Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.
paper
Cited
Public
Unavailable
- Authors
- Saunders, Christopher T; Wong, Wendy S W; Swamy, Sajani; Becq, Jennifer; Murray, Lisa J; Cheetham, R Keira
- Year
- 2012
- Journal
- Bioinformatics (Oxford, England)
- PMID
- 22581179
- DOI
- 10.1093/bioinformatics/bts271
MOTIVATION: Whole genome and exome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized to model this problem so as to sensitively call variants at any practical level of tumor impurity. RESULTS: We describe Strelka, a method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples. The method uses a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. We demonstrate that the method has superior accuracy and sensitivity on impure samples compared with approaches based on either diploid genotype likelihoods or general allele-frequency tests. AVAILABILITY: The Strelka workflow source code is available at ftp://strelka@ftp.illumina.com/. CONTACT: csaunders@illumina.com
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| DNA Mismatch Repair Gene Variant Classification: Evaluating the Utility of Somatic Mutations and Mismatch Repair Deficient Colonic Crypts and Endometrial Glands. | Walker R et al. | β | 2023 | β |
| Evaluating Multiple Next-Generation Sequencing-Derived Tumor Features to Accurately Predict DNA Mismatch Repair Status. | Walker R et al. | β | 2023 | β |
| GeNeo: A Bioinformatics Toolbox for Genomics-Guided Neoepitope Prediction. | Al Seesi S et al. | β | 2023 | β |
| Genetic characterization of primary and metastatic high-grade serous ovarian cancer tumors reveals distinct features associated with survival. | Kotnik EN et al. | β | 2023 | β |
| Genetic trajectory and clonal evolution of multiple primary lung cancer with lymph node metastasis. | Tian H et al. | β | 2023 | β |
| Genetic Variants Associated with Bronchial Asthma Specific to the Population of the Russian Federation. | Akhmerova YN et al. | β | 2023 | β |
| Genomics of <i>ERBB2</i>-Positive Breast Cancer in Young Women Before and After Exposure to Chemotherapy Plus Trastuzumab. | Lipsyc-Sharf M et al. | β | 2023 | β |
| Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer. | Kamran SC et al. | β | 2023 | β |
| Genomic variant benchmark: if you cannot measure it, you cannot improve it. | Majidian S et al. | β | 2023 | β |
| Homologous recombination deficiency signatures in gastrointestinal and thoracic cancers correlate with platinum therapy duration. | Tsang ES et al. | β | 2023 | β |
| Human 8-cell embryos enable efficient induction of disease-preventive mutations without off-target effect by cytosine base editor. | Wei Y et al. | β | 2023 | β |
| Identifying primary and secondary MLH1 epimutation carriers displaying low-level constitutional MLH1 methylation using droplet digital PCR and genome-wide DNA methylation profiling of colorectal cancers. | Joo JE et al. | β | 2023 | β |
| Immune Activation following Irbesartan Treatment in a Colorectal Cancer Patient: A Case Study. | Titmuss E et al. | β | 2023 | β |
| In situ tumour arrays reveal early environmental control of cancer immunity. | Ortiz-MuΓ±oz G et al. | β | 2023 | β |
| Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer. | Cotto KC et al. | β | 2023 | β |
| Integrated molecular characterization of esophageal basaloid squamous cell carcinoma: a subtype with distinct RNA expression pattern and immune characteristics, but no specific genetic mutations. | Li Y et al. | β | 2023 | β |
| Integrated multi-omics approach to distinct molecular characterization and classification of early-onset colorectal cancer. | Du M et al. | β | 2023 | β |
| Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin. | Liang WW et al. | β | 2023 | β |
