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Related Concept Videos

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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...
Pharmacogenetic Phenotypes: Alterations in Pharmacokinetics, Drug Targets and Biologic Milieu01:29

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Genetic variations significantly influence drug response through pharmacokinetics, receptor interactions, and biologic milieu modifications. Pharmacokinetic alterations impact drug metabolism and clearance, affecting efficacy and toxicity. Variants in drug-metabolizing enzymes, such as CYP2C9 and CYP2C19, alter drug activation and elimination. For example, CYP2C9 loss-of-function variants require lower warfarin doses to prevent excessive bleeding, while CYP2C19 variants reduce clopidogrel...
Pharmacogenomics: Identification of New Drug Targets01:29

Pharmacogenomics: Identification of New Drug Targets

Advances in genomics have profoundly influenced drug discovery by increasing both the speed and accuracy of pharmaceutical development. Pharmacogenomics, which examines how genetic variation influences drug response, facilitates the identification of novel therapeutic targets and enables patient stratification for personalized treatment. These strategies contribute to improved drug efficacy, minimized adverse effects, and more efficient clinical trial design.Mapping genetic differences...
Polygenic Traits01:18

Polygenic Traits

When more than one gene is responsible for a given phenotype, the trait is considered polygenic. Human height is a polygenic trait. Studies have uncovered hundreds of loci that influence height, and there are believed to be many more. Due to the high number of genes involved, as well as environmental and nutritional factors, height varies significantly within a given population. The distribution of height forms a bell-shaped curve, with relatively few individuals in the population at the...
Polygenic Traits01:18

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Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...

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Updated: May 15, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects.

Sriram Pendyala1, Katie Partington2, Nicholas Bradley3

  • 1Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA.

Cell
|May 13, 2026
PubMed
Summary
This summary is machine-generated.

Variant in situ sequencing (VIS-seq) reveals how genetic variants affect cell structure and protein behavior. This new imaging method captures complex phenotypic changes, aiding in understanding disease-associated variants.

Keywords:
functional genomicsgenetic variationmultiplexed assays of variant effectoptical pooled screeningpleiotropy

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Area of Science:

  • Genomics
  • Cell Biology
  • Bioinformatics

Background:

  • Genetic variants often have complex phenotypic effects that are difficult to measure with current methods.
  • Understanding these effects is crucial for diagnosing and treating genetic diseases.

Purpose of the Study:

  • To develop and validate a novel method, variant in situ sequencing (VIS-seq), for comprehensively assessing variant effects on cellular phenotypes.
  • To apply VIS-seq to a large set of LMNA and PTEN variants to characterize their impact on molecular and cellular phenotypes.

Main Methods:

  • VIS-seq is a pooled, image-based assay that measures variant effects on molecular and cellular phenotypes across diverse cell types.
  • The method generates high-dimensional morphological profiles by analyzing cell images at scale.
  • Applied to ~3,000 LMNA and PTEN variants.

Main Results:

  • VIS-seq successfully captured detailed phenotypic profiles, including changes in protein abundance, localization, activity, and cell architecture.
  • Specific LMNA variant subsets were linked to distinct changes in nuclear circularity.
  • Autism-associated PTEN variants were identified as mislocalized, and VIS-seq distinguished them from control and other disease-linked variants.
  • Most variants affected a complex phenotypic continuum not detectable by single readouts.

Conclusions:

  • VIS-seq provides a powerful framework for dissecting the complex, multi-dimensional phenotypic effects of genetic variants.
  • The method links genetic variants to cellular phenotypes at scale, illuminating how molecular changes cascade to affect cellular structures and function.
  • VIS-seq offers a new approach to resolve the complexity of variant function and its role in disease.