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

Improving Translational Accuracy02:07

Improving Translational Accuracy

2.6K
2.6K
Improving Translational Accuracy02:07

Improving Translational Accuracy

11.5K
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...
11.5K
RNA-seq03:21

RNA-seq

9.1K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.1K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

12.2K
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...
12.2K
Homologous Recombination02:31

Homologous Recombination

6.1K
6.1K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

14.1K
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,...
14.1K

You might also read

Related Articles

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

Sort by
Same author

Early Detriment Analysis of First-Line Nivolumab plus Ipilimumab-Based Therapy in Patients with Metastatic Non-Small Cell Lung Cancer.

Clinical cancer research : an official journal of the American Association for Cancer Research·2026
Same author

Adipose Tissue Depots and Blood Pressure Regulation: Mechanisms, Biomarkers, and Targets Beyond Obesity.

American journal of hypertension·2026
Same author

Gdf15 expression in thermogenic adipocytes regulates diet-induced weight gain in a sex-dependent manner.

Molecular medicine (Cambridge, Mass.)·2026
Same author

Analyzing the performance of deep learning splice prediction algorithms.

PloS one·2026
Same author

Bioinformatics strategies and biomarker refinement using high-throughput transcriptome data in transplantation.

Frontiers in bioinformatics·2026
Same author

GFRAL is required to mediate changes in systemic metabolism in response to mitochondrial stress in brown adipose tissue.

Journal of molecular medicine (Berlin, Germany)·2026
Same journal

Guided immunotherapy for residual solid tumor: integrating platelets and CAR T cells to reduce post-surgical recurrence.

Biomarker research·2026
Same journal

Immunological decoding of adult T cell leukemia - its cell of origin and oncogenesis.

Biomarker research·2026
Same journal

Malignant epithelial states drive immune dysfunction in ampulla of Vater carcinoma.

Biomarker research·2026
Same journal

TAF15-mediated m5C modification of MTHFD2 RNA reveals a novel therapeutic target for IDH mutant gliomas.

Biomarker research·2026
Same journal

Biology-aligned cervical cancer screening: target-centric biomarkers and next-generation diagnostic platforms.

Biomarker research·2026
Same journal

CD163<sup>+</sup> macrophages coordinate erythroblastic Island formation and iron metabolism to enable glucocorticoid-induced erythropoiesis.

Biomarker research·2026
See all related articles

Related Experiment Video

Updated: Apr 23, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

23.3K

The use of haplotype-specific transcripts improves sample annotation consistency.

Nicole Hartmann1, Evert Luesink1, Edward Khokhlovich1

  • 1Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland.

Biomarker Research
|October 7, 2014
PubMed
Summary
This summary is machine-generated.

A new transcript marker panel using human leukocyte antigen (HLA) genes can identify sample donor inconsistencies in microarray datasets. This robust method aids pharmacogenomics research by ensuring accurate sample annotation.

Keywords:
BiomarkersDip testHLA-DQA1HLA-DRB4Microarray quality control (QC)mRNA

More Related Videos

Author Spotlight: Decoding RNA Methylation's Role in Pancreatic Cancer - A Single-Base Resolution Study
06:57

Author Spotlight: Decoding RNA Methylation's Role in Pancreatic Cancer - A Single-Base Resolution Study

Published on: July 7, 2023

1.7K
Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
09:30

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Published on: September 13, 2018

7.9K

Related Experiment Videos

Last Updated: Apr 23, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

23.3K
Author Spotlight: Decoding RNA Methylation's Role in Pancreatic Cancer - A Single-Base Resolution Study
06:57

Author Spotlight: Decoding RNA Methylation's Role in Pancreatic Cancer - A Single-Base Resolution Study

Published on: July 7, 2023

1.7K
Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
09:30

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Published on: September 13, 2018

7.9K

Area of Science:

  • Genomics
  • Pharmacogenomics
  • Molecular Biology

Background:

  • Accurate sample annotation is critical for pharmacogenomics research using expression microarray data.
  • Ensuring data integrity is essential for reliable downstream analysis and interpretation.

Purpose of the Study:

  • To develop and validate a novel transcript marker panel for accurate sample annotation in microarray datasets.
  • To assess the utility of human leukocyte antigen (HLA) genes as molecular identifiers for sample fingerprinting.

Main Methods:

  • Applied Hartigan's dip test statistics to a human whole genome microarray dataset to identify candidate markers.
  • Validated marker performance using 188 serial samples from 53 donors across five public microarray datasets with variable tissue origins.

Main Results:

  • A panel of three probe sets, including human leukocyte antigens HLA-DQA1 and HLA-DRB4, was identified as a qualified transcript marker.
  • This panel detected sample donor identifier inconsistencies in 6 out of 188 test samples (approximately 3%).

Conclusions:

  • The developed HLA-DQA1 and HLA-DRB4 transcript marker panel is a robust and tissue-independent tool for improving donor annotation concordance at the transcript level.
  • The allele-selectivity of HLA genes makes them suitable for donor-specific expression pattern "fingerprinting" in genomic studies.