DRAGEN Publications

The following list of publications summarises the extensive applications of the Illumina DRAGEN™ Bio-IT Platform.

2022

Akkad N, Kodgule R, Duncavage EJ, et al. Evaluation of Breast Implant-associated Anaplastic Large Cell Lymphoma With Whole Exome and Genome Sequencing [published online ahead of print, 2022 Nov 10]. Aesthet Surg J. 2022;sjac282. doi:10.1093/asj/sjac282

Baban A, Alesi V, Magliozzi M, et al. Cardiovascular Involvement in Pediatric FLNC Variants: A Case Series of Fourteen Patients. J Cardiovasc Dev Dis. 2022;9(10):332. Published 2022 Sep 30. doi: 10.3390/jcdd9100332

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. Published 2022 Dec 13. doi:10.1038/s41598-022-26181-3

Bilal MY, Klutts JS. Molecular Epidemiological Investigations of Localized SARS-CoV-2 Outbreaks-Utility of Public Algorithms. Epidemiologia (Basel). 2022;3(3):402-411. Published 2022 Sep 19. doi: 10.3390/epidemiologia3030031

Yıldız Bölükbaşı E, Karolak JA, Szafranski P, et al. High-level gonosomal mosaicism for a pathogenic non-coding CNV deletion of the lung-specific FOXF1 enhancer in an unaffected mother of an infant with ACDMPV. Mol Genet Genomic Med. 2022;10(11):e2062. doi: 10.1002/mgg3.2062

*Clark CR Hardison MT, Houdeshell H, et al. Evaluation of an optimized protocol and Illumina ARTIC V4 primer pool for sequencing of SARS-CoV-2 using COVIDSeq™ and DRAGEN™ COVID Lineage App workflow. bioRxiv 2022.01.07.475443; https://www.biorxiv.org/content/10.1101/2022.01.07.475443v1.full

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

Coelho AVC, Mascaro-Cordeiro B, Lucon DR, et al. The Brazilian Rare Genomes Project: Validation of Whole Genome Sequencing for Rare Diseases Diagnosis. Front Mol Biosci. 2022;9:821582. Published 2022 May 2. doi:10.3389/fmolb.2022.821582

*Ding Y, Owen M, Le J, et al. Scalable, high quality, whole genome sequencing from archived, newborn, dried blood spots. MedRxiv 2022.07.27.22278102 https://www.medrxiv.org/content/10.1101/2022.07.27.22278102v1

Donzelli S, Ciuffreda L, Pontone M, et al. Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking. Comput Struct Biotechnol J. 2022;20:2558-2563. doi:10.1016/j.csbj.2022.05.033

Funingana IG, Ambrose J, Hosking K, Demiris N, Sosinsky A, Brenton JD. 28MO Real-world whole sequencing data of ovarian cancer patients. Annals of Oncology. 2022;33:S395. doi: 10.1016/j.annonc.2022.04.046

Goswami C, Sheldon M, Bixby C, et al. Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program. BMC Infect Dis. 2022;22(1):404. Published 2022 Apr 25. doi:10.1186/s12879-022-07374-7

Guruju N, Nallamilli BRR, Jump V, Collins C, Hegde M. eP356: Exome sequencing expands the sensitivity and specificity of identification of sequence variants and CNVs in phenotypic females with DSD. Genetics in Medicine. 2022;24(3):S223-S224. doi: 10.1016/j.gim.2022.01.391

Hallermayr A, Wohlfrom T, Steinke-Lange V, et al. Somatic copy number alteration and fragmentation analysis in circulating tumor DNA for cancer screening and treatment monitoring in colorectal cancer patients. J Hematol Oncol. 2022;15(1):125. Published 2022 Sep 2. doi: 10.1186/s13045-022-01342-z

Haworth A, Homfray T, Drury S, et al. eP360: Exome analysis of prenatal and postnatal cases referred with skeletal dysplasia-overview of phenotypic and genomic and findings. Genetics in Medicine. 2022;24(3, Supplement):S226. doi:10.1016/j.gim.2022.01.395

Hu Y, Shin J, Roy S, Burkard ME. Abstract P4-07-05: Tumor mutational profiles of extreme long-term survivors with metastatic breast cancer. Cancer Research. 2022 Feb 15;82(4_Supplement):P4-07. doi: 10.1158/1538-7445.SABCS21-P4-07-05

Jezkova J, Shaw S, Taverner NV, Williams HJ. Rapid genome sequencing for pediatrics. Hum Mutat. 2022;43(11):1507-1518. doi: 10.1002/humu.24466

Khanna C, Le Coz C, Vaccaro C, et al. Lymphocytes Utilize Somatic Mutations, Epigenetic Silencing, and the Proteasome to Escape Truncated WASP Expression. J Clin Immunol. 2022;42(4):753-759. doi: 10.1007/s10875-022-01224-6

