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Next-generation Sequencing

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....

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Updated: Feb 27, 2026

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

A massively parallel strategy for STR marker development, capture, and genotyping.

Logan Kistler^1,2, Stephen M Johnson², Mitchell T Irwin³

¹Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.

Nucleic Acids Research

|July 2, 2017

Summary

This summary is machine-generated.

This study introduces a new method for recovering short tandem repeat (STR) markers from sequencing data without a reference genome. This approach enables efficient genetic analysis for conservation and ecological studies, even with degraded DNA samples.

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Last Updated: Feb 27, 2026

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Area of Science:

Genetics
Conservation Biology
Bioinformatics

Background:

Short tandem repeats (STRs) are crucial polymorphic markers for population genetics, conservation, and ecological research.
Existing methods for STR recovery are not optimized for scalable, high-throughput sequencing.
Developing new tools is essential for advancing population genetic studies in non-model organisms.

Purpose of the Study:

To develop a novel pipeline for efficient short tandem repeat (STR) marker recovery directly from high-throughput shotgun sequencing data without requiring a reference genome.
To establish a cost-effective and scalable method for generating large STR and single nucleotide polymorphism (SNP) datasets for any species.
To demonstrate the utility of this approach for conservation genetics using endangered lemurs.

Main Methods:

A pipeline was developed to identify and capture STRs from shotgun sequencing data, bypassing the need for a reference genome.
The method was applied to capture 5000 STRs from diademed sifakas (Propithecus diadema).
The approach was further tested using fecal DNA from P. diadema, assessing its robustness and efficiency.

Main Results:

The developed pipeline achieved highly efficient recovery of targeted STR loci (97.3-99.6% with ≥10x coverage) from diademed sifakas.
The method successfully generated large, genome-wide single nucleotide polymorphism (SNP) panels from flanking STR regions.
The STR capture strategy proved robust when tested on fecal DNA, indicating potential for degraded samples.

Conclusions:

This novel method offers a scalable and cost-effective solution for rapid recovery of extensive STR and SNP datasets across diverse species, even without a reference genome.
The approach is particularly valuable for conservation and ecological studies, enabling genetic analysis from suboptimal DNA sources.
The pipeline significantly advances the application of high-throughput sequencing in population genetics and conservation efforts.