Complex Disease Research Methods

Introduction to Genomic Methods for Complex Disease Research

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
Application Method Suggested Products

Common Variant Discovery

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
Infinium OmniZhongHua-8 Kit
Asian Screening Array
Multi-Ethnic Global-8 Kit

Rare Variant Discovery

WGS enables discovery of rare 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

Variant Confirmation

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


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

AmpliSeq for Illumina Custom DNA Panel
TruSight Cardio Sequencing Kit

Gene Expression/Differential Expression

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

TruSeq Stranded Total RNA

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

Methylation Profiling

Methylation sequencing
Whole-genome bisulfite sequencing (WGBS) and targeted methylation sequencing (Methyl-Seq) enable a deeper understanding of the methylome.

TruSeq Methyl Capture EPIC

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

Infinium MethylationEPIC Kit

Chromatin Accessibility

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

Illumina Tagment DNA TDE1 Enzyme and Buffer Kits

Transcription Factor Binding

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

TruSeq ChIP Library Prep Kit

Featured Sequencing Platforms

MiSeq System
MiSeq System

With the MiSeq System you can access focused applications such as targeted resequencing, metagenomics, small genome sequencing, targeted gene expression profiling, and more. MiSeq reagents enable up to 15 Gb of output with 25 million sequencing reads and 2 × 300 bp read lengths.

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NextSeq 2000
NextSeq 2000

The NextSeq 2000 System supports a broad range of emerging and mid-throughput sequencing applications. The system offers significant reductions in sequencing costs compared to other benchtop sequencing platforms, and secondary analysis in as little as 2 hours.

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The NovaSeq 6000 System
The NovaSeq 6000 System

High-quality, high-coverage sequencing offers a comprehensive view of the genome to detect variants accurately, characterize isoforms, and more. With increased throughput and reduced price per sample, the NovaSeq 6000 System is ideal for data-intensive applications.

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Featured Analysis Products

Illumina DRAGEN Bio-IT Platform
Illumina DRAGEN Bio-IT Platform

The Illumina DRAGEN (Dynamic Read Analysis for GENomics) Bio-IT Platform provides accurate, ultra-rapid secondary analysis of sequencing data.

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BaseSpace Sequence Hub
BaseSpace Sequence Hub

Data management and simplified bioinformatics for labs getting started and for rapidly scaling next-generation sequencing (NGS) operations.

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BaseSpace Correlation Engine
BaseSpace Correlation Engine

BaseSpace Correlation Engine mines over 23,000 (and growing) scientific studies to get data-driven answers for genes, experiments, drugs and phenotypes for your research.

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Featured Complex Disease Literature

Learn valuable insights about the single-cell sequencing
Single-Cell Sequencing Workflow: Critical Steps and Considerations

Want to learn valuable insights about the single-cell sequencing workflow?

Download eBook

Gene Expression Profiling with RNA-Seq
Gene Expression Profiling with RNA-Seq

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

Download eBook