Sanford Kobayashi E, Batalov S, Wenger AM, et al. Approaches to long-read sequencing in a clinical setting to improve diagnostic rate. Sci Rep. 2022;12(1):16945. Published 2022 Oct 9. doi: 10.1038/s41598-022-20113-x

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

Lázaro-Guevara JM, Flores-Robles BJ, Garrido-Lopez KM, et al. Identification of RP1 as the genetic cause of retinitis pigmentosa in a multi-generational pedigree using Extremely Low-Coverage Whole Genome Sequencing (XLC-WGS). Gene. 2023;851:146956. doi: 10.1016/j.gene.2022.146956

Leibler C, John S, Elsner RA, et al. Genetic dissection of TLR9 reveals complex regulatory and cryptic proinflammatory roles in mouse lupus. Nat Immunol. 2022;23(10):1457-1469. doi: 10.1038/s41590-022-01310-2

Lin PC, Tsai YS, Yeh YM, Shen MR. Cutting-Edge AI Technologies Meet Precision Medicine to Improve Cancer Care. Biomolecules. 2022;12(8):1133. Published 2022 Aug 17. doi: 10.3390/biom12081133

Lowe DR, Forson B, Butler MG, et al. Abstract 537: Development of blood TMB (bTMB) reference materials for validation of cfDNA-based targeted NGS assays that measure tumor mutational burden (TMB) in patient blood samples. Cancer Research. 2022 Jun 15;82(12_Supplement):537-. doi: 10.1158/1538-7445.AM2022-537

Lu Z, Brunton AE, Mohebnasab M, et al. Community-Based SARS-CoV-2 Testing Using Saliva or Nasopharyngeal Swabs to Compare the Performance of Weekly COVID-19 Screening to Wastewater SARS-CoV-2 Signals. ACS ES&T Water. 2022;2(10):1667-1677. doi: 10.1021/acsestwater.2c00177

Miller M, Jansen M, Silver M, et al. eP376: NGS detection of NUDT15 6-bp insertion and UGT1A1 (TA) repeat polymorphism on a preventative genomics assay. Genetics in Medicine. 2022;24(3):S236-S237. doi: 10.1016/j.gim.2022.01.411

Muñoz-Valle JF, Venancio-Landeros AA, Sánchez-Sánchez R, et al. An Upgrade on the Surveillance System of SARS-CoV-2: Deployment of New Methods for Genetic Inspection. Int J Mol Sci. 2022;23(6):3143. Published 2022 Mar 15. doi:10.3390/ijms23063143

Myasnikov RP, Kulikova OV, Meshkov AN, et al. A Splice Variant of the MYH7 Gene Is Causative in a Family with Isolated Left Ventricular Noncompaction Cardiomyopathy. Genes (Basel). 2022;13(10):1750. Published 2022 Sep 28. doi:10.3390/genes13101750

Narang A, Lacaze P, Ronaldson KJ, et al. Whole-genome sequencing analysis of clozapine-induced myocarditis. Pharmacogenomics J. 2022;22(3):173-179. doi: 10.1038/s41397-022-00271-x

*Nikolaienko O, Lønning P. E, Knappskog S. EpialleleR: an R/BioC package for sensitive allele-specific methylation analysis in NGS data. bioRxiv 2022.06.30.498213; doi: 10.1101/2022.06.30.498213

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 Genom. 2022;2(5):100129. doi: 10.1016/j.xgen.2022.100129

Owen MJ, Lefebvre S, Hansen C, et al. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun. 2022;13(1):4057. Published 2022 Jul 26. doi: 10.1038/s41467-022-31446-6

Rapini N, Patera PI, Schiaffini R, et al. Monogenic diabetes clinic (MDC): 3-year experience [published online ahead of print, 2022 Sep 30] [published correction appears in Acta Diabetol. 2022 Nov 5;:]. Acta Diabetol. 2022;10.1007/s00592-022-01972-2. doi: 10.1007/s00592-022-01972-2

Sahraeian SME, Fang LT, Karagiannis K, et al. Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample. Genome Biol. 2022;23(1):12. Published 2022 Jan 7. doi: 10.1186/s13059-021-02592-9

Schaefer IM, Hemming ML, Lundberg MZ, et al. Concurrent inhibition of CDK2 adds to the anti-tumour activity of CDK4/6 inhibition in GIST. Br J Cancer. 2022;127(11):2072-2085. doi: 10.1038/s41416-022-01990-5

Sellers H, Stein M, Tandale P, et al. OP040: Clinical validation of tagmentation-based genome sequencing for germline disorders. Genetics in Medicine. 2022;24(3):S366. doi: 10.1016/j.gim.2022.01.588

