Founder population size, demographic changes (eg. population bottlenecks or rapid expansion) can lead to variation in recombination rates across different populations. Previous research has shown that using population-specific reference panels has a significant effect on downstream population genomic analysis like haplotype phasing, genotype imputation and association, especially in the context of population isolates. Here, we developed a high-resolution recombination rate mapping at 10kb and 50kb scale using high-coverage (20-30x) whole-genome sequenced 55 family trios from Finland and compared it to recombination rates of non-Finnish Europeans (NFE). We tested the downstream effects of the population-specific recombination rates in statistical phasing and genotype imputation in Finns as compared to the same analyses performed by using the NFE-based recombination rates. We found that Finnish recombination rates have a moderately high correlation (Spearman coefficient =0.67-0.79) with NFE, although on average (across all autosomal chromosomes), Finnish rates (2.268±0.4209 cM/Mb) are 12-14% lower than NFE (2.641±0.5032 cM/Mb). Finnish recombination map was found to have no significant effect in haplotype phasing accuracy (switch error rates ~ 2%) and average imputation concordance rates (97-98% for common, 92-96% for low frequency and 78-90% for rare variants). Our results suggest that downstream population genomic analyses like haplotype phasing and genotype imputation mostly depend on population-specific contexts like appropriate reference panels and their sample size, but not on population-specific recombination maps or effective population sizes. Currently, available HapMap recombination maps seem robust for population-specific phasing and imputation pipelines, even in the context of relatively isolated populations like Finland.

中文翻译：

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高分辨率人群特异性重组率及其对分期和基因型估算的影响

创始人人口规模，人口变化（例如人口瓶颈或快速扩张）可能导致不同人群的重组率发生变化。先前的研究表明，使用特定于人群的参考面板对下游人群基因组分析（例如单倍型定相，基因型插补和关联）具有重大影响，尤其是在人群分离的情况下。在这里，我们使用来自芬兰的高覆盖率（20-30x）全基因组测序55家庭三重奏组，开发了10kb和50kb规模的高分辨率重组率图谱，并将其与非芬兰欧洲人（NFE）的重组率进行了比较。与使用基于NFE的重组率进行的相同分析相比，我们在芬兰人的统计定相和基因型估算中测试了特定人群重组率的下游影响。我们发现芬兰重组率与NFE具有中等程度的相关性（Spearman系数= 0.67-0.79），尽管平均而言（在所有常染色体上），芬兰的重组率（2.268±0.4209 cM / Mb）比NFE低12-14％ （2.641±0.5032 cM / Mb）。发现芬兰重组图对单倍型定相准确度（切换错误率〜2％）和平均插补一致性率（常见为97-98％，低频为92-96％，稀有变异为78-90％）没有显着影响）。我们的结果表明，下游种群基因组学分析（如单倍型定相和基因型插补）主要取决于特定人群的情况，例如适当的参考面板及其样本大小，而不取决于特定人群的重组图或有效人群大小。当前，即使在像芬兰这样相对孤立的人群的情况下，可用的HapMap重组图对于特定于人群的定相和插补管线似乎也很健壮。