De novo mutations in children born after medical assisted reproduction

Abstract

STUDY QUESTION Are there more de novo mutations (DNMs) present in the genomes of children born through medical assisted reproduction (MAR) compared to spontaneously conceived children? SUMMARY ANSWER In this pilot study, no statistically significant difference was observed in the number of DNMs observed in the genomes of MAR children versus spontaneously conceived children. WHAT IS KNOWN ALREADY DNMs are known to play a major role in sporadic disorders with reduced fitness such as severe developmental disorders, including intellectual disability and epilepsy. Advanced paternal age is known to place offspring at increased disease risk, amongst others by increasing the number of DNMs in their genome. There are very few studies reporting on the effect of MAR on the number of DNMs in the offspring, especially when male infertility is known to be affecting the potential fathers. With delayed parenthood an ongoing epidemiological trend in the 21st century, there are more children born from fathers of advanced age and more children born through MAR every day. STUDY DESIGN, SIZE, DURATION This observational pilot study was conducted from January 2015 to March 2019 in the tertiary care centre at Radboud University Medical Center. We included a total of 53 children and their respective parents, forming 49 trios (mother, father and child) and two quartets (mother, father and two siblings). One group of children was born after spontaneous conception (n = 18); a second group of children born after IVF (n = 17) and a third group of children born after ICSI combined with testicular sperm extraction (ICSI-TESE) (n = 18). In this pilot study, we also subdivided each group by paternal age, resulting in a subgroup of children born to younger fathers (<35 years of age at conception) and older fathers (>45 years of age at conception). PARTICIPANTS/MATERIALS, SETTING, METHODS Whole-genome sequencing (WGS) was performed on all parent-offspring trios to identify DNMs. For 34 of 53 trios/quartets, WGS was performed twice to independently detect and validate the presence of DNMs. Quality of WGS-based DNM calling was independently assessed by targeted Sanger sequencing. MAIN RESULTS AND THE ROLE OF CHANCE No significant differences were observed in the number of DNMs per child for the different methods of conception, independent of parental age at conception (multi-factorial ANOVA, f(2) = 0.17, P-value = 0.85). As expected, a clear paternal age effect was observed after adjusting for method of conception and maternal age at conception (multiple regression model, t = 5.636, P-value = 8.97 × 10−7), with on average 71 DNMs in the genomes of children born to young fathers (<35 years of age) and an average of 94 DNMs in the genomes of children born to older fathers (>45 years of age). LIMITATIONS, REASONS FOR CAUTION This is a pilot study and other small-scale studies have recently reported contrasting results. Larger unbiased studies are required to confirm or falsify these results. WIDER IMPLICATIONS OF THE FINDINGS This pilot study did not show an effect for the method of conception on the number of DNMs per genome in offspring. Given the role that DNMs play in disease risk, this negative result is good news for IVF and ICSI-TESE born children, if replicated in a larger cohort. STUDY FUNDING/COMPETING INTEREST(S) This research was funded by the Netherlands Organisation for Scientific Research (918-15-667) and by an Investigator Award in Science from the Wellcome Trust (209451). The authors have no conflicts of interest to declare. TRIAL REGISTRATION NUMBER N/A.

Comparing Clinical and Genetic Characteristics of De Novo and Inherited COL1A1/COL1A2 Variants in a Large Chinese Cohort of Osteogenesis Imperfecta

“…Errors in DNA replication, exposure to mutagens, or failure to repair DNA damage can result in de novo mutations ( 12 ). Nowadays, advanced paternal age at conception has been considered the predominant factor associated with an increasing number of de novo mutations ( 9 , 11 , 42 , 43 ). However, in our study, the average paternal age at conception was 29.2 years, significantly younger than the data of the US ( 29 ).…”

“…In addition, Wong et al (44) reported that medically assisted conception would increase the incidence of de novo mutations compared with natural conception. However, recently, a pilot study by Smits et al (11) showed no impact of assisted reproductive technologies on the number of de novo mutations in the genome of the offspring. In our study, the majority of the pedigrees (98.04%) with de novo mutations were spontaneous conception, which limited us to investigate the impact of different methods of conception on de novo mutations.…”

“…Approximately 80% of all de novo germline point mutations occur on the paternal allele because oocytes experience only one additional round of DNA replication during their evolution into a mature ovum, whereas spermatogonia will encounter hundreds of DNA replication and cell fission before becoming sperm cells. What's more, it has been demonstrated that most types of de novo mutations are much more correlated with increased paternal age at birth (9)(10)(11). Rare sporadic diseases in the population are associated with de novo mutations (12).…”

Phasing of de novo mutations using a scaled-up multiple amplicon long-read sequencing approach

“…Supplementary Table 9 Dataset from Smits et al, 2022 used to calculate the percentage of DNMs that have an iSNP within 5kb ranges.…”

“…Cases where an iSNP could not be found in the coding region had primers designed to cover 5 kb regions around the DNM position for parent and proband samples (Figure 1.b3). We chose the 5 kb region based on the analysis of 4344 DNMs identified in 53 whole genome sequenced individuals/children (Smits et al, 2022). This revealed the presence of at least 1 iSNP within 5 kb of any given DNM in 81% of cases (Supplementary Tables 8 and 9).…”