Related Concept Videos
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
01:25What is Population Genetics?
A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, they pass down their genes to their offspring. Many of these genes are polymorphic, meaning that they occur in multiple variants. Such variations of a gene are referred to as alleles. The collective set of all the alleles within a population is known as the gene pool.
01:05Single Nucleotide Polymorphisms-SNPs
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Related Experiment Video
Updated: May 16, 2026
04:52
Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
A population model for genotyping indels from next-generation sequence data.
Haojing Shao1, Evangelos Bellos, Hanjiudai Yin
1BGI-Shenzhen, Shenzhen 518083, China.
Nucleic Acids Research
|December 11, 2012
Summary
Accurate plant and animal genome analysis is improved using a new indel genotyping algorithm. This method significantly reduces errors in low-coverage sequencing data, enhancing genomic variation studies.
Area of Science:
- Genomics
- Bioinformatics
- Population Genetics
Background:
- Insertion and deletion polymorphisms (indels) are key drivers of genomic variation in plants and animals.
- Accurate indel genotyping is difficult with low-coverage and exome next-generation sequencing data.
Purpose of the Study:
- To develop an efficient population clustering algorithm for accurate indel genotyping in diploids and polyploids.
- To address the challenges of genotyping from low-coverage and exome sequencing data.
Main Methods:
- Developed a novel population clustering algorithm for indel genotyping.
- Tested the algorithm on a dataset comprising 2000 exomes.
- Evaluated performance against existing genotyping methods.
Main Results:
- Achieved a 4-fold reduction in overall indel genotype error rates.
- Demonstrated a 9-fold reduction in error rates specifically in low-coverage regions.
- The algorithm proved efficient for both diploid and polyploid species.
Conclusions:
- The new algorithm significantly improves the accuracy of indel genotyping, especially from challenging low-coverage and exome sequencing data.
- This advancement facilitates more reliable genomic variation studies in diverse plant and animal populations.