6Department of Oncology (2009)
Justin Lamb, Sridhar Ramaswamy, Heide L. Ford, Bernardo Contreras, Robert V. Martinez, Frances S. Kittrell, ...
Here we describe how patterns of gene expression in human tumors have been deconvoluted to reveal a mechanism of action for the cyclin D1 oncogene. Com-putational analysis of the expression patterns...
Reich, David, Nalls, Michael A, Kao, W H Linda, Akylbekova, Ermeg L, Tandon, Arti, Patterson, Nick, ...
Persistently low white blood cell count (WBC) and neutrophil count is a well-described phenomenon in persons of African ancestry, whose etiology remains unknown. We recently used admixture mapping to...
Microsatellites Are Molecular Clocks That Support Accurate Inferences about History (2009)
Sun, James X., Mullikin, James C., Patterson, Nick, Reich, David E.
Microsatellite length mutations are often modeled using the generalized stepwise mutation process, which is a type of random walk. If this model is sufficiently accurate, one can estimate the...
The role of the CD58 locus in multiple sclerosis (2009)
Baecher-Allan, Clare, Maier, Lisa M, Arthur, Ariel T, Ottoboni, Linda, Barcellos, Lisa, ...
Multiple sclerosis (MS) is an inflammatory disease of the central nervous system associated with demyelination and axonal loss. A whole genome association scan suggested that allelic variants in the...
ARTICLE A Genomewide Admixture Map for Latino Populations (2008)
Alkes L. Price, Nick Patterson, Fuli Yu, David R. Cox, Alicja Waliszewska, Gavin J. Mcdonald, ...
Admixture mapping is an economical and powerful approach for localizing disease genes in populations of recently mixed ancestry and has proven successful in African Americans. The method holds equal...
Keating, Brendan J, Tischfield, Sam, Murray, Sarah S, Bhangale, Tushar, Price, Thomas S, Glessner, Joseph T, ...
A wealth of genetic associations for cardiovascular and metabolic phenotypes in humans has been accumulating over the last decade, in particular a large number of loci derived from recent genome wide...
Discerning the Ancestry of European Americans in Genetic Association Studies (2008)
Alkes L. Price, Johannah Butler, Nick Patterson, Cristian Capelli, Vincenzo L. Pascali, Francesca Scarnicci, ...
European Americans are often treated as a homogeneous group, but in fact form a structured population due to historical immigration of diverse source populations. Discerning the ancestry of European...
Discerning the ancestry of European Americans in genetic association studies (2007)
Alkes Price, Johannah L. Butler, Nick Patterson, Cristian Capelli, Vincenzo L. Pascali, Francesca Scarnicci, ...
European Americans are often treated as a homogeneous group, but in fact form a structured population due to historical immigration of diverse source populations. Discerning the ancestry of European...
A High-Density Admixture Scan in 1,670 African Americans with Hypertension (2007)
Rahul C. Deo, Nick Patterson, Arti Tandon, Gavin J. McDonald, Christopher A. Haiman, Kristin Ardlie, ...
Hypertension (HTN) is a devastating disease with a higher incidence in African Americans than European Americans, inspiring searches for genetic variants that contribute to this difference. We report...
A second generation human haplotype map of over 3.1 million SNPs (2007)
Frazer, Kelly A., Ballinger, Dennis G., Cox, David R., Hinds, David A., Stuve, Laura L., Gibbs, Richard A., ...
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and...
A High-Density Admixture Scan in 1,670 African Americans with Hypertension (2007)
Rahul Deo, Nick Patterson, Arti Tandon, Gavin McDonald, Christopher A. Haiman, Kristin Ardlie, ...
Hypertension (HTN) is a devastating disease with a higher incidence in African Americans than European Americans, inspiring searches for genetic variants that contribute to this difference. We report...
Genetic Structure of Chimpanzee Populations (2007)
Celine Becquet, Nick Patterson, Anne C. Stone, Molly Przeworski, David Reich
Little is known about the history and population structure of our closest living relatives, the chimpanzees, in part because of an extremely poor fossil record. To address this, we report the largest...
