A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER ESTIMATION USING SNP ARRAYS (2009)
Scharpf, Robert B., Ruczinski, Ingo, Carvalho, Benilton, Doan, Betty, Chakravarti, Aravinda, Irizarry, Rafael A.
Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that...
A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER ESTIMATION USING SNP ARRAYS (2009)
Scharpf, Robert B., Ruczinski, Ingo, Carvalho, Benilton, Doan, Betty, Chakravarti, Aravinda, Irizarry, Rafael A.
Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that...
A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER ESTIMATION USING SNP ARRAYS (2009)
Scharpf, Robert B., Ruczinski, Ingo, Carvalho, Benilton, Doan, Betty, Chakravarti, Aravinda, Irizarry, Rafael A.
Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that...
A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER ESTIMATION USING SNP ARRAYS (2009)
Scharpf, Robert B., Ruczinski, Ingo, Carvalho, Benilton, Doan, Betty, Chakravarti, Aravinda, Irizarry, Rafael A.
Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that...
A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER USING SNP ARRAYS (2009)
Scharpf, Robert B., Ruczinski, Ingo, Carvalho, Benilton, Doan, Betty, Chakravarti, Aravinda, Irizarry, Rafael A.
Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that...
A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER USING SNP ARRAYS (2009)
Scharpf, Robert B., Ruczinski, Ingo, Carvalho, Benilton, Doan, Betty, Chakravarti, Aravinda, Irizarry, Rafael A.
Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that...
A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER USING SNP ARRAYS (2009)
Scharpf, Robert B., Ruczinski, Ingo, Carvalho, Benilton, Doan, Betty, Chakravarti, Aravinda, Irizarry, Rafael A.
Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that...
A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER USING SNP ARRAYS (2009)
Scharpf, Robert B., Ruczinski, Ingo, Carvalho, Benilton, Doan, Betty, Chakravarti, Aravinda, Irizarry, Rafael A.
Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that...
Arking, Dan E, Khera, Amit, Xing, Chao, Kao, W H Linda, Post, Wendy, Boerwinkle, Eric, ...
Extremes of electrocardiographic QT interval are associated with increased risk for sudden cardiac death (SCD); thus, identification and characterization of genetic variants that modulate QT interval...
SanGiovanni, John Paul, Arking, Dan E., Iyengar, Sudha K., Elashoff, Michael, Clemons, Traci E., Reed, George F., ...
BACKGROUND: Age-related macular degeneration (AMD), a chronic neurodegenerative and neovascular retinal disease, is the leading cause of blindness in elderly people of western European origin. While...
Positional identification of variants of Adamts16 linked to inherited hypertension (2009)
Joe, Bina, Saad, Yasser, Lee, Norman H., Frank, Bryan C., Achinike, Ovokeraye H., Luu, Truong V., ...
A previously reported blood pressure (BP) quantitative trait locus on rat Chromosome 1 was isolated in a short congenic segment spanning 804.6 kb. The 804.6 kb region contained only two genes,...
A Genome-Wide Scan for Obesity in African-Americans (2008)
Xiaofeng Zhu, Richard S. Cooper, Amy Luke, Guanjie Chen, Xiaodong Wu, Donghui Kan, ...
A genome-wide scan using 387 short tandem repeat markers was conducted for obesity among 618 black individuals from 202 families residing in a suburb of Chicago. Evidence for linkage was evaluated...
Lin, Shin, Carvalho, Benilton, Cutler, David J, Arking, Dan E, Chakravarti, Aravinda, Irizarry, Rafael A
Abstract Multiple algorithms have been developed for the purpose of calling single nucleotide polymorphisms (SNPs) from Affymetrix microarrays. We extend and validate the algorithm CRLMM, which...
Tara Matise And, Tara Cox Matise, Mark Perlin, Copyright Tara Matise, Tara Matise, Aravinda Chakravarti, ...
This documentation and the MultiMap program are copyrighted. The program may be copied freely for nonprofit research uses only and may not be used for commercial purposes without the specific...
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...
Angelo Scuteri, Serena Sanna, Wei-Min Chen, Manuela Uda, Giuseppe Albai, James Strait, ...
The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not...
Population Bottlenecks as a Potential Major Shaping Force of Human Genome Architecture (2007)
Adrian Gherman, Peter E. Chen, Tanya M. Teslovich, Pawel Stankiewicz, Marjorie Withers, Carl S. Kashuk, ...
The modern synthetic view of human evolution proposes that the fixation of novel mutations is driven by the balance among selective advantage, selective disadvantage, and genetic drift. When...
Wen, Gen, Wessel, Jennifer, Zhou, Weidong, Ehret, Georg B., Rao, Fangwen, Stridsberg, Mats, ...
Granins regulate secretory vesicle formation in neuroendocrine cells and granin-derived peptides are co-released with neurotransmitters as modulatory signals at sympathetic sites. We report evidence...
