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Human whole-genome sequencing

A detailed view into the genetic variants that encode human traits and disease

An unbiased view of the entire human genome

Human whole-genome sequencing (WGS) offers the most detailed view into our genetic code. WGS has the ability to evaluate every base in the genome and navigate the complexity of genomic variants that make us unique.

Previously a challenging application, human whole-genome sequencing is now one of the simplest. Advances in library preparation, sequencing, bioinformatics, and variant analysis have made it possible for researchers to go from sample to data in less than 30 hours. Whether you’re performing a comprehensive genomic evaluation or using the genome as a foundation for other studies, human whole-genome sequencing has never been more accessible.

novaseq-x loading reagent

Production-scale whole-genome sequencing workflow

Illumina Genomics Architecture v3 delivers a streamlined, scalable solution for high-throughput human WGS with the NovaSeq X Plus System—reducing manual effort and turnaround time for consistent, site-ready results.

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Comprehensive variant detection with human WGS

The human genome is complex, with variations from small, single nucleotide changes to large chromosomal rearrangements, and virtually everything in between. Examples of variants include single nucleotide variants (SNVs), insertions and deletions (indels), structural variants (SVs), copy number variants (CNVs), and others. Human whole-genome sequencing is the most comprehensive method for detecting all of these variant types in a single assay.1-8

Mapped reads

Expanded genomics insights from long-distance data

Resolve challenging-to-map regions of the genome, generate phased sequencing data, and simplify your sequencing workflow. Illumina mapped read technology enhances short-read genome sequencing with long-distance information for exceptional genome mapping and insights.

Learn more about mapped read technology
Read the TruPath Genome sample performance technical note

Featured human whole-genome sequencing workflow

Powered by proximity mapped read technology, TruPath Genome for research applications enables human germline whole-genome sequencing with unprecedented simplicity, higher accuracy variant detection, and improved coverage.

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1
Library Prep

TruPath™ Genome

Highly accurate, comprehensive germline human whole-genome sequencing for research applications with ~10 min of hands-on time and no traditional library prep.

2
Sequencing

NovaSeq™ X Series

The NovaSeq X Series delivers extraordinary throughput and accuracy to perform data-intensive applications at production scale.

3
Data analysis

DRAGEN™ Germline

DRAGEN Germline is an accurate and efficient (FASTQ to VCF) secondary analysis solution for whole genome, whole exome, and targeted panel NGS data.

Our three-step human whole-genome sequencing workflow for research applications provides a fully featured, rapid solution for labs. The resulting WGS delivers high-quality insights across the entire genome for virtually all variant classes.

1
Library Prep

Illumina DNA PCR-free Prep

An efficient, fast, and integrated library preparation workflow for research studies that yields highly accurate data for sensitive sequencing applications.

2
Sequencing

NovaSeq 6000 System

The NovaSeq 6000 System offers deep, broad coverage through advanced applications for a comprehensive view of the genome.

NovaSeq X Series

The NovaSeq X Series delivers extraordinary throughput and accuracy to perform data-intensive applications at production scale.

3
Data analysis

DRAGEN secondary analysis

DRAGEN secondary analysis enables labs of all sizes and disciplines to maximize the value of the genome with powerful, cutting-edge data analysis tools.

Featured workflow products

Illumina DNA PCR-free prep

A high-performing, fast, and integrated workflow for sensitive applications such as human whole-genome sequencing.

NovaSeq X Series

Extraordinary throughput and accuracy to perform data-intensive applications at production scale.

New insights into haplotype phasing

Hear from Tim Steiert, PhD, from the Competence Centre for Genome Analysis Kiel (CCGA) to learn how TruPath Genome unlocks long-range insights from short-read data, how TruPath Genome Phasing compares to long-read approaches and more.

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Bioinformatics innovations

Short-read sequencing with long-range insights

Discover how TruPath Genome and the DRAGEN Germline application fundamentally extend the reach of sequencing-by-synthesis (SBS), enabling long-distance phasing and variant/haplotype discovery in genomic regions that were previously inaccessible.

Advancing genomic research with AI

Explore how Illumina applies AI across the genomic workflow to help researchers gain faster, more accurate, and reproducible insights from complex biological data.

How scientists use human WGS

WGS drives innovation in rare disease research

Dr Matt Might is Professor and Director of the Hugh Kaul Precision Medicine Institute. His son, Bertrand, was the first person diagnosed with NGLY1 deficiency, an ultra-rare disorder.

From exomes to whole genomes

The DRAGEN secondary analysis platform enables GeneDx to scale to whole-genome analysis and identify variants with precision.

XLEAP-SBS

The debut of XLEAP-SBS chemistry

NovaSeq X Series Reagent Kits are powered by a faster, more accurate, and robust update to traditional sequencing by synthesis (SBS) chemistry that supports consistent, reliable data generation for results you can trust. Improvements in XLEAP-SBS reagents allow for shipping and storage in lyophilized form, minimizing environmental impact for significant reductions in packaging size, weight, plastic mass, and waste.

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Related resources

Rare disease genomics

Understanding the genomics of rare diseases can help scientists pinpoint the causes of these disorders.

WGS for rare diseases

Whole-genome sequencing enables researchers to uncover genetic variants associated with rare diseases and detect multiple variant types at once.

Population genomics

Population genomics programs integrate large-scale genomic and clinical data into a learning health system, driving health care innovation.

References

  1. Lionel AC, Costain G, Monfared N, et al. Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test. Genet Med. 2018;20(4):435-443. doi:10.1038/gim.2017.119
  2. Sanghvi RV, Buhay CJ, Powell BC, et al. Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers. Genet Med. 2018;20(8):855-866. doi:10.1038/gim.2017.192
  3. Dolzhenko E, van Vugt JJFA, Shaw RJ, et al. Detection of long repeat expansions from PCR-free whole-genome sequence data. Genome Res. 2017;27(11):1895-1903. doi:10.1101/gr.225672.117
  4. Gross AM, Ajay SS, Rajan V, et al. Copy-number variants in clinical genome sequencing: deployment and interpretation for rare and undiagnosed disease. Genet Med. 2019;21(5):1121-1130. doi:10.1038/s41436-018-0295-yv
  5. Alfares A, Aloraini T, Subaie LA, et al. Whole-genome sequencing offers additional but limited clinical utility compared with reanalysis of whole-exome sequencing. Genet Med. 2018;20(11):1328-1333. doi:10.1038/gim.2018.41
  6. Lindstrand A, Eisfeldt J, Pettersson M, et al. From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. Genome Med. 2019;11(1):68. Published 2019 Nov 7. doi:10.1186/s13073-019-0675-1
  7. Chen X, Sanchis-Juan A, French CE, et al. Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data. Genet Med. 2020;22(5):945-953. doi:10.1038/s41436-020-0754-0
  8. Chen X, Schulz-Trieglaff O, Shaw R, et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016;32(8):1220-1222. doi:10.1093/bioinformatics/btv710