MitoH3: Mitochondrial Haplogroup and Homoplasmic/Heteroplasmic Variant Calling Pipeline for Alzheimer's Disease Sequencing Project

Congcong Zhu; Tong Tong; John J Farrell; Eden R Martin; William S Bush; Margaret A Pericak-Vance; Li-San Wang; Gerard D Schellenberg; Jonathan L Haines; Kathryn L Lunetta; Lindsay A Farrer; Xiaoling Zhang

doi:10.3233/ADR-230120

MitoH3: Mitochondrial Haplogroup and Homoplasmic/Heteroplasmic Variant Calling Pipeline for Alzheimer's Disease Sequencing Project

J Alzheimers Dis Rep. 2024 Apr 8;8(1):575-587. doi: 10.3233/ADR-230120. eCollection 2024.

Authors

Congcong Zhu¹, Tong Tong^{1

2}, John J Farrell¹, Eden R Martin³, William S Bush⁴, Margaret A Pericak-Vance³, Li-San Wang⁵, Gerard D Schellenberg⁵, Jonathan L Haines⁴, Kathryn L Lunetta⁶, Lindsay A Farrer^{1

2

6

7

8

9

10

11}, Xiaoling Zhang^{1

2

6

10

11}

Affiliations

¹ Department of Medicine (Biomedical Genetics), Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
² Bioinformatics Program, Boston University, Boston, MA, USA.
³ John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.
⁴ Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
⁵ Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
⁶ Departments of Biostatistics Boston University School of Public Health, Boston, MA, USA.
⁷ Departments of Epidemiology, Boston University School of Public Health, Boston, MA, USA.
⁸ Departments of Neurology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
⁹ Departments of Ophthalmology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
¹⁰ Framingham Heart Study, Boston University School of Medicine, Framingham, MA, USA.
¹¹ Alzheimer's Disease Research Center, Boston University School of Medicine, Boston, MA, USA.

Abstract

Background: Mitochondrial DNA (mtDNA) is a double-stranded circular DNA and has multiple copies in each cell. Excess heteroplasmy, the coexistence of distinct variants in copies of mtDNA within a cell, may lead to mitochondrial impairments. Accurate determination of heteroplasmy in whole-genome sequencing (WGS) data has posed a significant challenge because mitochondria carrying heteroplasmic variants cannot be distinguished during library preparation. Moreover, sequencing errors, contamination, and nuclear mtDNA segments can reduce the accuracy of heteroplasmic variant calling.

Objective: To efficiently and accurately call mtDNA homoplasmic and heteroplasmic variants from the large-scale WGS data generated from the Alzheimer's Disease Sequencing Project (ADSP), and test their association with Alzheimer's disease (AD).

Methods: In this study, we present MitoH3-a comprehensive computational pipeline for calling mtDNA homoplasmic and heteroplasmic variants and inferring haplogroups in the ADSP WGS data. We first applied MitoH3 to 45 technical replicates from 6 subjects to define a threshold for detecting heteroplasmic variants. Then using the threshold of 5% ≤variant allele fraction≤95%, we further applied MitoH3 to call heteroplasmic variants from a total of 16,113 DNA samples with 6,742 samples from cognitively normal controls and 6,183 from AD cases.

Results: This pipeline is available through the Singularity container engine. For 4,311 heteroplasmic variants identified from 16,113 samples, no significant variant count difference was observed between AD cases and controls.

Conclusions: Our streamlined pipeline, MitoH3, enables computationally efficient and accurate analysis of a large number of samples.

Keywords: Alzheimer’s disease; haplogroup; homoplasmic and heteroplasmic variant calling; mitochondrial DNA; whole genome sequencing.