Genetic structure of chimpanzee populations (2007)
Celine Becquet, Nick Patterson, Anne C. Stone, Molly Przeworski, David Reich
Little is known about the history and population structure of our closest living relatives, the chimpanzees, in part because of an extremely poor fossil record. To address this, we report the largest...
Population Structure and Eigenanalysis (2006)
Nick Patterson, Alkes L. Price, David Reich
Current methods for inferring population structure from genetic data do not provide formal significance tests for population differentiation. We discuss an approach to studying population structure...
Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men (2006)
Freedman, Matthew L., Haiman, Christopher A., Patterson, Nick, McDonald, Gavin J., Tandon, Arti, Waliszewska, Alicja, ...
A whole-genome admixture scan in 1,597 African Americans identified a 3.8Mbinterval on chromosome 8q24 as significantly associated with susceptibility to prostate cancer [logarithm of odds (LOD)7.1]....
Population structure and eigenanalysis (2006)
Nick Patterson, Alkes L. Price, David Reich
Current methods for inferring population structure from genetic data do not provide formal significance tests for population differentiation. We discuss an approach to studying population structure...
A comparison of phasing algorithms for trios and unrelated individuals (2006)
Jonathan Marchini, David Cutler, Nick Patterson, Matthew Stephens, Eleazar Eskin, Eran Halperin, ...
Knowledge of haplotype phase is valuable for many analysis methods in the study of disease, population, and evolutionary genetics. Considerable research effort has been devoted to the development of...
The Case for Selection at CCR5-Δ32 (2005)
Pardis C. Sabeti, Emily Walsh, Steve F. Schaffner, Patrick Varilly, Ben Fry, Holli B. Hutcheson, ...
Sabeti and colleagues use dense genetic maps to show that the HIV-resistance CCR5-Δ32 allele is more than 5,000 years old and is likely to have been under mainly neutral selection.
The Case for Selection at CCR5-Δ32 (2005)
Pardis C. Sabeti, Emily Walsh, Steve F. Schaffner, Patrick Varilly, Ben Fry, Holli B. Hutcheson, ...
The C-C chemokine receptor 5, 32 base-pair deletion (CCR5-Δ32) allele confers strong resistance to infection by the AIDS virus HIV. Previous studies have suggested that CCR5-Δ32 arose within the...
A High-Density Admixture Map for Disease Gene Discovery in African Americans (2004)
Smith, Michael W, Patterson, Nick, Lautenberger, James A, Truelove, Ann L, McDonald, Gavin J, Waliszewska, Alicja, ...
Admixture mapping (also known as “mapping by admixture linkage disequilibrium,” or MALD) provides a way of localizing genes that cause disease, in admixed ethnic groups such as African Americans,...
Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. L
In Kellis et al. (2003), we reported the genome sequences of S. paradoxus, S. mikatae and S. bayanus and compared these three yeast species to their close relative, S. cerevisiae. Genome-wide...
Manolis Kamvysselis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric L
In [13] we reported the genome sequences of S. paradoxus, S. mikatae and S. bayanus and compared these three yeast species to their close relative, S. cerevisiae. Genome-wide comparative analysis...
Mootha, Vamsi K., Handschin, Christoph, Arlow, Dan, Xie, Xiaohui, St. Pierre, Julie, Sihag, Smita, ...
Recent studies have shown that genes involved in oxidative phosphorylation (OXPHOS) exhibit reduced expression in skeletal muscle of diabetic and prediabetic humans. Moreover, these changes may be...
The Case for Selection at CCR5-Δ32
Sabeti, Pardis C, Walsh, Emily, Schaffner, Steve F, Varilly, Patrick, Fry, Ben, Hutcheson, Holli B, ...
The C-C chemokine receptor 5, 32 base-pair deletion (CCR5-Δ32) allele confers strong resistance to infection by the AIDS virus HIV. Previous studies have suggested that CCR5-Δ32 arose within the...
