Aravinda Chakravarti

Summary

Affiliation: Johns Hopkins University
Country: USA

Publications

  1. pmc Next-generation sequencing of human mitochondrial reference genomes uncovers high heteroplasmy frequency
    Maria Ximena Sosa
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
    PLoS Comput Biol 8:e1002737. 2012
  2. pmc Quantifying and modeling birth order effects in autism
    Tychele Turner
    Center for Complex Disease Genomics, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 6:e26418. 2011
  3. pmc Copy number variants in candidate genes are genetic modifiers of Hirschsprung disease
    Qian Jiang
    Center for Complex Disease Genomics, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 6:e21219. 2011
  4. pmc Genome-wide association study identifies GPC5 as a novel genetic locus protective against sudden cardiac arrest
    Dan E Arking
    Center for Complex Diseases Genomics, McKusick Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 5:e9879. 2010
  5. pmc A genome-wide linkage and association scan reveals novel loci for autism
    Lauren A Weiss
    Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
    Nature 461:802-8. 2009
  6. doi Distilling pathophysiology from complex disease genetics
    Aravinda Chakravarti
    Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA Electronic address
    Cell 155:21-6. 2013
  7. pmc Massively parallel rare disease genetics
    Kathleen H Burns
    Department of Pathology, Johns Hopkins University School of Medicine, Ross Building Room 524, 720 Rutland Avenue, Baltimore, MD 21205, USA
    Genome Med 3:29. 2011
  8. pmc Evidence for a gene influencing heart rate on chromosome 5p13-14 in a meta-analysis of genome-wide scans from the NHLBI Family Blood Pressure Program
    Jason M Laramie
    Department of Neurology, Boston University School of Medicine, Boston, MA, USA
    BMC Med Genet 7:17. 2006
  9. pmc A compelling genetic hypothesis for a complex disease: PRODH2/DGCR6 variation leads to schizophrenia susceptibility
    Aravinda Chakravarti
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
    Proc Natl Acad Sci U S A 99:4755-6. 2002
  10. doi Obituary: Victor Almon McKusick (1921-2008)
    Aravinda Chakravarti
    Aravinda Chakravarti is at the McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21093, USA
    Nature 455:46. 2008

Research Grants

  1. GENETIC ANALYSIS OF HIRSCHSPRUNG DISEASE
    Aravinda Chakravarti; Fiscal Year: 2000
  2. Genome-Wide Association Analysis in Essential Hypertension (FEHGAS study)
    Aravinda Chakravarti; Fiscal Year: 2009
  3. Human Genomic Polymorphism in Autism
    Aravinda Chakravarti; Fiscal Year: 2006
  4. GENETIC ANALYSIS OF HIRSCHSPRUNG DISEASE
    Aravinda Chakravarti; Fiscal Year: 2007
  5. GENETIC ANALYSIS OF HIRSCHSPRUNG DISEASE
    Aravinda Chakravarti; Fiscal Year: 2006
  6. Human Genomic Polymorphism in Autism
    Aravinda Chakravarti; Fiscal Year: 2005
  7. Human Genomic Polymorphisms And Haplotypes
    Aravinda Chakravarti; Fiscal Year: 2004
  8. GENETIC ANALYSIS OF HIRSCHSPRUNG DISEASE
    Aravinda Chakravarti; Fiscal Year: 2005
  9. HUMAN GENOMIC POLYMORPHISMS
    Aravinda Chakravarti; Fiscal Year: 2000
  10. GENETIC ANALYSIS OF HIRSCHSPRUNG DISEASE
    Aravinda Chakravarti; Fiscal Year: 2000

Detail Information

Publications87

  1. pmc Next-generation sequencing of human mitochondrial reference genomes uncovers high heteroplasmy frequency
    Maria Ximena Sosa
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
    PLoS Comput Biol 8:e1002737. 2012
    ..These results demonstrate that next-generation sequencing technologies allow interrogation of the mitochondrial genome in greater depth than previously possible which may be of value in biology and medicine...
  2. pmc Quantifying and modeling birth order effects in autism
    Tychele Turner
    Center for Complex Disease Genomics, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 6:e26418. 2011
    ..A search for genes considering these patterns is likely to increase statistical power and uncover novel molecular etiologies...
