scispace - formally typeset
Search or ask a question
Author

Adam Auton

Other affiliations: Broad Institute, Cornell University, University of Oxford  ...read more
Bio: Adam Auton is an academic researcher from Albert Einstein College of Medicine. The author has contributed to research in topics: Genome-wide association study & Population. The author has an hindex of 47, co-authored 94 publications receiving 51799 citations. Previous affiliations of Adam Auton include Broad Institute & Cornell University.


Papers
More filters
Journal ArticleDOI
TL;DR: The largest genetic study to date of morphology in domestic dogs identifies genes controlling nearly 100 morphological traits and identifies important trends in phenotypic variation within this species.
Abstract: Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (≤3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species.

431 citations

Journal ArticleDOI
Richard Karlsson Linnér1, Richard Karlsson Linnér2, Pietro Biroli3, Edward Kong4, S. Fleur W. Meddens1, S. Fleur W. Meddens2, Robbee Wedow, Mark Alan Fontana5, Mark Alan Fontana6, Maël Lebreton7, Stephen P. Tino8, Abdel Abdellaoui2, Anke R. Hammerschlag2, Michel G. Nivard2, Aysu Okbay2, Cornelius A. Rietveld1, Pascal Timshel9, Pascal Timshel10, Maciej Trzaskowski11, Ronald de Vlaming2, Ronald de Vlaming1, Christian L. Zund3, Yanchun Bao12, Laura Buzdugan13, Laura Buzdugan3, Ann H. Caplin, Chia-Yen Chen14, Chia-Yen Chen4, Peter Eibich15, Peter Eibich16, Peter Eibich17, Pierre Fontanillas, Juan R. González18, Peter K. Joshi19, Ville Karhunen20, Aaron Kleinman, Remy Z. Levin21, Christina M. Lill22, Gerardus A. Meddens, Gerard Muntané18, Gerard Muntané23, Sandra Sanchez-Roige21, Frank J. A. van Rooij1, Erdogan Taskesen2, Yang Wu11, Futao Zhang11, Adam Auton, Jason D. Boardman24, David W. Clark19, Andrew Conlin20, Conor C. Dolan2, Urs Fischbacher25, Patrick J. F. Groenen1, Kathleen Mullan Harris26, Gregor Hasler27, Albert Hofman4, Albert Hofman1, Mohammad Arfan Ikram1, Sonia Jain21, Robert Karlsson28, Ronald C. Kessler4, Maarten Kooyman, James MacKillop29, James MacKillop30, Minna Männikkö20, Carlos Morcillo-Suarez18, Matthew B. McQueen24, Klaus M. Schmidt31, Melissa C. Smart12, Matthias Sutter32, Matthias Sutter33, Matthias Sutter17, Roy Thurik1, André G. Uitterlinden1, Jon White34, Harriet de Wit35, Jian Yang11, Lars Bertram22, Lars Bertram36, Dorret I. Boomsma2, Tõnu Esko37, Ernst Fehr3, David A. Hinds, Magnus Johannesson38, Meena Kumari12, David Laibson4, Patrik K. E. Magnusson28, Michelle N. Meyer39, Arcadi Navarro18, Arcadi Navarro40, Abraham A. Palmer21, Tune H. Pers10, Tune H. Pers9, Danielle Posthuma2, Daniel Schunk41, Murray B. Stein21, Rauli Svento20, Henning Tiemeier1, Paul R. H. J. Timmers19, Patrick Turley42, Patrick Turley14, Patrick Turley4, Robert J. Ursano43, Gert G. Wagner15, Gert G. Wagner17, James F. Wilson19, James F. Wilson44, Jacob Gratten11, Jacob Gratten45, James J. Lee46, David Cesarini47, Daniel J. Benjamin42, Daniel J. Benjamin48, Philipp Koellinger2, Philipp Koellinger15, Jonathan P. Beauchamp8 
TL;DR: This paper found evidence of substantial shared genetic influences across risk tolerance and the risky behaviors: 46 of the 99 general risk tolerance loci contain a lead SNP for at least one of their other GWAS, and general risk-tolerance is genetically correlated with a range of risky behaviors.
Abstract: Humans vary substantially in their willingness to take risks. In a combined sample of over 1 million individuals, we conducted genome-wide association studies (GWAS) of general risk tolerance, adventurousness, and risky behaviors in the driving, drinking, smoking, and sexual domains. Across all GWAS, we identified hundreds of associated loci, including 99 loci associated with general risk tolerance. We report evidence of substantial shared genetic influences across risk tolerance and the risky behaviors: 46 of the 99 general risk tolerance loci contain a lead SNP for at least one of our other GWAS, and general risk tolerance is genetically correlated ([Formula: see text] ~ 0.25 to 0.50) with a range of risky behaviors. Bioinformatics analyses imply that genes near SNPs associated with general risk tolerance are highly expressed in brain tissues and point to a role for glutamatergic and GABAergic neurotransmission. We found no evidence of enrichment for genes previously hypothesized to relate to risk tolerance.

