Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Genome-wide Association Studies-GWAS

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...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

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...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

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,...

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

Pedigree Analysis

Pedigree Analysis

You might also read

Related Articles

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

Sort by

Same author

Transposable element small RNAs and large RNAs in aging brains and implications in Huntington's and Parkinson's disease.

Genome research·2026

Same author

Whole genome sequencing analysis of over 3500 individuals dementia-free over 85 years old.

Journal of Alzheimer's disease : JAD·2026

Same author

Variant Prioritization by Pedigree-Based Haplotyping.

Genetic epidemiology·2026

Same author

Multiple-testing corrections in case-control studies using identity-by-descent segments.

American journal of human genetics·2026

Same author

The Impact of Structural Variation on Alzheimer's Disease in the Alzheimer's Disease Sequencing Project.

Research square·2026

Same author

Application of the STAAR framework in detecting rare variant associations with Alzheimer disease and related dementias: Insights and implications.

HGG advances·2026

Search research articles

Related Experiment Video

Updated: Jul 14, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies.

Jason M Laramie¹, Jemma B Wilk, Anita L DeStefano

¹Department of Neurology, Boston University School of Medicine, Boston, MA, USA. laramiej@bu.edu

Bioinformatics (Oxford, England)

|June 26, 2007

Summary

This study introduces HaploBuild, a novel program for identifying genetic associations. It constructs biologically relevant haplotypes by analyzing non-contiguous single nucleotide polymorphisms (SNPs), improving upon traditional sliding window methods.

More Related Videos

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

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

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

Published on: June 21, 2018

Related Experiment Videos

Last Updated: Jul 14, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

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

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

Published on: June 21, 2018

Area of Science:

Genetics
Bioinformatics
Computational Biology

Background:

Haplotype association tests are crucial for genetic studies.
Current methods often rely on 'sliding window' approaches for haplotype construction.
These traditional methods can be limited by arbitrary haplotype lengths and contiguous SNP requirements.

Purpose of the Study:

To develop a new computational program, HaploBuild, for haplotype association analysis.
To overcome limitations of existing methods by allowing non-contiguous single nucleotide polymorphisms (SNPs) to define haplotypes.
To enable the construction of more biologically relevant haplotypes.

Main Methods:

Developed a program that searches densely genotyped regions for associated non-contiguous haplotypes.
Employed a standard family-based haplotype association test.
Allowed subsets of single nucleotide polymorphisms (SNPs) to drive haplotype construction, moving beyond fixed-size windows.

Main Results:

HaploBuild successfully identifies associated non-contiguous haplotypes in densely genotyped regions.
The program constructs haplotypes based on biologically relevant SNP combinations, not arbitrary windows.
This approach offers greater flexibility and biological relevance compared to traditional methods.

Conclusions:

HaploBuild provides a powerful new tool for genetic association studies.
The ability to construct non-contiguous haplotypes enhances the biological relevance of findings.
This method expands the capabilities of haplotype-based genetic analysis.