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The release of the draft reference human genome sequence in 2001 was undoubtedly one of the most significant achievements of modern biology (1). However, it was immediately realized that if we were to tap the full potential of the sequence information in terms of understanding of genotype-phenotype correlation, mapping disease causing variations, pharmacogenomics and personalized medicine, a large number of individuals need to be sequenced at a much faster pace and at astronomically lesser cost. This led to the advent of next generation sequencing technologies and enabled sequencing of whole genomes with several orders of magnitude reduction in cost and time (2). These technological advancements fuelled several large scale individual sequencing projects (3-8). As of now, data from over 120,000 human genome sequences is currently available in the public domain and a lot is being generated through nationwide projects (9,10), international consortium (6) as well as by consumer genomics companies (11). It is estimated that by 2025 the total number of genome sequences would be anywhere between 100 million to 2 billion (12). With this the variation data will also multiply multiple folds. On an average there are 4.1 million to 5.0 million single nucleotide differences in any two human genomes, suggesting that apart from the raw sequence data, one also needs to cater for 4-5 million variant sites if the comparison was done to reference the human genome alone (4). In disease context, the comparison may have to be done to several normal genomes so as to zoom into the variations responsible for the disease phenotype and subtract the silent ones.
