Comparison of mitochondrial DNA sequences from whole blood and lymphoblastoid cell lines

Chunyu Liu,Poching Liu,Jessica L Fetterman,Yan Luo,Kaiyu Yan,Jun Zhu,Jun Ding,Daniel Levy,Xianbang Sun

doi:10.1038/s41598-022-05814-7

Abstract

Lymphoblastoid cell lines (LCLs) provide an unlimited source of genomic DNA for genetic studies. Here, we compared mtDNA sequence variants, heteroplasmic or homplasmic, between LCL (sequenced by mitoRCA-seq method) and whole blood samples (sequenced through whole genome sequencing approach) of the same 130 participants in the Framingham Heart Study. We applied harmonization of sequence coverages and consistent quality control to mtDNA sequences. We identified 866 variation sites in the 130 LCL samples and 666 sites in the 130 blood samples. More than 94% of the identified homoplasmies were present in both LCL and blood samples while more than 70% of heteroplasmic sites were uniquely present either in LCL or in blood samples. The LCL and whole blood samples carried a similar number of homoplasmic variants (p = 0.45) per sample while the LCL carried a greater number of heteroplasmic variants than whole blood per sample (p < 2.2e−16). Furthermore, the LCL samples tended to accumulate low level heteroplasmies (heteroplasmy level in 3–25%) than their paired blood samples (p = 0.001). These results suggest that cautions should be taken in the interpretation and comparison of findings when different tissues/cell types or different sequencing technologies are applied to obtain mtDNA sequences.

Highlights

Whole blood and cell lines are two common sources of DNA for genetic studies
With an alternative allele fraction (AAF) 3–97% threshold, we identified 866 sites being homoplasmic and/or heteroplasmic in the 130 Lymphoblastoid cell lines (LCLs) samples; we identified 666 sites in the 130 blood samples (Fig. 1)
The haplogroups identified for the 130 Framingham Heart Study (FHS) participants were identical using the homoplasmies in the 130 LCL and 130 whole blood samples (Supplementary Table 2)

Summary

Introduction

Whole blood and cell lines are two common sources of DNA for genetic studies. In contrast to the a limited supply of DNA from whole blood samples, an Epstein–Barr Virus (EBV) transformed lymphoblastoid cell line (LCL) provides an unlimited source of genomic DNA1. Each cell contains many copies of mtDNA molecules, and mutations can either affect all mtDNA molecules (termed homoplasmy) or a proportion of mtDNA molecules (termed heteroplasmy)[8] To date, it remains unclear if LCL samples is suitable to be used as an unlimited source (i.e., the replacement for whole blood) to study mtDNA sequence variations. Previous study compared the mtDNA sequence variations in independent LCL and blood samples with WES of low depth coverage. Among the above samples, LCL and blood, mtDNA sequencing data from 130 participants (45% women) This present study was aimed to investigate the comparability of mtDNA sequencing variations (homoplasmy and heteroplasmy) between the paired LCL samples and whole blood samples of the same 130 FHS participants. We performed comprehensive and consistent quality control procedures to identify mtDNA sequence variations from the two DNA sources

Methods

Results

Conclusion