Shao X, Le Stunff C, Cheung W, et al. Differentially methylated CpGs in response to growth hormone administration in children with idiopathic short stature. Clin Epigenetics. 2022;14(1):65. Published 2022 May 18. doi: 10.1186/s13148-022-01281-z

Suzuki H, Nozaki M, Yoshihashi H, et al. Genome Analysis in Sick Neonates and Infants: High-yield Phenotypes and Contribution of Small Copy Number Variations. J Pediatr. 2022;244:38-48.e1. doi: 10.1016/j.jpeds.2022.01.033

Urnikyte A, Pranckeniene L, Domarkiene I, et al. Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift. Genes (Basel). 2022;13(4):569. Published 2022 Mar 23. doi: 10.3390/genes13040569

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 Med. 2022;14(1):34. Published 2022 Mar 28. doi: 10.1186/s13073-022-01031-z

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

Wright D, Chan C, Chaochaisit W, et al. Rapid Displacement of SARS-CoV-2 Variants within Japan Correlates with Cycle Threshold Values on Routine RT-PCR Testing. Archives of Clinical and Biomedical Research. 2022;6(5):722-731. https://www.fortunejournals.com/articles/rapid-displacement-of-sarscov2-variants-within-japan-correlates-with-cycle-threshold-values-on-routine-rtpcr-testing.html

Yamanishi K, Doe N, Mukai K, et al. Acute stress induces severe neural inflammation and overactivation of glucocorticoid signaling in interleukin-18-deficient mice. Transl Psychiatry. 2022;12(1):404. Published 2022 Sep 23. doi: 10.1038/s41398-022-02175-7

2021

Adadey SM, Schrauwen I, Aboagye ET, et al. Further confirmation of the association of SLC12A2 with non-syndromic autosomal-dominant hearing impairment. J Hum Genet. 2021;66(12):1169-1175. doi: 10.1038/s10038-021-00954-6

*AlAli AK, Al-Enazi A, Ammar A, et al. Whole‐Exome Sequencing of a Saudi Epilepsy Cohort Reveals Association Signals in Known and Potentially Novel Loci. Research Square; 2021. DOI: 10.21203/rs.3.rs-915593/v1

Alcoba-Florez J, Lorenzo-Salazar JM, Gil-Campesino H, et al. Monitoring the rise of the SARS-CoV-2 lineage B.1.1.7 in Tenerife (Spain) since mid-December 2020. J Infect. 2021;82(6):e1-e3. doi: 10.1016/j.jinf.2021.04.005

Bamborschke D, Özdemir Ö, Kreutzer M, et al. Ultra-rapid emergency genomic diagnosis of Donahue syndrome in a preterm infant within 17 hours. Am J Med Genet A. 2021;185(1):90-96. doi: 10.1002/ajmg.a.61917

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. Published 2021 Feb 17. doi: 10.1371/journal.pone.0247115

Biswas P, Kurmanov B, Hong K, et al.; Identification of unique variants as the underlying cause of IRD in pedigrees that remained unresolved after initial whole genome sequence analysis.. Invest. Ophthalmol. Vis. Sci. 2021;62(8):1523. Published 2021 June. doi: https://iovs.arvojournals.org/article.aspx?articleid=2775244

Farswan A, Jena L, Kaur G, et al. Branching clonal evolution patterns predominate mutational landscape in multiple myeloma. Am J Cancer Res. 2021;11(11):5659-5679. Published 2021 Nov 15. eCollection 2021. PMCID: PMC8640818

Gupta R, Kaur G, Farswan A, et al. P-047: Clonal evolution in multiple myeloma evaluated by Whole Exome Sequencing. Clinical Lymphoma Myeloma and Leukemia. 2021;21:S64. doi: 10.1016/S2152-2650(21)02181-9

Hongo H, Kosaka T, Suzuki Y, Mikami S, Fukada J, Oya M. Topoisomerase II alpha inhibition can overcome taxane-resistant prostate cancer through DNA repair pathways. Sci Rep. 2021;11(1):22284. Published 2021 Nov 15. doi: 10.1038/s41598-021-01697-2

Hoq MI, Bhuiyan RH, Rahman MKR, et al. Genome Sequence of a SARS-CoV-2 Strain from a COVID-19 Clinical Sample from the Khagrachari District of Bangladesh. Microbiol Resour Announc. 2021;10(13):e00189-21. Published 2021 Apr 1. doi:10.1128/MRA.00189-21

Hossain MU, Ahammad I, Bhattacharjee A, et al. Whole genome sequencing for revealing the point mutations of SARS-CoV-2 genome in Bangladeshi isolates and their structural effects on viral proteins. RSC Adv. 2021;11(61):38868-38879. Published 2021 Dec 3. doi: 10.1039/d1ra05327b

*Jaksik R, Rosiak J, Zawadzki P, et al. Accuracy of somatic variant detection workflows for whole genome sequencing experiments. bioRxiv 2021.06.10.446467; https://www.biorxiv.org/content/10.1101/2021.06.10.446467v2

