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Illumina sequences African trio genome to benefit disease studies

Illumina : 06 May, 2008  (Company News)
The genomes of an anonymous African Trio (Yoruba from Ibadan, Nigeria) have been completely sequenced by Illumina scientists using the company's Genome Analyzer sequencing platform.
Illumina previously announced the sequencing of the first of these HapMap samples, that of the adult male, in February 2008. The company initiated sequencing of the two additional samples in April and generated an average of 14 fold coverage of each genome within weeks. Illumina scientists were able to rapidly generate the data by incorporating system improvements in the Genome Analyzer that yielded single flowcell runs exceeding 7.5 billion bases (GB) of high-quality data.

In addition, with software improvements which will be commercially available this summer, Illumina scientists have demonstrated that the same runs can yield 10GB of high quality data with 50-base paired end reads. In April, Illumina deposited the sequence data for the adult male into the National Center for Biotechnology Information (NCBI) database, and the Company intends to deposit the sequence data for the female adult and the offspring into the NCBI database to enable researchers anywhere to access and analyse the data.

'The high-quality data generated from the sequencing of this West African Trio is important to enrich our knowledge of human genetic variation in individuals, to map out detailed inheritance patterns in single genomes, and ultimately to identify new mutational events as they arise,' said David Bentley, PhD, vice president and chief scientist at Illumina. 'The data for this trio will be freely available in the public domain to extend and complement ongoing human genetic studies, including the 1000 Genomes Project. As Illumina enables researchers worldwide to routinely generate high-quality individual human-genome sequences our understanding of human genetics and disease will rise to a new level in the coming year.'

Illumina scientists generated over 45GB of high-quality aligned data for each of the adult female and the offspring using recent advances in chemistry, software, and protocols for the Genome Analyzer. These advances include both short insert Paired End reads and long insert Mate Pair reads with both reads at 50 base pairs or longer to increase mapping accuracy; increased cluster density for significantly higher output; and improved algorithms to generate higher quality data. Illumina's unique Paired Read and Mate Pair library generation methods enabled reads in excess of 50 base pairs from each end of a read, with some runs generating reads of up to 75 base pairs from each end of a fragment.

'The latest advances on the Genome Analyzer demonstrate the scalability of the system,' said Christian Henry, acting general manager of Illumina's Sequencing Business. 'We are now internally generating runs of nearly 15GB of data. Furthermore, we have active programmes, which will further increase the read length, the throughput per day, and the quality of the data generated by the Genome Analyzer.

We expect that the combination of these improvements will enable our customers to achieve this level of high-quality data on a single flowcell later this year. These improvements, which rely solely on chemistry and software developments, can be readily implemented on the existing Genome Analyzer platform. By continually working to optimise our system, we will enable our customers to extract more data from their systems and in the process drive the cost per genome sequenced down significantly.'
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