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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
RNA-seq03:21

RNA-seq

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 microarray-based...

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Capturing Chromosome Conformation Across Length Scales
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Capturing Chromosome Conformation Across Length Scales

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Capturing native long-range contiguity by in situ library construction and optical sequencing.

Jerrod J Schwartz1, Choli Lee, Joseph B Hiatt

  • 1Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.

Proceedings of the National Academy of Sciences of the United States of America
|November 1, 2012
PubMed
Summary

This study introduces a novel method for DNA sequencing, enabling longer read lengths for improved genome assembly and structural variation detection. The technique captures contiguity information and primary sequence in a single, efficient process.

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Last Updated: May 17, 2026

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10:15

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Published on: January 20, 2023

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Amplicon Sequencing using the Long-Read Sequencing Technologies
08:57

Amplicon Sequencing using the Long-Read Sequencing Technologies

Published on: August 29, 2025

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Short DNA read lengths from cost-effective sequencing limit de novo genome assembly, structural variation detection, and haplotype-resolved sequencing.
  • A need exists for methods capturing contiguity information at high throughput for massively parallel sequencing.

Purpose of the Study:

  • To propose and demonstrate in situ library construction and optical sequencing for capturing contiguity and primary sequence data simultaneously.
  • To address the limitations of short-read sequencing technologies in complex genomic analyses.

Main Methods:

  • In situ library construction on standard Illumina flow cells.
  • Optical sequencing to capture paired-end reads with varying insert sizes (1-3 kb).
  • Stretching of single DNA molecules (3-8 kb) on flow cell surfaces prior to library construction.

Main Results:

  • >30,000 Escherichia coli paired-end reads generated with 1, 2, or 3 kb separation.
  • Demonstrated feasibility of stretching single DNA molecules to relate physical distance to genomic distance.
  • Successful capture of both contiguity information and primary sequence using a single technology.

Conclusions:

  • In situ library construction and optical sequencing offer an efficient approach to enhance DNA sequencing capabilities.
  • This method has the potential to improve de novo genome assembly, structural variation detection, and haplotype resolution.
  • The technique provides a scalable solution for capturing genomic contiguity information at high throughput.