| Integrative proteogenomic characterization of early esophageal cancer. | Li L et al. | β | 2023 | β |
| Integrative Single-Cell Analysis Reveals Transcriptional and Epigenetic Regulatory Features of Clear Cell Renal Cell Carcinoma. | Yu Z et al. | β | 2023 | β |
| Molecular characterisation of pancreatic ductal adenocarcinoma with <i>NTRK</i> fusions and review of the literature. | Allen MJ et al. | β | 2023 | β |
| Molecular characterization of genomic breakpoints of ALK rearrangements in non-small cell lung cancer. | Wang Z et al. | β | 2023 | β |
| Molecular Characterization of Multifocal Granular Cell Tumors. | Dehner CA et al. | β | 2023 | β |
| Molecular characterization of sub-frontal recurrent medulloblastomas reveals potential clinical relevance. | Chen Z et al. | β | 2023 | β |
| Monitoring Sarcoma Response to Immune Checkpoint Inhibition and Local Cryotherapy with Circulating Tumor DNA Analysis. | Bui NQ et al. | β | 2023 | β |
| Multimodal molecular landscape of response to Y90-resin microsphere radioembolization followed by nivolumab for advanced hepatocellular carcinoma. | Kaya NA et al. | β | 2023 | β |
| Multiplatform molecular profiling uncovers two subgroups of malignant peripheral nerve sheath tumors with distinct therapeutic vulnerabilities. | Suppiah S et al. | β | 2023 | β |
| Mutational Landscape of Bladder Cancer in Mexican Patients: <i>KMT2D</i> Mutations and chr11q15.5 Amplifications Are Associated with Muscle Invasion. | PΓ©rez-Montiel MD et al. | β | 2023 | β |
| Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma. | Abbas S et al. | β | 2023 | β |
| Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma. | Patel R et al. | β | 2023 | β |
| Neoantigen-specific CD4<sup>+</sup> tumor-infiltrating lymphocytes are potent effectors identified within adoptive cell therapy products for metastatic melanoma patients. | Hall MS et al. | β | 2023 | β |
| Neoantigens: promising targets for cancer therapy. | Xie N et al. | β | 2023 | β |
| Non-viral precision Tβcell receptor replacement for personalized cell therapy. | Foy SP et al. | β | 2023 | β |
| NOTCH4<sup>ΞL12_16</sup> sensitizes lung adenocarcinomas to EGFR-TKIs through transcriptional down-regulation of HES1. | Zhang B et al. | β | 2023 | β |
| Novel insights into molecular patterns of ROS1 fusions in a large Chinese NSCLC cohort: a multicenter study. | Zhou S et al. | β | 2023 | β |
| NR4A3 Expression Is Consistently Absent in Acinic Cell Carcinomas of the Breast: A Potential Nosologic Shift. | Richardson ET et al. | β | 2023 | β |
| Persistent mutation burden drives sustained anti-tumor immune responses. | Niknafs N et al. | β | 2023 | β |
| Predictive modelling of response to neoadjuvant therapy in HER2+ breast cancer. | Cosgrove N et al. | β | 2023 | β |
| Prior anti-CTLA-4 therapy impacts molecular characteristics associated with anti-PD-1 response in advanced melanoma. | Campbell KM et al. | β | 2023 | β |
| Prioritizing candidate peptides for cancer vaccines through predicting peptide presentation by HLA-I proteins. | Zhou LY et al. | β | 2023 | β |
| Proteogenomic insights suggest druggable pathways in endometrial carcinoma. | Dou Y et al. | β | 2023 | β |
| Quantification of rare somatic single nucleotide variants by droplet digital PCR using SuperSelective primers. | Pablo-Fontecha V et al. | β | 2023 | β |
| Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics. | Jun SH et al. | β | 2023 | β |
| Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia. | Loukas I et al. | β | 2023 | β |
| Simple combination of multiple somatic variant callers to increase accuracy. | Trevarton AJ et al. | β | 2023 | β |
| Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma. | Yao L et al. | β | 2023 | β |
| Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia. | Nowicki-Osuch K et al. | β | 2023 | β |
