DRAGEN Publications
The following list of selected publications summarizes the extensive applications of Illumina DRAGEN Secondary Analysis Software.
Expand each section to view publications by year.
Definitions
Genetic Disease – Publications using DRAGEN for germline variant analysis to study inherited and rare diseases using whole‑genome, whole‑exome, or targeted sequencing data.
Oncology – Publications applying DRAGEN to cancer genomics workflows, including somatic variant calling, tumor–normal analysis, and detection of low‑frequency variants.
Multiomics – Publications demonstrating the use of DRAGEN across multiple data types, such as DNA, RNA, epigenomic, or single‑cell sequencing, within integrated analysis workflows.
Population Health – Publications leveraging DRAGEN for large‑scale cohort and biobank studies, emphasizing scalability, joint calling, and population‑level variant analysis.
Plant and Animal – Publications using DRAGEN for genomic analysis of non‑human organisms, including agricultural, model organism, and comparative genomics research.
Infectious Disease – Publications applying DRAGEN to microbial or viral sequencing data for pathogen detection, variant analysis, and genomic surveillance.
Benchmarking – Publications evaluating the accuracy, performance, and scalability of DRAGEN through comparisons with other bioinformatics tools or pipelines.
2026
Clinical validation of a high-performance somatic exome sequencing assay: from target-enrichment strategy to variant calling
npj Genomic Medicine / link
Oncology, Clinical Diagnostics
2025
Evaluation of false positive and false negative errors in targeted next generation sequencing
Genome Biology / link
Oncology
Characterization of subclonal variants in HG002 Genome in a Bottle reference material as a resource for benchmarking variant callers
Cell Genomics / link
Benchmarking
Comprehensive investigation of gene mutations in canine large cell gastrointestinal lymphoma
Frontiers in Veterinary Science / link
Oncology
Comparisons of performances of structural variants detection algorithms in solitary or combination strategy
PLOS ONE / link
Population Genomics
Comparative genomics reveals phylogenetic intermixing of Stomoxys fly, manure, and bovine mastitis-associated bacteria in dairy settings
biorxiv / link
Population Genomics
Comparative analysis of the Mexico City Prospective Study and the UK Biobank identifies ancestry-specific effects on clonal hematopoiesis
nature genetics / link
Population Genomics
Clinical characteristics of the Ala21Val variant in the myelin proteolipid protein 1 (PLP1) gene associated with Pelizaeus-Merzbacher disease in a Brazilian male patient
Human Genome Variation / link
Genetic Disease
Classification of acute myeloid leukemia based on multi-omics and prognosis prediction value
Molecular Oncology / link
Oncology
CIROZ is dispensable in ancestral vertebrates but essential for left-right patterning in humans
The American Journal of Human Genetics / link
Genetic Disease
Case Report: Importance of high-throughput genetic investigations in the differential diagnosis of unexplained erythrocytosis
National Library of Medicine / link
Genetic Disease
Building a growing genomic repository for maternal and fetal health through the PING Consortium
Nature / link
Genetic Disease
Blood DNA virome associates with autoimmune diseases and COVID-19
nature genetics / link
Population Genomics
Bi-Allelic MARVELD2 Variant Identified with Exome Sequencing in a Consanguineous Multiplex Ghanaian Family Segregating Non-Syndromic Hearing Loss
MDPI / link
Genetic Disease
Beyond the BRCA1/2 genes in ovarian cancer: the clinical and prognostic role of germline pathogenic variants in the ATM gene
Research Square / link
Genetic Disease
Beneficial mutualistic fungus Suillus luteus provided excellent buffering insurance in Scots pine defense responses under pathogen challenge at transcriptome level
BMC Plant Biology / link
Genomic Factory
Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications
Bioinformatics Advances / link
Genomic Factory
Bacteriophage Treatment Induces Phenotype Switching and Alters Antibiotic Resistance of ESBL Escherichia coli
MDPI / link
Genomic Factory
BACH2 regulates T cell lineage states to overcome dysfunction driven by tonic CAR signaling
Research Square / link
Oncology
Assessment of candidate high-grade serous ovarian carcinoma predisposition genes through integrated germline and tumour sequencing
npj Genomic Medicine / link
Genetic Disease
Assessing the Impact of Cell Isolation Method on B cell Gene Expression using Next-Generation Sequencing
Experimental Hematology / link
Genomic Factory
Assessing the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases
Nature Communications / link
Genetic Disease
APOBEC3A drives ovarian cancer metastasis by altering epithelial-mesenchymal transition
JCI Insight / link
Oncology
Analysis of Population-Level Avirulence and Virulence Genetic Frequencies Provides Insight Into Resistance Gene Rotation and Plant Disease Epidemiology
Plant Pathology / link
Population Genomics
