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Related Experiment Video

Updated: Nov 2, 2025

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

Protocol for detecting introgressed archaic variants with SPrime.

Ying Zhou¹, Sharon R Browning²

¹Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

|June 7, 2021

Summary

This summary is machine-generated.

This study introduces SPrime, a tool to detect ancient archaic human DNA (Neanderthal and Denisovan) in modern human populations. A protocol is provided for analyzing Han Chinese data from the 1000 Genomes Project.

Keywords:

Bioinformatics Genetics

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Published on: March 7, 2019

Area of Science:

Human evolutionary genetics
Population genetics
Paleogenomics

Background:

Modern humans carry genetic material inherited from archaic hominins like Neanderthals and Denisovans.
Identifying and characterizing this ancient introgression is crucial for understanding human evolution and adaptation.

Purpose of the Study:

To present the SPrime program for detecting archaic introgression in contemporary human populations.
To provide a specific protocol for identifying Neanderthal and Denisovan introgression in the Han Chinese population (CHB) using 1000 Genomes Project data.

Main Methods:

Utilizing the SPrime software for variant detection.
Applying a detailed protocol to analyze whole-genome sequencing data from the 1000 Genomes Project.
Focusing on the CHB population for specific introgression analysis.

Main Results:

Demonstration of SPrime's capability to identify Neanderthal and Denisovan introgression.
Successful application of the protocol to a specific modern human population (CHB).

Conclusions:

SPrime is an effective tool for detecting archaic introgression.
The provided protocol enables researchers to investigate Neanderthal and Denisovan genetic contributions in specific populations.