| Small-scale mutations are infrequent as mechanisms of resistance in post-PARP inhibitor tumour samples in high grade serous ovarian cancer. | Burdett NL et al. | β | 2023 | β |
| Somatic mutational landscape of hereditary hematopoietic malignancies caused by germline variants in RUNX1, GATA2, and DDX41. | Homan CC et al. | β | 2023 | β |
| Spatial and clonality-resolved 3D cancer genome alterations reveal enhancer-hijacking as a potential prognostic marker for colorectal cancer. | Kim K et al. | β | 2023 | β |
| The genome-wide mutational consequences of DNA hypomethylation. | Besselink N et al. | β | 2023 | β |
| The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes. | Kazachenka A et al. | β | 2023 | β |
| Transcriptomic classes of BCR-ABL1 lymphoblastic leukemia. | Kim JC et al. | β | 2023 | β |
| TSC2 inactivation, low mutation burden and high macrophage infiltration characterise hepatic angiomyolipomas. | Giannikou K et al. | β | 2023 | β |
| Validation of genetic variants from NGS data using deep convolutional neural networks. | Vaisband M et al. | β | 2023 | β |
| WEE1 inhibitor adavosertib in combination with carboplatin in advanced TP53 mutated ovarian cancer: A biomarker-enriched phase II study. | Embaby A et al. | β | 2023 | β |
| Whole exome analysis reveals the genomic profiling related to chemo-resistance in Chinese population with limited-disease small cell lung cancer. | Yu J et al. | β | 2023 | β |
| Whole-genome sequencing of 20 cholangiocarcinoma cases reveals unique profiles in patients with cirrhosis and primary sclerosing cholangitis. | Holzapfel N et al. | β | 2023 | β |
| Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues. | Abelin JG et al. | β | 2023 | β |
| Accurate determination of CRISPR-mediated gene fitness in transplantable tumours. | Eirew P et al. | β | 2022 | β |
| All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons. | Sarangi V et al. | β | 2022 | β |
| A multicenter clinical study: personalized medication for advanced gastrointestinal carcinomas with the guidance of patient-derived tumor xenograft (PDTX). | Cheng Y et al. | β | 2022 | β |
| An acquired phosphatidylinositol 4-phosphate transport initiates T-cell deterioration and leukemogenesis. | Zhong W et al. | β | 2022 | β |
| Analysis of genetic profiling, pathomics signature, and prognostic features of primary lymphoepithelioma-like carcinoma of the renal pelvis. | Fan B et al. | β | 2022 | β |
| A patient-driven clinicogenomic partnership for metastatic prostate cancer. | Crowdis J et al. | β | 2022 | β |
| A platform for oncogenomic reporting and interpretation. | Reisle C et al. | β | 2022 | β |
| A recurrent somatic missense mutation in GNAS gene identified in familial thyroid follicular cell carcinomas in German longhaired pointer dogs. | Yu Y et al. | β | 2022 | β |
| Association between germline variants and somatic mutations in colorectal cancer. | Barfield R et al. | β | 2022 | β |
| Basal cell carcinomas acquire secondary mutations to overcome dormancy and progress from microscopic to macroscopic disease. | Trieu KG et al. | β | 2022 | β |
| Bias and inconsistency in the estimation of tumour mutation burden. | Makrooni MA et al. | β | 2022 | β |
| cfTrack: A Method of Exome-Wide Mutation Analysis of Cell-free DNA to Simultaneously Monitor the Full Spectrum of Cancer Treatment Outcomes Including MRD, Recurrence, and Evolution. | Li S et al. | β | 2022 | β |
| Characteristics of TP53 germline variants and their correlations with Li-Fraumeni syndrome or Li-Fraumeni-like syndrome in Chinese tumor patients. | Tian P et al. | β | 2022 | β |
| Characterization of disease-propagating stem cells responsible for myeloproliferative neoplasm-blast phase. | Wang X et al. | β | 2022 | β |
