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Updated: Jun 20, 2026

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

Published on: August 17, 2022

Personalized copy number and segmental duplication maps using next-generation sequencing.

Can Alkan¹, Jeffrey M Kidd, Tomas Marques-Bonet

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

Nature Genetics

|September 1, 2009

Summary

This summary is machine-generated.

New algorithm mrFAST accurately maps duplicated regions in genomes. This reveals significant copy number variation in genes, primarily due to segmental duplications, impacting human genetic diversity.

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Area of Science:

Genomics
Bioinformatics
Human Genetics

Background:

Duplicated genomic regions are crucial for gene innovation and phenotypic variation.
Accurately resolving the structure, copy number, and sequence of duplicated regions is challenging.

Purpose of the Study:

To develop a comprehensive algorithm for mapping next-generation sequencing reads.
To enable accurate prediction of absolute copy-number variation in duplicated segments and genes.

Main Methods:

Developed mrFAST, an algorithm for comprehensive next-generation sequence read mapping.
Applied mrFAST to analyze three human genomes.
Experimentally validated genome-wide copy number differences.

Main Results:

mrFAST accurately predicts absolute copy-number variation of duplicated segments and genes.
An average of 73-87 genes per individual exhibit copy number variation.
Genic copy number differences strongly correlate with segmental duplications (OR=135, P<2.2x10^-16).
The method distinguishes highly identical gene copies for precise gene content assessment.

Conclusions:

mrFAST provides a robust method for analyzing complex genomic duplications.
Segmental duplications are a major driver of gene copy number variation in humans.
This approach enhances understanding of functional constraint and genetic diversity.