Thermo Fisher Scientific said today it has partnered with The Wellcome Trust Sanger Institute to co-develop the Applied Biosystems Axiom Africa Array, designed to capture genome-wide variation in African populations, as well as Asian and European populations.
The Array, which uses the Axiom genotyping technology of Thermo Fisher’s Applied Biosciences brand, is designed to accelerate and support initiatives in global health and population research by combining Wellcome Trust Sanger’s expertise in human genomic analysis with Thermo Fisher’s in informatics.
Thermo Fisher, which announced the Array’s commercial launch, said the Array will address the need for new tools for genomic studies in Africa, where populations have been shown to have the greatest diversity in their genomes and the highest numbers of continental and population-specific genetic variants.
To begin addressing that need, Wellcome Trust Sanger and the University of Cambridge co-led a whole-genome sequencing effort of 4,956 individuals from populations in Africa to create the African Genome Resources (AGR) haplotype reference panel. AGR was initiated through a collaborative network of scientists, primarily from the African Partnership for Chronic Disease Research, and involved African partner institutes that included the Medical Research Council/Ugandan Virus Research Institute and the University of KwaZulu Natal.
The AGR resource now contains 94.5 million SNPs, of which 21.7 million are unique to AGR. The whole-genome sequencing effort of AGR has encompassed populations from across Africa, including from Ethiopia (Gumuz, Wolayta, Amhara, Oromo, Somali), Egypt, Namibia (Nama/Khoesan) and South Africa (Zulu). Genomes of 2,000 individuals from Uganda (Baganda, Banyarwanda, Barundi and others) were also included.
Axiom Africa Array leverages content from AGR and offers a comprehensive imputation-aware genotyping microarray containing 925,000 variants, according to Thermo Fisher. The array tags at least 90% of common genetic variation in 12 diverse African populations, and also includes pre-selected evidence-based genetic variants important in the context of disease research and pharmacogenomics in global populations. The Axiom Africa Array is supported by AGR, which integrated with 1,000 genomes phase 3, provides a reference panel for imputation.
“We are pleased to see our efforts in this area being translated to a genotyping array that we expect will become the standard for large-scale medical and population genetic studies in Africa, and globally—demonstrated by its ability to also capture genome variation in European and Asian populations,” Dr. Manjinder Sandhu, Ph.D., Senior Group Leader, Global Health & Populations Group at The Wellcome Trust Sanger Institute and the University of Cambridge.
Axiom Africa Array shares all attributes with other Axiom genotyping arrays, including imputation-aware algorithms applied in the development of several biobank arrays in various longitudinal cohort studies.
"We pride ourselves on being the platform of choice to support global medical and population research initiatives that aim to understand genetic risk factors for disease development and on contributing to advancements in medical research for millions of individuals,” added Laurent Bellon, Ph.D., vice president and general manager, microarray business, Thermo Fisher Scientific.
Thermo Fisher Scientific has disclosed details of the Array in a poster presentation, PgmNr 2925/F, at the 2017 Annual meeting of the American Society of Human Genetics.