| Characterization of the Genomic and Immunologic Diversity of Malignant Brain Tumors through Multisector Analysis. | Schaettler MO et al. | β | 2022 | β |
| Clinical, Pathologic, and Molecular Prognostic Factors in Patients with Early-Stage EGFR-Mutant NSCLC. | Jung HA et al. | β | 2022 | β |
| Clinicopathological and genetic study of a rare occurrence: Malignant transformation of fibrous dysplasia of the jaws. | Shi R et al. | β | 2022 | β |
| Clinicopathologic and molecular analysis of a <i>BCOR-CCNB3</i> undifferentiated sarcoma of the kidney reveals significant epigenetic alterations. | Hagoel TJ et al. | β | 2022 | β |
| Clonal evolution in primary breast cancers under sequential epirubicin and docetaxel monotherapy. | Venizelos A et al. | β | 2022 | β |
| Collision of germline POLE and PMS2 variants in a young patient treated with immune checkpoint inhibitors. | Berrino E et al. | β | 2022 | β |
| Combinatorial and Machine Learning Approaches for Improved Somatic Variant Calling From Formalin-Fixed Paraffin-Embedded Genome Sequence Data. | Dodani DD et al. | β | 2022 | β |
| Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma. | Freeman SS et al. | β | 2022 | β |
| Common anti-cancer therapies induce somatic mutations in stem cells of healthy tissue. | Kuijk E et al. | β | 2022 | β |
| Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients. | Zhu B et al. | β | 2022 | β |
| Comprehensive characterization of pre- and post-treatment samples of breast cancer reveal potential mechanisms of chemotherapy resistance. | Hoogstraat M et al. | β | 2022 | β |
| Comprehensive Genomic Profiling of Cell-Free Circulating Tumor DNA Detects Response to Ribociclib Plus Letrozole in a Patient with Metastatic Breast Cancer. | Silveira C et al. | β | 2022 | β |
| CT Radiomics and Whole Genome Sequencing in Patients with Pancreatic Ductal Adenocarcinoma: Predictive Radiogenomics Modeling. | Hinzpeter R et al. | β | 2022 | β |
| De Novo myelodysplastic syndromes in patients 20-50 years old are enriched for adverse risk features. | Epstein-Peterson ZD et al. | β | 2022 | β |
| Design of Personalized Neoantigen RNA Vaccines Against Cancer Based on Next-Generation Sequencing Data. | Alburquerque-GonzΓ‘lez B et al. | β | 2022 | β |
| Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers. | Symer DE et al. | β | 2022 | β |
| DNA Methylation Profiling Identifies Subgroups of Lung Adenocarcinoma with Distinct Immune Cell Composition, DNA Methylation Age, and Clinical Outcome. | Guidry K et al. | β | 2022 | β |
| Effects of Two Distinct Psychoactive Microbes, <i>Lacticaseibacillus rhamnosus</i> JB-1 and <i>Limosilactobacillus reuteri</i> 6475, on Circulating and Hippocampal mRNA in Male Mice. | Haas-Neill S et al. | β | 2022 | β |
| Efficacy of the Ketogenic Diet for Pediatric Epilepsy According to the Presence of Detectable Somatic mTOR Pathway Mutations in the Brain. | Ko A et al. | β | 2022 | β |
| Elucidating minimal residual disease of paediatric B-cell acute lymphoblastic leukaemia by single-cell analysis. | Zhang Y et al. | β | 2022 | β |
| Epigenetic priming in chronic liver disease impacts the transcriptional and genetic landscapes of hepatocellular carcinoma. | Gallon J et al. | β | 2022 | β |
| ESR1 hotspot mutations in endometrial stromal sarcoma with high-grade transformation and endocrine treatment. | Dessources K et al. | β | 2022 | β |
| Exceptional response to combination ipilimumab and nivolumab in metastatic uveal melanoma: Insights from genomic analysis. | Yu IS et al. | β | 2022 | β |
| Exome sequencing reveals a distinct somatic genomic landscape in breast cancer from women with germline PTEN variants. | Brewer T et al. | β | 2022 | β |
| Expanding cross-presenting dendritic cells enhances oncolytic virotherapy and is critical for long-term anti-tumor immunity. | Svensson-Arvelund J et al. | β | 2022 | β |