395 citations

Journal ArticleDOI
TL;DR: The results suggest future genome-wide association scans in Hispanic/Latino populations may require correction for local genomic ancestry at a subcontinental scale when associating differences in the genome with disease risk, progression, and drug efficacy, as well as for admixture mapping.
Abstract: Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped on the Illumina 610-Quad arrays and 112 Mexicans genotyped on Affymetrix 500K platform. Intersecting these data with previously collected high-density SNP data from 4,305 individuals, we use principal component analysis and clustering methods FRAPPE and STRUCTURE to investigate genome-wide patterns of African, European, and Native American population structure within and among Hispanic/Latino populations. Comparing autosomal, X and Y chromosome, and mtDNA variation, we find evidence of a significant sex bias in admixture proportions consistent with disproportionate contribution of European male and Native American female ancestry to present-day populations. We also find that patterns of linkage-disequilibria in admixed Hispanic/Latino populations are largely affected by the admixture dynamics of the populations, with faster decay of LD in populations of higher African ancestry. Finally, using the locus-specific ancestry inference method LAMP, we reconstruct fine-scale chromosomal patterns of admixture. We document moderate power to differentiate among potential subcontinental source populations within the Native American, European, and African segments of the admixed Hispanic/Latino genomes. Our results suggest future genome-wide association scans in Hispanic/Latino populations may require correction for local genomic ancestry at a subcontinental scale when associating differences in the genome with disease risk, progression, and drug efficacy, as well as for admixture mapping.

384 citations

Journal ArticleDOI
29 Mar 2013-Science
TL;DR: Findings indicate that ancient balancing selection has shaped human variation and point to genes involved in host-pathogen interactions as common targets.
Abstract: Instances in which natural selection maintains genetic variation in a population over millions of years are thought to be extremely rare. We conducted a genome-wide scan for long-lived balancing selection by looking for combinations of SNPs shared between humans and chimpanzees. In addition to the major histocompatibility complex (MHC), we identified 125 regions in which the same haplotypes are segregating in the two species, all but two of which are non-coding. In six cases, there is evidence for an ancestral polymorphism that persisted to the present in humans and chimpanzees. Regions with shared haplotypes are significantly enriched for membrane glycoproteins, and a similar trend is seen among shared coding polymorphisms. These findings indicate that ancient balancing selection has shaped human variation and point to genes involved in host-pathogen interactions as common targets.

289 citations

Journal ArticleDOI
13 Apr 2012-Science
TL;DR: A fine-scale genetic map of the Western chimpanzee is constructed from high-throughput sequence data and shows that chimpanzee recombination is dominated by hotspots, which show no overlap with those of humans even though rates are similarly elevated around CpG islands and decreased within genes.
Abstract: To study the evolution of recombination rates in apes, we developed methodology to construct a fine-scale genetic map from high-throughput sequence data from 10 Western chimpanzees, Pan troglodytes verus. Compared to the human genetic map, broad-scale recombination rates tend to be conserved, but with exceptions, particularly in regions of chromosomal rearrangements and around the site of ancestral fusion in human chromosome 2. At fine scales, chimpanzee recombination is dominated by hotspots, which show no overlap with those of humans even though rates are similarly elevated around CpG islands and decreased within genes. The hotspot-specifying protein PRDM9 shows extensive variation among Western chimpanzees, and there is little evidence that any sequence motifs are enriched in hotspots. The contrasting locations of hotspots provide a natural experiment, which demonstrates the impact of recombination on base composition.

288 citations


Cited by
More filters
Journal ArticleDOI
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Abstract: As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

37,898 citations

28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
Adam Auton1, Gonçalo R. Abecasis2, David Altshuler3, Richard Durbin4  +514 moreInstitutions (90)
01 Oct 2015-Nature
TL;DR: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
Abstract: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

12,661 citations

Journal ArticleDOI
TL;DR: In this article, the authors present an approach for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.
Abstract: Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

10,798 citations

Journal ArticleDOI
TL;DR: VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.
Abstract: Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. Availability: http://vcftools.sourceforge.net Contact: [email protected]

10,164 citations