Population Bottlenecks as a Potential Major Shaping Force of Human Genome Architecture (2007)
Adrian Gherman, Peter E. Chen, Tanya Teslovich, Pawel Stankiewicz, Marjorie Withers, Carl S Kashuk, ...
The modern synthetic view of human evolution proposes that the fixation of novel mutations is driven by the balance between selective advantage, selective disadvantage and genetic drift. When...
Angelo Scuteri, Serena Sanna, Wei-Min Chen, Manuela Uda, Giuseppe Albai, James Strait, ...
The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not...
ESTIMATING GENOME-WIDE COPY NUMBER USING ALLELE SPECIFIC MIXTURE MODELS (2006)
Wang , Wenyi, Caravalho, Benilton, Miller, Nate, Pevsner, Jonathan, Chakravarti, Aravinda, Irizarry, Rafael A
Genomic changes such as copy number alterations are thought to be one of the major underlying causes of human phenotypic variation among normal and disease subjects [23,11,25,26,5,4,7,18]. These...
ESTIMATING GENOME-WIDE COPY NUMBER USING ALLELE SPECIFIC MIXTURE MODELS (2006)
Wang , Wenyi, Caravalho, Benilton, Miller, Nate, Pevsner, Jonathan, Chakravarti, Aravinda, Irizarry, Rafael A
Genomic changes such as copy number alterations are thought to be one of the major underlying causes of human phenotypic variation among normal and disease subjects [23,11,25,26,5,4,7,18]. These...
ESTIMATING GENOME-WIDE COPY NUMBER USING ALLELE SPECIFIC MIXTURE MODELS (2006)
Wang , Wenyi, Caravalho, Benilton, Miller, Nate, Pevsner, Jonathan, Chakravarti, Aravinda, Irizarry, Rafael A
Genomic changes such as copy number alterations are thought to be one of the major underlying causes of human phenotypic variation among normal and disease subjects [23,11,25,26,5,4,7,18]. These...
ESTIMATING GENOME-WIDE COPY NUMBER USING ALLELE SPECIFIC MIXTURE MODELS (2006)
Wang , Wenyi, Caravalho, Benilton, Miller, Nate, Pevsner, Jonathan, Chakravarti, Aravinda, Irizarry, Rafael A
Genomic changes such as copy number alterations are thought to be one of the major underlying causes of human phenotypic variation among normal and disease subjects [23,11,25,26,5,4,7,18]. These...
Laramie, Jason M, Wilk, Jemma B, Hunt, Steven C, Ellison, R Curtis, Chakravarti, Aravinda, Boerwinkle, Eric, ...
Abstract Background Elevated resting heart rate has been shown in multiple studies to be a strong predictor of cardiovascular disease. Previous family studies have shown a significant heritable...
Human embryonic stem cells have a unique epigenetic signature (2006)
Bibikova, Marina, Chudin, Eugene, Wu, Bonnie, Zhou, Lixin, Garcia, Eliza Wickham, Liu, Ying, ...
Human embryonic stem (hES) cells originate during an embryonic period of active epigenetic remodeling. DNA methylation patterns are likely to be critical for their self-renewal and pluripotence. We...
Human embryonic stem cells have a unique epigenetic signature (2006)
Bibikova, Marina, Chudin, Eugene, Wu, Bonnie, Zhou, Lixin, Wickham Garcia, Eliza, Liu, Ying, ...
Human embryonic stem (hES) cells originate during an embryonic period of active epigenetic remodeling. DNA methylation patterns are likely to be critical for their self-renewal and pluripotence. We...
J. Hunter Young, Jean-Paul Chretien, Michael J. Klag, Michael A. Levine, ...
Hypertension is a leading cause of stroke, heart disease, and kidney failure. The genetic basis of blood pressure variation is largely unknown but is likely to involve genes that influence renal salt...
J Hunter Young, Jean-Paul Chretien, Michael J. Klag, Michael A. Levine, ...
Hypertension is a leading cause of stroke, heart disease, and kidney failure. The genetic basis of blood pressure variation is largely unknown but is likely to involve genes that influence renal salt...
On the probability that a novel variant is a disease-causing mutation (2005)
Mitchell, Adele A., Chakravarti, Aravinda, Cutler, David J.
When a novel variant is found in a patient and not in a group of controls, it becomes a candidate for the disease-causing mutation in that patient. At present, no sampling theory exists for assessing...
Grice, Elizabeth A., Rochelle, Erin S., Green, Eric D., Chakravarti, Aravinda, McCallion, Andrew S.
Evolutionary sequence conservation is now a relatively common approach for the prediction of functional DNA sequences. However, the fraction of conserved non-coding sequences with regulatory...
On the probability that a novel variant is a disease-causing mutation (2005)
Mitchell, Adele A., Chakravarti, Aravinda, Cutler, David J.
