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Variation of BMP3 contributes to dog breed skull diversity.

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TLDR
This study reveals the causal variant for a canine QTL contributing to a major morphologic trait and uncovers a missense mutation in BMP3.
Abstract
Since the beginnings of domestication, the craniofacial architecture of the domestic dog has morphed and radiated to human whims. By beginning to define the genetic underpinnings of breed skull shapes, we can elucidate mechanisms of morphological diversification while presenting a framework for understanding human cephalic disorders. Using intrabreed association mapping with museum specimen measurements, we show that skull shape is regulated by at least five quantitative trait loci (QTLs). Our detailed analysis using whole-genome sequencing uncovers a missense mutation in BMP3. Validation studies in zebrafish show that Bmp3 function in cranial development is ancient. Our study reveals the causal variant for a canine QTL contributing to a major morphologic trait.

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A comprehensive transcriptional map of primate brain development

Trygve E. Bakken, +98 more
- 21 Jul 2016 - 
TL;DR: A high-resolution transcriptional atlas of rhesus monkey (Macaca mulatta) brain development is described that combines dense temporal sampling of prenatal and postnatal periods with fine anatomical division of cortical and subcortical regions associated with human neuropsychiatric disease.
Journal ArticleDOI

Genome-wide analysis points to roles for extracellular matrix remodeling, the visual cycle, and neuronal development in myopia

TL;DR: The largest ever genome-wide association study on myopia in Europeans performs a survival analysis on age of myopia onset and identifies 22 significant associations, two of which are replications of earlier associations with refractive error.
Posted Content

Genome-wide analysis points to roles for extracellular matrix remodeling, the visual cycle, and neuronal development in myopia

TL;DR: In this paper, the authors performed a survival analysis on age of myopia onset and identified 19 significant associations (p < 5e-8), two of which are replications of earlier associations with refractive error.
References
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Journal ArticleDOI

The Sequence Alignment/Map format and SAMtools

TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI

PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

TL;DR: This work introduces PLINK, an open-source C/C++ WGAS tool set, and describes the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation, which focuses on the estimation and use of identity- by-state and identity/descent information in the context of population-based whole-genome studies.
Journal ArticleDOI

A method and server for predicting damaging missense mutations.

TL;DR: A new method and the corresponding software tool, PolyPhen-2, which is different from the early tool polyPhen1 in the set of predictive features, alignment pipeline, and the method of classification is presented and performance, as presented by its receiver operating characteristic curves, was consistently superior.
Journal ArticleDOI

R: A Language for Data Analysis and Graphics

TL;DR: In this article, the authors discuss their experience designing and implementing a statistical computing language, which combines what they felt were useful features from two existing computer languages, and they feel that the new language provides advantages in the areas of portability, computational efficiency, memory management, and scope.
Journal ArticleDOI

ggplot2: Elegant Graphics for Data Analysis

TL;DR: ggplot2 as mentioned in this paper is an implementation in R of The Grammar of Graphics, a systematic approach to the specification of statistical graphics that was introduced in a book previously reviewed in the Journal of Statistical Software by Cox (2007).
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