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Related Concept Videos

Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
Single Nucleotide Polymorphisms-SNPs01:05

Single 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,...
Next-generation Sequencing03:00

Next-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.
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
Genetic Variation01:25

Genetic Variation

Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles, which...
Human Genetics01:28

Human Genetics

Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Current software for genotype imputation.

David Ellinghaus1, Stefan Schreiber, Andre Franke

  • 1Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany. d.ellinghaus@ikmb.uni-kiel.de

Human Genomics
|August 27, 2009
PubMed
Summary
This summary is machine-generated.

Genotype imputation using software like BEAGLE, IMPUTE, and MACH is crucial for genetic association studies. All evaluated programs performed well, but user-friendliness and specific strengths influence software choice.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Genotype imputation for single nucleotide polymorphisms (SNPs) is a standard procedure in genetic association studies.
  • It allows the inclusion of genetic markers without direct genotyping, increasing study power.
  • Several software programs exist for genotype imputation, with user-friendliness often guiding selection.

Purpose of the Study:

  • To evaluate the usability of three publicly available genotype imputation programs: BEAGLE, IMPUTE, and MACH.
  • To compare their performance with HapMap reference data.
  • To identify strengths and weaknesses of each program for different scenarios in genetic association studies.

Main Methods:

  • Usability evaluation of BEAGLE, IMPUTE, and MACH software.
  • Performance assessment using HapMap reference data.
  • Analysis of data preparation and subsequent association analysis effort.

Main Results:

  • All three imputation programs (BEAGLE, IMPUTE, MACH) demonstrated good performance with HapMap data.
  • Minimal effort was required for data preparation and association analysis across the programs.
  • Each program exhibits distinct advantages and disadvantages, indicating no single program is universally optimal.

Conclusions:

  • BEAGLE, IMPUTE, and MACH are effective tools for genotype imputation in genetic association studies.
  • The choice of imputation software should consider specific project needs and user preferences regarding usability.
  • Further evaluation may be needed to determine the best fit for diverse research applications.