An orally available P1′-5-fluorinated Mpro inhibitor blocks SARS-CoV-2 replication without booster and exhibits high genetic barrier
PNAS Nexus / link
Genomic Factory
An Exploratory Genomic and Transcriptomic Analysis Between Choloepus didactylus and Homo sapiens
Genes / link
Genomic Factory
AMPed up immunity: 418 whole genomes reveal intraspecific diversity of koala antimicrobial peptides
Immunogenetics / link
Population Genomics
Adrenal mixed corticomedullary tumors: report of a case with molecular characterization and systematic review
Virchows Archiv / link
Oncology
Activated cardiac fibroblasts are a primary source of high-molecular-weight hyaluronan production
American Journal of Physiology-Cell Physiology / link
Genetic Disease
Acquired sperm hypomethylation by gestational arsenic exposure is re-established in both the paternal and maternal genomes of post-epigenetic reprogramming embryos
Epigenetics & Chromatin / link
Genetic Disease
A triad of somatic mutagenesis converges in self-reactive B cells to cause a virus-induced autoimmune disease
Immunity / link
Genetic Disease
A phase II trial of mTORC1/2 inhibition in STK11 deficient non small cell lung cancer
npj Precision Oncology / link
Oncology
A nationwide comprehensive genomic profiling and molecular tumor board platform for patients with advanced cancer
npj Precision Oncology / link
Oncology
A comparative template-switching cDNA approach for HTS-based multiplex detection of three viruses and one viroid commonly found in apple trees
Nature / link
Genomic Factory
Effect of DNA input on analytical and clinical parameters of a circulating tumor DNA assay for comprehensive genomic profiling
Journal of Laboratory Medicine / link
P260: Enhancing copy number variant analysis in exome sequencing with backbone probe optimization
-- / link
Identification of technically challenging variants: Whole-genome sequencing improves diagnostic yield in patients with high clinical suspicion of rare diseases
HGG Advances / link
Genetic Disease
Benchmarking of variant calling software for whole-exome sequencing using gold standard datasets
Nature / link
Evaluating Discordant Somatic Calls Across Mutation Discovery Approaches to Minimize False-Negative Drug-Resistant Findings
The Journals of Molecular Diagnostics / link
2024
Analysis of tumor mutational burden and mutational landscape comparing whole-exome sequencing and comprehensive genomic profiling in patients with resectable early-stage non-small-cell lung cancer
Therapeutic Advances in Medical Oncology / link
v3.10; TMB
Whole genome sequencing in paediatric channelopathy and cardiomyopathy
Frontiers in Cardiovascular Medicine / link
BSSH; Germline Pipeline; Joint genotyping; v3.9.5
Somatic CAG repeat instability in intermediate alleles of the HTT gene and its potential association with a clinical phenotype
European Journal of Human Genetics / link
ExpansionHunter; Germline Pipeline
High fusion and cytopathy of SARS-CoV-2 variant B.1.640.1
Journal of Virology / link
COVIDSeq Test pipeline; DRAGEN server
Interleukin‐4 induced 1 ‐mediated resistance to an immune checkpoint inhibitor through suppression of CD8 + T cell infiltration in melanoma
Cancer Science / link
BSSH; Differential Expression; RNA pipeline; v3.6.3
Oxytocin-induced birth causes sex-specific behavioral and brain connectivity changes in developing rat offspring
Iscience / link
v3.9.3
Prevalence and impact of sarcopenia in individuals with heart failure with reduced ejection fraction (the SARC-HF study): A prospective observational study protocol
Plos one / link
BSSH; Enrichment pipeline
PKHD1L1, a gene involved in the stereocilia coat, causes autosomal recessive nonsyndromic hearing loss
Human Genetics / link
CNV pipeline
LncRNAs expression profile in a family household cluster of COVID ‐19 patients
Journal of Cellular and Molecular Medicine / link
COVID Lineage App; v3.5.7; BSSH
A protective role for type I interferon signaling following infection with Mycobacterium tuberculosis carrying the rifampicin drug resistance-conferring RpoB mutation H445Y
PLoS pathogens / link
RNA seq; v3.9.3
Successful skipping of abnormal pseudoexon by antisense oligonucleotides in vitro for a patient with beta-propeller protein-associated neurodegeneration
Scientific reports / link
v3.5
A novel framework for human leukocyte antigen (HLA) genotyping using probe capture-based targeted next-generation sequencing and computational analysis
Computational and Structural Biotechnology Journal / link
v4.2.4
Genetics of psycho-emotional well-being: genome-wide association study and polygenic risk score analysis
Frontiers in Psychiatry / link
Claudin-10 Expression and the Gene Expression Pattern of Thick Ascending Limb Cells
International Journal of Molecular Sciences / link
v3.10.11
Insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme
Nature Medicine / link
alignment
Whole-genome sequencing of tetraploid potato varieties reveals different strategies for drought tolerance
Scientific Reports / link
DRAGEN-GATK
Prospective cohort study of genomic newborn screening: BabyScreen+ pilot study protocol
BMJ open / link
SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation?
