indel variant
Evidence from:
primary |
all sources
Related entities (21)
| Subject | Relation | Object | p-value | Evidence |
|---|---|---|---|---|
| AA | associated_with | indel | — | 1 |
| EAs | associated_with | indel | — | 1 |
| Impute2 | interacts_with | indel | — | 1 |
| indel | associated_with | African American | — | 1 |
| indel | associated_with | Alzheimer’s disease | — | 1 |
| indel | risk_factor_for | autism | — | 1 |
| indel | associated_with | cancer | — | 1 |
| indel | associated_with | cis-eQTL | — | 1 |
| indel | associated_with | coding variant | — | 1 |
| indel | associated_with | cognition | — | 1 |
| indel | associated_with | diabetes | — | 1 |
| indel | associated_with | European population | — | 1 |
| indel | associated_with | Hispanic | — | 1 |
| indel | associated_with | miRNA | — | 1 |
| indel | associated_with | noncoding variant | — | 1 |
| indel | associated_with | Parkinson’s disease | — | 1 |
| indel | risk_factor_for | schizophrenia | — | 2 |
| indel | associated_with | SNP | — | 1 |
| indel | associated_with | SNV | — | 1 |
| indel | risk_factor_for | Tourette syndrome | — | 1 |
| indel | associated_with | trans-eQTL | — | 1 |
Mentioned in (133)
Papers in which this entity is mentioned.
- Large-scale exome analyses reveal new rare variant contributions in amyotrophic lateral sclerosis. (2026)
- Advancing regulatory variant effect prediction with AlphaGenome. (2026)
- Comprehensive repertoire of the chromosomal alteration and mutational signatures across 16 cancer types. (2026)
- Whole-genome landscapes of 1,364 breast cancers. (2026)
- Whole genome sequencing approach to assess homologous recombination deficiency in a pan-cancer cohort. (2026)
- Stratified Medicine Pediatrics: Cell-Free DNA and Serial Tumor Sequencing Identifies Subtype-Specific Cancer Evolution and Epigenetic States. (2025)
- FET fusion oncoproteins disrupt physiologic DNA repair and create a targetable opportunity for ATR inhibitor therapy. (2025)
- Genome-wide association testing beyond SNPs. (2025)
- Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition. (2025)
- Nucleotide Transformer: building and evaluating robust foundation models for human genomics. (2025)
- Yield of genetic association signals from genomes, exomes and imputation in the UK Biobank. (2024)
- Molecular profiling of 888 pediatric tumors informs future precision trials and data-sharing initiatives in pediatric cancer. (2024)
- Transient loss of Polycomb components induces an epigenetic cancer fate. (2024)
- Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders. (2024)
- Nanopore sequencing with unique molecular identifiers enables accurate mutation analysis and haplotyping in the complex lipoprotein(a) KIV-2 VNTR. (2024)
- Insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme. (2024)
- The Application of Long-Read Sequencing to Cancer. (2024)
- A harmonized public resource of deeply sequenced diverse human genomes. (2024)
- Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates. (2024)
- Proving sequence aligners can guarantee accuracy in almost ( log ) time through an average-case analysis of the seed-chain-extend heuristic. (2023)
- Machine learning for genetics-based classification and treatment response prediction in cancer of unknown primary. (2023)
- A survey of mapping algorithms in the long-reads era. (2023)
- Comprehensive analysis of mutational signatures reveals distinct patterns and molecular processes across 27 pediatric cancers. (2023)
- Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors. (2023)
- Single-cell analysis of somatic mutations in human bronchial epithelial cells in relation to aging and smoking. (2022)
- Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data. (2022)
- Variant interpretation using population databases: Lessons from gnomAD. (2022)
- Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers. (2022)
- Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA. (2021)
- Application of third-generation sequencing in cancer research. (2021)
- A practical guide to cancer subclonal reconstruction from DNA sequencing. (2021)
- Genetic scores for adult subcortical volumes associate with subcortical volumes during infancy and childhood. (2021)
- Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. (2021)
- Discovery of regulatory noncoding variants in individual cancer genomes by using cis-X. (2020)
- Best practices for variant calling in clinical sequencing. (2020)
- Structural variation in the sequencing era. (2020)
- Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring. (2020)
- Pan-cancer analysis of whole genomes. (2020)
- Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases. (2020)
- Inferring structural variant cancer cell fraction. (2020)
- The repertoire of mutational signatures in human cancer. (2020)
- Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. (2020)
- Pan-cancer landscape of homologous recombination deficiency. (2020)
- The mutational constraint spectrum quantified from variation in 141,456 humans. (2020)
- Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers. (2020)
- Transcriptomic signatures across human tissues identify functional rare genetic variation. (2020)
- Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers. (2019)
- Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. (2019)
- The mutational footprints of cancer therapies. (2019)
- The mutational constraint spectrum quantified from variation in 141,456 humans (2019)
- Tumor mutational burden standardization initiatives: Recommendations for consistent tumor mutational burden assessment in clinical samples to guide immunotherapy treatment decisions. (2019)
- The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment. (2019)
- Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study. (2019)
- VCF2CNA: A tool for efficiently detecting copy-number alterations in VCF genotype data and tumor purity. (2019)
- A multi-task convolutional deep neural network for variant calling in single molecule sequencing. (2019)
- HLA*LA-HLA typing from linearly projected graph alignments. (2019)
- Assessment of tumor mutation burden calculation from gene panel sequencing data. (2019)
- Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project. (2019)
- Best practices for bioinformatic characterization of neoantigens for clinical utility. (2019)
- A Compendium of Mutational Signatures of Environmental Agents. (2019)
