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 Concept Videos

Genetic Screens02:46

Genetic Screens

5.9K
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
5.9K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.2K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
7.2K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

16.6K
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...
16.6K
Genomics02:02

Genomics

41.7K
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...
41.7K

You might also read

Related Articles

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

Sort by
Same author

Solutions to problems of nonexistence of parameter estimates and sparse data bias in Poisson regression.

Statistical methods in medical research·2021
Same author

Association of Rare Coding Mutations With Alzheimer Disease and Other Dementias Among Adults of European Ancestry.

JAMA network open·2019
Same author

Correction to: Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer's disease resilience.

Genome medicine·2018
Same author

Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer's disease resilience.

Genome medicine·2017
Same author

Incorporation of subject-level covariates in quantile normalization of miRNA data.

BMC genomics·2015
Same author

Exploiting Linkage Disequilibrium for Ultrahigh-Dimensional Genome-Wide Data with an Integrated Statistical Approach.

Genetics·2015
Same journal

Geographic distribution of sex chromosome polymorphism in Anastrepha fraterculus sp. 1 from Argentina.

BMC genetics·2020
Same journal

Development and characterization of a pupal-colour based genetic sexing strain of Anastrepha fraterculus sp. 1 (Diptera: Tephritidae).

BMC genetics·2020
Same journal

Improvement on the genetic engineering of an invasive agricultural pest insect, the cherry vinegar fly, Drosophila suzukii.

BMC genetics·2020
Same journal

Precise single base substitution in the shibire gene by CRISPR/Cas9-mediated homology directed repair in Bactrocera tryoni.

BMC genetics·2020
Same journal

Climate stress resistance in male Queensland fruit fly varies among populations of diverse geographic origins and changes during domestication.

BMC genetics·2020
Same journal

Genetic structure and symbiotic profile of worldwide natural populations of the Mediterranean fruit fly, Ceratitis capitata.

BMC genetics·2020
See all related articles

Related Experiment Video

Updated: Mar 28, 2026

Large-Scale Screens of Metagenomic Libraries
16:05

Large-Scale Screens of Metagenomic Libraries

Published on: May 28, 2007

9.3K

A forest-based feature screening approach for large-scale genome data with complex structures.

Gang Wang1, Guifang Fu2, Christopher Corcoran3

  • 1Department of Mathematics and Statistics, Utah State University, 3900 Old Main, Logan, 84322, UT, USA. gang.wang@aggiemail.usu.edu.

BMC Genetics
|December 25, 2015
PubMed
Summary
This summary is machine-generated.

Random Forest (RF) based feature screening effectively identifies complex genetic effects in genome-wide association studies (GWAS). This method surpasses traditional approaches by considering SNP interactions, offering a powerful tool for analyzing large-scale genomic data.

More Related Videos

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
07:35

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

8.1K
Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens
09:33

Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens

Published on: August 25, 2023

1.9K

Related Experiment Videos

Last Updated: Mar 28, 2026

Large-Scale Screens of Metagenomic Libraries
16:05

Large-Scale Screens of Metagenomic Libraries

Published on: May 28, 2007

9.3K
Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
07:35

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

8.1K
Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens
09:33

Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens

Published on: August 25, 2023

1.9K

Area of Science:

  • Genomics
  • Statistical Genetics
  • Bioinformatics

Background:

  • Genome-wide association studies (GWAS) face limitations with increasing SNP numbers and limited sample sizes.
  • Traditional p-value based methods struggle with ultrahigh dimensional genomic data.
  • Feature screening is an effective approach for handling high-dimensional data but is underutilized in GWAS.

Purpose of the Study:

  • To explore the performance of a Random Forest (RF) based feature screening procedure in GWAS.
  • To identify Single Nucleotide Polymorphisms (SNPs) with complex genetic effects, including nonlinear and interactive effects.
  • To evaluate RF's utility for analyzing continuous phenotypes in large-scale genomic datasets.

Main Methods:

  • Utilized a Random Forest (RF) based feature screening procedure.
  • Employed simulation studies and real data analysis to assess the method's power.
  • Compared RF screening with five other popular feature screening approaches.
  • Used Permutation Variable Importance Measure (PVIM) for displaying SNP significance.

Main Results:

  • RF-based feature screening effectively accommodates complex genetic effects like nonlinear, interactive, correlative, and joint effects.
  • The method demonstrated comparable or superior performance to traditional approaches in simulations.
  • Permutation Variable Importance Measure (PVIM) provides valuable information for visualizing SNP significance, similar to traditional Manhattan plots.

Conclusions:

  • RF-based feature screening is an efficient, implementable, and accurate method for analyzing complex whole-genome data.
  • This approach is well-suited for identifying epistatic and polygenic variants regulating complex traits.
  • The study advocates for the broader adoption of feature screening in GWAS to meet the demands of modern genomic data analysis.