| FGFR1 is a potential therapeutic target in neuroblastoma. | Cimmino F et al. | β | 2022 | β |
| Gemcitabine combined with apatinib and toripalimab in recurrent or metastatic nasopharyngeal carcinoma. | You R et al. | β | 2022 | β |
| Genetic Alterations in Papillary Thyroid Carcinoma With Hashimoto<sup>'</sup>s ThyroiditisοΌ <i>ANK3</i>, an Indolent Maintainer of Papillary Thyroid Carcinoma. | Zeng C et al. | β | 2022 | β |
| Genetic Analyses of Cell-Free DNA in Pancreatic Juice or Bile for Diagnosing Pancreatic Duct and Biliary Tract Strictures. | Nagai K et al. | β | 2022 | β |
| Genetic mutation and tumor microbiota determine heterogenicity of tumor immune signature: Evidence from gastric and colorectal synchronous cancers. | Yang W et al. | β | 2022 | β |
| Genetic subtypes of smoldering multiple myeloma are associated with distinct pathogenic phenotypes and clinical outcomes. | Bustoros M et al. | β | 2022 | β |
| Genomic analysis of focal nodular hyperplasia with associated hepatocellular carcinoma unveils its malignant potential: a case report. | Ercan C et al. | β | 2022 | β |
| Genomic and epigenomic <i>BRCA</i> alterations predict adaptive resistance and response to platinum-based therapy in patients with triple-negative breast and ovarian carcinomas. | Menghi F et al. | β | 2022 | β |
| Genomic and microbial factors affect the prognosis of anti-pd-1 immunotherapy in nasopharyngeal carcinoma. | Xu L et al. | β | 2022 | β |
| Genomic characterization of small cell carcinomas of the uterine cervix. | Schultheis AM et al. | β | 2022 | β |
| Genomic Correlates of Outcome in Tumor-Infiltrating Lymphocyte Therapy for Metastatic Melanoma. | Creasy CA et al. | β | 2022 | β |
| Genomic Features of Muscle-invasive Bladder Cancer Arising After Prostate Radiotherapy. | Mossanen M et al. | β | 2022 | β |
| Genomic landscapes of canine splenic angiosarcoma (hemangiosarcoma) contain extensive heterogeneity within and between patients. | Wong S et al. | β | 2022 | β |
| Genomic predictors of response to PD-1 inhibition in children with germline DNA replication repair deficiency. | Das A et al. | β | 2022 | β |
| Germline and sporadic mTOR pathway mutations in low-grade oncocytic tumor of the kidney. | Kapur P et al. | β | 2022 | β |
| Grouped-seq for integrated phenotypic and transcriptomic screening of patient-derived tumor organoids. | Wu Y et al. | β | 2022 | β |
| HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade. | Shao XM et al. | β | 2022 | β |
| Identification of missing persons through kinship analysis by microhaplotype sequencing of single-source DNA and two-person DNA mixtures. | Bai Z et al. | β | 2022 | β |
| Identification of neoantigens for individualized therapeutic cancer vaccines. | Lang F et al. | β | 2022 | β |
| Identification of RET fusions in a Chinese multicancer retrospective analysis by next-generation sequencing. | Shi M et al. | β | 2022 | β |
| Immune biomarkers of response to immunotherapy in patients with high-risk smoldering myeloma. | Sklavenitis-Pistofidis R et al. | β | 2022 | β |
| Implementation of a prostate cancer-specific targeted sequencing panel for credentialing of patient-derived cell lines and genomic characterization of patient samples. | Stover EH et al. | β | 2022 | β |
| Increased Tumor Intrinsic Growth Potential and Decreased Immune Function Orchestrate the Progression of Lung Adenocarcinoma. | Zhao Y et al. | β | 2022 | β |
| Integrated DNA and RNA Sequencing Reveals Drivers of Endocrine Resistance in Estrogen Receptor-Positive Breast Cancer. | Xia Y et al. | β | 2022 | β |
| Integrated genomic analyses identify high-risk factors and actionable targets in T-cell acute lymphoblastic leukemia. | Zhu H et al. | β | 2022 | β |