- Pan-cancer whole-genome analyses of metastatic solid tumours. (2019)
- Alcohol and endogenous aldehydes damage chromosomes and mutate stem cells. (2018)
- Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. (2018)
- Widespread Selection for Oncogenic Mutant Allele Imbalance in Cancer. (2018)
- Comprehensive Characterization of Cancer Driver Genes and Mutations. (2018)
- Genome-wide somatic variant calling using localized colored de Bruijn graphs. (2018)
- The Immune Landscape of Cancer. (2018)
- Human Genetics of Addiction: New Insights and Future Directions. (2018)
- Comprehensive Cancer-Predisposition Gene Testing in an Adult Multiple Primary Tumor Series Shows a Broad Range of Deleterious Variants and Atypical Tumor Phenotypes. (2018)
- Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes (2018)
- Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome. (2018)
- The fractured landscape of RNA-seq alignment: the default in our STARs. (2018)
- SvABA: genome-wide detection of structural variants and indels by local assembly. (2018)
- Patterns and mechanisms of structural variations in human cancer. (2018)
- Picky comprehensively detects high-resolution structural variants in nanopore long reads. (2018)
- Copy number signatures and mutational processes in ovarian carcinoma. (2018)
- Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome (2017)
- HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures. (2017)
- Universal Patterns of Selection in Cancer and Somatic Tissues. (2017)
- Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma. (2017)
- Orthotopic patient-derived xenografts of paediatric solid tumours. (2017)
- GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly. (2017)
- The fractured landscape of RNA-seq alignment: The default in our STARs (2017)
- Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. (2017)
- Mapping and phasing of structural variation in patient genomes using nanopore sequencing. (2017)
- A method to reduce ancestry related germline false positives in tumor only somatic variant calling. (2017)
- De Novo Coding Variants Are Strongly Associated with Tourette Disorder. (2017)
- PGBD5 promotes site-specific oncogenic mutations in human tumors. (2017)
- The impact of structural variation on human gene expression. (2017)
- Fast and Accurate Genomic Analyses using Genome Graphs (2017)
- New insights into the generation and role of de novo mutations in health and disease. (2016)
- Integrated digital error suppression for improved detection of circulating tumor DNA. (2016)
- KAT2B polymorphism identified for drug abuse in African Americans with regulatory links to drug abuse pathways in human prefrontal cortex. (2016)
- Landscape of somatic mutations in 560 breast cancer whole-genome sequences. (2016)
- A genomic case study of desmoplastic small round cell tumor: comprehensive analysis reveals insights into potential therapeutic targets and development of a monitoring tool for a rare and aggressive disease. (2016)
- Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel). (2016)
- Development and clinical application of an integrative genomic approach to personalized cancer therapy. (2016)
- GenVisR: Genomic Visualizations in R. (2016)
- Tools and best practices for data processing in allelic expression analysis. (2015)
- Recent genetic findings in schizophrenia and their therapeutic relevance. (2015)
- Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia. (2015)
- A global reference for human genetic variation. (2015)
- Integrative Clinical Sequencing in the Management of Refractory or Relapsed Cancer in Youth. (2015)
- A global reference for human genetic variation. (2015)
- RADIA: RNA and DNA integrated analysis for somatic mutation detection. (2014)
- Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations. (2014)
- Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma. (2014)
- An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. (2014)
- Genetic variability in the regulation of gene expression in ten regions of the human brain. (2014)
- In search of rare variants: preliminary results from whole genome sequencing of 1,325 individuals with psychophysiological endophenotypes. (2014)
- PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. (2014)
- Signatures of mutational processes in human cancer. (2013)
- ACMG clinical laboratory standards for next-generation sequencing. (2013)
- A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains. (2013)
- A comparative analysis of algorithms for somatic SNV detection in cancer. (2013)
- The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation. (2013)
- Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. (2013)
- High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. (2012)
- An integrated map of genetic variation from 1,092 human genomes. (2012)
- Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. (2012)
- Mutational processes molding the genomes of 21 breast cancers. (2012)
- Annotation of functional variation in personal genomes using RegulomeDB. (2012)
- Novel mutations target distinct subgroups of medulloblastoma. (2012)
- Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. (2012)
- Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. (2012)
- A promoter polymorphism in the Per3 gene is associated with alcohol and stress response. (2012)
- VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. (2012)
- A framework for variation discovery and genotyping using next-generation DNA sequencing data. (2011)
- Fast and accurate long-read alignment with Burrows-Wheeler transform. (2010)
- BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. (2009)
- Fast and accurate short read alignment with Burrows-Wheeler transform. (2009)
- VarScan: variant detection in massively parallel sequencing of individual and pooled samples. (2009)
- Fast and accurate short read alignment with Burrows-Wheeler transform. (2009)
Merged raw entities (6)
All extracted name/type variants the normalize job merged into this entity. Use this to spot wrong merges, or aliases that should be split off.
| Raw name | Type | Papers | Mentions |
|---|---|---|---|
| indel | variant | 105 | 259 |
| indels | variant | 70 | 118 |
| insertion-deletion | variant | 5 | 5 |
| insertion/deletion polymorphisms | variant | 1 | 1 |
| insertion-deletion variant | variant | — | — |
| small insertions or deletions | variant | — | — |