Frontiers in Microbiology / link
COVID Lineage App; v3.5.4
Detection of SARS-CoV-2 in Wastewater Associated with Scientific Stations in Antarctica and Possible Risk for Wildlife
Microorganisms / link
COVID Lineage App
Generation of murine tumor models refractory to αPD-1/-L1 therapies due to defects in antigen processing/presentation or IFNγ signaling using CRISPR/Cas9
PLOS ONE / link
Somatic variant calling
Chronic stress alters hepatic metabolism and thermodynamic respiratory efficiency affecting epigenetics in C57BL/6 mice
iScience / link
Germline Pipeline; v3.9.5
Synchronous Epidermodysplasia Verruciformis and Intraepithelial Lesion of the Vulva Is Caused by Coinfection With Alpha-Human Papillomavirus and Beta-Human Papillomavirus Genotypes and Facilitated by Mutations in Cell-Mediated Immunity Genes
Archives of Pathology & Laboratory Medicine / link
Immune infiltration, aggressive pathology, and poor survival outcomes in RECQL helicase deficient breast cancers
Neoplasia / link
Somatic pipeline; v4.0.3
Extending DeepTrio for sensitive detection of complex de novo mutation patterns
NAR Genomics and Bioinformatics / link
v3.6
Spatial Mapping of Hematopoietic Clones in Human Bone Marrow
Blood Cancer Discovery / link
alignment; v3.10.4
The contributions of deleterious rare alleles in NLRP12 and inflammasome-related genes to polymyalgia rheumatica
Scientific Reports / link
Myxoid liposarcoma with nuclear pleomorphism: a clinicopathological and molecular study
Virchows Archiv / link
RNA app
Targeting cell-type-specific, choroid-peripheral immune signaling to treat age-related macular degeneration
Cell Reports Medicine / link
alignment; DRAGEN server; v3.9.3
Two novel non-coding single nucleotide variants in the DNase1 hypersensitivity site of PRDM13 causing North Carolina macular dystrophy in Korea
Molecular Vision / link
DRAGEN-GATK
A Mutational Hotspot in The LAMP2 Gene: Unravelling Intrafamilial Phenotypic Variation and Global Distribution of The c.877C>T Variant: A Descriptive Study
Cell Journal (Yakhteh) / link
iPSC-Derived Endothelial Cells Reveal LDLR Dysfunction and Dysregulated Gene Expression Profiles in Familial Hypercholesterolemia
International Journal of Molecular Sciences / link
v3.9.5
Divergent HLA variations and heterogeneous expression but recurrent HLA loss-of- heterozygosity and common HLA-B and TAP transcriptional silencing across advanced pediatric solid cancers
Frontiers in Immunology / link
v3.10; HLA
Secondary bone marrow graft loss after third-party virus-specific T cell infusion: Case report of a rare complication
Nature Communications / link
BSSH; Germline Pipeline; v3.4.5
Changes in DNA methylation associated with a specific mode of delivery: a pilot study
Frontiers in Medicine / link
Methylation pipeline
Directing the migration of serum-free, ex vivo-expanded Vγ9Vδ2 T cells
Frontiers in Immunology / link
AWS; v3.10.4a
Targeting TRIP13 in favorable histology Wilms tumor with nuclear export inhibitors synergizes with doxorubicin
Communications Biology / link
v3.5.7
Immune evasion, infectivity, and fusogenicity of SARS-CoV-2 BA.2.86 and FLip variants
Cell / link
COVID Lineage App
Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state
Nature Communications / link
DRAGEN server; v3.10
Mapping breast and prostate cancer in the Brazilian public health system: study protocol of the Onco-Genomas Brasil
Frontiers in Oncology / link
alignment; v3.10.4
Disease-associated AIOLOS variants lead to immune deficiency/dysregulation by haploinsufficiency and redefine AIOLOS functional domains