A Comparison of Phasing Algorithms for Trios and Unrelated Individuals
Marchini, Jonathan, Cutler, David, Patterson, Nick, Stephens, Matthew, Eskin, Eleazar, Halperin, Eran, ...
Knowledge of haplotype phase is valuable for many analysis methods in the study of disease, population, and evolutionary genetics. Considerable research effort has been devoted to the development of...
Mootha, Vamsi K., Handschin, Christoph, Arlow, Dan, Xie, Xiaohui, St. Pierre, Julie, Sihag, Smita, ...
Recent studies have shown that genes involved in oxidative phosphorylation (OXPHOS) exhibit reduced expression in skeletal muscle of diabetic and prediabetic humans. Moreover, these changes may be...
An Integrated Haplotype Map of the Human Major Histocompatibility Complex
Walsh, Emily C., Mather, Kristie A., Schaffner, Stephen F., Farwell, Lisa, Daly, Mark J., Patterson, Nick, ...
Numerous studies have clearly indicated a role for the major histocompatibility complex (MHC) in susceptibility to autoimmune diseases. Such studies have focused on the genetic variation of a small...
A High-Density Admixture Map for Disease Gene Discovery in African Americans
Smith, Michael W., Patterson, Nick, Lautenberger, James A., Truelove, Ann L., McDonald, Gavin J., Waliszewska, Alicja, ...
Admixture mapping (also known as “mapping by admixture linkage disequilibrium,” or MALD) provides a way of localizing genes that cause disease, in admixed ethnic groups such as African Americans,...
Methods for High-Density Admixture Mapping of Disease Genes
Patterson, Nick, Hattangadi, Neil, Lane, Barton, Lohmueller, Kirk E., Hafler, David A., Oksenberg, Jorge R., ...
Admixture mapping (also known as “mapping by admixture linkage disequilibrium,” or MALD) has been proposed as an efficient approach to localizing disease-causing variants that differ in frequency...
Abecasis, Goncalo, Cox, Nancy, Daly, Mark J., Kruglyak, Leonid, Laird, Nan, Markianos, Kyriacos, ...
Genetic Signatures of Strong Recent Positive Selection at the Lactase Gene
Bersaglieri, Todd, Sabeti, Pardis C., Patterson, Nick, Vanderploeg, Trisha, Schaffner, Steve F., Drake, Jared A., ...
In most human populations, the ability to digest lactose contained in milk usually disappears in childhood, but in European-derived populations, lactase activity frequently persists into adulthood...
The Case for Selection at CCR5-Δ32
Sabeti, Pardis C, Walsh, Emily, Schaffner, Steve F, Varilly, Patrick, Fry, Ben, Hutcheson, Holli B, ...
The C-C chemokine receptor 5, 32 base-pair deletion (CCR5-Δ32) allele confers strong resistance to infection by the AIDS virus HIV. Previous studies have suggested that CCR5-Δ32 arose within the...
A Comparison of Phasing Algorithms for Trios and Unrelated Individuals
Marchini, Jonathan, Cutler, David, Patterson, Nick, Stephens, Matthew, Eskin, Eleazar, Halperin, Eran, ...
Knowledge of haplotype phase is valuable for many analysis methods in the study of disease, population, and evolutionary genetics. Considerable research effort has been devoted to the development of...
Population Structure and Eigenanalysis
Patterson, Nick, Price, Alkes L, Reich, David
Current methods for inferring population structure from genetic data do not provide formal significance tests for population differentiation. We discuss an approach to studying population structure...
Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men
Freedman, Matthew L., Haiman, Christopher A., Patterson, Nick, McDonald, Gavin J., Tandon, Arti, Waliszewska, Alicja, ...
A whole-genome admixture scan in 1,597 African Americans identified a 3.8 Mb interval on chromosome 8q24 as significantly associated with susceptibility to prostate cancer [logarithm of odds (LOD) =...
Genetic Structure of Chimpanzee Populations
Becquet, Celine, Patterson, Nick, Stone, Anne C, Przeworski, Molly, Reich, David
Little is known about the history and population structure of our closest living relatives, the chimpanzees, in part because of an extremely poor fossil record. To address this, we report the largest...