| Integrated proteogenomic characterization of urothelial carcinoma of the bladder. | Xu N et al. | β | 2022 | β |
| Integrated proteomic analysis of low-grade gliomas reveals contributions of 1p-19q co-deletion to oligodendroglioma. | Wong D et al. | β | 2022 | β |
| Integrating whole genome sequencing, methylation, gene expression, topological associated domain information in regulatory mutation prediction: A study of follicular lymphoma. | Farooq A et al. | β | 2022 | β |
| Integrative analysis reveals a clinicogenomic landscape associated with liver metastasis and poor prognosis in hepatoid adenocarcinoma of the stomach. | Jiang J et al. | β | 2022 | β |
| Integrative genomic analysis reveals low T-cell infiltration as the primary feature of tobacco use in HPV-positive oropharyngeal cancer. | Wahle BM et al. | β | 2022 | β |
| Integrative Genomic Profiling Uncovers Therapeutic Targets of Acral Melanoma in Asian Populations. | Shi Q et al. | β | 2022 | β |
| Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages. | Ng CKY et al. | β | 2022 | β |
| Interrogating breast cancer heterogeneity using single and pooled circulating tumor cell analysis. | RothΓ© F et al. | β | 2022 | β |
| Intratumor genetic heterogeneity and clonal evolution to decode endometrial cancer progression. | Mota A et al. | β | 2022 | β |
| InΒ vitro germ cell induction from fertile and infertile monozygotic twin research participants. | Pandolfi EC et al. | β | 2022 | β |
| KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas. | Rudd ML et al. | β | 2022 | β |
| Leveraging big data of immune checkpoint blockade response identifies novel potential targets. | Bareche Y et al. | β | 2022 | β |
| Mapping molecular subtype specific alterations in breast cancer brain metastases identifies clinically relevant vulnerabilities. | Cosgrove N et al. | β | 2022 | β |
| Molecular and clinical characteristics of IDH mutations in Chinese NSCLC patients and potential treatment strategies. | Chen S et al. | β | 2022 | β |
| Molecular characterization of biphenotypic epithelioid and plexiform melanoma with deep penetrating nevus-like features. | Giubellino A et al. | β | 2022 | β |
| Molecular Subclasses of Clear Cell Ovarian Carcinoma and Their Impact on Disease Behavior and Outcomes. | Bolton KL et al. | β | 2022 | β |
| Molecular Typing and Clinical Characteristics of Synchronous Multiple Primary Colorectal Cancer. | Zhao Y et al. | β | 2022 | β |
| Monoallelic <i>Heb/Tcf12</i> Deletion Reduces the Requirement for NOTCH1 Hyperactivation in T-Cell Acute Lymphoblastic Leukemia. | Veiga DFT et al. | β | 2022 | β |
| Morphologic and Genomic Characteristics of Breast Cancers Occurring in Individuals with Lynch Syndrome. | Schwartz CJ et al. | β | 2022 | β |
| Multi-omic cross-sectional cohort study of pre-malignant Barrett's esophagus reveals early structural variation and retrotransposon activity. | Katz-Summercorn AC et al. | β | 2022 | β |
| Multiregional single-cell proteogenomic analysis of ccRCC reveals cytokine drivers of intratumor spatial heterogeneity. | Miheecheva N et al. | β | 2022 | β |
| MuSE: A Novel Approach to Mutation Calling with Sample-Specific Error Modeling. | Ji S et al. | β | 2022 | β |
| Mutational landscape of non-functional adrenocortical adenomas. | Wu L et al. | β | 2022 | β |
| Neoantigen-specific CD4<sup>+</sup> TΒ cells in human melanoma have diverse differentiation states and correlate with CD8<sup>+</sup> TΒ cell, macrophage, and B cell function. | Veatch JR et al. | β | 2022 | β |
| NeoScore Integrates Characteristics of the Neoantigen:MHC Class I Interaction and Expression to Accurately Prioritize Immunogenic Neoantigens. | Borden ES et al. | β | 2022 | β |
| Next-generation sequencing of homologous recombination genes could predict efficacy of platinum-based chemotherapy in non-small cell lung cancer. | Zhang L et al. | β | 2022 | β |