The Journal of Clinical Investigation / link
DNA pipeline
A de novo nonsense variant in the DMD gene associated with X-linked dystrophin-deficient muscular dystrophy in a cat
Journal of Veterinary Internal Medicine / link
v4.0.3; joint genotyper
Utility of polygenic scores across diverse diseases in a hospital cohort for predictive modeling
Nature Communications / link
Genome pipeline
SALL4 deletion and kidney and cardiac defects associated with VACTERL association
Pediatric Nephrology / link
v3.5
Functional variants in a TTTG microsatellite on 15q26.1 cause familial nonautoimmune thyroid abnormalities
Nature Genetics / link
v3.9.5
Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort
Genetics in Medicine / link
DNA identification of monozygotic twins
Forensic Science International: Genetics / link
Somatic pipeline v4.0.3
Sequencing technologies and hardware-accelerated parallel computing transform computational genomics research
Frontiers in Bioinformatics / link
review
Genome sequencing as a generic diagnostic strategy for rare disease
Genome Medicine / link
v3.5.7; ExpansionHunter; Germline pipeline; SMA caller; CYP21A2 caller
SARS-CoV-2 among liver transplant recipients: clinical course and mutational analysis
Journal of Clinical Virology Plus / link
COVID-19 associated pulmonary aspergillosis in critically-ill patients: a prospective multicenter study in the era of Delta and Omicron variants
Annals of Intensive Care / link
COVIDSeq Test pipeline; DRAGEN server
Phenotypic and transcriptional changes in lens epithelial cells following acute and fractionated ionizing radiation exposure
International Journal of Radiation Biology / link
Novel hemizygous single-nucleotide duplication in RPGR in a patient with retinal dystrophy and sensorineural hearing loss
Molecular Genetics & Genomic Medicine / link
CNV caller; Haplotype variant calling
Simultaneous detection and characterization of common respiratory pathogens in wastewater through genomic sequencing
Water Research / link
RNA pathogen detection pipeline
Germline mutations of homologous recombination genes and clinical outcomes in pancreatic cancer: a multicenter study in Taiwan
Journal of Biomedical Science / link
BSSH; Enrichment app
Inherited defects of piRNA biogenesis cause transposon de-repression, impaired spermatogenesis, and human male infertility
-- / link
v4.2
CpG methylation changes associated with hyperglycemia in type 1 diabetes occur at angiogenic glomerular and retinal gene loci
-- / link
Epigenome pipeline
Mpox Viral Lineage Analysis and Technique Development Using Next-generation Sequencing Approach
The Journal of Infectious Diseases / link
Large-scale DNA sequencing identifies rare variants associated with Systemic Lupus Erythematosus susceptibility in known risk genes
Gene / link
alignment; Variant calling
Characterisation of a LINE-1 Insertion in the RP1 Gene by Targeted Adaptive Nanopore Sequencing in a Family with Retinitis Pigmentosa
Human Mutation / link
v3.9
Rare De Novo and Inherited Genes in Familial and Nonfamilial Pediatric Attention-Deficit/Hyperactivity Disorder
JAMA pediatrics / link
Treatment and prognostic implications of strong PD-L1 expression in primary hepatic sarcomatoid carcinoma
Immunotherapy / link
Cellular and molecular alterations in a human hepatocellular in vitro model of nonalcoholic fatty liver disease development and stratification
Journal of Environmental Science and Health, Part C / link
Cost-effectiveness of genetic testing of endocrine tumor patients using a comprehensive hereditary cancer gene panel
