DRAGEN Publications

The following list of selected publications summarizes the extensive applications of the Illumina DRAGEN™ secondary analysis.

2024

Behera S, Catreux S, Rossi M, et al. Comprehensive genome analysis and variant detection at scale using DRAGEN. Nat Biotechnol. October 2024:1-15. doi:10.1038/s41587-024-02382-1

Behera S, Belyeu JR, Chen X, et al. Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk. BMC Medical Genomics. 2024;17(1):255. doi:10.1186/s12920-024-02024-0

Piening BD, Wagner JT, Welle JT, et al. Development and Validation of a Whole Genome Sequencing-Based Test for Cytogenetic Characterization of Acute Myeloid Leukemia. Blood. 2024;144:7494. doi:10.1182/blood-2024-210937

Silver LW, McLennan EA, Beaman J, et al. Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas. Immunogenetics. 2024;76(5):381-395. doi:10.1007/s00251-024-01356-6

Schobers G, Derks R, den Ouden A, et al. Genome sequencing as a generic diagnostic strategy for rare disease. Genome Med. 2024;16(1):32. doi:10.1186/s13073-024-01301-y

Schilling F, Schumacher C, Köhl K, et al. Whole-genome sequencing of tetraploid potato varieties reveals different strategies for drought tolerance. Scientific Reports. 2024;14(1):5476. doi:10.1038/s41598-024-55669-3

Ruiz de Sabando A, Ciosi M, Galbete A, Cumming SA, Monckton DG, Ramos-Arroyo MA. Somatic CAG repeat instability in intermediate alleles of the HTT gene and its potential association with a clinical phenotype. European Journal of Human Genetics. 2024:1-9. doi:10.1038/s41431-024-01546-6

Mitchell J, Milite S, Bartram J, et al. Clinical application of tumour-in-normal contamination assessment from whole genome sequencing. Nat Commun. 2024;15(1):323. doi:10.1038/s41467-023-44158-2

Masood D, Ren L, Nguyen C, et al. Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome. Genome Biology. 2024;25(1):163. doi:10.1186/s13059-024-03294-8

Kim SW, Lee H, Song DY, et al. Whole genome sequencing analysis identifies sex differences of familial pattern contributing to phenotypic diversity in autism. Genome Medicine. 2024;16(1):114. doi:10.1186/s13073-024-01385-6

Grobecker P, Berri S, Peden JF, et al. A dedicated caller for DUX4 rearrangements from whole-genome sequencing data. June 2024:2024.05.23.595509. doi:10.1101/2024.05.23.595509

Bick AG, Metcalf GA, Mayo KR, et al. Genomic data in the All of Us Research Program. Nature. 2024;627(8003):340-346. doi:10.1038/s41586-023-06957-x

Betschart RO, Riccio C, Aguilera-Garcia D, et al. Biostatistical Aspects of Whole Genome Sequencing Studies: Preprocessing and Quality Control. doi:10.1002/bimj.202300278

Betschart RO, Koliopanos G, Garg P, et al. Comprehensive Analysis of the Genetic Variation in the LPA Gene from Short-Read Sequencing. BioMed. 2024;4(2):156-170. doi:10.3390/biomed4020013

2023

Derrien J, Gastineau S, Frigout A, et al. Acquired resistance to a GPRC5D-directed T-cell engager in multiple myeloma is mediated by genetic or epigenetic target inactivation. Nat Cancer. 2023;4(11):1536-1543. doi:10.1038/s43018-023-00625-9

Vormittag-Nocito E, Acosta AM, Agarwal S, et al. In-Depth Comparison of Genetic Variants Demonstrates a Close Relationship Between Invasive and Intraductal Components of Prostate Cancer. Modern Pathology. 2023;36(6):100130. doi:10.1016/j.modpat.2023.100130

Vanni I, Pastorino L, Tanda ET, et al. Whole-Exome Sequencing and cfDNA Analysis Uncover Genetic Determinants of Melanoma Therapy Response in a Real-World Setting. International Journal of Molecular Sciences. 2023;24(5):4302. doi:10.3390/ijms24054302

Torkildsen CF, Thomsen LCV, Sande RK, et al. Molecular and phenotypic characteristics influencing the degree of cytoreduction in high‐grade serous ovarian carcinomas. Cancer Medicine. 2023;12(13):14183-14195. doi:10.1002/cam4.6085

Schmidt JK, Kim YH, Strelchenko N, et al. Whole genome sequencing of CCR5 CRISPR-Cas9-edited Mauritian cynomolgus macaque blastomeres reveals large-scale deletions and off-target edits. Front Genome Ed. 2023;4. doi:10.3389/fgeed.2022.1031275

Scheffler K, Catreux S, O’Connell T, et al. Somatic small-variant calling methods in Illumina DRAGEN^TM Secondary Analysis. March 2023:2023.03.23.534011. doi:10.1101/2023.03.23.534011

2022

Wagner J, Olson ND, Harris L, et al. Curated variation benchmarks for challenging medically relevant autosomal genes. Nat Biotechnol. 2022;40(5):672-680. doi:10.1038/s41587-021-01158-1

Venner E, Muzny D, Smith JD, et al. Whole-genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program. Genome Medicine. 2022;14(1):34. doi:10.1186/s13073-022-01031-z

Toffoli M, Chen X, Sedlazeck FJ, et al. Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson’s disease-associated GBA gene. Commun Biol. 2022;5(1):1-10. doi:10.1038/s42003-022-03610-7

