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

Accuracy and Errors in Hypothesis Testing01:13

Accuracy and Errors in Hypothesis Testing

198
Hypothesis testing is a fundamental statistical tool that begins with the assumption that the null hypothesis H0 is true. During this process, two types of errors can occur: Type I and Type II. A Type I error refers to the incorrect rejection of a true null hypothesis, while a Type II error involves the failure to reject a false null hypothesis.
In hypothesis testing, the probability of making a Type I error, denoted as α, is commonly set at 0.05. This significance level indicates a 5%...
198
Improving Translational Accuracy02:07

Improving Translational Accuracy

10.3K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
10.3K
Sample Proportion and Population Proportion01:20

Sample Proportion and Population Proportion

5.3K
Collecting samples or responses from an entire population takes significant time and effort, so a researcher collects responses from only a sample of that population. Suppose a study needs to collect information about a specific mobile application. After sample collection, the researcher analyzes the data and discovers that most individuals in the sample use that specific mobile application. The sample proportion measures the number of individuals in a sample who either use or don't use the...
5.3K
What is Population Genetics?01:25

What is Population Genetics?

57.9K
A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, they pass down their genes to their offspring. Many of these genes are polymorphic, meaning that they occur in multiple variants. Such variations of a gene are referred to as alleles. The collective set of all the alleles within a population is known as the gene pool.
57.9K
Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

34.4K
Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
34.4K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.7K
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...
5.7K

You might also read

Related Articles

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

Sort by
Same author

Challenges and recommendations in establishing national human diversity genomic projects.

Nature methods·2026
Same author

Incorporating dietary information to enhance polygenic prediction models with applications to body mass index and type 2 diabetes.

Genes & nutrition·2026
Same author

Meta-analysis of over 8,000 individuals from Hawai'i and Samoa for genetic associations to cardiometabolic phenotypes.

medRxiv : the preprint server for health sciences·2026
Same author

Polygenic predisposition modifies the associations of fish oil supplementation with circulating omega-3 fatty acids: a cross-sectional gene-diet interaction study in UK Biobank.

medRxiv : the preprint server for health sciences·2026
Same author

The Multiethnic Cohort: A Resource for the Study of Genetic and Nongenetic Cancer Risk across Populations.

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology·2026
Same author

Mechanistic Insights into Phenanthrene Uptake in Three Major Crops: Root Exudate Metabolomic Evidence.

Bulletin of environmental contamination and toxicology·2026
Same journal

Comparison of methods for assessing effects of risk factors on disease progression in Mendelian randomization under index event bias.

American journal of human genetics·2026
Same journal

Deciding "what" to screen for and "when": The importance of natural history information.

American journal of human genetics·2026
Same journal

Homologous recombination deficiency-driven genomic instability in ovarian cancer as an indicator of BRCA1 and BRCA2 variant pathogenicity.

American journal of human genetics·2026
Same journal

Individuals who deviate from polygenic expectation are enriched for damaging variants in genes linked to rare disease.

American journal of human genetics·2026
Same journal

Integrating social determinants of health and genetic risk in disease risk models.

American journal of human genetics·2026
Same journal

De novo variants in LDB1 are linked to distinct neurodevelopmental phenotypes determined by variant location and differing pathomechanisms.

American journal of human genetics·2026
See all related articles

Related Experiment Video

Updated: Jun 28, 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

15.2K

Imputation accuracy across global human populations.

Jordan L Cahoon1, Xinyue Rui2, Echo Tang3

  • 1Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA; Department of Computer Science, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA.

American Journal of Human Genetics
|April 11, 2024
PubMed
Summary
This summary is machine-generated.

Genotype imputation accuracy is lower for non-European populations due to underrepresentation in reference panels. Increasing diversity in genetic research is crucial for equitable genomic studies.

More Related Videos

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

39.0K
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.1K

Related Experiment Videos

Last Updated: Jun 28, 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

15.2K
Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

39.0K
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.1K

Area of Science:

  • Genomics
  • Population Genetics
  • Bioinformatics

Background:

  • Genotype imputation is essential for genome-wide association studies (GWAS).
  • Current imputation reference panels, including the Trans-Omics for Precision Medicine (TOPMed) initiative, show underrepresentation of non-European ancestries.
  • This underrepresentation leads to disparities in imputation accuracy across diverse global populations.

Purpose of the Study:

  • To assess global genotype imputation accuracy across diverse populations.
  • To identify specific populations with suboptimal imputation performance.
  • To evaluate the impact of genetic distance from European references on imputation accuracy.

Main Methods:

  • Genotype imputation was performed for over 43,000 individuals across 123 populations.
  • Imputation accuracy was measured using r-squared (Rsq) values, comparing results to sequencing data.
  • A meta-imputation strategy using the Taiwan Biobank was assessed to improve imputation for non-European ancestries.

Main Results:

  • Significant disparities in imputation accuracy were observed, with lower Rsq values for non-European populations compared to European ancestries.
  • Populations such as Saudi Arabians, Vietnamese, Thai, and Papua New Guineans showed notably lower imputation accuracy (Rsq 0.62-0.79) than European populations (Rsq 0.90-0.93).
  • Rsq may overestimate imputation accuracy in non-European groups, and meta-imputation did not universally improve performance.

Conclusions:

  • The underrepresentation of diverse ancestries in imputation reference panels creates significant inequities in genetic research.
  • Improving imputation accuracy for underrepresented populations requires larger and more diverse reference datasets.
  • Increased diversity in genomic data is paramount for advancing equitable and robust genetic discoveries worldwide.