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Related Experiment Video

Updated: Jul 12, 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

A deep population reference panel of tandem repeat variation.

Helyaneh Ziaei Jam¹, Yang Li², Ross DeVito¹

¹Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.

Nature Communications

|October 23, 2023

Summary

This summary is machine-generated.

This study characterizes tandem repeat (TR) genetic variation using whole genome sequencing, developing a new method (EnsembleTR) to genotype over 1.7 million TR loci. The findings offer insights into TRs

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Last Updated: Jul 12, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Published on: June 23, 2012

Digital Polymerase Chain Reaction Assay for the Genetic Variation in a Sporadic Familial Adenomatous Polyposis Patient Using the Chip-in-a-tube Format

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Area of Science:

Genomics
Human Genetics
Population Genetics

Background:

Tandem repeats (TRs) are significant sources of human genetic variation.
TRs are associated with various human phenotypes.
Understanding TR variation is crucial for human genetic studies.

Purpose of the Study:

To deeply characterize tandem repeat (TR) variation in diverse human populations.
To develop and validate a robust method for high-quality TR genotyping.
To create a valuable resource for future research on TRs and human health.

Main Methods:

High-coverage whole genome sequencing of 3550 individuals from the 1000 Genomes Project and H3Africa cohorts.
Development of EnsembleTR, a method integrating genotypes from four separate TR callers.
Genotyping of over 1.7 million TR loci.

Main Results:

Identification of novel sequence features influencing TR heterozygosity.
Discovery of population-specific trinucleotide expansions.
Detection of hundreds of novel TR-associated expression quantitative trait loci (eQTL) signals.
Generation of a phased haplotype panel for accurate TR imputation from single nucleotide polymorphisms (SNPs).

Conclusions:

The EnsembleTR method provides high-quality genotypes across a vast number of TR loci.
The catalog reveals new insights into the genetic architecture and population dynamics of TRs.
The generated TR genotypes and haplotype panel are valuable resources for future genetic studies.
This work advances our understanding of TRs' role in human variation and phenotypes.