  3. pmc Copy number variants in candidate genes are genetic modifiers of Hirschsprung disease
    Qian Jiang
    Center for Complex Disease Genomics, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 6:e21219. 2011
    ..A much larger study will be necessary both for replication and for identifying the full spectrum of small CNV effects...
  4. pmc Genome-wide association study identifies GPC5 as a novel genetic locus protective against sudden cardiac arrest
    Dan E Arking
    Center for Complex Diseases Genomics, McKusick Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 5:e9879. 2010
    ..We performed a GWAS to identify genetic determinants of SCA...
  5. pmc A genome-wide linkage and association scan reveals novel loci for autism
    Lauren A Weiss
    Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
    Nature 461:802-8. 2009
    ..The linkage regions reported here provide targets for rare variation screening whereas the discovery of a single novel association demonstrates the action of common variants...
  6. doi Distilling pathophysiology from complex disease genetics
    Aravinda Chakravarti
    Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA Electronic address
    Cell 155:21-6. 2013
    ..Here we propose a set of criteria, akin to Koch's postulates for infectious disease, for assigning causality between genetic variants and human disease phenotypes. ..
  7. pmc Massively parallel rare disease genetics
    Kathleen H Burns
    Department of Pathology, Johns Hopkins University School of Medicine, Ross Building Room 524, 720 Rutland Avenue, Baltimore, MD 21205, USA
    Genome Med 3:29. 2011
    ..A report on the 'Genomic Disorders 2011 - The Genomics of Rare Diseases' meeting, Wellcome Trust Sanger Institute, Hinxton, UK, 23-26 March 2011...
  8. pmc Evidence for a gene influencing heart rate on chromosome 5p13-14 in a meta-analysis of genome-wide scans from the NHLBI Family Blood Pressure Program
    Jason M Laramie
    Department of Neurology, Boston University School of Medicine, Boston, MA, USA
    BMC Med Genet 7:17. 2006
    ..Previous family studies have shown a significant heritable component to heart rate with several groups conducting genomic linkage scans to identify quantitative trait loci...
  9. pmc A compelling genetic hypothesis for a complex disease: PRODH2/DGCR6 variation leads to schizophrenia susceptibility
    Aravinda Chakravarti
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
    Proc Natl Acad Sci U S A 99:4755-6. 2002
  10. doi Obituary: Victor Almon McKusick (1921-2008)
    Aravinda Chakravarti
    Aravinda Chakravarti is at the McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21093, USA
    Nature 455:46. 2008
  11. ncbi Nature, nurture and human disease
    Aravinda Chakravarti
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Jefferson Street Building, 2 109, Baltimore, Maryland 21287, USA
    Nature 421:412-4. 2003
    ..We argue here that the environment exerts its influence at the DNA level and so will need to be understood before the underlying causal factors of common human diseases can be fully recognized...
  12. pmc Differential contributions of rare and common, coding and noncoding Ret mutations to multifactorial Hirschsprung disease liability
    Eileen Sproat Emison
    Center for Complex Disease Genomics, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Am J Hum Genet 87:60-74. 2010
    ..The RET allelic series, and its genotype-phenotype correlations, shows that success in variant identification in complex disorders may strongly depend on which patients are studied...
  13. pmc Multiple independent genetic factors at NOS1AP modulate the QT interval in a multi-ethnic population
    Dan E Arking
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 4:e4333. 2009
    ..These results highlight the consistent and complex role of NOS1AP genetic variants in modulating QT interval...
  14. ncbi A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk
    Eileen Sproat Emison
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Nature 434:857-63. 2005
    ..Thus, common low-penetrance variants, identified by association studies, can underlie both common and rare diseases...
  15. pmc Phenotype-genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence
    Carl S Kashuk
    McKusick Nathans Institute of Genetic Medicine and Department of Comparative Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 102:8949-54. 2005
    ....
  16. ncbi Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studies
    Shin Lin
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Broadway Research Building, Suite 475, 733 N Broadway, Baltimore, Maryland 21205, USA
    Nat Genet 36:1181-8. 2004
    ..These results show that the theoretical benefits of genome-wide association studies are at last realizable...
