Illumina to Conduct Large-Scale Genotyping Study

Illumina, Inc. has announced that it has signed a multi-phase genotyping services agreement to support colorectal cancer researchers funded by Cancer Research UK.

The multi-million dollar agreement extends over several years and includes two major phases.

In the first phase of the project, Illumina's service group will conduct dense, whole-genome genotyping (500,000 single nucleotide polymorphisms, or SNPs, per sample) for at least 4,000 well-classified colorectal patients and controls.

In the second phase, Illumina will genotype over 10,000 samples using a custom, multi-sample BeadChip that will enable analysis of 20,000 SNPs per sample.

Both phases will use Illumina's Sentrix® Arrays and Infinium™ Assay with the option to employ related assay methods.

Illumina's genotyping services group will support work being driven scientifically by a collaboration comprising two major Cancer Research UK-funded research groupings in the UK investigating the genetic basis of colorectal cancer.

The aim of the work is to investigate the role of common genetic variation in the etiology of large bowel cancer.

Harpal Kumar, Chief Operating Officer of Cancer Research UK, describes the study as “fully consistent with our organizational objective of conducting world-class research into the biology and causes of cancer.”

“We're very keen to work with Illumina on this project and we believe that the results will help Cancer Research UK pave the way for better understanding of cancer and improved quality of life for cancer patients,” Kumar stated.

Phase I of the project will include at least 4,000 well-classified colorectal patients and controls.

Each sample will be genotyped with the Sentrix HumanHap-1 BeadChip and the Sentrix HumanHap-1S BeadChip using Illumina's Infinium assay.

SNP content for the two BeadChips is derived largely from high-value TagSNPs identified in the recently completed HapMap Project.

Together, the two BeadChips will enable genotyping of over 500,000 SNPs per sample, with comprehensive genomic coverage and industry-leading data quality.

Phase I will focus predominantly on: 1) finding candidate genes that may confer susceptibility to colorectal cancer; 2) charting the prevalence of genetic mutations and associated risk factors in these genes; and 3) understanding how these factors affect the epidemiology, or progression, of the disease.

Following analysis of Phase I data, Illumina will develop a custom, multi-sample BeadChip that enables the study of 20,000 SNPs per sample using the Infinium assay.

Research teams will analyze data from over 10,000 samples genotyped on the custom BeadChip with the goal of identifying low-prevalence, high-effect markers and functionally important SNPs exhibiting unequivocal association to colorectal cancer and disease predisposition.

“We're very pleased to be working with Cancer Research UK to help their research teams gain insight into the genetic basis of colorectal cancer,” said Jay Flatley, Illumina President and CEO.

“To our knowledge, this will be the largest and most informative genotyping study of its kind ever conducted.”

“The study design is made possible by the HapMap-derived tools that will allow Illumina to perform very efficient whole-genome genotyping, providing the Edinburgh and London Research teams the statistical power for significant cancer discovery.”