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

Combinatorial Gene Control02:33

Combinatorial Gene Control

9.4K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
9.4K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.5K
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%...
18.5K
Law of Independent Assortment02:03

Law of Independent Assortment

62.1K
While Mendel’s Law of Segregation states that the two alleles for one gene are separated into different gametes, a different question of how different genes are inherited remains. For example, is the gene for tall plants inherited with the gene for green peas? Mendel asked this question by experimenting with a dihybrid cross; a cross in which both parents are homozygous for two distinct traits resulting in an F1 generation that are heterozygous for both traits.
62.1K
Sampling Plans01:23

Sampling Plans

842
Sampling is a crucial step in analytical chemistry, allowing researchers to collect representative data from a large population. Common sampling methods include random, judgmental, systematic, stratified, and cluster sampling.
Random sampling is a method where each member of the population has an equal chance of being selected for the sample. It involves selecting individuals randomly, often using random number generators or lottery-type methods. For example, when analyzing the properties of a...
842
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

6.6K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
6.6K

You might also read

Related Articles

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

Sort by
Same author

Likelihood-based optimization enables accurate copy number estimation for paralogous genes using exome data.

Bioinformatics (Oxford, England)·2026
Same author

Single-cell RNA profiling of oligodendroglial lineage cells derived from iPSCs carrying Parkinson's disease-relevant LRRK2-G2019S mutation.

iScience·2026
Same author

Hemophagocytic Lymphohistiocytosis and Fibroblast Growth Factor 23 (FGF23)-Induced Hypophosphatemia.

American journal of kidney diseases : the official journal of the National Kidney Foundation·2026
Same author

Knowledge and perspectives on pharmacogenomic-guided antidepressant treatment among psychiatrists and primary care practitioners.

Pharmacogenetics and genomics·2026
Same author

Analytical Validation of Short-Read Genome Sequencing for Diagnostic Panel and Exome Testing.

The Journal of molecular diagnostics : JMD·2026
Same author

Delivering pharmacogenomic results via electronic health record patient portals: Impacts of health literacy and genetics knowledge.

Patient education and counseling·2026

Related Experiment Video

Updated: Jan 3, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
09:45

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

12.0K

VarCover: Allele Min-Set Cover Software.

Erick R Scott1, Vikas Bansal2, Carl Meacham3

  • 1Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, New York.

The Journal of Molecular Diagnostics : JMD
|November 22, 2019
PubMed
Summary
This summary is machine-generated.

VarCover software helps clinical labs select minimal reference samples for genetic testing. This open-source tool efficiently identifies samples covering targeted alleles, reducing validation costs and lab effort.

More Related Videos

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

3.8K
Competitive Genomic Screens of Barcoded Yeast Libraries
11:59

Competitive Genomic Screens of Barcoded Yeast Libraries

Published on: August 11, 2011

18.7K

Related Experiment Videos

Last Updated: Jan 3, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
09:45

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

12.0K
Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

3.8K
Competitive Genomic Screens of Barcoded Yeast Libraries
11:59

Competitive Genomic Screens of Barcoded Yeast Libraries

Published on: August 11, 2011

18.7K

Area of Science:

  • Genomics
  • Bioinformatics
  • Clinical Genetics

Background:

  • Clinical genetic testing laboratories require efficient reference material selection.
  • Identifying optimal reference sets for variant coverage is challenging.
  • Existing methods may not be computationally efficient for large variant sets.

Purpose of the Study:

  • To develop and evaluate VarCover, an open-source software for selecting a minimum set of reference samples.
  • To streamline the process of identifying reference materials for clinical genetic testing.
  • To reduce the costs and effort associated with molecular genetic test validation.

Main Methods:

  • Developed VarCover software utilizing the SetCoverPy package.
  • Implemented sample weighting based on minor allele frequency.
  • Employed preselection of samples possessing singleton target alleles.
  • Tested VarCover on 237 variants in 56 ACMG-recommended genes using the 1000 Genomes Project dataset.

Main Results:

  • VarCover identified 140 reference samples from the 1000 Genomes Project to cover 237 variants.
  • Sample weighting improved allele coverage in the solution set.
  • Preselection of singleton-possessing samples reduced processing time for larger variant sets.
  • The software provides a programmatic interface for efficient reference set identification.

Conclusions:

  • VarCover offers an efficient solution for selecting minimum reference sample sets for clinical genetic testing.
  • The software reduces the effort and cost of molecular genetic test validation.
  • VarCover's approach enhances the selection of reference materials for covering targeted alleles.