When a novel variant is found in a patient and not in a group of controls, it becomes a candidate for the disease-causing mutation in that patient. At present, no sampling theory exists for assessing...
Grice, Elizabeth A., Rochelle, Erin S., Green, Eric D., Chakravarti, Aravinda, McCallion, Andrew S.
Evolutionary sequence conservation is now a relatively common approach for the prediction of functional DNA sequences. However, the fraction of conserved noncoding sequences with regulatory potential...
Haplotype and Missing Data Inference in Nuclear Families (2004)
Lin, Shin, Chakravarti, Aravinda, Cutler, David J.
Determining linkage phase from population samples with statistical methods is accurate only within regions of high linkage disequilibrium (LD). Yet, affected individuals in a genetic mapping study,...
Mitchell, Adele A., Zwick, Michael E., Chakravarti, Aravinda, Cutler, David J.
Three recent publications have examined the quality and completeness of dbSNP and have come to dramatically different conclusions regarding dbSNP's false positive rate and the proportion of dbSNPs...
Haplotype and Missing Data Inference in Nuclear Families (2004)
Lin, Shin, Chakravarti, Aravinda, Cutler, David J.
Determining linkage phase from population samples with statistical methods is accurate only within regions of high linkage disequilibrium (LD). Yet, affected individuals in a genetic mapping study,...
Maitra, Anirban, Cohen, Yoram, Gillespie, Susannah E.D., Mambo, Elizabeth, Fukushima, Noriyoshi, Hoque, Mohammad O., ...
Somatic mitochondrial mutations are common in human cancers, and can be used as a tool for early detection of cancer. We have developed a mitochondrial Custom Reseq™ microarray as an array-based...
Mitchell, Adele A., Zwick, Michael E., Chakravarti, Aravinda, Cutler, David J.
Three recent publications have examined the quality and completeness of dbSNP and have come to dramatically different conclusions regarding dbSNP's false positive rate and the proportion of dbSNPs...
Safety issues in cell-based intervention trials (2003)
Bateman-House, Alison S, Mueller Agnew, Dawn, Bok, Hilary, Brock, Dan W, Chakravarti, Aravinda, ...
We report on the deliberations of an interdisciplinary group of experts in science, law, and philosophy who convened to discuss novel ethical and policy challenges in stem cell research. In this...
Public stem cell banks: considerations of justice in stem cell research and therapy (2003)
Dawson, Liza, Bateman-House, Alison S, Agnew, Dawn Mueller, Bok, Hilary, Brock, Dan W, ...
Phoebe R. Berman Bioethics Institute, Johns Hopkins University, USA.
McCallion, Andrew S., Stames, Erine, Conlon, Ronald A., Chakravarti, Aravinda
Clinical expression of Hirschsprung disease (HSCR) requires the interaction of multiple susceptibility genes. Molecular genetic analyses have revealed that interactions between mutations in the genes...
Peri, Suraj, Navarro, J. Daniel, Amanchy, Ramars, Kristiansen, Troels Z., Jonnalagadda, Chandra Kiran, Surendranath, Vineeth, ...
Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of...
Zhu, Xiaofeng, Yan, Denise, Cooper, Richard S., Luke, Amy, Ikeda, Morna A., Chang, Yen-Pei C., ...
Association studies of candidate genes with complex traits have generally used one or a few single nucleotide polymorphisms (SNPs), although variation in the extent of linkage disequilibrium (LD)...
Segregation Analysis of Blood Pressure and Body Mass Index in a Rural US Community (2002)
Chakravarti, Aravinda., Chen, Chien-Hsiun., Cooper, Richard., Weder, Alan., Schork, Nicholas J.
Human Biology - Volume 74, Number 1, February 2002
ViewGene: a graphical tool for polymorphism visualization and characterization. (2002)
Kashuk, Carl, SenGupta, Sanghamitra, Eichler, Evan, Chakravarti, Aravinda
The human genome project is producing an enormous amount of sequence data, based on which single base changes between individuals can be identified. Unfortunately, computer tools that were adequate...
viewGene: A Graphical Tool for Polymorphism Visualization and Characterization (2002)
Kashuk, Carl, SenGupta, Sanghamitra, Eichler, Evan, Chakravarti, Aravinda
Sequence variation within the fragile X locus. (2001)
Mathews, Debra J., Kashuk, Carl, Brightwell, Gale, Eichler, Evan E., Chakravarti, Aravinda
The human genome provides a reference sequence, which is a template for resequencing studies that aim to discover and interpret the record of common ancestry that exists in extant genomes. To...
High-throughput variation detection and genotyping using microarrays. (2001)
Cutler, David J., Zwick, Michael E., Carrasquillo, Minerva M., Yohn, Christopher T., Tobin, Katherine P., Kashuk, Carl, ...
