Causal Variant Discovery

High-throughput genomic technologies enable screening of large sample numbers quickly to find disease-related causal variants. Many single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are associated with disease. Causal variant identification can lead to further studies of gene targets to characterize disease mechanisms.

SNP Genotyping to Identify Causal Variants

Large-scale investigations of the genome can be performed using arrays or next-generation sequencing (NGS). These surveys can generate statistically significant disease associations and identify potential causal variants of interest for future studies.

Identifying SNPs Using Arrays

Large-scale genome-wide association studies (GWAS) using arrays enable you to interrogate tens of thousands of samples at one time. GWAS are effective for identifying common variants associated with disease, uncovering multiple genes for further study.

Identifying SNPs Using NGS

While arrays are effective for finding common variants, they are limited in detecting rare variants. Whole-genome and whole-exome sequencing are common approaches for finding causal variants in rare or complex disease cases. Sequencing individuals or trios is a sensitive, unbiased approach to variant detection that can potentially reveal more variants than array-based approaches.

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CNV Detection for Causal Variant Discovery

CNVs are genomic alterations that result in an abnormal number of copies of one or more genes. They are usually caused by structural rearrangements. Like SNPs, certain CNVs have been associated with disease susceptibility.

Detecting CNVs Using Arrays

Array-based approaches for detecting de novo CNVs (not present in or transmitted by either parent) offer efficient and reliable large-scale analysis. You can profile genomic variations such as amplifications, deletions, rearrangements, and copy-neutral loss of heterozygosity.

Illumina offers several types of array solutions for CNV detection, to facilitate causal variant discovery:

  • The CytoSNP-850K BeadChip provides comprehensive coverage of cytogenetically relevant genes correlated with high disease risk.
  • Human genotyping arrays make cost-effective, large-scale genome-wide and phenome-wide association studies possible.

Detecting CNVs Using NGS

While efficient for large CNV detection, genotyping arrays are less sensitive for small CNVs (< 50 kilobases). NGS offers base-pair resolution that can detect the small CNVs missed by arrays. This knowledge can be useful for studies of missing heritability in complex diseases. The high resolution of sequencing complements the high throughput of arrays, enabling a complete view of the genome.

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Next Steps

After a genetic variant is associated with a disease, further study can reveal its effects on gene expression and/or regulation. Learn more about analyzing the downstream effects of disease-associated variants.

Understanding Function Through Genetic Data

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Dr. Tuuli Lappalainen discusses integrating genome and transcriptome sequencing data to understand functional variation in human genomes.
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Complex Disease Research

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Studying Inherited Condition-Associated Causal Variants

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Pharmacogenomics and Cardiovascular Disease

See how researchers used an Illumina microarray to identify responder genotypes in a failed cholesterol drug trial.
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Driving Advances in Psychiatric Genetics Research

Learn how Dr. Abraham Palmer at the University of Chicago uses the HiSeq 2500 System to identify genes that influence behavior.
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NGS Services for Variant Discovery

Illumina FastTrack Sequencing Services offer highly accurate, complete whole genome sequencing.
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