  17. pmc Genetic variations in nitric oxide synthase 1 adaptor protein are associated with sudden cardiac death in US white community-based populations
    W H Linda Kao
    Department of Epidemiology, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA
    Circulation 119:940-51. 2009
    ....
  18. pmc Effects of rare and common blood pressure gene variants on essential hypertension: results from the Family Blood Pressure Program, CLUE, and Atherosclerosis Risk in Communities studies
    Khanh Dung H Nguyen
    Center for Complex Disease Genomics, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
    Circ Res 112:318-26. 2013
    ..Hypertension affects ≈30% of adults in industrialized countries and is the major risk factor for cardiovascular disease...
  19. pmc Associations between genetic variants in the NOS1AP (CAPON) gene and cardiac repolarization in the old order Amish
    Wendy Post
    Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
    Hum Hered 64:214-9. 2007
    ..The purpose of the current study was to replicate this association in the Old Order Amish...
  20. pmc Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study
    Georg B Ehret
    Center for Complex Diseases Genomics, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Eur J Hum Genet 17:1650-7. 2009
    ..The failure to identify common variants is either because of low statistical power or the existence of rare coding variants in specific families or both, which require additional studies to clarify...
  21. pmc Defining the contribution of CNTNAP2 to autism susceptibility
    Srirangan Sampath
    Center for Complex Disease Genomics, McKusick Nathans Institute of Genetics Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 8:e77906. 2013
    ..9 x10(-5)). Consequently, this study suggests that although CNTNAP2 dysregulation plays a role in some cases, its population contribution to autism susceptibility is limited. ..
  22. pmc Estimating genome-wide copy number using allele-specific mixture models
    Wenyi Wang
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
    J Comput Biol 15:857-66. 2008
    ..Software to implement this procedure will be available in the Bioconductor oligo package (www.bioconductor.org)...
  23. pmc A common genetic variant in the neurexin superfamily member CNTNAP2 increases familial risk of autism
    Dan E Arking
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Am J Hum Genet 82:160-4. 2008
    ..Importantly, the genetic variant displays a parent-of-origin and gender effect recapitulating the inheritance of autism...
  24. pmc Rapid and efficient human mutation detection using a bench-top next-generation DNA sequencer
    Qian Jiang
    Center for Complex Disease Genomics, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Hum Mutat 33:281-9. 2012
    ..We identified five missense mutations in these three genes that may potentially be involved in the pathogenesis of HSCR and need to be studied in larger patient samples...
  25. pmc Population bottlenecks as a potential major shaping force of human genome architecture
    Adrian Gherman
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
    PLoS Genet 3:e119. 2007
    ....
  26. pmc Polymorphisms in the mitochondrial DNA control region and frailty in older adults
    Ann Z Moore
    Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
    PLoS ONE 5:e11069. 2010
    ..Mitochondrial genetic variation may contribute to altered susceptibility to the frailty syndrome in older adults...
  27. pmc Multiple genes for essential-hypertension susceptibility on chromosome 1q
    YEN PEI CHRISTY CHANG
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Am J Hum Genet 80:253-64. 2007
    ..Because the associated alleles in these genes are relatively common (frequency >5%), these three genes are important contributors to elevated BP in the population at large...
  28. pmc Haplotype and missing data inference in nuclear families
    Shin Lin
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
    Genome Res 14:1624-32. 2004
    ..Furthermore, our algorithm can estimate allelic status for missing data at high accuracy (>95%). Finally, the input capacity of the program is vast, easily handling thousands of segregating sites in > or = 1000 chromosomes...
  29. ncbi Public stem cell banks: considerations of justice in stem cell research and therapy
    Ruth R Faden
    Phoebe R Berman Bioethics Institute, Johns Hopkins University, USA
    Hastings Cent Rep 33:13-27. 2003
  30. ncbi Discrepancies in dbSNP confirmation rates and allele frequency distributions from varying genotyping error rates and patterns
    Adele A Mitchell
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 600 N Wolfe Street, Jefferson Street Building, 2 120, Baltimore, MD 21287, USA
    Bioinformatics 20:1022-32. 2004
    ..We conclude that the dbSNP false positive rate is approximately 15-17% and that the reported confirmation studies have vastly different genotyping error rates and patterns...
