Complex disease research methods

Uncover which methods and applications are best for your research

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Introduction to genomic methods for complex disease research

Complex disease-associated variants are not limited to mutations in the DNA sequence. There are multiple levels of possible sources of variability including transcription and gene expression, and epigenetic modifications. Complex disease research requires the ability to interrogate the genomes, transcriptomes, and epigenomes of multiple individuals across populations to identify genes, gene networks, and pathways that underlie a complex trait. Illumina offers array and NGS solutions and collaborative expertise to support customer success.

Explore popular genomic methods by application

Method Suggested Products

Whole-genome sequencing (WGS)
WGS enables discovery of common variants associated with complex diseases.

Illumina DNA Prep

Human genotyping arrays
Genome-wide genotyping arrays provide a cost-effective solution for common variant discovery through GWAS across and within diverse populations.

Global Screening Array
Global Diversity Array
Asian Screening Array


Method Suggested Products

Whole-genome sequencing (WGS)
WGS enables discovery of common variants associated with complex diseases.

Illumina DNA Prep

Whole-exome sequencing (WES)
WES enables discovery of rare variants within gene coding regions.

Illumina DNA Prep with Enrichment


Method Suggested Products

Targeted genotyping arrays
Targeted arrays enable variant discovery within a particular subset of complex diseases.

Infinium HTS iSelect Custom Beadchips
Infinium ImmunoArray-24 v2 BeadChip Kit

Targeted sequencing
Targeted sequencing enables gene variant confirmation as well as novel variant discovery in known genes.

AmpliSeq for Illumina Custom DNA Panel
Illumina DNA Prep with Enrichment

Method Suggested Products

Total RNA-Seq
Total RNA sequencing enables whole-transcriptome analysis including coding and multiple forms of noncoding RNA.

TruSeq Stranded Total RNA

mRNA-Seq
mRNA sequencing enables analysis of coding RNA across the transcriptome for applications such as eQTL mapping.

TruSeq Stranded mRNA

Single-Cell RNA-Seq
Single-cell RNA sequencing enables whole-transciptome analysis of individual cells, revealing differential responses to environmental stimuli, molecular mechanisms of disease, and interactions in the immune response.

NextSeq 2000 System
Illumina Single Cell 3' RNA Prep

Method Suggested Products

Methylation sequencing
The Illumina 5-base solution enables simultaneous methylation profiling and high-accuracy genetic variant calling.

Illumina 5-Base DNA Prep
Illumina 5-Base DNA Prep with Enrichment

Methylation arrays
Methylation arrays enable cost-effective DNA methylation analysis of coding and noncoding regulatory regions throughout the genome.

Infinium MethylationEPIC Kit

Method Suggested Products

ATAC-Seq
Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-Seq) enables interrogation of chromatin accessibility genome-wide.

Illumina Tagment DNA TDE1 Enzyme and Buffer Kits

Method Suggested Products

ChIP-Seq
Chromatin immunoprecipitation sequencing (ChIP-Seq) enables identification of genome-wide DNA binding sites for transcription factors and other proteins.

TruSeq ChIP Library Prep Kit

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Featured sequencing platforms

NovaSeq 6000 System ordering

Perform powerful high-throughput sequencing studies with the NovaSeq 6000 System. Match data output and time to results to project needs.

MiSeq i100 Series ordering

Simplified operations, advanced chemistry, and onboard informatics provide an easy-to-use, fast, and flexible instrument supporting a broad range of applications.

Featured analysis products

DRAGEN secondary analysis ordering

Maximize genomic insights with Illumina DRAGEN secondary analysis, learn about the latest updates, read FAQs, and find product support.

BaseSpace Sequence Hub ordering

Manage runs, analyze, store, and share sequencing data in BaseSpace Sequence Hub. Find applications, subscription options, and documentation.

Correlation Engine

An interactive omics knowledge base and data search engine that puts private data into biological context with highly curated public omics data.

Featured complex disease literature

Single-Cell sequencing workflow: critical steps and considerations

Download this eBook to learn valuable insights about the single-cell sequencing workflow.

Gene expression profiling with RNA-Seq

RNA sequencing is empowering transcriptomics like never before. Get the complete picture of gene expression profiling here.