The Journal of Clinical Endocrinology & Metabolism / link
v4.0.3; Germline pipeline
Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives
Cells / link
review
The Application of Knowledge Engineering via the Use of a Biomimetic Digital Twin Ecosystem, Phenotype-Driven Variant Analysis, and Exome Sequencing to Understand the Molecular Mechanisms of Disease
The Journal of Molecular Diagnostics / link
Germline
Photoperiod associated late flowering reaction norm: Dissecting loci and genomic-enviromic associated prediction in maize
Field Crops Research / link
Germline small variant caller
Characterization of carboxylated cellulose nanofibrils and oligosaccharides from Kraft pulp fibers and their potential elicitor effect on the gene expression of Capsicum annuum
International Journal of Biological Macromolecules / link
RNA pipeline; Differential expression pipeline
An Exome Capture-Based RNA-Sequencing Assay for Genome-Wide Identification and Prioritization of Clinically Important Fusions in Pediatric Tumors
The Journal of Molecular Diagnostics / link
v3.9.3
Analytical Performance Evaluation of a 523-Gene Circulating Tumor DNA Assay for Next-Generation Sequencing–Based Comprehensive Tumor Profiling in Liquid Biopsy Samples
The Journal of Molecular Diagnostics / link
TSO500 ctDNA v1.1; DRAGEN server v3
Whole genome sequencing followed by functional analysis of genomic deletion encompassing ERCC8 and NDUFAF2 genes in a non-consanguineous Indian family reveals dysfunctional mitochondrial bioenergetics leading to infant mortality
Mitochondrion / link
v3.3.1
DPF2-related Coffin-Siris syndrome type 7 in two generations
European Journal of Medical Genetics / link
v3.9
Beyond Single Diagnosis: Exploring Multidiagnostic Realities in Pediatric Patients through Genome Sequencing
Human Mutation / link
Variant calling; alignment
Whole-genome sequencing of Chromobacterium subtsugae strains exhibiting toxicity to Drosophila melanogaster
Microbiology Resource Announcements / link
v3.10.12
Gut microbiome composition: link between sports performance and protein absorption?
Journal of the International Society of Sports Nutrition / link
Metagenomics pipeline
Performance of amplicon and capture based next-generation sequencing approaches for the epidemiological surveillance of Omicron SARS-CoV-2 and other variants of concern
PLOS ONE / link
PRKD1-related telangiectasia-ectodermal dysplasia-brachydactyly-cardiac anomaly syndrome: Case report and review of the literature
European Journal of Medical Genetics / link
Good Manufacturing Practice–compliant human induced pluripotent stem cells: from bench to putative clinical products
Cytotherapy / link
PPP2R5D heterozygous pathogenic variant causes early-onset parkinsonism and treatment implications: A case report
Parkinsonism & Related Disorders / link
DRAGEN-GATK
Oncogenic cell tagging and single-cell transcriptomics reveal cell type-specific and time-resolved responses to Vhl inactivation in the kidney
Cancer Research / link
BCL convert
Strategies for diagnosis and management of CMMRD in low-resource countries: report of a Tunisian family
Familial Cancer / link
Enrichment tool
Sudden unexpected postnatal collapse and BUB1B mutation: first forensic case report
International Journal of Legal Medicine / link
Germline
Novel mutation of COG5 in a Taiwanese girl with congenital disorders of glycosylation manifesting as developmental delay
Molecular Genetics and Metabolism Reports / link
alignment
Intraarticular Nodular Fasciitis of the Elbow Confirmed by USP6-MYH9 Gene Fusion.
