The Mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates

Abstract

In the past decade, several studies have estimated the human per-generation germline mutation rate using large pedigrees. More recently, estimates for various non-human species have been published. However, methodological differences among studies in detecting germline mutations and estimating mutation rates make direct comparisons difficult. Here, we describe the many different steps involved in estimating pedigree-based mutation rates, including sampling, sequencing, mapping, variant calling, filtering, and how to appropriately account for false-positive and false-negative rates. For each step, we review the different methods and parameter choices that have been used in the recent literature. Additionally, we present the results from a 'Mutationathon', a competition organized among five research labs to compare germline mutation rate estimates for a single pedigree of rhesus macaques. We report almost a two-fold variation in the final estimated rate among groups using different post-alignment processing, calling, and filtering criteria and provide details into the sources of variation across studies. Though the difference among estimates is not statistically significant, this discrepancy emphasizes the need for standardized methods in mutation rate estimations and the difficulty in comparing rates from different studies. Finally, this work aims to provide guidelines for computational and statistical benchmarks for future studies interested in identifying germline mutations from pedigrees.

Sequence variants affect the genome-wide rate of germline microsatellite mutations

“…Using motif length specific mutation rates and the average number of markers available for each trio to extrapolate to the full set of 1,394,292 microsatellites gives an expected number of 63.7 mDNMs (95% CI: 61.9-65.4) per offspring per generation 32 . This extrapolated number is comparable with the de novo mutational load of SNPs and indels detected through short read sequencing 34,35 .…”

Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans

“…To test the performance of our pipeline for SNM identification, we applied the whole pipeline to trio data from rhesus macaques, as recently used by the ‘Mutationathon’ study (Bergeron, et al 2022). Of the 33 SNMs there validated by PCR, our pipeline recovered 27, which was more than the other presented pipelines ( supplementary fig.…”

“…The central challenge in calling rare heterozygous de novo mutations in highly diverse diploid genomes is to distinguish true mutations from read-mapping errors (Keightley, et al 2014; Bergeron, et al 2022). For each family, we used GATK-version 4.2.2 (McKenna, et al 2010) ‘SelectVariants’ to select single nucleotide variants (SNVs) in the VCF file and then used ‘VariantsToTable’ to extract relevant information for each SNV, including chromosomes (CHROM), positions (POS), reference allele (REF), alternative allele (ALT), genotype (GT), depth (DP), genotype quality (GQ), allele depth (AD), allele depth on forward reads (ADF) and allele depth on reverse reads (ADR).…”

Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes

“…This, again, is similar to the rate we assumed for warthogs. Recently, Zhang et al (2022) used domestic pig pedigrees to estimate a much lower mutation rate of 3.6 × 10 −9 per site per generation, but mutation rates estimated through pedigrees are very sensitive to filtering choices as they depend on the ability to successfully distinguish between low numbers of true de novo mutations and sequencing errors or other artifacts ( Bergeron et al 2022 ). We note that inferred dates scale about linearly with the assumed mutation rate, so our dating estimates can be readily converted should more accurate estimates of the suid mutation rate become available.…”