Dragen platform

Manufactured by Illumina

The DRAGEN Platform is a high-performance genomic analysis solution developed by Illumina. It is designed to accelerate secondary analysis of sequencing data by leveraging field-programmable gate array (FPGA) technology. The DRAGEN Platform provides rapid and efficient processing of raw sequencing reads, enabling fast data analysis and interpretation.

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Lab products found in correlation

Novaseq 6000 sequencing system, by Illumina (1 mentions) Bcl2fastq 2.20, by Illumina (1 mentions) Truseq nano dna library prep kit, by Illumina (1 mentions) Nextera dna flex library prep kit, by Illumina (1 mentions) Quant it picogreen dsdna assay, by Thermo Fisher Scientific (1 mentions)

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DRAGEN Bio-IT Platform (29 citations) DRAGEN (13 citations) DRAGEN Bio-IT Platform Germline Pipeline v3.0.7 (7 citations) Dragen Bio-IT Platform version 3.8 (3 citations) DRAGEN Bio-IT Platform Germline Pipeline (3 citations) DRAGEN 2 platform (2 citations)

4 protocols using dragen platform

Whole-Genome Sequencing of Lithuanian Trios

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Whole-genome sequencing (WGS) was performed for 25 trios of Lithuanian origin at coverage of 26.88–61.38× (an average of 36.27×), Table S1. Overall, the sample size was 75 individuals: 25 newborns, 25 mothers, and 25 fathers. WGS was performed at the CeGaT company (Tubingen, Germany). 100 ng DNA was paired-end sequenced in 2 × 150 bp mode on state-of-the-art Illumina NovaSeq™ 6000 Sequencing System using TruSeq^® Nano DNA Library Prep Kit (Illumina Inc., San Diego, CA, USA).
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20). Adapters were trimmed with Skewer (version 0.2.2) [10 (link)]. Quality trimming of the reads has not been performed. Analysis of sequencing data was performed using the Illumina DRAGEN platform (version 3.6.4). The DRAGEN DNA Pipeline uses the current industry standard, BWA-MEM and GATK-HC software. Reads were mapped to the reference genome hg19 (present on the Illumina DRAGEN platform v.3.6.4) and duplicates were marked. Calling of small variants, regions of homozygosity, and structural variants was performed with default parameters. SNVs found at higher frequencies than 1% in the population were qualified as SNPs. The quality of the FASTQ files was analyzed with FastQC (version 0.11.5-cegat) [11 ]. Sequencing quality control Q30 values were above 88.59% (Figures S1–S3).

Urnikyte A., Pranckeniene L., Domarkiene I., Dauengauer-Kirliene S., Molyte A., Matuleviciene A., Pilypiene I, & Kučinskas V. (2022). Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift. Genes, 13(4), 569.

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Rapid Genomic Sequencing for Rare Disease

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The rGS was performed at Rady Children’s Institute for Genomic Medicine using previously described methods.^{3 (link),14 (link)} PCR-free library preparation was performed, and sequencing was conducted on the NovaSeq6000 systems using S1 or S2 flow cells. Genome sequences were aligned to human genome assembly GRCh37 (hg19), and sequence variants were identified with the DRAGEN Platform (Illumina).
Sequence variants were filtered to retain those with allele frequencies of <0.5% in the gnomAD database and classified according to the American College of Medical Genetics and Genomics/Association of Molecular Pathology guidelines. CNVs were identified with Manta and CNVnator and filtered to retain those coding regions of 8000 known disease genes with allele frequencies <2% in the Rady Children’s Institute of Genomic Medicine database. Starting in June 2020, CNV calling was performed using the DRAGEN Platform, and filters were expanded to include all known consensus coding sequence genes. Nucleotide and CNVs were automatically annotated and ranked using Opal Clinical (Fabric Genomics). If a provisional diagnosis was made, it was immediately conveyed to the providers by phone. Reported variants were confirmed by Sanger sequencing or multiplex ligation-dependent probe amplification (MLPA).

Joo D.M., Ng N, & Calendar R. (1997). A σ32 mutant with a single amino acid change in the highly conserved region 2.2 exhibits reduced core RNA polymerase affinity. Proceedings of the National Academy of Sciences of the United States of America, 94(10), 4907-4912.

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Benchmarking Variant Calling Pipelines

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We compared the performance of Giraffe, VG-MAP, Illumina’s Dragen platform, and BWA-MEM for genotyping SNVs and short indels. The design of each calling pipeline is described in S4 in the supplement (17 ) and the parameters and indexes for each experiment is described in Table S22. The variants produced by each pipeline were compared against the Genome In a Bottle (GIAB) v4.2.1 HG002 high confidence variant calling benchmark (24 ) using the RealTimeGenomics vcfeval tool (47 ) and Illumina’s hap.py tool (48 ). This benchmark set covers 92.2% of the GRCh38 sequence.
We also evaluated a DeepVariant (25 ) pipeline that uses Giraffe mappings (17 ). Using the default DeepVariant 1.1.0 trained model, we tested genotyping the HG003 sample across the entire genome. This sample was not used in training the model.

Sirén J., Monlong J., Chang X., Novak A.M., Eizenga J.M., Markello C., Sibbesen J.A., Hickey G., Chang P.C., Carroll A., Gupta N., Gabriel S., Blackwell T.W., Ratan A., Taylor K.D., Rich S.S., Rotter J.I., Haussler D., Garrison E, & Paten B. (2021). Pangenomics enables genotyping known structural variants in 5,202 diverse genomes. Science (New York, N.Y.), 374(6574), abg8871.

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Sequencing of Dried Blood Spot DNA

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Sequencing libraries were prepared from 10 μl of EDTA blood or five 3-mm punches from a Nucleic-Card Matrix dried blood spot (Thermo Fisher Scientific) with Nextera DNA Flex Library Prep kits (Illumina) and five cycles of PCR, as described (35 ). For SV analysis, libraries were prepared by Hyper kits (KAPA Biosystems), as described above. Libraries were quantified with Quant-iT PicoGreen dsDNA assays (Thermo Fisher Scientific). Libraries were sequenced (2 × 101 nt) without indexing on the S1 FC with NovaSeq 6000 S1 reagent kits (Illumina). Sequences were aligned to human genome assembly GRCh37 (hg19), and nucleotide variants were identified with the DRAGEN Platform (v.2.5.1, Illumina; table S16) (16 (link)).

Clark M.M., Hildreth A., Batalov S., Ding Y., Chowdhury S., Watkins K., Ellsworth K., Camp B., Kint C.I., Yacoubian C., Farnaes L., Bainbridge M.N., Beebe C., Braun J.J., Bray M., Carroll J., Cakici J.A., Caylor S.A., Clarke C., Creed M.P., Friedman J., Frith A., Gain R., Gaughran M., George S., Gilmer S., Gleeson J., Gore J., Grunenwald H., Hovey R.L., Janes M.L., Lin K., McDonagh P.D., McBride K., Mulrooney P., Nahas S., Oh D., Oriol A., Puckett L., Rady Z., Reese M.G., Ryu J., Salz L., Sanford E., Stewart L., Sweeney N., Tokita M., Van Der Kraan L., White S., Wigby K., Williams B., Wong T., Wright M.S., Yamada C., Schols P., Reynders J., Hall K., Dimmock D., Veeraraghavan N., Defay T, & Kingsmore S.F. (2019). Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation. Science translational medicine, 11(489), eaat6177.

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