Merge pull request #16 from quinlan-lab/incorporate_kelley_revision_e…

…dits

Incorporate Kelley revision edits

build/build.sh

@@ -18,7 +18,7 @@ DOCKER_RUNNING="$(docker info &> /dev/null && echo "true" || (true && echo "fals
 # Set option defaults
 CI="${CI:-false}"
 BUILD_PDF="${BUILD_PDF:-true}"
-BUILD_DOCX="${BUILD_DOCX:-false}"
+BUILD_DOCX="${BUILD_DOCX:-true}"
 BUILD_LATEX="${BUILD_LATEX:-false}"
 SPELLCHECK="${SPELLCHECK:-true}"
 MANUBOT_USE_DOCKER="${MANUBOT_USE_DOCKER:-$DOCKER_RUNNING}"

content/01.abstract.md

@@ -8,10 +8,8 @@ DNA replication and repair proteins often recognize particular sequence motifs o
 Thus, we might expect that the spectrum of *de novo* mutations — that is, the frequency of each individual mutation type (C>T, A>G, etc.) — will differ between genomes that harbor either a mutator or wild-type allele at a given locus. 
 Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene *Mutyh* that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs [@PMID:35545679;@PMID:33472028].
 
-> In this study we developed a new method, called "aggregate mutation spectrum distance," to detect alleles associated with mutation spectrum variation. 
-> By applying this approach to mutation data from the BXDs, we confirmed the presence of the germline mutator locus near *Mutyh* and discovered an additional C>A mutator locus on chromosome 6 that overlaps *Ogg1*, a DNA glycosylase involved in the same base-excision repair network as *Mutyh* [@PMID:17581577].
-
+In this study we developed a new method, called "aggregate mutation spectrum distance," to detect alleles associated with mutation spectrum variation. 
+By applying this approach to mutation data from the BXDs, we confirmed the presence of the germline mutator locus near *Mutyh* and discovered an additional C>A mutator locus on chromosome 6 that overlaps *Ogg1*, a DNA glycosylase involved in the same base-excision repair network as *Mutyh* [@PMID:17581577].
 The effect of a chromosome 6 mutator allele depended on the presence of a mutator allele near *Mutyh*, and BXDs with mutator alleles at both loci had even greater numbers of C>A mutations than those with mutator alleles at either locus alone. 
-
 Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles, and may be applicable to mutation data from humans and other model organisms. 
 

content/02.introduction.md

@@ -5,13 +5,13 @@ For example, parental age is an important determinant of mutation rate variabili
 Rates of germline mutation accumulation are also variable across human families [@PMID:26656846;@PMID:31549960], likely due to either genetic variation or differences in environmental exposures.
 Although numerous protein-coding genes contribute to the maintenance of genome integrity, genetic variants that increase germline mutation rates, known as *mutator alleles*, have proven difficult to discover in mammals.
 
-The dearth of observed germline mutators in mammalian genomes is not necessarily surprising, since alleles that lead to elevated germline mutation rates would likely have deleterious consequences and be purged by negative selection [@PMID:27739533].
+The dearth of observed germline mutators in mammalian genomes is not necessarily surprising, since alleles that lead to elevated germline mutation rates would likely have deleterious consequences and be purged by negative selection if their effect sizes are large [@PMID:27739533].
 Moreover, germline mutation rates are relatively low, and direct mutation rate measurements require whole-genome sequencing data from both parents and their offspring.
 As a result, large-scale association studies — which have been used to map the contributions of common genetic variants to many complex traits — are not currently well-powered to investigate the polygenic architecture of germline mutation rates [@PMID:31964835].  
 
 Despite these challenges, less traditional strategies have been used to identify a small number of mutator alleles in humans, macaques [@doi:10.1101/2023.03.27.534460], and mice. 
 By focusing on families with rare genetic diseases, a recent study discovered two mutator alleles that led to significantly elevated rates of *de novo* germline mutation in human genomes [@PMID:35545669]. 
-Another group observed mutator phenotypes in the sperm and somatic tissues of adults who carry cancer-predisposing inherited mutations in the POLE/POLD1 exonucleases [@PMID:34594041].
+Other groups have observed mutator phenotypes in the germlines and somatic tissues of adults who carry cancer-predisposing inherited mutations in the POLE/POLD1 exonucleases [@PMID:34594041;@PMID:37336879].
 Candidate mutator loci were also found by identifying human haplotypes from the Thousand Genomes Project with excess counts of derived alleles in genomic windows [@PMID:28095480].
 
