Navigation Links
BGI develops new strategy to uncover structural variations of human genomes
Date:7/25/2011

July 25, 2011 Shenzhen, China -- The study on single-nucleotide resolution structural variations (SVs) of an Asian and African genome was published online in Nature Biotechnology. This study was performed by BGI (previously known as the Beijing Genomics Institute), the largest genomics organization in the world, and demonstrates that whole genome de novo assembly could serve as a new solution for developing a more comprehensive SV map of individuals.

With the rapid development of genomics, more and more experts focus upon the studies of human genome variations by identification and annotation of SNPs in the context of structure, function, and disease. However, recent studies have shown that there are a large number of SVs that have been discovered in the human genome putatively having equal or greater functional impacts than SNPs.

Although many methods have been used to characterize SVs in previous studies, each may have some disadvantages due to technological limitations and the complexity of SVs, making it necessary to find a high accuracy detection method to identify and characterize SVs of human genomes.

"The research focusing on SVs is a real challenge," said Yingrui Li, Director of Science and Technology Department at BGI and the co-lead author of the study, "The study was confronted with many difficulties at the start, such as alignment accuracy, rearranged structure (non-linear), breakpoint recovery, and background noises."

"As a solution," he explained, 'researchers discovered a novel pipeline for detecting SVs in Whole Genome Assembly with a lower cost and faster speed." Based on large-scale genome assembly data from next-generation sequencing technologies, small and intermediate size homozygous SVs (1- 50kbp) can be detected, including insertions, deletions, inversions, and complex rearrangements with precise breakpoints and genotypes previously difficult to define by other approaches.

Through this new method, researchers identified 277,243 SVs, ranging from 1bp to 23kbp in assembled regions of both genomes. Meanwhile, the researchers performed validation using computational and experimental methods and the results indicated a high accuracy of detection. They also carried out characterization of genome-wide patterns of these SVs on different genomic features and studied their potential biological impacts. Profiling using 106 individuals of the 1000 Genomes Project indicates that the extent of diversity in SVs between individuals exceeds that of SNPs. These findings demonstrate whole genome de novo assembly could serve as a new solution to a more comprehensive SV map.

"Here we provide a new method, at a relatively low cost and high speed, to establish in greater detail the presence and patterns of SVs in different genomes, and the results have a high accuracy and a wider range of length spectrum coverage in comparison with previous methods," said Honglong Wu, bioinformatician at BGI and one senior author of the study.

Furthermore, researchers reported, SVs are more individual-specific than SNPs, which may play a significant role underlying the phenotypic differences between individuals. "This study makes us understand we need to consider all kinds of genetic variations and potential differences in their impacts on disease and various other phenotypes in medical genomics studies in the future." added Yingrui Li.

Professor Jun Wang, Executive Director of BGI, said, "With further progresses in de novo assembling by new technologies, assembly-based approaches will be of greater importance and potentially an ultimate solution to SV determination. The study of SVs is likely to attract even more attention in the future."

This study also reveals that de novo assembly can develop more complete personal genomes than resequencing based mapping. Researchers recommend using de novo sequencing technology to decode many more human genomes in the future.


'/>"/>

Contact: Lei Su
BGI-Marketing@genomics.cn
86-075-525-283-805
Beijing Genomics Institute
Source:Eurekalert

Related biology news :

1. Iowa State researcher develops new treatment method for canine eye diseases
2. Hypertension develops early, silently, in African-American men
3. MIT develops new way to fuse cells
4. Fujitsu Develops HDD Security Technology Based on Opal SSC Standards
5. When acute hepatitis develops into chronic hepatitis
6. MIT student develops new innovations to selectively kill cancer cells
7. CSHL team develops mouse models of leukemia that predict response to chemotherapy
8. HudsonAlpha investigator develops rapid response swine flu test
9. Carnegie Mellon develops innovative method to detect genetic causes of complex diseases
10. Epigentek Develops a New Method of Measuring Global DNA Methylation
11. GSU professor develops new method to help keep fruit, vegetables and flowers fresh
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:4/19/2017)... 2017 The global military biometrics ... marked by the presence of several large global players. ... five major players - 3M Cogent, NEC Corporation, M2SYS ... nearly 61% of the global military biometric market in ... global military biometrics market boast global presence, which has ...
(Date:4/13/2017)... 2017 UBM,s Advanced Design and Manufacturing event ... emerging and evolving technology through its 3D Printing and ... alongside the expo portion of the event and feature ... focused on trending topics within 3D printing and smart ... event will take place June 13-15, 2017 at the Jacob ...
(Date:4/11/2017)... Research and Markets has announced the addition of the ... ... to grow at a CAGR of 30.37% during the period 2017-2021. ... been prepared based on an in-depth market analysis with inputs from ... prospects over the coming years. The report also includes a discussion ...
Breaking Biology News(10 mins):
(Date:5/24/2017)... , ... May 23, 2017 ... ... premier provider of high quality relocatable and permanent modular buildings, announced the ... management tools and modern office design characteristics to help support on-site teamwork ...
(Date:5/23/2017)... ... 2017 , ... A recent survey conducted by the Weed Science Society of ... in 12 categories of broadleaf crops, fruits and vegetables, while common lambsquarters ranks as ... Canada participated in the 2016 survey, the second conducted by WSSA. A 2015 ...
(Date:5/23/2017)... ... May 23, 2017 , ... Vortex Biosciences , provider ... isolation of prostate circulating tumor cells using Vortex microfluidic technology ” in Nature Precision ... collaboration with Dr. Dino Di Carlo and Dr. Matthew Rettig at the University of ...
(Date:5/23/2017)... ... May 23, 2017 , ... Customers often prefer ... again and again. METTLER TOLEDO has released two new videos that show how ... integration of the ACT350 into Siemens and Allen Bradley PLCs is easy and ...
Breaking Biology Technology: