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

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

14.9K
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...
14.9K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.3K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
18.3K
Significance Testing: Overview01:04

Significance Testing: Overview

8.8K
Significance testing is a set of statistical methods used to test whether a claim about a parameter is valid. In analytical chemistry, significance testing is used primarily to determine whether the difference between two values comes from determinate or random errors. The effect of a particular change in the measurement protocol, analyst, or sample itself can cause a deviation from the expected result. In the case of a suspected deviation/outlier, we need to be able to confirm mathematically...
8.8K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

17.3K
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,...
17.3K
Incomplete Dominance01:43

Incomplete Dominance

28.8K
Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.
28.8K

You might also read

Related Articles

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

Sort by
Same author

Community Disadvantage Is Associated With More Severe Motor Symptoms in Parkinson Disease.

Neurology. Clinical practice·2025
Same author

A multi-omics resource of B cell activation reveals genetic mechanisms for immune-mediated diseases.

medRxiv : the preprint server for health sciences·2025
Same author

Psychosocial Stress and Risk for Intracerebral Hemorrhage in the ERICH (Ethnic/Racial Variations of Intracerebral Hemorrhage) Study.

Journal of the American Heart Association·2025
Same author

The REpeated ASSEssment of SurvivorS in intracerebral haemorrhage: protocol for a multicentre, prospective observational study.

BMJ open·2025
Same author

Digital Otoscopy With Computer-Aided Composite Image Generation: Impact on the Correct Diagnosis, Confidence, and Time.

Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery·2024
Same author

High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus.

Nature communications·2024

Related Experiment Video

Updated: Nov 18, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.5K

Identification of Influential Variants in Significant Aggregate Rare Variant Tests.

Rachel Z Blumhagen1,2, David A Schwartz3, Carl D Langefeld4,5,6

  • 1Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA, rachel.blumhagen@cuanschutz.edu.

Human Heredity
|February 10, 2021
PubMed
Summary
This summary is machine-generated.

The Rare Variant Influential Filtering Tool (RIFT) effectively prioritizes rare variants associated with diseases. RIFT achieves a high true positive rate and low false positive rate, aiding in identifying disease-driving genetic variants.

Keywords:
Genetic association testsIdiopathic pulmonary fibrosisLocalizationRare variants

More Related Videos

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
07:15

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Published on: January 16, 2019

11.2K
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

34.3K

Related Experiment Videos

Last Updated: Nov 18, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.5K
Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
07:15

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Published on: January 16, 2019

11.2K
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

34.3K

Area of Science:

  • Genetics and Genomics
  • Statistical Genetics
  • Computational Biology

Background:

  • Rare genetic variants play a role in complex diseases.
  • Identifying specific causal variants within aggregate sets is challenging.
  • Existing methods for variant prioritization have limitations.

Purpose of the Study:

  • To introduce a novel method for prioritizing rare variants after a significant aggregate association test.
  • To quantify the influence of individual variants on aggregate association tests.
  • To identify a subset of variants that influence disease association.

Main Methods:

  • Developed the Rare Variant Influential Filtering Tool (RIFT) using outlier detection methods (Tukey fences, median absolute deviation, SD).
  • Evaluated RIFT's performance through simulations, comparing true and false positive rates against adaptive combination of p values (ADA) and BeviMed.
  • Applied RIFT to targeted resequencing data from idiopathic pulmonary fibrosis (IPF) studies.

Main Results:

  • RIFT and other outlier detection methods showed higher sensitivity for uncommon variants (0.001 < MAF < 0.03) than very rare variants (MAF < 0.001).
  • RIFT demonstrated a lower median false positive rate than ADA for uncommon variants.
  • Both ADA and RIFT achieved significantly higher true positive rates compared to BeviMed.
  • In IPF data, 6 polymorphisms were identified as highly influential in disease association.

Conclusions:

  • RIFT is an effective tool for prioritizing rare variants in association studies, offering a high true positive rate and low false positive rate.
  • This method enhances the resolution of rare variant signals within aggregate sets.
  • RIFT provides an objective basis for prioritizing variants for experimental validation and understanding biological pathways.