Related Experiment Video
Updated: Apr 14, 2026
09:34
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
35.1K
Analysis of human triallelic SNPs by next-generation sequencing
Min Cao1, Juan Shi1, Jiqiu Wang1
1Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Department of Endocrinology and Metabolism, Shanghai Key Laboratory for Endocrine Tumors and E-Institute of Shanghai Universities, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, China.
Annals of Human Genetics
|April 25, 2015
Summary
This study identified 2,002 triallelic single-nucleotide polymorphisms (SNPs) in Chinese individuals using next-generation sequencing. These triallelic SNPs, particularly coding variants, may be influenced by natural selection, warranting further investigation.
Area of Science:
- Genetics
- Genomics
- Population Genetics
Background:
- Single-nucleotide polymorphisms (SNPs) are crucial for studying genetic variation.
- Triallelic SNPs, a specific type of SNP with three possible alleles, remain understudied.
- Next-generation sequencing (NGS) offers a powerful method for identifying triallelic sites in large populations.
Purpose of the Study:
- To identify and characterize triallelic single-nucleotide polymorphisms (SNPs) in a Chinese population.
- To investigate the frequency, novelty, and functional implications of triallelic SNPs.
- To explore the potential influence of natural selection on triallelic SNP evolution.
Main Methods:
- Exome sequencing data from 221 Chinese individuals were analyzed.
- High-depth sequencing (average 70-fold coverage) was employed.
- Identification and characterization of single-nucleotide polymorphisms (SNPs), including triallelic sites.
Main Results:
- A total of 382,901 SNPs were identified, with 2,002 (0.52%) being triallelic sites.
- Among triallelic SNPs, 17.3% were coding SNPs (cSNPs), and 78.3% were novel.
- Variant alleles at triallelic sites were more likely to cause nonsynonymous variations, suggesting functional impact.
- Evidence suggests natural selection may play a role in the evolution of triallelic SNPs.
Conclusions:
- Triallelic SNPs are a notable component of genetic variation, with a significant proportion being novel coding variants.
- These sites exhibit a propensity for nonsynonymous changes and appear to be under the influence of natural selection.
- Further research with larger sample sizes is necessary to fully elucidate the characteristics and evolutionary significance of triallelic SNPs.
Related Concept Videos
03:00Next-generation Sequencing
101.9K
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....
101.9K
01:05Single Nucleotide Polymorphisms-SNPs
20.1K
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,...
20.1K
01:57Sanger Sequencing
780.2K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
780.2K
02:26Comparing Copy Number Variations and SNPs
19.4K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
19.4K
03:21RNA-seq
12.7K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
12.7K
01:29Modern Molecular Taxonomy
861
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
861