Jerebtsova M, Nekhai S. Sickle Cell Hemoglobin Induces Autophagy in Human Macrophages. Blood. 2021;138(Supplement 1):952-952. doi: 10.1182/blood-2021-151349

Keehan L, Jiang MM, Li X, et al. A novel de novo intronic variant in ITPR1 causes Gillespie syndrome. Am J Med Genet A. 2021;185(8):2315-2324. doi: 10.1002/ajmg.a.62232

Kurmanov B, Biswas P, Lajoie B, et al. Identification of causative mutations in ten pedigrees with inherited retinal degeneration by whole genome analysis (WGS). Investigative Ophthalmology & Visual Science. 2021;62(8):1546-1546. https://iovs.arvojournals.org/article.aspx?articleid=2775224

Liu Y, Chang X, Qu HQ, et al. Rare Recurrent Variants in Noncoding Regions Impact Attention-Deficit Hyperactivity Disorder (ADHD) Gene Networks in Children of both African American and European American Ancestry. Genes (Basel). 2021;12(2):310. Published 2021 Feb 22. doi: 10.3390/genes12020310

Kumari N, Nouraie M, Ahmad A, et al. Restriction of HIV-1 infection in sickle cell trait. Blood Adv. 2021;5(23):4922-4934. doi:10.1182/bloodadvances.2021004247

Rueca M, Giombini E, Messina F, et al. The Easy-to-Use SARS-CoV-2 Assembler for Genome Sequencing: Development Study. JMIR Bioinform Biotech. 2022;3(1):e31536. Published 2022 Mar 14. doi: 10.2196/31536

Singh S, Sutcliffe MD, Repich K, Atkins KA, Harvey JA, Janes KA. Pan-Cancer Drivers Are Recurrent Transcriptional Regulatory Heterogeneities in Early-Stage Luminal Breast Cancer. Cancer Res. 2021;81(7):1840-1852. doi: 10.1158/0008-5472.CAN-20-1034

Zou D, Wang L, Liao J, et al. Genome sequencing of 320 Chinese children with epilepsy: a clinical and molecular study. Brain. 2021;144(12):3623-3634. doi: 10.1093/brain/awab233

2020

Dimmock DP, Clark MM, Gaughran M, et al. An RCT of Rapid Genomic Sequencing among Seriously Ill Infants Results in High Clinical Utility, Changes in Management, and Low Perceived Harm. Am J Hum Genet. 2020;107(5):942-952. doi:10.1016/j.ajhg.2020.10.003

Fan X, Desmond R, Winkler T, et al. Eltrombopag for patients with moderate aplastic anemia or uni-lineage cytopenias. Blood Adv. 2020;4(8):1700-1710. doi:10.1182/bloodadvances.2020001657

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

Scheffler K, Kim S, Jain V, et al. Accuracy improvements in somatic whole-genome small-variant calling with the DRAGEN platform. Cancer Research. 2020 Aug 15;80(16_Supplement):5463-. doi: 10.1158/1538-7445.AM2020-5463

Yamada M, Suzuki H, Watanabe A, et al. Role of chimeric transcript formation in the pathogenesis of birth defects. Congenit Anom (Kyoto). 2021;61(3):76-81. doi: 10.1111/cga.12400

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(1):20222. Published 2020 Nov 19. doi: 10.1038/s41598-020-77218-4

2019

Clark MM, Hildreth A, Batalov S, et al. Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation. Science Translational Medicine. 2019;11(489). Published 2019 Apr 24. doi: 10.1126/scitranslmed.aat6177

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. Published 2019 Apr 1. doi:10.1101/mcs.a003756

Kingsmore SF, Cakici JA, Clark MM, et al. A Randomized, Controlled Trial of the Analytic and Diagnostic Performance of Singleton and Trio, Rapid Genome and Exome Sequencing in Ill Infants. Am J Hum Genet. 2019;105(4):719-733. doi:10.1016/j.ajhg.2019.08.009

Russell MW, Moldenhauer JS, Rychik J, et al. Effect of parental origin of damaging variants in pro-angiogenic genes on fetal growth in patients with congenital heart defects: Data and analyses. Data Brief. 2019;25:104311. Published 2019 Jul 26. doi:10.1016/j.dib.2019.104311

Triska P, Kaneva K, Merkurjev D, et al. Landscape of Germline and Somatic Mitochondrial DNA Mutations in Pediatric Malignancies. Cancer Res. 2019;79(7):1318-1330. doi: 10.1158/0008-5472.CAN-18-2220

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. Published 2017 Mar. 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 Med. 2015;7:100. Published 2015 Sep 30. doi: 10.1186/s13073-015-0221-8

* Pre-print, not peer reviewed by a journal