-- / link
fusion detection; RNA app
Phase I/II study of the WEE1 inhibitor adavosertib (AZD1775) in combination with carboplatin in children with advanced malignancies: Arm C of the AcSé-ESMART trial
Clinical Cancer Research / link
Identification of a novel GNAS mutation in a family with pseudohypoparathyroidism type 1A
BMC Pediatrics / link
Germline pipeline
Biallelic NDUFA4 Deletion Causes Mitochondrial Complex IV Deficiency in a Patient with Leigh Syndrome
Genes / link
DNA pipeline v3.9.3
Virus sequencing performance during the SARS-CoV-2 pandemic: a retrospective analysis of data from multiple rounds of external quality assessment in Austria
Frontiers in Molecular Biosciences / link
Introducing Exome Sequencing as Part of the Diagnostic Algorithm for Pediatric Nephrology Patients in Bulgaria: A Single-Center Experience
Nephron / link
Leveraging Off-Target Reads in Panel Sequencing for Homologous Recombination Repair Deficiency Screening in Tumor
The Journal of Molecular Diagnostics / link
v3.10.9
Development and validation of a pharmacogenomics reporting workflow based on the illumina global screening array chip
Frontiers in Pharmacology / link
v3.7.6
Management of SARS-CoV-2 and Persistent Viral Detection in Solid Organ Transplant Recipients
Current Pulmonology Reports / link
COVID Lineage App
Evolution of a Distinct SARS-CoV-2 Lineage Identified during an Investigation of a Hospital Outbreak
Viruses / link
COVID Lineage App; BSSH
Expanding the phenotypic spectrum of LHCGR signal peptide insertion variant: novel clinical and allelic findings causing Leydig cell hypoplasia type II
Hormones / link
BSSH; Germline pipeline
Colonic tubular adenoma with clear cell change–case report with whole exome sequencing and updated review of the literature
Pathobiology: Journal of Immunopathology, Molecular and Cellular Biology / link
Mapping Whole Exome Sequencing to In Vivo Imaging with Stereotactic Localization and Deep Learning
-- / link
The Scalable Variant Call Representation: Enabling Genetic Analysis Beyond One Million Genomes
-- / link
A deep intronic variant in MME causes autosomal recessive Charcot-Marie-Tooth neuropathy through aberrant splicing
-- / link
DRAGEN-GATK; GATK HaplotypeCaller
AutScore – An integrative scoring approach for prioritization of ultra-rare autism spectrum disorder candidate variants from whole exome sequencing data
-- / link
Clinical application of Complete Long Read genome sequencing identifies a 16kb intragenic duplication in EHMT1 in a patient with suspected Kleefstra syndrome
-- / link
BSSH; ICLR WGS pipeline app v2.0.6
Comprehensive analysis of the genetic variation in the LPA gene from short-read sequencing
-- / link
LPA caller
Functional Analysis of G6PD Variants Associated With Low G6PD Activity in the All of Us Research Program
-- / link
Genome-wide study of gene-by-sex interactions identifies risks for cleft palate
-- / link
Germline pipeline v3.7.5
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
-- / link
Pan-Cancer Interrogation of B7-H3 (CD276) as an Actionable Therapeutic Target across Human Malignancies
Cancer Research Communications / link
A 39 kb structural variant causing Lynch Syndrome detected by optical genome mapping and nanopore sequencing
European Journal of Human Genetics / link
SV caller
A framework for the evaluation and reporting of incidental findings in clinical genomic testing
European Journal of Human Genetics / link
Natural Killer Cell Infiltration in Prostate Cancers Predict Improved Patient Outcomes
Prostate Cancer and Prostatic Diseases / link
demultiplexing
Antimicrobial susceptibility and resistome of Actinobacillus pleuropneumoniae in Taiwan: a next-generation sequencing analysis
Veterinary Quarterly / link
Clinical exome sequencing by general pediatricians: high clinical utility and no evidence of inappropriate testing
Frontiers in Pediatrics / link
DRAGEN server v3
Integrated analysis of transcriptome and genome variations in pediatric T cell acute lymphoblastic leukemia: data from north Indian tertiary care center
BMC Cancer / link
Unveiling the impact of temperature shift on microbial community dynamics and metabolic pathways in anaerobic digestion
Process Safety and Environmental Protection / link
Metagenomics pipeline
Two Cases of Sporadic Amyotrophic Lateral Sclerosis With Contrasting Clinical Phenotypes: Genetic Insights
Cureus / link
Variant calling
Molecular profiling and the impact of treatment on outcomes in adenoid cystic carcinoma (ACC) type-I and II
