Techniques | RNA, Messenger - metabolism | Alzheimer Disease - pathology | Membrane Glycoproteins - genetics | Genetic Variation | Exome - genetics | Animals | Brain - pathology | Heterozygote | Aged | Mice | Mutation | Alzheimer Disease - genetics | Receptors, Immunologic - genetics | Sequence Analysis, DNA - methods | Receptors, Immunologic - metabolism | Gene mutations | Genetic variation | Causes of | Genetic aspects | Research | Apolipoproteins | Alzheimer's disease | Health aspects | Proteins | Genetics | Genomes | Alzheimers disease
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