Perfect Genome Assembly - BGI's Solution

We came across a paper co-authored by members of Complete Genomics (bought by BGI) and BGI.

Next generation sequencing (NGS) technologies, primarily based on massively parallel sequencing, have touched and radically changed almost all aspects of research worldwide. These technologies have allowed for the rapid analysis, to date, of the genomes of more than 2,000 different species. In humans, NGS has arguably had the largest impact. Over 100,000 genomes of individual humans (based on various estimates) have been sequenced allowing for deep insights into what makes individuals and families unique and what causes disease in each of us. Despite all of this progress, the current state of the art in sequence technology is far from generating a perfect genome sequence and much remains to be understood in the biology of human and other organisms genomes. In the article that follows, we outline why the perfect genome in humans is important, what is lacking from current human whole genome sequences, and a potential strategy for achieving the perfect genome in a cost effective manner.

Strategy -

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FIGURE 1. The concept of read co-barcoding for advanced whole genome sequencing (WGS). All four critical requirements are depicted. (1) A genomic library is prepared from long DNA (e.g., 30300 kb) representing 10 or more cells. Multiple staggered long DNA fragments for each genomic region are generated as a result of random fragmenting during cell lysis (three fragments depicted under each parental chromosome). In the co-barcoded read libraries these redundant long fragments allow variant phasing, a more accurate assembly of the genome, and ultimately de novo assembly. In this example a pair of long proximate repeat elements, longer than the read and mate-pair length, is shown by the large gray boxes. A and C denote single base differences between copies of these repeat elements. Long, overlapping, staggered genomic fragments allow for the proper placement of these repeats in the final assembly by exclusive linking of repeat members to surrounding unique sequences provided by the long DNA fragments that start or end between repeats. (2) Sequence reads generated from each long fragment (i.e., subfragments used to produce these reads) are tagged (small colored curved lines) with the same barcode (co-barcoded). There are many (usually 10s100s) of reads per long DNA fragment, most if not all having the same barcode. Reads belonging to related (i.e., overlapped) long fragments mostly have different barcodes. Consequently maternal (red) and paternal (blue) fragments for a genomic region have different barcodes as indicated by the distinct barcode numbers (253, 112, and X for mom, 27, 367, and Y for dad). After MPS, barcodes are used to aggregate reads from the original long fragment. Such read aggregation, even without sequence assembly per long fragment, provides information for variant phasing and repeat resolving when reads from overlapping long fragments, representing the same chromosome, are used together in the assembly process. (3) Sequence reads must cover >30% and preferably the majority of bases in each long fragment. Consecutive continuous reads (depicted here) or overlapping mate-pair reads (two shorter reads from the ends of the same subfragment) can provide the needed coverage. Sequencing the majority of bases of each fragment with co- barcoded reads links alleles in haplotypes as, on average, 10 or more heterozygous sites occur per long DNA fragment. (4) The read or mate-pair length is longer than the frequent dispersed repeats (e.g., Alu, depicted by the small gray boxes) and are correctly assembled primarily using read level data.

Cost mentioned in the paper - $200/genome