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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
AbCD: arbitrary coverage design for sequencing-based genetic studies.
Jian Kang1, Kuan-Chieh Huang, Zheng Xu
1Faculty of Kinesiology, University of Calgary, Calgary, AB T2N1N4, Canada.
Bioinformatics (Oxford, England)
|January 30, 2013
Summary
AbCD is a new tool that helps design genetic sequencing studies by estimating effective sample sizes for various coverage levels and ethnic groups. This cost-effective approach aids researchers in planning genetic research efficiently.
Area of Science:
- Genomics
- Bioinformatics
- Population Genetics
Background:
- Advances in sequencing technologies have transformed genetic studies.
- High-coverage sequencing offers comprehensive variant detection but is costly.
- Low-coverage sequencing presents a cost-effective alternative for genetic studies.
Purpose of the Study:
- To introduce AbCD, a user-friendly interface for designing sequencing-based studies.
- To provide pre-estimated effective sample sizes for arbitrary coverage and sample sizes.
- To support study designs across diverse ethnic groups and data combinations.
Main Methods:
- AbCD utilizes pre-estimated effective sample sizes for minor allele frequency categories.
- Two software tools, ShotGun and DesignPlanner, were developed to generate these estimates.
- ShotGun simulates short-read sequencing data with customizable parameters.
- DesignPlanner integrates simulation, SNP discovery, genotype calling, and effective sample size estimation.
Main Results:
- AbCD offers effective sample size estimates for coverage from 0.5-30× and sample sizes from 20-10,000.
- Estimates are provided for four major ethnic groups: Europeans, Africans, Asians, and African Americans.
- The system supports combined data strategies, such as low-depth whole-genome and high-depth exonic sequencing.
Conclusions:
- AbCD facilitates cost-effective design of genetic sequencing studies.
- The tool supports flexible study designs, including combinations of sequencing and existing genotype data.
- AbCD enhances the planning and efficiency of genetic research by providing crucial sample size estimations.
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