The genetic dissection of complex traits may ultimately require a large number of SNPs to be genotyped in multiple individuals who exhibit phenotypic variation in a trait of interest. Microarray...
RESPONSE: Testing for Colon Neoplasia Susceptibility Variants at the Human COX2 Locus (2001)
Wiesner, Georgia L., Platzer, Petra, Buxbaum, Sarah G., Lewis, Susan, Macmillen, Melissa, Willis, Joseph, ...
High-Throughput Variation Detection and Genotyping Using Microarrays (2001)
Cutler, David J., Zwick, Michael E., Carrasquillo, Minerva M., Yohn, Christopher T., Tobin, Katherine P., Kashuk, Carl, ...
Sequence Variation Within the Fragile X Locus (2001)
Mathews, Debra J., Kashuk, Carl, Brightwell, Gale, Eichler, Evan E., Chakravarti, Aravinda
Testing for Colon Neoplasia Susceptibility Variants at the Human COX2 Locus (2001)
Wiesner, Georgia L., Platzer, Petra, Buxbaum, Sarah, Lewis, Susan, MacMillen, Mellissa, Olechnowicz, Joseph, ...
Background: Siblings and other first-degree relatives of patients with “sporadic” (i.e., apparently nonfamilial) colorectal cancer or precursor adenomatous colon polyps have an increased risk of...
High-Throughput Variation Detection and Genotyping Using Microarrays (2001)
Cutler, David J., Zwick, Michael E., Carrasquillo, Minerva M., Yohn, Christopher T., Tobin, Katherine P., Kashuk, Carl, ...
High-Throughput Variation Detection and Genotyping Using Microarrays (2001)
Cutler, David J., Zwick, Michael E., Carrasquillo, Minerva M., Yohn, Christopher T., Tobin, Katherine P., Kashuk, Carl, ...
Schork, Nicholas J., Nath, Swapan K., Fallin, Daniele, Chakravarti, Aravinda
Linkage disequilibrium (LD) mapping has been applied to many simple, monogenic, overtly Mendelian human traits, with great success. However, extensions and applications of LD mapping approaches to...
Bolk, Stacey, Pelet, Anna, Hofstra, Robert M. W., Angrist, Misha, Salomon, Remi, Croaker, David, ...
Reduced penetrance in genetic disorders may be either dependent or independent of the genetic background of gene carriers. Hirschsprung disease (HSCR) demonstrates a complex pattern of inheritance...
Bailey, Jeffrey A., Carrel, Laura, Chakravarti, Aravinda, Eichler, Evan E.
X inactivation is a chromosome-specific form of genetic regulation in which thousands of genes on one homologue become silenced early in female embryogenesis. Although many aspects of X inactivation...
Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. (2000)
Fan, Jian-Bing, Chen, Xiaoqiong, Halushka, Marc K., Berno, Anthony, Huang, Xiaohua, Ryder, Thomas, ...
Large scale human genetic studies require technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. We describe a highly parallel...
Patterns of Meiotic Recombination on the Long Arm of Human Chromosome 21 (2000)
Lynn, Audrey, Kashuk, Carl, Petersen, Michael B., Bailey, Jeffrey A., Cox, David R., Antonarakis, Stylianos E., ...
Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays (2000)
Fan, Jian-Bing, Chen, Xiaoqiong, Halushka, Marc K., Berno, Anthony, Huang, Xiaohua, Ryder, Thomas, ...
The Sox10Dom Mouse: Modeling the Genetic Variation of Waardenburg-Shah (WS4) Syndrome (1999)
Southard-Smith, E. Michelle, Angrist, Misha, Ellison, Jane S., Agarwala, Richa, Baxevanis, Andreas D., Chakravarti, Aravinda, ...
Shaw, Sarah H., Carrasquillo, Minerva M., Kashuk, Carl, Puffenberger, Erik G., Chakravarti, Aravinda
Age, Sex, and the Familial Risk of Rheumatoid Arthritis (1996)
Kwoh, C. Kent, Venglish, Colleen, Lynn, Audrey H., Whitley, Deborah M., Young, Elizabeth, Chakravarti, Aravinda
The familial aggregation of rheumatoid arthritis was examined to determine factors modifying the risk of rheumatoid arthritis in first degree relatives of 165 cases ascertained from January 1, 1987,...
Talbot, C.Conover, Avramopouls, Dimitris, Gerken, Steven, Chakravarti, Aravinda, Armour, John A., Matsunami, Norisada, ...
Six novel polymorphic short sequence repeats were identified and localized on the linkage map of human chromosome 21 by genotyping the CEPH reference pedigrees. One of these markers, the tetrameric...
Mutation analysis of the RET receptor tyrosine kinase in Hirschsprung disease (1995)
Angrist, Misha, Bolk, Stacey, Thiel, Bonnie, Puffenberger, Erik G., Hofstra, Robert M., ...
