Varanto: variant enrichment analysis and annotation

Timonen, Oskari; Särkkä, Mikko; Fülöp, Tibor; Mattsson, Anton; Kekäläinen, Juha; Paananen, Jussi

doi:10.1093/bioinformatics/btz046

Cited by 1 publication

(1 citation statement)

References 18 publications

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“…All figures were made using the ggplot2 package in R (v. 3.5.1). Significance of enrichment within each functional category, PolyPhen and SIFT scores were assessed using Varanto (http://bioinformatics.uef.fi/varanto/), against the reference Ilumina Human660W-Quad [56].…”

Section: Quantification and Statistical Analysis Detecting Natural Sementioning

confidence: 99%

Reconstruction of nine thousand years of agriculture-based diet and impact on human genetic diversity in Asia

Raj

Pei

Foll

et al. 2019

Preprint

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Domestication of crops and animals during the Holocene epoch played a critical role in shaping human culture, diet and genetic variation. This domestication process took place across a span of time and space, especially in Asia. We hypothesize that domestication of plants and animals around the world must have influenced the human genome differentially among human populations to a far greater degree than has been appreciated previously. The range of domesticated foods that were available in different regions can be expected to have created regionally distinct nutrient intake profiles and deficiencies. To capture this complexity, we used archaeobotanical evidence to construct two models of dietary nutrient composition over a 9000 year time span in Asia: one based on Larson et al. (2014) and measured through composition of 8 nutrients, and another taking into account a wider range of crops, cooking and lifestyle variation, and the dietary variables glycemic index and carbohydrate content. We hypothesize that the subtle dietary shifts through time and space have also influenced current human genetic variation among Asians. We used statistical methods BayeScEnv, BayeScan and Baypass, to examine the impact of our reconstructed long-term dietary habits on genome-wide genetic variation in 29 current-day Asian populations ( Figure S1, Figure 1, Figure 2). Our results show that genetic variation in diet-related pathways is correlated with dietary differences among Asian populations. SNPs in five genes, GHR, LAMA1, SEMA3A, CAST and TCF7L2, involved in the gene ontologies 'salivary gland morphogenesis' and 'negative regulation of type B pancreatic cell apoptotic process' suggest that metabolism may have been primary targets of selection driven by dietary shifts. These shifts may have influenced biological pathways in ways that have a lasting impact on health. We present a case that archaeobotanical evidence can provide valuable insight for understanding how historical human niche construction might have influenced modern human genetic variation. Results:The dietary models were constructed to capture different aspects of long-term nutritional information. They incorporate the following unique features: 1) an estimation of a preagricultural diet base, which we term a 'hunter-gatherer diet'; 2) proportionate variation of different dietary components; 3) variation in the length of exposure to dietary components; 4) inclusion of different food processing techniques to obtain nutritional estimates; 5) the use of glycemic index and carbohydrate content to measure nutrition, as both highlight the impact of increased carbohydrate consumption through time and may play a role in diabetes risk [1][2][3]. The first dietary model we constructed examines relative differences in the change of nutrient levels in each of the three ADMIXTURE-defined groups ( Figure S1). In the second model, unlike the first, we incorporate information on pre-domestication diet by including a baseline dietary model for our populations. We assume that the con...

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Section: Quantification and Statistical Analysis Detecting Natural Sementioning

confidence: 99%