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dragen variant calling algorithm  (Illumina Inc)


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    Structured Review

    Illumina Inc dragen variant calling algorithm
    Dragen Variant Calling Algorithm, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/variant+calling+algorithms/somatic+variant+caller+algorithm/pm40305610-213-9-9
    Average 90 stars, based on 1 article reviews
    dragen variant calling algorithm - by Bioz Stars, 2026-10
    90/100 stars

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    other:

    Article Title: Investigation of Exome-Wide Tumor Heterogeneity on Colorectal Tissue-Based Single Cells.
    Article Snippet: Dragen Somatic Variant Caller v. 4.2.7 (Illumina Inc.) was run in tumor-normal mode for the CRC and NAT samples.

    Article Title: Clonal hematopoiesis is associated with distinct rheumatoid arthritis phenotypes.
    Article Snippet: The panel of normals was then included in the Illumina DRAGEN variant calling algorithm.

    Produced:

    Article Title: Acquired sperm hypomethylation by gestational arsenic exposure is re-established in both the paternal and maternal genomes of post-epigenetic reprogramming embryos.
    Article Snippet: .. An N-masked reference genome that is based on the GRCm38/mm10 reference genome and N-masked at SNP positions between the GRCm38/mm10 and C3H/HeN genomes was produced from a variant call file made on Dragen (Illumina). ..

    Variant Assay:

    Article Title: Acquired sperm hypomethylation by gestational arsenic exposure is re-established in both the paternal and maternal genomes of post-epigenetic reprogramming embryos.
    Article Snippet: .. An N-masked reference genome that is based on the GRCm38/mm10 reference genome and N-masked at SNP positions between the GRCm38/mm10 and C3H/HeN genomes was produced from a variant call file made on Dragen (Illumina). ..

    Article Title: Machine learning based on multiplatform tests assists in subtype classification of mature B-cell neoplasms.
    Article Snippet: © 2024 British Society for Haematology and John Wiley & Sons Ltd. Junwei Lin and Yafei Mu contributed equally to this article.. 1Guangzhou Medical University, Guangzhou, China 2Guangzhou KingMed Transformative Medicine Institute Co., Ltd., Guangzhou, China 3Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China 4Department of Hematology, The Third Affiliated Hospital of Sun Yatsen University and Sun Yatsen Institute of Hematology, Guangzhou, China 5Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, China 6Guangzhou KingMed Diagnostics Group Co., Ltd., Guangzhou, China

    Article Title: Photoperiod associated late flowering reaction norm: Dissecting loci and genomic-enviromic associated prediction in maize
    Article Snippet: Context: Tropical maize lines are known to have extended flowering times when grown in northern temperate environments, a response largely due to the prolonged day length.. This adaptation challenge is referred to as Photoperiod Associated Late Flowering (PALF) and poses a significant barrier to using tropical maize genetics in temperate agricultural settings.. Objectives: This study aims to (i) investigate the genomic and environmental factors that influence PALF in recombinant inbred lines (RILs) derived from a tropical parent crossed with three temperate-adapted maize lines. (ii) Evaluate the performance of these RILs under different environmental conditions in Texas, Iowa, and Wisconsin over the years 2018–2021. (iii) Explore the efficacy of combining enviromic and genomic data to predict flowering times more accurately.

    Article Title: Evaluation of whole genome sequencing utility in identifying driver alterations in cancer genome
    Article Snippet: .. For SNVs and indels, somatic and germline variants were identified using the DRAGEN Somatic Variant Caller and Small Variant Caller (Illumina), respectively. ..

    Article Title: Localization of epidermal growth factor receptor-mutations using PNA:DNA probes in clinical specimens from patients with non-small cell lung cancer.
    Article Snippet: .. For SNVs and indel mutations, somatic and germline variants were identified using the DRAGEN Somatic Variant Caller and Small Variant Caller (Illumina), respectively. ..



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    Main characteristics of the studies included in the present systematic review.

    Journal: Diagnostics

    Article Title: The Need for Standardization in Next-Generation Sequencing Studies for Classic Hodgkin Lymphoma: A Systematic Review

    doi: 10.3390/diagnostics12040963

    Figure Lengend Snippet: Main characteristics of the studies included in the present systematic review.

    Article Snippet: ctDNA as a feasible strategy for genotyping and monitoring , Variants in SOCS1 (28%), IGLL5 (36%), TNFAIP3 (23%), GNA13 (23%) and STAT6 (21%). Poor prognosis features correlated with ctDNA concentration , VarScan2 and DGCaller algorithms for variant calling. RefSeq database for functional annotation , Illumina, San Diego, CA, USA , ctDNA , 60 cases of newly diagnosed cHL , Identify cHL somatic variants , Alcoceba et al., (2021) [ ] .

    Techniques: Sequencing, Software, Concentration Assay, Variant Assay, Functional Assay, Control, Biomarker Discovery, Isolation, Selection