Hirschsprung disease (HSCR), or congenital agangiionic megacolon, is the most common cause of congenital bowel obstruction with an incidence of 1 in 5000 live births. Recently, linkage of an...
G.Puffenberger, Erik, R.Kauffman, Erick, Bolk, Stacey, C.Matise, Tara, S.Washington, Sarah, Angrist, Misha, ...
Hirschsprung disease (HSCR) is a congenital disorder of unknown etiology characterized by the absence of enteric ganglia In the distal colon. We have ascertained a large, inbred, Mennonite kindred...
Dinucleotide repeat polymorphisms at the D13S192 and D13S193 loci (1993)
Hong, Hee-Kyung, Giorda, Roberto, Trucco, Massimo, Chakravarti, Aravinda
Mutirangura, Apiwat, Greenberg, Frank, Butler, Merlin G., Malcolm, Sue, Nicholls, Robert D., Chakravarti, Aravinda, ...
Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are distinct mental retardation disorders caused by a deficiency of paternal (PWS) or maternal (AS) contributions for chromosome 15 by either...
Microsatellite repeat polymorphism at the D13S197 locus (1993)
Hong, Hee-Kyung, Giorda, Roberto, Yu, Ling Mei, Trucco, Massimo, Chakravarti, Aravinda
Dinucleotide repeat polymorphism at the DXS1146 locus (1993)
Hong, Hee-Kyung, Giorda, Roberto, Trucco, Massimo, Chakravarti, Aravinda
The utility of linked marker genes in genetic counseling /--by Aravinda Chakravarti. (1979)
Thesis (Ph. D.)--University of Texas Health Science Center at Houston. Graduate School of Biomedical Sciences, 1979.
Bailey, Jeffrey A., Carrel, Laura, Chakravarti, Aravinda, Eichler, Evan E.
X inactivation is a chromosome-specific form of genetic regulation in which thousands of genes on one homologue become silenced early in female embryogenesis. Although many aspects of X inactivation...
Bolk, Stacey, Pelet, Anna, Hofstra, Robert M. W., Angrist, Misha, Salomon, Remi, Croaker, David, ...
Reduced penetrance in genetic disorders may be either dependent or independent of the genetic background of gene carriers. Hirschsprung disease (HSCR) demonstrates a complex pattern of inheritance...
Sequence variations in the public human genome data reflect a bottlenecked population history
Marth, Gabor, Schuler, Greg, Yeh, Raymond, Davenport, Ruth, Agarwala, Richa, Church, Deanna, ...
Single-nucleotide polymorphisms (SNPs) constitute the great majority of variations in the human genome, and as heritable variable landmarks they are useful markers for disease mapping and resolving...
McCallion, Andrew S., Stames, Erine, Conlon, Ronald A., Chakravarti, Aravinda
Clinical expression of Hirschsprung disease (HSCR) requires the interaction of multiple susceptibility genes. Molecular genetic analyses have revealed that interactions between mutations in the genes...
Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays
Fan, Jian-Bing, Chen, Xiaoqiong, Halushka, Marc K., Berno, Anthony, Huang, Xiaohua, Ryder, Thomas, ...
Large scale human genetic studies require technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. We describe a highly parallel...
Sequence Variation Within the Fragile X Locus
Mathews, Debra J., Kashuk, Carl, Brightwell, Gale, Eichler, Evan E., Chakravarti, Aravinda
The human genome provides a reference sequence, which is a template for resequencing studies that aim to discover and interpret the record of common ancestry that exists in extant genomes. To...
High-Throughput Variation Detection and Genotyping Using Microarrays
Cutler, David J., Zwick, Michael E., Carrasquillo, Minerva M., Yohn, Christopher T., Tobin, Katherine P., Kashuk, Carl, ...
The genetic dissection of complex traits may ultimately require a large number of SNPs to be genotyped in multiple individuals who exhibit phenotypic variation in a trait of interest. Microarray...
Hong, Hee-Kyung, Chakravarti, Aravinda, Takahashi, Joseph S.
The spontaneous autosomal recessive mouse mutant for hydrocephaly with hop gait (hyh) exhibits dramatic cystic dilation of the ventricles at birth and invariably develops hopping gait. We show that...
Peri, Suraj, Navarro, J. Daniel, Amanchy, Ramars, Kristiansen, Troels Z., Jonnalagadda, Chandra Kiran, Surendranath, Vineeth, ...
Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of...
Zhu, Xiaofeng, Yan, Denise, Cooper, Richard S., Luke, Amy, Ikeda, Morna A., Chang, Yen-Pei C., ...
Association studies of candidate genes with complex traits have generally used one or a few single nucleotide polymorphisms (SNPs), although variation in the extent of linkage disequilibrium (LD)...