| Origins and Timing of Emerging Lesions in Advanced Renal Cell Carcinoma. | Wallace A et al. | β | 2022 | β |
| Ovarian cancer mutational processes drive site-specific immune evasion. | VΓ‘zquez-GarcΓa I et al. | β | 2022 | β |
| Parental mosaicism for apparent de novo genetic variants: Scope, detection, and counseling challenges. | Zemet R et al. | β | 2022 | β |
| Patient-derived tumor organoids for personalized medicine in a patient with rare hepatocellular carcinoma with neuroendocrine differentiation: a case report. | Meier MA et al. | β | 2022 | β |
| PBRM1 presents a potential prognostic marker and therapeutic target in duodenal papillary carcinoma. | He X et al. | β | 2022 | β |
| Personalized ctDNA micro-panels can monitor and predict clinical outcomes for patients with triple-negative breast cancer. | Barnell EK et al. | β | 2022 | β |
| Personalized neoantigen vaccine NEO-PV-01 with chemotherapy and anti-PD-1 as first-line treatment for non-squamous non-small cell lung cancer. | Awad MM et al. | β | 2022 | β |
| Postzygotic mutations and where to find them - Recent advances and future implications in the field of non-neoplastic somatic mosaicism. | Wasilewska K et al. | β | 2022 | β |
| Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma. | Tong Y et al. | β | 2022 | β |
| Racial and ethnic differences in clonal hematopoiesis, tumor markers, and outcomes of patients with multiple myeloma. | Peres LC et al. | β | 2022 | β |
| Recapitulating whole genome based population genetic structure for Indian wild tigers through an ancestry informative marker panel. | Khan A et al. | β | 2022 | β |
| Recent Major Transcriptomics and Epitranscriptomics Contributions toward Personalized and Precision Medicine. | Mubarak G et al. | β | 2022 | β |
| Recurrent noncoding somatic and germline WT1 variants converge to disrupt MYB binding in acute promyelocytic leukemia. | Song H et al. | β | 2022 | β |
| Single-cell genomic variation induced by mutational processes in cancer. | Funnell T et al. | β | 2022 | β |
| Somatic and Germline Genomic Alterations in Very Young Women with Breast Cancer. | Waks AG et al. | β | 2022 | β |
| Somatic and Germline Variant Calling from Next-Generation Sequencing Data. | Chang TC et al. | β | 2022 | β |
| Somatic Mutational Landscape in Mexican Patients: <i>CDH1</i> Mutations and chr20q13.33 Amplifications Are Associated with Diffuse-Type Gastric Adenocarcinoma. | Cerrato-Izaguirre D et al. | β | 2022 | β |
| Somatic whole genome dynamics of precancer in Barrett's esophagus reveals features associated with disease progression. | Paulson TG et al. | β | 2022 | β |
| Spatial profiling reveals association between WNT pathway activation and T-cell exclusion in acquired resistance of synovial sarcoma to NY-ESO-1 transgenic T-cell therapy. | Campbell KM et al. | β | 2022 | β |
| Statins mediate anti- and pro-tumourigenic functions by remodelling the tumour microenvironment. | Kamata T et al. | β | 2022 | β |
| The Clinical Features and Molecular Mechanism of Pituitary Adenoma Associated With Vestibular Schwannoma. | Zhu H et al. | β | 2022 | β |
| The Clinically Actionable Molecular Profile of Early versus Late-Stage Non-Small Cell Lung Cancer, an Individual Age and Sex Propensity-Matched Pair Analysis. | McGuire AL et al. | β | 2022 | β |
| The first successful treatment and genetic sequencing of primary hepatic adenosarcoma with sarcomatous overgrowth: a case report. | Hu H et al. | β | 2022 | β |
| The genomic landscape of canine diffuse large B-cell lymphoma identifies distinct subtypes with clinical and therapeutic implications. | Giannuzzi D et al. | β | 2022 | β |
| The Genomic Landscape of Early-Stage Ovarian High-Grade Serous Carcinoma. | Cheng Z et al. | β | 2022 | β |