  31. pmc Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays
    Shin Lin
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, N Broadway, Baltimore, MD 21205, USA
    Genome Biol 9:R63. 2008
    ..Also, we tie our call confidence metric to percent accuracy. We intend that our validation datasets and methods, refered to as SNPaffycomp, serve as standard benchmarks for future SNP calling algorithms...
  32. ncbi Genomic alterations in cultured human embryonic stem cells
    Anirban Maitra
    McKusick Nathans Institute of Genetic Medicine, Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Nat Genet 37:1099-103. 2005
    ....
  33. pmc Exploring biologically relevant pathways in frailty
    Yen Yi Ho
    Division of Geriatric Medicine and Gerontology, Johns Hopkins University School of Medicine, 5505 Bayview Circle, Baltimore, MD 21224, USA
    J Gerontol A Biol Sci Med Sci 66:975-9. 2011
    ..As with longevity research, genetic analyses may help to provide insights into biologically relevant pathways that contribute to frailty...
  34. doi Understanding cardiovascular disease through the lens of genome-wide association studies
    Dan E Arking
    Center for Complex Disease Genomics, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Trends Genet 25:387-94. 2009
    ..Although GWAS face several technical challenges, including the potential for both false-positive and false-negative findings, they are starting to provide a unique view of the genetic architecture of a common disease...
  35. pmc From the Cover: Whole-genome association study identifies STK39 as a hypertension susceptibility gene
    Ying Wang
    Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Proc Natl Acad Sci U S A 106:226-31. 2009
    ..Thus, variants in STK39 may influence BP by increasing STK39 expression and consequently altering renal Na(+) excretion, thus unifying rare and common BP-regulating alleles in the same physiological pathway...
  36. pmc A multilevel model to address batch effects in copy number estimation using SNP arrays
    Robert B Scharpf
    Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Biostatistics 12:33-50. 2011
    ..The software is open source and implemented in the R package crlmm at Bioconductor (http:www.bioconductor.org)...
  37. ncbi Identifying allelic loss and homozygous deletions in pancreatic cancer without matched normals using high-density single-nucleotide polymorphism arrays
    Eric S Calhoun
    Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutes, Baltimore, MD 21231, USA
    Cancer Res 66:7920-8. 2006
    ..This study provides previously unavailable high-resolution allelotype and deletion breakpoint maps in widely shared pancreatic cancer cell lines and effectively eliminates the need for matched normal tissue to define informative loci...
  38. ncbi Variation in the ciliary neurotrophic factor gene and muscle strength in older Caucasian women
    Dan E Arking
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University, 733 N Broadway, Baltimore, MD 21205, USA
    J Am Geriatr Soc 54:823-6. 2006
    ..To determine whether genetic variants in the ciliary neurotrophic factor (CNTF) gene are associated with muscle strength in older women...
  39. ncbi A common genetic variant in the NOS1 regulator NOS1AP modulates cardiac repolarization
    Dan E Arking
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Nat Genet 38:644-51. 2006
    ..Approximately 60% of subjects of European ancestry carry at least one minor allele of the NOS1AP genetic variant, which explains up to 1.5% of QT interval variation...
  40. pmc On the probability that a novel variant is a disease-causing mutation
    Adele A Mitchell
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Genome Res 15:960-6. 2005
    ..Thus, discovery of a variant in a patient and not in a group of controls is, on its own, very weak evidence of involvement with disease...
  41. ncbi Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer
    Elizabeth A Grice
    McKusick Nathans Institute of Genetic Medicine, Department of Comparative Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Hum Mol Genet 14:3837-45. 2005
    ..Importantly, this sequence also modulates expression in the enteric nervous system consistent with its proposed role in HSCR...
  42. pmc Hybrids of aneuploid human cancer cells permit complementation of simple and complex cancer defects
    David A Dezentje
    Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
    Cancer Biol Ther 8:347-55. 2009
    ..Fusing CIN cell lines to form mapped hybrids offers new tools for positional cloning or classification of simple and complex cancer phenotypes, including mechanical defects and altered drug responses...
  43. pmc Interaction between a chromosome 10 RET enhancer and chromosome 21 in the Down syndrome-Hirschsprung disease association
    Stacey Arnold
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Hum Mutat 30:771-5. 2009
    ..This is the first report of a genetic interaction between a common functional variant (rs2435357) and a not infrequent copy number error (chromosome 21 dosage) in two human developmental disorders...
