Pilot Screening of Cell-Free mtDNA in NIPT: Quality Control, Variant Calling, and Haplogroup Determination.

Alisa Morshneva,Natalia Dvoynova,Anastasia Chentsova,Tatyana Ivashchenko,Olga Talantova,Polina Kozyulina,Elena Serebryakova,Olesya Bespalova,Vladislav Baranov,Igor Kogan,Dmitrii Ivanov,Olga Tarasenko,Aitalina Sukhomyasova,Elena Vashukova,Andrey Glotov,Nadezhda Maksimova,Alexander Koroteev

doi:10.3390/genes12050743

Abstract

Clinical tests based on whole-genome sequencing are generally focused on a single task approach, testing one or several parameters, although whole-genome sequencing (WGS) provides us with large data sets that can be used for many supportive analyses. In spite of low genome coverage, data of WGS-based non-invasive prenatal testing (NIPT) contain fully sequenced mitochondrial DNA (mtDNA). This mtDNA can be used for variant calling, ancestry analysis, population studies and other approaches that extend NIPT functionality. In this study, we analyse mtDNA pool from 645 cell-free DNA (cfDNA) samples of pregnant women from different regions of Russia, explore the effects of transportation and storing conditions on mtDNA content, analyse effects, frequency and location of mitochondrial variants called from samples and perform haplogroup analysis, revealing the most common mitochondrial superclades. We have shown that, despite the relatively low sequencing depth of unamplified mtDNA from cfDNA samples, the mtDNA analysis in these samples is still an informative instrument suitable for research and screening purposes.

Highlights

Discovery of the foetal DNA in maternal plasma made in 1997 by Denis Lo has marked the beginning of a new era in prenatal testing [1]
MtDNA Pool Is Better Presented in cellfree DNA (cfDNA) Samples from Streck Collection Tubes
The same trend can be observed for the mitochondrial DNA (mtDNA) coverage: the vast majority of samples with more than 75% mtDNA coverage belongs to the Streck group (Figure 1B)

Summary

Introduction

Discovery of the foetal DNA in maternal plasma made in 1997 by Denis Lo has marked the beginning of a new era in prenatal testing [1]. DNA (cfDNA)-based testing for foetal Down syndrome detection, the functionality of the method is constantly expanding [2]. CfDNA fraction was reported to contain the full mitochondrial genome [8], compared to fairly low nuclear genomic DNA coverage. This can be explained by the higher copy number and relatively small size of mitochondrial DNA (16,569 bp) in comparison to genomic DNA (3 Gbp) [9]. Mitochondrial genes can undergo natural transfer to nuclear DNA so the nuclear copies of mtDNA (NUMTs) are formed [10]. NUMTs can be a source of contamination in mtDNA analyses [11]

Methods

Results

Conclusion