| The Impact of Inflammation-Induced Tumor Plasticity during Myeloid Transformation. | Yeaton A et al. | β | 2022 | β |
| The impact of rare germline variants on human somatic mutation processes. | Vali-Pour M et al. | β | 2022 | β |
| The impact of whole genome and transcriptome analysis (WGTA) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies. | Tessier-Cloutier B et al. | β | 2022 | β |
| The NHS England 100,000 Genomes Project: feasibility and utility of centralised genome sequencing for children with cancer. | Trotman J et al. | β | 2022 | β |
| The spatio-temporal evolution of multiple myeloma from baseline to relapse-refractory states. | Rasche L et al. | β | 2022 | β |
| Tissue-resident memory and circulating T cells are early responders to pre-surgical cancer immunotherapy. | Luoma AM et al. | β | 2022 | β |
| Transcriptomic profiles of neoantigen-reactive T cells in human gastrointestinal cancers. | Zheng C et al. | β | 2022 | β |
| Vaccination with Designed Neopeptides Induces Intratumoral, Cross-reactive CD4+ T-cell Responses in Glioblastoma. | Wang J et al. | β | 2022 | β |
| Whole exome sequencing of high-risk neuroblastoma identifies novel non-synonymous variants. | PrzybyΕa W et al. | β | 2022 | β |
| Whole exome sequencing reveals novel risk genes of pituitary neuroendocrine tumors. | Peculis R et al. | β | 2022 | β |
| Whole-genome and transcriptome analysis of advanced adrenocortical cancer highlights multiple alterations affecting epigenome and DNA repair pathways. | Lavoie JM et al. | β | 2022 | β |
| Whole-genome sequencing reveals the evolutionary trajectory of HBV-related hepatocellular carcinoma early recurrence. | Zhou SL et al. | β | 2022 | β |
| Whole genome sequencing reveals the independent clonal origin of multifocal ileal neuroendocrine tumors. | MΓ€kinen N et al. | β | 2022 | β |
| A clinically applicable integrative molecular classification of meningiomas. | Nassiri F et al. | β | 2021 | β |
| Activation of unfolded protein response overcomes Ibrutinib resistance in diffuse large B-cell lymphoma. | Zhang XT et al. | β | 2021 | β |
| A first-generation pediatric cancer dependency map. | Dharia NV et al. | β | 2021 | β |
| An adaptive method of defining negative mutation status for multi-sample comparison using next-generation sequencing. | Hutson N et al. | β | 2021 | β |
| An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome. | Desai S et al. | β | 2021 | β |
| An Integrative DNA Sequencing and Methylation Panel to Assess Mismatch Repair Deficiency. | Oldfield LE et al. | β | 2021 | β |
| A novel genomic classification system of gastric cancer via integrating multidimensional genomic characteristics. | Wang H et al. | β | 2021 | β |
| A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells. | Cheng S et al. | β | 2021 | β |
| A showcase study on personalized in silico drug response prediction based on the genetic landscape of muscle invasive bladder cancer. | Krentel F et al. | β | 2021 | β |
| Associations among the mutational landscape, immune microenvironment, and prognosis in Chinese patients with hepatocellular carcinoma. | Hu ZQ et al. | β | 2021 | β |
| Canine tumor mutational burden is correlated with TP53 mutation across tumor types and breeds. | Alsaihati BA et al. | β | 2021 | β |
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| Unraveling the chaotic genomic landscape of primary and metastatic canine appendicular osteosarcoma with current sequencing technologies and bioinformatic approaches. | Chu S et al. | β | 2021 | β |
| Validation of an NGS Panel Designed for Detection of Actionable Mutations in Tumors Common in Latin America. | Salvo M et al. | β | 2021 | β |
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