A mitochondrial D loop variant associated with reduced risk of embryonic aneuploidy

Abstract

Mitochondria are integral to oocyte and embryo energy production, spindle formation, and chromosomal segregation. Single nucleotide variants within the mitochondrial genome have been associated with susceptibility to many disease processes, including autoimmune and inflammatory processes. These variants could influence functions essential to early embryo development. The aim of this study was to assess if any association existed between rates of embryonic aneuploidy and sequence variants in the mitochondrial genome. Retrospective genetic association study. All patients underwent IVF at a single center with comprehensive chromosomal screening. 469 patients were identified as either being young with atypically high embryonic aneuploidy rates or older with low aneuploidy rates. Patient DNA was obtained from an on-site repository and used for analysis. Mitochondrial DNA was amplified with Takara LA PCR Kits™ and mitochondria specific primers. Whole genome sequencing was accomplished using an Ion PGM™ system utilizing Ion 318™ Sequencing Chips in order to achieve 20x depth reads. Individual variants were identified by comparing sequence reads to the Cambridge reference sequence. Patients were also assigned a haplogroup using the HaploFind software (https://haplofind.unibo.it). Individual variants and mitochondrial haplogroup frequencies were calculated and compared between the two study populations using logistical regression and chi squared contingency tables. Sequencing revealed 1,475 SNPs amongst 469 tested patients. A variant at position 16,390 (G>A) was significantly more common in patients with low aneuploidy rates (p.0.0008), which survived multiple test correction. Additionally, 443 individuals were assigned into 1 of 9 known European haplogroups (H, I, J, K, T, U, V, W, X) and analyzed in this study. The remaining patients were grouped as other. Haplogroup H contained the largest proportion of patients (41.4%). No association was found between aneuploidy rate and haplogroup inheritance. Although prior studies suggested an association between haplogroup variants and the incidence of oocyte chromosomal errors the present study found no association with a significantly larger sample size. However, with the availability of sequence data for the entire mitochondrial genome a significantly associated single nucleotide variant was identified in patients with lower risk of embryonic aneuploidy. The variant is located within the D-loop, a non-coding region of the mitochondrial genome involved with replication and transcription. It is possible that this variant confers a reproductive advantage given its distinct location. Additional studies need to be performed in order to further investigate the role of this variant in embryo development.