Jove
Visualize
Contact Us
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

Related Experiment Videos

Probe selection algorithm for oligonucleotide array-based medium-resolution genotyping.

Y Zhou1, S Peng, H Gao

  • 1Department of Biological Sciences & Biotechnology, Tsinghua University, Beijing, China.

Medical & Biological Engineering & Computing
|December 14, 2004
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

The distinctive characteristics of the micro-vasculature and immune cell infiltration in cystic pancreatic neuroendocrine tumors.

Journal of endocrinological investigation·2020
Same author

[A summary of China's 70 years of development in diagnosis and treatment targeting corneal diseases].

[Zhonghua yan ke za zhi] Chinese journal of ophthalmology·2020
Same author

[A special on epidemic prevention and control: ophthalmologic research and prevention of 2019 novel coronavirus based on ocular manifestations of viral diseases].

[Zhonghua yan ke za zhi] Chinese journal of ophthalmology·2020
Same author

Transmission of viral pathogens in a social network of university students: the eX-FLU study.

Epidemiology and infection·2020
Same author

Long noncoding RNA UCA1 promotes proliferation and metastasis of thyroid cancer cells by sponging miR-497-3p.

European review for medical and pharmacological sciences·2020
Same author

[Bronchiolar adenoma: a clinicopathological analysis of 15 cases].

Zhonghua bing li xue za zhi = Chinese journal of pathology·2020
Same journal

Anti-aliasing-enhanced WaveUNet for clinically reliable 12-lead ECG reconstruction from limited 3-lead input.

Medical & biological engineering & computing·2026
Same journal

Deep multi-modal features based spatio-temporal video regression for non-invasive hemoglobin estimation.

Medical & biological engineering & computing·2026
Same journal

Reduced mechanical strength correlates with decreased elastin content in aortic intima-media tissue: association with dissection in human ascending aortas.

Medical & biological engineering & computing·2026
Same journal

How plaque morphology and stenosis severity govern stent-artery interaction and deployment outcomes: a computational study.

Medical & biological engineering & computing·2026
Same journal

Investigating a relation between amyloid beta plaque burden and accumulated neurotoxicity caused by amyloid beta oligomers.

Medical & biological engineering & computing·2026
Same journal

A robot-assisted eye positioning method with high precision and repeatability for ocular particle therapy: mechanical and geometric assessment.

Medical & biological engineering & computing·2026
See all related articles

This study introduces a novel algorithm for designing oligonucleotide arrays for medium-resolution genotyping. The method significantly reduces the number of probes needed while maintaining high accuracy in DNA sequencing, making genotyping more cost-effective.

Area of Science:

  • Genetics and Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Medium-resolution genotyping aims to differentiate subgroups within a population.
  • Oligonucleotide arrays offer a cost-effective, high-throughput method for identifying DNA sequence variations essential for genotyping.
  • Increasing probe numbers in array design escalates costs and complexity, necessitating probe selection for efficient medium-resolution genotyping.

Purpose of the Study:

  • To develop and report the first algorithm for designing and selecting probes for oligonucleotide array-based medium-resolution typing.
  • To minimize the number of probes selected from a large set while preserving genotyping resolution.
  • To optimize oligonucleotide array design for cost-efficiency and high-throughput genetic analysis.

Main Methods:

Related Experiment Videos

  • An algorithm based on information theory principles, including entropy, conditional entropy, and mutual information, was developed.
  • The algorithm was designed to select a minimal probe set from a larger collection, minimizing resolution loss.
  • The algorithm's efficacy was validated using human leukocyte antigen (HLA) sequence data.

Main Results:

  • For HLA-A, 30 probes were selected from an initial set of 390, and for HLA-B, 60 probes were selected from 767.
  • Probe count was reduced by approximately tenfold.
  • Distinguishability decreased minimally: 0.45% for HLA-A (99.90% to 99.45%) and 0.27% for HLA-B (99.84% to 99.57%).

Conclusions:

  • The developed algorithm provides a practical and satisfactory method for selecting a minimum number of probes for medium-resolution genotyping.
  • This approach significantly reduces the complexity and cost of oligonucleotide array design.
  • The findings demonstrate a viable strategy for efficient high-throughput genetic analysis using optimized probe sets.