Clinical Cancer Research / link
COVID-19 in hematopoietic stem cell transplant recipients during three years of the pandemic: a multicenter study in Brazil
Revista do Instituto de Medicina Tropical de São Paulo / link
v3.5.13
Repair of leukemia-associated single nucleotide variants via interallelic gene conversion
-- / link
Somatic pipeline
Expanding the Phenotype of the CACNA1C-Associated Neurological Disorders in Children: Systematic Literature Review and Description of a Novel Mutation
Children / link
Symptomatology and IgG Levels Before and After SARS-CoV-2 Omicron Breakthrough Infections in Vaccinated Individuals
-- / link
CCR5 and CCL5 gene expression in colorectal cancer: comprehensive profiling and clinical value
Journal for Immunotherapy of Cancer / link
Nuclear Factor κB Signaling Deficiency in CD11c-Expressing Phagocytes Mediates Early Inflammatory Responses and Enhances Mycobacterium tuberculosis Control
The Journal of Infectious Diseases / link
ELMO2 biallelic pathogenic variants in a patient with gingival hypertrophy and cherubism phenotype: Case report and molecular review
American Journal of Medical Genetics Part A / link
High Comorbidity of Pediatric Cancers in Patients with Birth Defects: Insights from Whole Genome Sequencing Analysis of Copy Number Variations
Translational Research / link
Another case of nuclear speckleopathy due to a novel NKAP pathogenic variant
Clinical Dysmorphology / link
Multiomics Analysis of PCB126’s Effect on a Mouse Chronic-Binge Alcohol Feeding Model
Environmental Health Perspectives / link
v1.2.1
Genetic Analysis of a Mosaic Fra(16)(q22)/Del(16)(q22) Karyotype in a Primary Infertile Woman
International Journal of Women's Health / link
Unveiling New Insights: Reinterpreting DES Mutation, p.Arg383His, through a Study of an Iranian Family with Isolated Hypertrophic Cardiomyopathy, Implication for Phenotype‒Genotype Correlation Analysis
-- / link
Evidence from 2100 index cases supports genome sequencing as a first-tier genetic test
Genetics in Medicine / link
Natural Killer Cells Do Not Attenuate a Mouse-Adapted SARS-CoV-2-Induced Disease in Rag2−/− Mice
Viruses / link
BSSH
Predominance of the recombinant SARS-CoV-2 lineages XBB in Rio Grande do Sul State, Brazil: a genomic surveillance study and impact on vaccine response
-- / link
Exome Sequencing Reveals Biallelic Mutations in MBTPS1 Gene in a Girl with a Very Rare Skeletal Dysplasia
Diagnostics / link
The clinical value of optical genome mapping in the rapid characterization of RB1 duplication and 15q23q24.2 triplication, for more appropriate prenatal genetic counselling
Molecular Genetics & Genomic Medicine / link
BCL convert
Spectrum of PHEX Mutations and FGF23 Profiles in a Taiwanese Cohort With X-Linked Hypophosphatemia Including 102 Patients
In Vivo / link
v3.7.5
Case report: Novel genotype of ALG2-CDG and confirmation of the heptasaccharide glycan (NeuAc-Gal-GlcNAc-Man2-GlcNAc2) as a specific diagnostic biomarker
Frontiers in Genetics / link
CNV pipeline
Establishing mesothelioma patient-derived organoid models from malignant pleural effusions
Lung Cancer / link
TSO 500 v2.1.0
A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population
Frontiers in Immunology / link
COVIDSeq Test pipeline; BSSH
Whole genome sequencing of a family with autosomal dominant features within the oculoauriculovertebral spectrum
-- / link
Systematic molecular analyses for 115 karyotypically normal men with isolated non-obstructive azoospermia
Human Reproduction / link
Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses
-- / link
Metagenomics pipeline
Molecular basis of DEL phenotype in the Indian population: Insights from next-generation sequencing analysis of two cases
Transfusion and Apheresis Science / link
v3.4
Acquired NF2 mutation confers resistance to TRK inhibition in an ex vivo LMNA::NTRK1-rearranged soft-tissue sarcoma cell model
The Journal of Pathology / link
alignment; RNA pipeline
The complement regulator CD55 modulates TLR9 signaling and supports survival in marginal zone B cells
-- / link
DRAGEN server; v3.9.3
Impact of Omicron variant sublineage BA.2.75 on the OnSite COVID-19 Ag Rapid Test: the applicability of rapid antigen test with universal transport media
Infectious Diseases / link
Surveillance Outcome and Genetic Findings in Individuals at High Risk of Pancreatic Cancer
Clinical and Translational Gastroenterology / link
SV caller