The Human MitoChip: A High-Throughput Sequencing Microarray for Mitochondrial Mutation Detection
Maitra, Anirban, Cohen, Yoram, Gillespie, Susannah E.D., Mambo, Elizabeth, Fukushima, Noriyoshi, Hoque, Mohammad O., ...
Somatic mitochondrial mutations are common in human cancers, and can be used as a tool for early detection of cancer. We have developed a mitochondrial Custom Reseq™ microarray as an array-based...
Haplotype and Missing Data Inference in Nuclear Families
Lin, Shin, Chakravarti, Aravinda, Cutler, David J.
Determining linkage phase from population samples with statistical methods is accurate only within regions of high linkage disequilibrium (LD). Yet, affected individuals in a genetic mapping study,...
Kashuk, Carl S., Stone, Eric A., Grice, Elizabeth A., Portnoy, Matthew E., Green, Eric D., Sidow, Arend, ...
The ability to discriminate between deleterious and neutral amino acid substitutions in the genes of patients remains a significant challenge in human genetics. The increasing availability of genomic...
On the probability that a novel variant is a disease-causing mutation
Mitchell, Adele A., Chakravarti, Aravinda, Cutler, David J.
When a novel variant is found in a patient and not in a group of controls, it becomes a candidate for the disease-causing mutation in that patient. At present, no sampling theory exists for assessing...
Schork, Nicholas J., Nath, Swapan K., Fallin, Daniele, Chakravarti, Aravinda
Linkage disequilibrium (LD) mapping has been applied to many simple, monogenic, overtly Mendelian human traits, with great success. However, extensions and applications of LD mapping approaches to...
Differential Susceptibility to Hypertension Is Due to Selection during the Out-of-Africa Expansion
Young, J. Hunter, Chang, Yen-Pei C, Kim, James Dae-Ok, Chretien, Jean-Paul, Klag, Michael J, Levine, Michael A, ...
Hypertension is a leading cause of stroke, heart disease, and kidney failure. The genetic basis of blood pressure variation is largely unknown but is likely to involve genes that influence renal salt...
viewGene: A Graphical Tool for Polymorphism Visualization and Characterization
Kashuk, Carl, SenGupta, Sanghamitra, Eichler, Evan, Chakravarti, Aravinda
The human genome project is producing an enormous amount of sequence data, based on which single base changes between individuals can be identified. Unfortunately, computer tools that were adequate...
Laramie, Jason M, Wilk, Jemma B, Hunt, Steven C, Ellison, R Curtis, Chakravarti, Aravinda, Boerwinkle, Eric, ...
Armanios, Mary, Chen, Jiunn-Liang, Chang, Yen-Pei Christy, Brodsky, Robert A., Hawkins, Anita, Griffin, Constance A., ...
Dyskeratosis congenita is a rare inherited disorder characterized by abnormal skin manifestations. Morbidity and mortality from this disease is usually due to bone marrow failure, but idiopathic...
Petersen, Michael B., Frantzen, Merete, Antonarakis, Stylianos E., Warren, Andrew C., Van Broeckhoven, Christine, Chakravarti, Aravinda, ...
Nondisjunction in trisomy 21 has traditionally been studied by cytogenetic heteromorphisms. Those studies assumed no crossing-over on the short arm of chromosome 21. Recently, increased accuracy of...
The meiotic stage of nondisjunction in trisomy 21: Determination by using DNA polymorphisms
Antonarakis, Stylianos E., Petersen, Michael B., McInnis, Melvin G., Adelsberger, Patricia A., Schinzel, Albert A., Binkert, Franz, ...
We have studied DNA polymorphisms at loci in the pericentromeric region on the long arm of chromosome 21 in 200 families with trisomy 21, in order to determine the meiotic origin of nondisjunction....
Chakravarti, Aravinda, Nei, Masatoshi
For a linked marker locus to be useful for genetic counseling, the counselee must be heterozygous for both disease and marker loci and his or her linkage phase must be known. It is shown that when...
Bailey, Jeffrey A., Carrel, Laura, Chakravarti, Aravinda, Eichler, Evan E.
X inactivation is a chromosome-specific form of genetic regulation in which thousands of genes on one homologue become silenced early in female embryogenesis. Although many aspects of X inactivation...
Bolk, Stacey, Pelet, Anna, Hofstra, Robert M. W., Angrist, Misha, Salomon, Remi, Croaker, David, ...
Reduced penetrance in genetic disorders may be either dependent or independent of the genetic background of gene carriers. Hirschsprung disease (HSCR) demonstrates a complex pattern of inheritance...
Sequence variations in the public human genome data reflect a bottlenecked population history
Marth, Gabor, Schuler, Greg, Yeh, Raymond, Davenport, Ruth, Agarwala, Richa, Church, Deanna, ...