 In mice, a germline mutator allele was recently discovered by sequencing a large family of inbred mice [@PMID:35545679].
@@ -21,21 +21,19 @@ Due to their husbandry in a controlled laboratory setting, the BXDs were largely
 
 In this previous study, whole-genome sequencing data from the BXD family were used to map a quantitative trait locus (QTL) for the C>A mutation rate [@PMID:35545679].
 Germline C>A mutation rates were nearly 50% higher in mice with *D* haplotypes at the QTL, likely due to genetic variation in the DNA glycosylase *Mutyh* that reduced the efficacy of oxidative DNA damage repair.
+Pathogenic variants of *Mutyh* also appear to act as mutators in normal human germline and somatic tissues [@PMID:35803914;@PMID:30753674].
 Importantly, the QTL did not reach genome-wide significance in a scan for variation in overall germline mutation rates, which were only modestly higher in BXDs with *D* alleles, demonstrating the utility of mutation spectrum analysis for mutator allele discovery.
 Close examination of the mutation spectrum is likely to be broadly useful for detecting mutator alleles, as genes involved in DNA proofreading and repair often recognize particular sequence motifs or excise specific types of DNA lesions [@PMID:32619789].
 Mutation spectra are usually defined in terms of $k$-mer nucleotide context; the 1-mer mutation spectrum, for example, consists of 6 mutation types after collapsing by strand complement (C>T, C>A, C>G, A>T, A>C, A>G), while the 3-mer mutation spectrum contains 96 (each of the 1-mer mutations partitioned by trinucleotide context).
 
 Although mutation spectrum analysis can enable the discovery of mutator alleles that affect the rates of specific mutation types, early implementations of this strategy have suffered from a few drawbacks. 
 For example, performing association tests on the rates or fractions of every $k$-mer mutation type can quickly incur a substantial multiple testing burden.
 Since germline mutation rates are generally quite low, estimates of $k$-mer mutation type frequencies from individual samples can also be noisy and imprecise.
-
-> Moreover, inbreeding duration can vary considerably across samples in populations of RILs; for example, some BXDs were inbred for only 20 generations, while others were inbred for nearly 200.
-> As a result, the variance of individual $k$-mer mutation rate estimates in those populations will be much higher than if all samples were inbred for the same duration.
-
+Moreover, inbreeding duration can vary considerably across samples in populations of RILs; for example, some BXDs were inbred for only 20 generations, while others were inbred for nearly 200.
+As a result, the variance of individual $k$-mer mutation rate estimates in those populations will be much higher than if all samples were inbred for the same duration.
 We were therefore motivated to develop a statistical method that could overcome the sparsity of *de novo* mutation spectra, eliminate the need to test each $k$-mer mutation type separately, and enable sensitive detection of alleles that influence the germline mutation spectrum.
 
-> Here, we present a new mutation spectrum association test, called "aggregate mutation spectrum distance," that minimizes multiple testing burdens and mitigates the challenges of sparsity in *de novo* mutation datasets. 
-
+Here, we present a new mutation spectrum association test, called "aggregate mutation spectrum distance," that minimizes multiple testing burdens and mitigates the challenges of sparsity in *de novo* mutation datasets. 
 We leverage this method to re-analyze germline mutation data from the BXD family and find compelling evidence for a second mutator allele that was not detected using previous approaches. 
 The new allele appears to interact epistatically with the mutator that was previously discovered in the BXDs, further augmenting the C>A germline mutation rate in a subset of inbred mice. 
 Our observation of epistasis suggests that mild DNA repair deficiencies can compound one another, as mutator alleles chip away at the redundant systems that collectively maintain germline integrity.