Jove
Visualize
Contact Us

Related Experiment Videos

Modeling haplotype block variation using Markov chains.

G Greenspan1, D Geiger

  • 1Computer Science Department, Technion, Haifa 32000, Israel. gdg@cs.technion.ac.il

Genetics
|December 20, 2005
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Early use of anakinra in adult-onset Still's disease myocarditis.

Scandinavian journal of rheumatology·2018
Same author

Evaluation of image quality, radiation dose and diagnostic performance of dual-energy CT datasets in patients with hepatocellular carcinoma.

Clinical radiology·2015
Same author

MR-guided focused ultrasound (MRgFUS) ablation for the treatment of nonspinal osteoid osteoma: a prospective multicenter evaluation.

The Journal of bone and joint surgery. American volume·2014
Same author

Visual and quantitative approach to bone marrow foci of increased glucose uptake on PET/CT in a case of aplastic anaemia.

Nuklearmedizin. Nuclear medicine·2010
Same author

Guard cell anion channel SLAC1 is regulated by CDPK protein kinases with distinct Ca2+ affinities.

Proceedings of the National Academy of Sciences of the United States of America·2010
Same author

Preliminary experience with MRA in evaluating the degree of carotid stenosis and plaque morphology using high-resolution sequences after gadofosveset trisodium (Vasovist) administration: comparison with CTA and DSA.

La Radiologia medica·2010
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

This study introduces a Markov chain model for haplotype blocks, improving linkage disequilibrium mapping accuracy. The model excels in regions with strong linkage disequilibrium, outperforming independent block models.

Area of Science:

  • Genomics
  • Statistical Genetics
  • Bioinformatics

Background:

  • Linkage disequilibrium (LD) mapping relies on models of genomic background variation.
  • Current methods often assume independence between haplotype blocks.
  • Accurate modeling of LD is crucial for genetic association studies.

Purpose of the Study:

  • To analyze a novel background model using Markov chains for haplotype blocks.
  • To compare its performance against the independent block model.
  • To understand the model's behavior in relation to linkage disequilibrium and allele diversity.

Main Methods:

  • Developed a Markov chain model representing dependencies between haplotype blocks.
  • Created an error measure to quantitatively compare models.

Related Experiment Videos

  • Utilized data from the International Haplotype Mapping project.

    • Main Results:

    • The Markov model demonstrates superior accuracy in regions with strong linkage disequilibrium.
    • The independent model's accuracy decreases with increasing linkage disequilibrium.
    • Theoretical analysis explains the Markov model's performance based on allele diversity.

    Conclusions:

    • Markov chain modeling of haplotype blocks offers enhanced accuracy for LD mapping.
    • This approach is particularly effective in genetically structured populations.
    • Understanding block dependencies improves genomic region analysis.