Will admixture mapping work to find disease genes?
Admixture mapping is the first experimentally practical method for carrying out a whole-genome association scan, and is thus a promising method for detecting risk factors for common disease. The goal...
Admixture Mapping of an Allele Affecting Interleukin 6 Soluble Receptor and Interleukin 6 Levels
Reich, David, Patterson, Nick, Ramesh, Vijaya, De Jager, Philip L., McDonald, Gavin J., Tandon, Arti, ...
Circulating levels of inflammatory markers can predict cardiovascular disease risk. To identify genes influencing the levels of these markers, we genotyped 1,343 single-nucleotide polymorphisms...
A High-Density Admixture Scan in 1,670 African Americans with Hypertension
Deo, Rahul C, Patterson, Nick, Tandon, Arti, McDonald, Gavin J, Haiman, Christopher A, Ardlie, Kristin, ...
Hypertension (HTN) is a devastating disease with a higher incidence in African Americans than European Americans, inspiring searches for genetic variants that contribute to this difference. We report...
Discerning the Ancestry of European Americans in Genetic Association Studies
Price, Alkes L, Butler, Johannah, Patterson, Nick, Capelli, Cristian, Pascali, Vincenzo L, Scarnicci, Francesca, ...
European Americans are often treated as a homogeneous group, but in fact form a structured population due to historical immigration of diverse source populations. Discerning the ancestry of European...
Keating, Brendan J., Tischfield, Sam, Murray, Sarah S., Bhangale, Tushar, Price, Thomas S., Glessner, Joseph T., ...
A wealth of genetic associations for cardiovascular and metabolic phenotypes in humans has been accumulating over the last decade, in particular a large number of loci derived from recent genome wide...
Effects of cis and trans Genetic Ancestry on Gene Expression in African Americans
Price, Alkes L., Patterson, Nick, Hancks, Dustin C., Myers, Simon, Reich, David, Cheung, Vivian G., ...
Variation in gene expression is a fundamental aspect of human phenotypic variation. Several recent studies have analyzed gene expression levels in populations of different continental ancestry and...
Deo, Rahul C., Reich, David, Tandon, Arti, Akylbekova, Ermeg, Patterson, Nick, Waliszewska, Alicja, ...
Genome-wide association analysis in populations of European descent has recently found more than a hundred genetic variants affecting risk for common disease. An open question, however, is how...
Reich, David, Nalls, Michael A., Kao, W. H. Linda, Akylbekova, Ermeg L., Tandon, Arti, Patterson, Nick, ...
Persistently low white blood cell count (WBC) and neutrophil count is a well-described phenomenon in persons of African ancestry, whose etiology remains unknown. We recently used admixture mapping to...
Long-Range LD Can Confound Genome Scans in Admixed Populations
Price, Alkes L., Weale, Michael E., Patterson, Nick, Myers, Simon R., Need, Anna C., Shianna, Kevin V., ...
Cheng, Ching-Yu, Kao, W. H. Linda, Patterson, Nick, Tandon, Arti, Haiman, Christopher A., Harris, Tamara B., ...
The prevalence of obesity (body mass index (BMI) ≥30 kg/m2) is higher in African Americans than in European Americans, even after adjustment for socioeconomic factors, suggesting that genetic...
Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations
Price, Alkes L., Tandon, Arti, Patterson, Nick, Barnes, Kathleen C., Rafaels, Nicholas, Ruczinski, Ingo, ...
Identifying the ancestry of chromosomal segments of distinct ancestry has a wide range of applications from disease mapping to learning about history. Most methods require the use of unlinked...
The role of the CD58 locus in multiple sclerosis
De Jager, Philip L., Baecher-Allan, Clare, Maier, Lisa M., Arthur, Ariel T., Ottoboni, Linda, Barcellos, Lisa, ...
Multiple sclerosis (MS) is an inflammatory disease of the central nervous system associated with demyelination and axonal loss. A whole genome association scan suggested that allelic variants in the...