DRAGEN Publications

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

2025

De La Vega FM, Irvine SA, Anur P, et al. Benchmarking of Germline Copy Number Variant Callers from Whole Genome Sequencing Data for Clinical Applications. Bioinformatics Advances. April 2025:vbaf071. doi:10.1093/bioadv/vbaf071
 

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 DRAGENTM 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