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

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

16.0K
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...
16.0K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

21.2K
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.
21.2K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.9K
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%...
18.9K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

18.8K
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,...
18.8K
Gene Conversion02:08

Gene Conversion

10.7K
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
10.7K

You might also read

Related Articles

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

Sort by
Same author

Complex structural variation, phylogeny, and disease associations of the mucin pangenome.

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

After hours: surgical end-time and postoperative complications in head and neck microvascular reconstruction.

Oral oncology·2026
Same author

Short-Read Sequencing Benchmarking with Donor-Specific Assemblies.

bioRxiv : the preprint server for biology·2026
Same author

Publisher Correction: Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription.

Nature structural & molecular biology·2026
Same author

3D Volumetric-Based resection modeling to optimize reconstructive outcomes for ablative oral cavity defects.

Oral oncology·2026
Same author

Germline hypomethylation shapes dynamic CpG reservoirs in ape genomes.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Feb 28, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

20.0K

Donor-specific assemblies enhance somatic structural variant detection in complex genomic regions.

Taralynn M Mack1, Jiadong Lin1, Luyao Ren1,2

  • 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.

Biorxiv : the Preprint Server for Biology
|February 27, 2026
PubMed
Summary
This summary is machine-generated.

Donor-specific assemblies (DSAs) significantly improve the detection of somatic structural variants (sSVs) compared to linear references. DSAs identify more validated sSVs, especially in challenging repeat regions, aiding genomic variation studies.

More Related Videos

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

15.8K
Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens
09:33

Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens

Published on: August 25, 2023

1.8K

Related Experiment Videos

Last Updated: Feb 28, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

20.0K
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

15.8K
Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens
09:33

Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens

Published on: August 25, 2023

1.8K

Area of Science:

  • Genomics
  • Cancer Genomics
  • Bioinformatics

Background:

  • Somatic structural variants (sSVs) are crucial in genomic variation and disease.
  • Detecting sSVs is challenging due to reference bias, mosaicism, and repetitive regions.
  • Linear reference genomes (e.g., GRCh38, CHM13) have limitations in capturing individual genomic structures.

Purpose of the Study:

  • To systematically assess the performance of donor-specific assemblies (DSAs) for sSV detection.
  • To benchmark DSA utility against linear references using multiple sSV callers and long-read platforms.
  • To evaluate sSV discovery in the COLO829 melanoma cell line using a matched DSA.

Main Methods:

  • Compared sSV detection using GRCh38, CHM13, and the COLO829BL_DSA.
  • Employed three sSV callers (Delly, Severus, Sniffles2) with long-read sequencing data.
  • Benchmarked performance on the COLO829 melanoma cell line with a matched normal sample.

Main Results:

  • The COLO829BL_DSA identified 1.8-fold more manually validated sSVs than linear references.
  • DSAs detected sSVs in both shared and unique regions, including difficult-to-resolve repeat-rich areas.
  • DSA-specific sSVs were found in genes, some associated with cancer.

Conclusions:

  • Donor-specific assemblies significantly enhance sSV detection capabilities.
  • DSAs are valuable tools for resolving complex structural variations, particularly in repetitive genomic regions.
  • Utilizing DSAs improves the discovery of disease-associated sSVs.