  44. pmc Identification of a sudden cardiac death susceptibility locus at 2q24.2 through genome-wide association in European ancestry individuals
    Dan E Arking
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS Genet 7:e1002158. 2011
    ..Consistent with epidemiological studies showing increased risk of SCD with prolonged QRS/QT intervals, the interval-prolonging alleles are in aggregate associated with increased risk for SCD (P = 0.006)...
  45. pmc Mitochondrial DNA variants of respiratory complex I that uniquely characterize haplogroup T2 are associated with increased risk of age-related macular degeneration
    John Paul SanGiovanni
    National Eye Institute NEI National Institutes of Health NIH, Bethesda, Maryland, United States of America
    PLoS ONE 4:e5508. 2009
    ....
  46. pmc Allele-specific expression in the germline of patients with familial pancreatic cancer: an unbiased approach to cancer gene discovery
    Aik Choon Tan
    The Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, USA
    Cancer Biol Ther 7:135-44. 2008
    ....
  47. pmc Haploinsufficiency of telomerase reverse transcriptase leads to anticipation in autosomal dominant dyskeratosis congenita
    Mary Armanios
    Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 102:15960-4. 2005
    ..This finding emphasizes the importance of telomere maintenance and telomerase dosage for maintaining tissue proliferative capacity and has relevance for understanding mechanisms of age-related changes...
  48. ncbi Genomics in sudden cardiac death
    Dan E Arking
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Room 580, Baltimore, MD 21205, USA
    Circ Res 94:712-23. 2004
    ..The development of novel strategies to identify contributors to susceptibility in common cardiac phenotypes is most likely to lead to new and relevant therapeutic targets for SCD...
  49. pmc A polymorphic 3'UTR element in ATP1B1 regulates alternative polyadenylation and is associated with blood pressure
    Megana K Prasad
    Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 8:e76290. 2013
    ..003) in a European-American population. Therefore, we have identified a novel multi-allelic TRS in the 3'UTR of ATP1B1 that is associated with higher BP and may mediate its effect by regulating the polyadenylation of the ATP1B1 mRNA. ..
  50. pmc Replication of the Wellcome Trust genome-wide association study of essential hypertension: the Family Blood Pressure Program
    Georg B Ehret
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Eur J Hum Genet 16:1507-11. 2008
    ..No replication could be shown for hypertension status, but there are differences in study design. This attempted replication highlights that essential hypertension studies will require more comprehensive and larger genetic screens...
  51. pmc Differential susceptibility to hypertension is due to selection during the out-of-Africa expansion
    J Hunter Young
    The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS Genet 1:e82. 2005
    ..This differential susceptibility is likely due to our history of adaptation to climate...
  52. pmc The Human MitoChip: a high-throughput sequencing microarray for mitochondrial mutation detection
    Anirban Maitra
    Department of Pathology, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Genome Res 14:812-9. 2004
    ..The MitoChip is a high-throughput sequencing tool for the reliable identification of mitochondrial DNA mutations from primary tumors in clinical samples...
  53. ncbi Genome-wide association study and mouse model identify interaction between RET and EDNRB pathways in Hirschsprung disease
    Minerva M Carrasquillo
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 600 N Wolfe St, Jefferson St Bldg, 2 109, Baltimore, Maryland 21287, USA
    Nat Genet 32:237-44. 2002
    ..Thus, genetic interaction between mutations in RET and EDNRB is an underlying mechanism for this complex disorder...
  54. pmc Undetected genotyping errors cause apparent overtransmission of common alleles in the transmission/disequilibrium test
    Adele A Mitchell
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
    Am J Hum Genet 72:598-610. 2003
    ..Therefore, we conclude that undetected genotyping errors may be contributing to an inflated false-positive rate among reported TDT-derived associations and that genotyping fidelity must be increased...
  55. ncbi Safety issues in cell-based intervention trials
    Liza Dawson
    Phoebe R Berman Bioethics Institute, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Fertil Steril 80:1077-85. 2003
    ..We recommend that scientists, policy makers, and the public discuss these issues responsibly, and further, that a national advisory committee to oversee human trials of cell therapies be established...
