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

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A comparative analysis of current phasing and imputation software.

Adriano De Marino¹, Abdallah Amr Mahmoud¹, Madhuchanda Bose¹

¹Research & Development, SelfDecode, Miami, FL, United States of America.

|October 19, 2022

Summary

This summary is machine-generated.

Beagle5.4, Impute5, and Minimac4 show high accuracy for whole-genome imputation. Beagle5.4 offers faster run times, while Minimac4 uses less memory, aiding genomic data analysis.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Whole-genome data accessibility has surged due to reduced sequencing costs and imputation methods.
Microarray chips combined with imputation enable near whole-genome data generation affordably.
Hidden Markov Models (HMM) are the predominant approach for imputation.

Purpose of the Study:

To compare the performance of leading HMM-based phasing and imputation tools.
To evaluate accuracy, speed, and memory usage across different datasets and chip densities.
To guide users in selecting optimal software and reference panels for imputation.

Main Methods:

Benchmarking of Beagle5.4, Eagle2.4.1, Shapeit4, Impute5, and Minimac4.
Testing on four datasets with varying microarray chip densities.
Assessment of imputation accuracy using concordance rates, IQS, and R2 metrics.
Evaluation of computational resources including run time and memory usage.

Main Results:

Beagle5.4 achieved the highest average concordance rate, followed by Impute5 and Minimac4.
Impute5 and Minimac4 excelled with low-frequency markers, while Beagle5.4 was more accurate for common markers (MAF>5%).
Beagle5.4 demonstrated lower run times; Minimac4 utilized the least memory among imputation tools.

Conclusions:

The choice of imputation tool and metric impacts interpretation of results.
Specific software combinations are best suited for different genomic analysis needs.
An automated pipeline was developed to assist users in creating customized imputation strategies.