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Related Concept Videos

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.
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...

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

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Qxpak.5: old mixed model solutions for new genomics problems.

Miguel Pérez-Enciso1, Ignacy Misztal

  • 1ICREA-CRAG-Universitat Autònoma de Barcelona, Bellaterra, Spain. miguel.perez@uab.es

BMC Bioinformatics
|May 27, 2011
PubMed
Summary

Qxpak v.5 is a versatile statistical genomics software package for sophisticated quantitative trait loci and association analyses. It simplifies complex genetic analyses using mixed models, offering broad applicability and flexibility.

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Area of Science:

  • Statistical genomics
  • Quantitative genetics

Background:

  • Mixed models are versatile statistical tools applicable to various genomics problems.
  • Their theoretical and algorithmic framework accommodates diverse situations.

Purpose of the Study:

  • To introduce Qxpak v.5, a software package for advanced statistical genomics analyses.
  • To enhance capabilities for quantitative trait loci (QTL) and association studies.

Main Methods:

  • Utilizes a unified approach based on mixed models.
  • Accommodates multiple loci, multiple traits, and complex genetic effects (imprinting, epistasis, sex-linked loci).
  • Incorporates relationship matrices from molecular data or user-defined files for genome selection and population structure correction.

Main Results:

  • Qxpak v.5 supports sophisticated analyses including genome selection and population structure correction.
  • The software can model diverse genetic scenarios in crosses, accommodating two parental lines.
  • New features enhance flexibility in handling relationship matrices.

Conclusions:

  • Qxpak software simplifies statistical genetic analyses through a unified mixed model approach.
  • It offers a flexible tool for a wide range of genetic and statistical modeling needs.
  • The software, manual, and examples are available online.