Single-nucleotide polymorphisms (SNPs) constitute the great majority of variations in the human genome, and as heritable variable landmarks they are useful markers for disease mapping and resolving...
McCallion, Andrew S., Stames, Erine, Conlon, Ronald A., Chakravarti, Aravinda
Clinical expression of Hirschsprung disease (HSCR) requires the interaction of multiple susceptibility genes. Molecular genetic analyses have revealed that interactions between mutations in the genes...
viewGene: A Graphical Tool for Polymorphism Visualization and Characterization
Kashuk, Carl, SenGupta, Sanghamitra, Eichler, Evan, Chakravarti, Aravinda
The human genome project is producing an enormous amount of sequence data, based on which single base changes between individuals can be identified. Unfortunately, computer tools that were adequate...
Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays
Fan, Jian-Bing, Chen, Xiaoqiong, Halushka, Marc K., Berno, Anthony, Huang, Xiaohua, Ryder, Thomas, ...
Large scale human genetic studies require technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. We describe a highly parallel...
Sequence Variation Within the Fragile X Locus
Mathews, Debra J., Kashuk, Carl, Brightwell, Gale, Eichler, Evan E., Chakravarti, Aravinda
The human genome provides a reference sequence, which is a template for resequencing studies that aim to discover and interpret the record of common ancestry that exists in extant genomes. To...
High-Throughput Variation Detection and Genotyping Using Microarrays
Cutler, David J., Zwick, Michael E., Carrasquillo, Minerva M., Yohn, Christopher T., Tobin, Katherine P., Kashuk, Carl, ...
The genetic dissection of complex traits may ultimately require a large number of SNPs to be genotyped in multiple individuals who exhibit phenotypic variation in a trait of interest. Microarray...
Hong, Hee-Kyung, Chakravarti, Aravinda, Takahashi, Joseph S.
The spontaneous autosomal recessive mouse mutant for hydrocephaly with hop gait (hyh) exhibits dramatic cystic dilation of the ventricles at birth and invariably develops hopping gait. We show that...
Haplotype Inference in Random Population Samples
Lin, Shin, Cutler, David J., Zwick, Michael E., Chakravarti, Aravinda
Contemporary genotyping and sequencing methods do not provide information on linkage phase in diploid organisms. The application of statistical methods to infer and reconstruct linkage phase in...
Peri, Suraj, Navarro, J. Daniel, Amanchy, Ramars, Kristiansen, Troels Z., Jonnalagadda, Chandra Kiran, Surendranath, Vineeth, ...
Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of...
Zhu, Xiaofeng, Yan, Denise, Cooper, Richard S., Luke, Amy, Ikeda, Morna A., Chang, Yen-Pei C., ...
Association studies of candidate genes with complex traits have generally used one or a few single nucleotide polymorphisms (SNPs), although variation in the extent of linkage disequilibrium (LD)...
The Human MitoChip: A High-Throughput Sequencing Microarray for Mitochondrial Mutation Detection
Maitra, Anirban, Cohen, Yoram, Gillespie, Susannah E.D., Mambo, Elizabeth, Fukushima, Noriyoshi, Hoque, Mohammad O., ...
Somatic mitochondrial mutations are common in human cancers, and can be used as a tool for early detection of cancer. We have developed a mitochondrial Custom Reseq™ microarray as an array-based...
Haplotype and Missing Data Inference in Nuclear Families
Lin, Shin, Chakravarti, Aravinda, Cutler, David J.
Determining linkage phase from population samples with statistical methods is accurate only within regions of high linkage disequilibrium (LD). Yet, affected individuals in a genetic mapping study,...
Kashuk, Carl S., Stone, Eric A., Grice, Elizabeth A., Portnoy, Matthew E., Green, Eric D., Sidow, Arend, ...
The ability to discriminate between deleterious and neutral amino acid substitutions in the genes of patients remains a significant challenge in human genetics. The increasing availability of genomic...
On the probability that a novel variant is a disease-causing mutation
Mitchell, Adele A., Chakravarti, Aravinda, Cutler, David J.
When a novel variant is found in a patient and not in a group of controls, it becomes a candidate for the disease-causing mutation in that patient. At present, no sampling theory exists for assessing...
Mitchell, Adele A., Cutler, David J., Chakravarti, Aravinda
The transmission/disequilibrium test (TDT), a family-based test of linkage and association, is a popular and intuitive statistical test for studies of complex inheritance, as it is nonparametric and...
Armanios, Mary, Chen, Jiunn-Liang, Chang, Yen-Pei Christy, Brodsky, Robert A., Hawkins, Anita, Griffin, Constance A., ...
Dyskeratosis congenita is a rare inherited disorder characterized by abnormal skin manifestations. Morbidity and mortality from this disease is usually due to bone marrow failure, but idiopathic...
