Illumina Publications

Thorpe E, Williams T, Shaw C, et al.

The impact of clinical genome sequencing in a global population with suspected rare genetic disease

AM J Hum Genet 111(7):1271-1281

2024

Shepherdson JL, Hutchison K, Don DW, et al.

Variants in ZFX are associated with an X-linked neurodevelopmental disorder with recurrent facial gestalt

AM J Hum Genet 111(3):487-508

2024

Zerella JR, Homan CC, Arts P, et al.

Germline ERG haploinsufficiency defines a new syndrome with cytopenia and hematological malignancy predisposition

Blood 144(17):1765-1780

2024

Kjar A, Haschert MR, Zepeda JC, et al.

Biofunctionalized gelatin hydrogels support development and maturation of iPSC-derived cortical organoids

Cell Reports 43(11):114874

2024

Hermosilla-Albala N, Silva FE, Cuadros-Espinoza S, Farh K K-H, et al.

Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism

Commun Biol 7(1):1283

2024

Rodriguez KM, Perofsky KL, Ramchandar N, et al.

Pathogen kinetics and detection by next-generation sequencing in pediatric complicated pneumonia

Diagn Microbiol Infect Dis 110(2):116468

2024

Wehn AK, Qiu P, Lunceford J, et al.

Concordance Between the FDA-Approved Companion Diagnostic and an Alternative Assay Kit for Assessing Homologous Recombination Deficiency in Ovarian Cancer

Gynecol Oncol 184:67-73

2024

Maghini DG, Dvorak M, Dahlen A, et al.

Quantifying bias introduced by sample collection in relative and absolute microbiome measurements

Nat Biotechnol 42(2):328-338

2024

Zhang M, Sjöström M, Cui X, Farh K, et al.

Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression

Nat Cell Biol 26(7):1176-1186

2024

Peretz CAC, Kennedy VE, Walia A, et al.

Multiomic single cell sequencing identifies stemlike nature of mixed phenotype acute leukemia

Nat Commun 15:8191

2024

Delgado-Vega AM, Cederroth H, Taylan F, et al.

Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon

Nat Genet 21 Oct

2024

Kuderna LFK, Ulirsch JC, Rashid S, Farh K K-H, et al.

Identification of constrained sequence elements across 239 primate genomes

Nature 625(7996):735-742

2024

Hunter O, Talkish J, Quick-Cleveland J, et al.

Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain

RNA 30(2):149-170

2024

Gong B, Li D, Łabaj PP, et al.

Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing

Sci Data 11(1):892

2024

Sundaram L, Kumar A, Zatzman M, Farh K K-H, et al.

Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers

Science 385(6713):eadk9217

2024

Natarajan A, Fremin BJ, Schmidtke DT, et al.

The Tomato Brown Rugose Fruit Virus Movement Protein Gene Is a Novel Microbial Source Tracking Marker

Appl Environ Micobiol 89(7):e0058323

2023

Peixoto C, Lopes MB, Martins M, Kaplan S, et al.

Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization

BMC Bioinform 24:17

2023

Tan A, Murugapiran S, Mikalauskas A, et al.

Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes

BMC Microbiol 23(1):299

2023

McBride DJ, Fielding C, Newington T, et al.

Whole-Genome Sequencing Can Identify Clinically Relevant Variants from a Single Sub-Punch of a Dried Blood Spot Specimen

Int J Neonatal Screen 9(3):52

2023

Valero C, Golkaram M, Vos JL, Kaplan S, et al.

Clinical-genomic determinants of immune checkpoint blockade response in head and neck squamous cell carcinoma

J Clin Invest 133(19):e169823

2023

Sarfaty M, Golkaram M, Funt SA, Kaplan S, et al.

Novel Genetic Subtypes of Urothelial Carcinoma With Differential Outcomes on Immune Checkpoint Blockade.

J Clin Oncol 41:17

2023

Dhondt B, Pinheiro C, Geeurickx E, et al.

Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics

J Extracell Vesicles 12(5):e12315

2023

Soto R, Paul L, Porucznik CA, et al.

Effectiveness of Self-Collected, Ambient Temperature-Preserved Nasal Swabs Compared to Samples Collected by Trained Staff for Genotyping of Respiratory Viruses by Shotgun RNA Sequencing: Comparative Study.

JMIR Form Res 7:e32848

2023

Jensen A, Swift F, de Vries D, Farh K, et al.

Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation

Mol Biol Evol 40(12):msad247

2023

Kuderna LFK, Gao H, Janiak MC, Farh K K-H, et al.

A global catalog of whole-genome diversity from 233 primate species

Science 380(6648):906-913

2023

Sørensen EF, Harris RA, Zhang L, Farh K K-H, et al.

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons

Science 380(6648):eabn8153

2023

Shao Y, Zhou L, Li F, Farh K K-H, et al.

Phylogenomic analyses provide insights into primate evolution

Science 380(6648):913-924

2023

Fiziev PP, McRae J, Ulirsch JC, Farh K K-H, et al.

Rare penetrant mutations confer severe risk of common diseases

Science 380(6648):eabo1131

2023

Gao H, Hamp T, Ede J, Farh K K-H, et al.

The landscape of tolerated genetic variation in humans and primates

Science 380(6648):eabn8153

2023

Silveira C, Sousa AC, Corredeira P, et al.

Comprehensive genomic profiling of cell-free circulating tumor DNA detects response to ribociclib plus letrozole in a patient with metastatic breast cancer

Biomol 12(12):1818

2022

Ameen M, Sundaram L, Shen M, Farh K, et al.

Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease

Cell 185(26):4937-4953.e23

2022

Sobral D, Martins M, Kaplan S

Genetic and microenvironmental intra-tumor heterogeneity impacts colorectal cancer evolution and metastatic development

Commun Biol 5:937

2022

Zhang Y, Blomquist TM, Kusko R, et al.

Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples

Genome Biol 23(1):141

2022

Golkaram M, Kuo F, Gupta S, et al.

Spatiotemporal evolution of the clear cell renal cell carcinoma microenvironment links intra-tumoral heterogeneity to immune escape

Genom Med 14:143

2022

Ibanez K, Polke J, Hagelstrom T, et al.

Whole genome sequencing for diagnosis of neurological repeat expansion disorders

Lancet Neurol 21(3):234-245

2022

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 13(1):4057

2022

Parikh VN, Ioannidis AG, Jimenez-Morales D, Farh K, et al.

Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy

Nat Commun 13(1):5107

2022

Moisse M, Zwamborn RAJ, van Vugt J, et al.

The Effect of SMN Gene Dosage on ALS Risk and Disease Severity

Ann Neurol 89(4):686-697

2021

Krishna C, DiNatale RG, Kuo F, et al.

Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy

Cancer Cell. 39(5):662-677

2021

Trevino AE, Müller F, Andersen J, Farh K, et al.

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

Cell 184(19):5053-5069.e23

2021

Galson JD, Schaetzle S, Bashford-Rogers RJM, et al.

Deep Sequencing of B Cell Receptor Repertoires From COVID-19 Patients Reveals Strong Convergent Immune Signatures

Front Immunol 11:605170

2021

Gong B, Li D, Kusko R, et al.

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

Genom Biol 22(1):109

2021

Rajan-Babu IS, Peng J, Chiu R, et al.

Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions

Genome Med 13(1):126

2021

Deveson IW, Gong B, Lai K, et al.

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

Nat Biotechnol 39:1115-1128

2021

Thornton CA, Mulqueen RM, Torkenczy KA, et al.

Spatially mapped single-cell chromatin accessibility

Nat Commun 12(1):1274

2021

van Rheenen W, van der Spek R, Bakker M, et al.

Common and rare variant association analyses in Amyotrophic Lateral Sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

Nat Genet 53(12):1636-1648

2021

Owen MJ, Niemi AK, Dimmock DP, et al.

Rapid Sequencing-Based Diagnosis of Thiamine Metabolism Dysfunction Syndrome

N Engl J Med 384(22):2159-2161

2021

Golkaram M, Salmans ML, Kaplan S, et al.

HERVs establish a distinct molecular subtype in stage II/III colorectal cancer with poor outcome

NPJ Genom Med 6:13

2021

Chen X, Shen F, Gonzaludo N, et al.

Cyrius: accurate CYP2D6 genotyping using whole-genome sequencing data

Pharmacogenomics J 21:251–261

2021

Cao J, O'Day DR, Pliner HA, et al.

A human cell atlas of fetal gene expression

Science 370(6518):eaba7721

2021

Domcke S, Hill AJ, Daza RM, et al.

A human cell atlas of fetal chromatin accessibility

Science 370(6518):eaba7612

2020

van Wietmarschen N, Sridharan S, Nathan WJ, et al.

Repeat expansions confer WRN dependence in microsatellite-unstable cancers

Nature 586(7828):292-298

2020

Fazal S, Danzi MC, Cintra VP, et al.

Large scale in silico characterization of repeat expansion variation in human genomes

Sci Data 7(1):294

2020

Cao J, Zhou W, Steemers F, Trapnell C, Shendure J

Sci-fate characterizes the dynamics of gene expression in single cells

Nat Biotechnol 38(8):980-988

2020

Trost B, Engchuan W, Nguyen CM, et al.

Genome-wide detection of tandem DNA repeats that are expanded in autism

Nature 586(7827):80-86

2020

Chua JPS, Go MK, Osothprarop T, et al.

Evolving a Thermostable Terminal Deoxynucleotidyl Transferase

ACS Synth Biol 9(7):1725-1735

2020

Munchel S, Rohrback S, Randise-Hinchliff C, et al.

Circulating transcripts in maternal blood reflect a molecular signature of early-onset preeclampsia

Sci Transl Med 12(550):eaaz0131

2020

Dolzhenko E, Bennett MF, Richmond PA, et al.

ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data

Genome Biol 21(1):102

2020

Hodge RD, Miller JA, Novotny M, et al.

Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons

Nat Commun 11(1):1172

2020

Chen, X., Sanchis-Juan, A., French, C.E. et al.

Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data

Genet Med 22, 945–953

2020

Helman G, Lajoie BR, Crawford J, et al.

Genome sequencing in persistently unsolved white matter disorders

Ann Clin 7(1):144-152

2020

Srivatsan SR, McFaline-Figueroa JL, Ramani V, et al.

Massively multiplex chemical transcriptomics at single-cell resolution

Science 367(6473):45-51

2020

Godsey JH, Silvestro A, Barrett JC, et al.

Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC’s Analytical Variables Working Group

Clin Chem 66(9):1156-1166

2020

Liu L, Toung JM, Jassowicz AF, et al.

Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification

Ann Oncol 29(6):1445-1453

2018

Janku F, Zhang S, Waters J, et al.

Development and validation of an ultradeep next-generation sequencing assay for testing of plasma cell-free DNA from patients with advanced cancer

Clin Cancer Res 23(18):5648-5656

2017

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Key peer-reviewed genomics publications showcasing research from Illumina scientists

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