Tag Archives: Beijing Genomics Institute

Structural Variation in Two Human Genomes Mapped by Whole Genome de novo Assembly

I found the Li et al. paper – “Structural Variation in Two Human Genomes Mapped by Whole Genome de novo Assembly” – published in the August issue of Nature Biotechnology interesting for a number of reasons.  As someone mainly interested in fungal and plant genomics this paper is somewhat outside my research focus, but I found both the novel approach to de novo genome assembly and the emphasis on structural genome variation over single nucleotide polymorphisms (SNPs) in explaining genetic diversity to be very interesting.

By using short read sequencing technology from the Illumina platform, the researchers began by sequencing the genomes of two individuals, one person of African descent (NA18507) and one of Asian descent (YH).  As with many genome sequencing studies, there were numerous problems during the assembly process, such as alignment accuracy, recovery of long contiguous stretches of nucleotides, stretches of low or no coverage, and identifying sequencing background noise.  The authors tried to eliminate these issues by developing a strategy focusing on de novo assembly instead of mapping reads to reference genomes.

The novel pipeline was able to identify structural variants – such as insertions, deletions, rearrangements, inversions, etc. – in each of the homozygous assembled genomes, some of which were upwards of 23,000 base pairs in length.  The researchers then validated the structural variations using both experimental and computational methods, and, using data generated for the 1000 Human Genomes Project, they mapped their identified structural variations in the genomes of 106 other individuals.

While SNPs are easier to observe (perhaps the reasons why they have been emphasized so much in recent years?) it seems that structural rearrangements are perhaps the major form of variation in human genomes, and maybe, all genomes.  Structural variations were less common than SNPs, but are more individual specific and appear to be associated with phenotypic characteristics.  A next research direction would be to observe the association of structural variations to disease traits or susceptibility.

This paper also suggests that accurately assembling long genomic regions are very important to understanding structural variation.  This can be accomplished by either using technologies that naturally generate longer reads (i.e. Sanger or PacBio sequencing) or ensuring that short reads can be accurately assembled by computational methods.

As an aside: this group at BGI (formerly the Beijing Genomics Institute) also sequenced the Giant Panda genome.

Conference on the Progress of the “1000 Plant & Animal Reference Genomes Project”

The organizers of the “Second International Conference on the Progress of the “1000 Plant & Animal Reference Genomes Project” have again announced a call for abstracts for the meeting, which will be held from the 10th to 12th of July in Shenzhen, China.  I’ve noticed a large increase in the number of meetings in China (see here) and this meeting is also sponsored by the Beijing Genomics Institute (BGI).

As you can gather from the name, the “100 Plant and Animal Reference Genome Project” seeks to provide a total of 1000 plant and animal genomes for the use of researchers (For more information on the “1000 Plant and Animal Reference Genomes Project” see here).

This meeting seeks to increase the number of collaborators, particularly from a global perspective, to this project.  To register for this meeting see here, and stay connected to this meeting and the BGI by following them on Twitter (@BGI-Events).  You can even enter yourself in a drawing to win a gift (a soft-drink soda!) when you provide proof you have re-tweeted meeting notices from the BGI.  The meeting with have two sessions: one on the progress and prospects of the 1000 plant and animal reference genome project and another on new developments in sequencing and bioinformatics technology.  There will be five workshops: crop genomics and breeding, aquaculture genomics, vegetable and flower genomics, forest and fruit tree genomics, and rare animal genomics (I’m not really sure what “rare” means in this sense).

Beijing Genomics Institute’s International Conference on Genomics 6

Seems like there are a whole series of symposia right now proclaiming to be the international conference on genomics and I do not know who holds the rights to the title.  I figure more meetings in this research area can’t hurt the state of the science.  The Beijing Genomics Institute has been sponsoring an annual series, The International Conference on Genomics, now on its 6th year, and, despite the name of “international conference”, it’s always held in or around Beijing.

This year’s meeting, The International Conference on Genomics 6 (ICG-VI) aims to promote research in basic and applied genomics by sponsoring a series of presentations focused on new sequencing techniques and bioinformatic strategies.  There will be sessions centered on new sequencing techniques, transcriptomics, epigenomics, metagenomics, proteomics, bioinformatics and data mining, and social issues relating to new genomic information.  Registration for the meeting can be found here.