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Semiconductor Sequencing for Preimplantation Genetic Testing for Aneuploidy

Semiconductor Sequencing for Preimplantation Genetic Testing for Aneuploidy

Published on: August 25, 2019

Noninvasive prenatal paternity testing by target sequencing microhaps.

Xueling Ou¹, Ning Qu¹

¹Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, PR China.

Forensic Science International. Genetics

|June 28, 2020

Summary

Non-invasive prenatal paternity testing (NIPPT) is feasible using cell-free DNA (cfDNA) and microhaplotypes (MHs). This massively parallel sequencing (MPS) method accurately determined paternity in 15 first-trimester cases.

Keywords:

Cell-free DNA (cfDNA)DNA mixtures Massively parallel sequencing (MPS)Microhaps Noninvasive prenatal paternity testing (NIPPT)Single nucleotide polymorphisms (SNPs)

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Area of Science:

Genetics
Forensic Science
Molecular Biology

Background:

Microhaplotypes (MHs) are multi-allelic markers useful in forensics.
Massively parallel sequencing (MPS) enables MH analysis.
Cell-free DNA (cfDNA) in maternal circulation offers non-invasive testing potential.

Purpose of the Study:

Evaluate the feasibility of non-invasive prenatal paternity testing (NIPPT) using polymorphic microhap markers.
Assess the efficacy of a custom MPS-based assay for cfDNA analysis in NIPPT.
Determine paternity with high accuracy using cfDNA and MHs in early pregnancy.

Main Methods:

Developed and applied a custom MPS-based assay targeting 60 microhap markers.
Utilized cfDNA samples from 15 first-trimester NIPPT cases (6-13 weeks gestation).
Employed the R package relMix with a regression dropout model for data interpretation.

Main Results:

Targeted sequencing with hybridization capture effectively sequenced microhaplotypes from cfDNA.
Paternity was correctly determined in all 15 cases with a combined paternity index (CPI) > 10^12.
High specificity was confirmed by excluding close relatives and distinguishing biological fathers from unrelated males.

Conclusions:

MPS-based microhap sequencing is a viable strategy for NIPPT.
This method advances NIPPT capabilities and addresses challenges with DNA mixtures.
The approach offers accurate and reliable paternity determination from maternal cfDNA.