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Pedigree Analysis

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Updated: Oct 20, 2025

Methyl-binding DNA capture Sequencing for Patient Tissues

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

A 2b-RAD parentage analysis pipeline for complex and mixed DNA samples.

Isaac Miller-Crews¹, Mikhail V Matz¹, Hans A Hofmann²

¹Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA.

Forensic Science International. Genetics

|September 12, 2021

Summary

This study introduces a cost-effective genotyping method using 2b-RAD sequencing for accurate parentage analysis. The new pipeline effectively infers familial relationships, even in complex or inbred populations.

Keywords:

2b-RADuencing Combined paternity index Identity-by-state matrix Next-generation sequencing Parentage analysis Paternity testing

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

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Last Updated: Oct 20, 2025

Methyl-binding DNA capture Sequencing for Patient Tissues

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

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:

Population genomics
Molecular ecology
Bioinformatics

Background:

Microsatellite markers are costly and limited for species-specific parentage analysis.
Next-generation sequencing offers advanced genotyping but requires specialized pipelines for parentage.
Existing methods struggle with inbred populations and mixed DNA samples.

Purpose of the Study:

To develop a cost-effective and robust pipeline for parentage analysis using 2b-RAD sequencing.
To infer familial relationships from mixed DNA samples and populations, including inbred individuals.
To overcome limitations of traditional genetic testing methods in complex population structures.

Main Methods:

Utilized 2b-RAD sequencing for uniform fragment generation across samples.
Developed a probabilistic genotyping pipeline incorporating a weighted outlier paternity index (WOPI).
Employed an identity-by-state (IBS) matrix-based clustering for pedigree reconstruction.

Main Results:

Successfully inferred parentage in a highly inbred East African cichlid fish population.
Demonstrated accurate familial relationship inference from pooled offspring samples (clutches).
Validated the pipeline's ability to handle closely related individuals and resolve mixed DNA samples.

Conclusions:

2b-RAD sequencing combined with the developed bioinformatics pipeline offers a versatile solution for parentage analysis.
This approach is cost-effective and applicable across diverse species, irrespective of available genomic resources.
The method effectively addresses challenges posed by inbreeding and mixed samples in genetic testing.