Olson ND, Wagner J, McDaniel J, et al. PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions. Cell Genomics. 2022;2(5):100129. doi:10.1016/j.xgen.2022.100129

Lee NY, Hum M, Amali AA, et al. Whole-exome sequencing of BRCA-negative breast cancer patients and case–control analyses identify variants associated with breast cancer susceptibility. Hum Genomics. 2022;16(1):61. doi:10.1186/s40246-022-00435-7

Kousathanas A, Pairo-Castineira E, Rawlik K, et al. Whole-genome sequencing reveals host factors underlying critical COVID-19. Nature. 2022;607(7917):97-103. doi:10.1038/s41586-022-04576-6

Hale VL, Dennis PM, McBride DS, et al. SARS-CoV-2 infection in free-ranging white-tailed deer. Nature. 2022;602(7897):481-486. doi:10.1038/s41586-021-04353-x

Clark LN, Gao Y, Wang GT, et al. Whole genome sequencing identifies candidate genes for familial essential tremor and reveals biological pathways implicated in essential tremor aetiology. eBioMedicine. 2022;85:104290. doi:10.1016/j.ebiom.2022.104290

Betschart RO, Thiéry A, Aguilera-Garcia D, et al. Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment. Sci Rep. 2022;12(1):21502. doi:10.1038/s41598-022-26181-3

Al Anazi AH, Ammar AS, Al-Hajj M, et al. Whole‐exome sequencing of a Saudi epilepsy cohort reveals association signals in known and potentially novel loci. Hum Genomics. 2022;16:71. doi:10.1186/s40246-022-00444-6

2021

Washington NL, Gangavarapu K, Zeller M, et al. Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. Cell. 2021;184(10):2587-2594.e7. doi:10.1016/j.cell.2021.03.052

Wang Q, Dhindsa RS, Carss K, et al. Rare variant contribution to human disease in 281,104 UK Biobank exomes. Nature. 2021;597(7877):527-532. doi:10.1038/s41586-021-03855-y

Locher M, Jukic E, Bohn JP, et al. Clonal dynamics in a composite chronic lymphocytic leukemia and hairy cell leukemia-variant. Genes, Chromosomes and Cancer. 2021;60(4):287-292. doi:10.1002/gcc.22925

*Jaksik R, Rosiak J, Zawadzki P, Sztromwasser P. Accuracy of somatic variant detection workflows for whole genome sequencing experiments. June 2021:2021.06.10.446467. doi:10.1101/2021.06.10.446467

Ivanova AS, Sivitskaya LN, Kulikova SL, Liaudanski AD, Davydenko OG. Application of Massive Parallel DNA Sequencing to Diagnose Drug-Resistant Epilepsy in Children. Mol Genet Microbiol Virol. 2021;36(4):189-191. doi:10.3103/S0891416821040091

Chen X, Shen F, Gonzaludo N, et al. Cyrius: accurate CYP2D6 genotyping using whole-genome sequencing data. Pharmacogenomics J. 2021;21(2):251-261. doi:10.1038/s41397-020-00205-5

Bhoyar RC, Jain A, Sehgal P, et al. High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing. PLOS ONE. 2021;16(2):e0247115. doi:10.1371/journal.pone.0247115

2020

Zhao S, Agafonov O, Azab A, Stokowy T, Hovig E. Accuracy and efficiency of germline variant calling pipelines for human genome data. Sci Rep. 2020;10:20222. doi:10.1038/s41598-020-77218-4

*McKernan KJ, Helbert Y, Kane LT, et al. Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes. January 2020:2020.01.03.894428. doi:10.1101/2020.01.03.894428

Chin CS, Wagner J, Zeng Q, et al. A diploid assembly-based benchmark for variants in the major histocompatibility complex. Nat Commun. 2020;11(1):4794. doi:10.1038/s41467-020-18564-9

Chen X, Sanchis-Juan A, French CE, et al. Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data. Genetics in Medicine. 2020;22(5):945-953. doi:10.1038/s41436-020-0754-0

2019

Thiffault I, Farrow E, Zellmer L, et al. Clinical genome sequencing in an unbiased pediatric cohort. Genetics in Medicine. 2019;21(2):303-310. doi:10.1038/s41436-018-0075-8

Laurenzano SE, McFall C, Nguyen L, et al. Neonatal diabetes mellitus due to a novel variant in the INS gene. Cold Spring Harb Mol Case Stud. 2019;5(4):a004085. doi:10.1101/mcs.a004085

Ji J, Shen L, Bootwalla M, et al. A semiautomated whole-exome sequencing workflow leads to increased diagnostic yield and identification of novel candidate variants. Cold Spring Harb Mol Case Stud. 2019;5(2):a003756. doi:10.1101/mcs.a003756

Cooper MS, Stark Z, Lunke S, Zhao T, Amor DJ. IREB2-associated neurodegeneration. Brain. 2019;142(8):e40. doi:10.1093/brain/awz183

2017

Goyal A, Kwon HJ, Lee K, et al. Ultra-Fast Next Generation Human Genome Sequencing Data Processing Using DRAGENTM Bio-IT Processor for Precision Medicine. Open Journal of Genetics. 2017;7(1):9-19. doi:10.4236/ojgen.2017.71002

2015

Miller NA, Farrow EG, Gibson M, et al. A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases. Genome Medicine. 2015;7(1):100. doi:10.1186/s13073-015-0221-8

* Pre-print