Schork, Nicholas J., Nath, Swapan K., Fallin, Daniele, Chakravarti, Aravinda
Linkage disequilibrium (LD) mapping has been applied to many simple, monogenic, overtly Mendelian human traits, with great success. However, extensions and applications of LD mapping approaches to...
Differential Susceptibility to Hypertension Is Due to Selection during the Out-of-Africa Expansion
Young, J. Hunter, Chang, Yen-Pei C, Kim, James Dae-Ok, Chretien, Jean-Paul, Klag, Michael J, Levine, Michael A, ...
Hypertension is a leading cause of stroke, heart disease, and kidney failure. The genetic basis of blood pressure variation is largely unknown but is likely to involve genes that influence renal salt...
Laramie, Jason M, Wilk, Jemma B, Hunt, Steven C, Ellison, R Curtis, Chakravarti, Aravinda, Boerwinkle, Eric, ...
Petersen, Michael B., Frantzen, Merete, Antonarakis, Stylianos E., Warren, Andrew C., Van Broeckhoven, Christine, Chakravarti, Aravinda, ...
Nondisjunction in trisomy 21 has traditionally been studied by cytogenetic heteromorphisms. Those studies assumed no crossing-over on the short arm of chromosome 21. Recently, increased accuracy of...
The meiotic stage of nondisjunction in trisomy 21: Determination by using DNA polymorphisms
Antonarakis, Stylianos E., Petersen, Michael B., McInnis, Melvin G., Adelsberger, Patricia A., Schinzel, Albert A., Binkert, Franz, ...
We have studied DNA polymorphisms at loci in the pericentromeric region on the long arm of chromosome 21 in 200 families with trisomy 21, in order to determine the meiotic origin of nondisjunction....
Chakravarti, Aravinda, Nei, Masatoshi
For a linked marker locus to be useful for genetic counseling, the counselee must be heterozygous for both disease and marker loci and his or her linkage phase must be known. It is shown that when...
Human embryonic stem cells have a unique epigenetic signature
Bibikova, Marina, Chudin, Eugene, Wu, Bonnie, Zhou, Lixin, Garcia, Eliza Wickham, Liu, Ying, ...
Human embryonic stem (hES) cells originate during an embryonic period of active epigenetic remodeling. DNA methylation patterns are likely to be critical for their self-renewal and pluripotence. We...
Scuteri, Angelo, Sanna, Serena, Chen, Wei-Min, Uda, Manuela, Albai, Giuseppe, Strait, James, ...
The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not...
Population Bottlenecks as a Potential Major Shaping Force of Human Genome Architecture
Gherman, Adrian, Chen, Peter E, Teslovich, Tanya M, Stankiewicz, Pawel, Withers, Marjorie, Kashuk, Carl S, ...
The modern synthetic view of human evolution proposes that the fixation of novel mutations is driven by the balance among selective advantage, selective disadvantage, and genetic drift. When...
Arking, Dan E., Cutler, David J., Brune, Camille W., Teslovich, Tanya M., West, Kristen, Ikeda, Morna, ...
Autism is a childhood neuropsychiatric disorder that, despite exhibiting high heritability, has largely eluded efforts to identify specific genetic variants underlying its etiology. We performed a...
Multiple Independent Genetic Factors at NOS1AP Modulate the QT Interval in a Multi-Ethnic Population
Arking, Dan E., Khera, Amit, Xing, Chao, Kao, W. H. Linda, Post, Wendy, Boerwinkle, Eric, ...
Extremes of electrocardiographic QT interval are associated with increased risk for sudden cardiac death (SCD); thus, identification and characterization of genetic variants that modulate QT interval...
Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays
Lin, Shin, Carvalho, Benilton, Cutler, David J, Arking, Dan E, Chakravarti, Aravinda, Irizarry, Rafael A
Extended and validated CRLMM is shown to be more accurate than the Affymetrix default programs, and datasets and methods for validation are presented that can serve as standard benchmarks by which...
SanGiovanni, John Paul, Arking, Dan E., Iyengar, Sudha K., Elashoff, Michael, Clemons, Traci E., Reed, George F., ...
Whole-genome association study identifies STK39 as a hypertension susceptibility gene
Wang, Ying, O'Connell, Jeffrey R., McArdle, Patrick F., Wade, James B., Dorff, Sarah E., Shah, Sanjiv J., ...
Hypertension places a major burden on individual and public health, but the genetic basis of this complex disorder is poorly understood. We conducted a genome-wide association study of systolic and...
Positional identification of variants of Adamts16 linked to inherited hypertension
Joe, Bina, Saad, Yasser, Lee, Norman H., Frank, Bryan C., Achinike, Ovokeraye H., Luu, Truong V., ...
A previously reported blood pressure (BP) quantitative trait locus on rat Chromosome 1 was isolated in a short congenic segment spanning 804.6 kb. The 804.6 kb region contained only two genes,...