Functional evaluation of a novel nonsense variant of the calcium-sensing receptor gene leading to hypocalcemia
European Journal of Endocrinology / link
Influence of TP53 Comutation on the Tumor Immune Microenvironment and Clinical Outcomes With Immune Checkpoint Inhibitors in STK11-Mutant Non–Small-Cell Lung Cancer
JCO Precision Oncology / link
Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania
Genes / link
BCL convert
Ex vivo modeling of acquired drug resistance in BRAF - mutated pancreatic cancer organoids uncovers individual therapeutic vulnerabilities
Cancer Letters / link
RNA pipeline
Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru
Tropical Medicine and Infectious Disease / link
BSSH
Consanguineous marriages increase the incidence of recurrent tuberculosis: Evidence from whole exome sequencing
Infection, Genetics and Evolution / link
alignment
Brain injury drives optic glioma formation through neuron-glia signaling
Acta Neuropathologica Communications / link
Antiviral response and HIV-1 inhibition in sickle cell disease
Iscience / link
Differential expression pipeline v3.6.3; RNA pipeline v3.8.4
Analysis of partial Y chromosome microdeletions and NGS data in Lithuanian infertile men
-- / link
v3.6.4
Chapter 6 - Assessing microbiota composition in the context of aging
Methods in Cell Biology / link
BSSH; Metagenomics pipeline
Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics
Frontiers in Microbiology / link
Intellectual disability syndrome associated with a homozygous founder variant in SGSM3 in Ashkenazi Jews
Journal of Medical Genetics / link
Molecular analysis and transfusion management in a rare case of cis-AB blood group: A report from India
Transfusion Clinique et Biologique / link
v3.4
Immune transcriptomic profile in adult female pigs: dominance status has more influence than environmental enrichment
-- / link
v3.8.4; RNA
Differential Responses to Immune Checkpoint Inhibitors are Governed by Diverse Mismatch Repair Gene Alterations
Clinical Cancer Research / link
Comparative molecular profiling of pancreatic ductal adenocarcinoma of the head versus body and tail
npj Precision Oncology / link
BCL convert
Beyond the kidney biopsy: genomic approach to undetermined kidney diseases
Clinical Kidney Journal / link
BCL convert
Myocardial Matrix Hydrogels Mitigate Negative Remodeling and Improve Function in Right Heart Failure Model
JACC: Basic to Translational Science / link
RNA pipeline; v3.10.12
Despite Recovery from Necrotizing Enterocolitis Infants Retain a Hyperinflammatory Response to Injury
Journal of Inflammation Research / link
BSSH; Differential Expression App v4.0.3
Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories
PLOS Neglected Tropical Diseases / link
v1.3
ACBD5-related retinal dystrophy with leukodystrophy due to novel mutations in ACBD5 and with additional features including ovarian insufficiency
American Journal of Medical Genetics Part A / link
BSSH
Genomic heterogeneity at baseline is associated with T790M resistance mutations in EGFR-mutated lung cancer treated with the first-/second-generation tyrosine kinase inhibitors
The Journal of Pathology: Clinical Research / link
alignment; v4.0.3
Genetic Markers Among the Israeli Druze Minority Population With End-Stage Kidney Disease
American Journal of Kidney Diseases / link
CNV
Preclinical Evidence for the Glucocorticoid-Sparing Potential of a Dual Toll-Like Receptor 7/8 Inhibitor in Autoimmune Diseases
Journal of Pharmacology and Experimental Therapeutics / link
High Frequencies of Genetic Variants in Patients with Atypical Femoral Fractures
International Journal of Molecular Sciences / link
Loss of function in NSD2 causes DNA methylation signature similar to that in Wolf-Hirschhorn syndrome
Genetics in Medicine Open / link
Concordance between an FDA-approved companion diagnostic and an alternative assay kit for assessing homologous recombination deficiency in ovarian cancer
Gynecologic Oncology / link
A Cataract-Causing Mutation in the TRPM3 Cation Channel Disrupts Calcium Dynamics in the Lens
Cells / link
v3.9
Homozygous variant in TKFC abolishing triokinase activities is associated with isolated immunodeficiency
Journal of Medical Genetics / link
Renal transcriptome analysis of uninephrectomized db/db mice identified a mechanism for the transition to severe diabetic nephropathy
Experimental Animals / link
The diversity and clinical implications of genetic variants influencing clopidogrel bioactivation and response in the Emirati population
Human Genomics / link
v4