  56. pmc Phenotype variation in two-locus mouse models of Hirschsprung disease: tissue-specific interaction between Ret and Ednrb
    Andrew S McCallion
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 100:1826-31. 2003
    ..Our data demonstrate that interaction between these genes is restricted to the enteric nervous system and does not affect renal, coat color, and retinal choroid development...
  57. pmc Relative contribution of genetic and nongenetic modifiers to intestinal obstruction in cystic fibrosis
    Scott M Blackman
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21287, USA
    Gastroenterology 131:1030-9. 2006
    ..Our aim was to determine the relative contribution of genetic and nongenetic modifiers to the development of this major complication of CF...
  58. pmc Haplotype inference in random population samples
    Shin Lin
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
    Am J Hum Genet 71:1129-37. 2002
    ..2 are analyzed and scored according to the fraction of neighbor relations correctly called, reconstructions are 95.2% accurate over entire 100-kb stretches and are 98.6% accurate within blocks of high LD...
  59. pmc Development of human protein reference database as an initial platform for approaching systems biology in humans
    Suraj Peri
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21287, USA
    Genome Res 13:2363-71. 2003
    ..hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era...
  60. pmc ViewGene: a graphical tool for polymorphism visualization and characterization
    Carl Kashuk
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
    Genome Res 12:333-8. 2002
    ..Manipulation, cross-referencing, and haplotype viewing of snp data are essential for quality assessment and identification of variants associated with genetic disease, and viewGene provides all three of these important functions...
  61. ncbi A genome-wide linkage analysis investigating the determinants of blood pressure in whites and African Americans
    Bonnie A Thiel
    Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
    Am J Hypertens 16:151-3. 2003
    ..0057 and .00023, respectively) was found on chromosome 1. Our results support the idea that BP regulation is most likely governed by multiple genetic loci, each with a relatively weak effect on BP in the population at large...
  62. ncbi An evaluation of the assembly of an approximately 15-Mb region on human chromosome 13q32-q33 linked to bipolar disorder and schizophrenia
    Susan L Christian
    Department of Psychiatry, The University of Chicago, Chicago, Illinois 60637, USA
    Genomics 79:635-56. 2002
    ..Overall, integration of the data from multiple sources is still needed for complete assembly of the 13q32-q33 region. (c)..
  63. pmc Linkage disequilibrium and haplotype diversity in the genes of the renin-angiotensin system: findings from the family blood pressure program
    Xiaofeng Zhu
    Department of Preventive Medicine and Epidemiology, Loyola Stritch School of Medicine, Maywood, Illinois 60153, USA
    Genome Res 13:173-81. 2003
    ..These findings have implications for candidate-gene association studies and indicate that variation between populations of European and African origin in haplotype diversity is characteristic of most genes...
  64. ncbi Associations between hypertension and genes in the renin-angiotensin system
    Xiaofeng Zhu
    Department of Preventive Medicine and Epidemiology, Loyola University Stritch School of Medicine, Maywood, Ill, USA
    Hypertension 41:1027-34. 2003
    ..Thus, in this biracial population sample, we find evidence that interindividual variation in the renin-angiotensin system genes contributes to hypertension risk...
  65. ncbi Erythrocyte sodium-lithium countertransport and blood pressure: a genome-wide linkage study
    Alan B Weder
    Division of Hypertension, University of Michigan, Ann Arbor, MI 48109, USA
    Hypertension 41:842-6. 2003
    ..Further studies confirming the presence of a quantitative trait locus in this region and evaluating these candidate genes may help explain the association of elevated sodium-lithium countertransport and hypertension...
  66. ncbi Haplotype association analysis of AGT variants with hypertension-related traits: the HyperGEN study
    C Charles Gu
    Division of Biostatistics, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
    Hum Hered 60:164-76. 2005
    ..We set out to examine a hypothesis that multiple genetic variants in the system act together in blood pressure regulation, via intermediate phenotypes such as blood pressure reactivity...
  67. ncbi A population association study of angiotensinogen polymorphisms and haplotypes with left ventricular phenotypes
    Laura J Rasmussen-Torvik
    Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
    Hypertension 46:1294-9. 2005
    ..The single SNP association was driven by a large group of SNPs in high linkage disequilibrium that includes the promoter SNP rs5051...
  68. pmc Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits
    Angelo Scuteri
    Unità Operativa Geriatria, Istituto per la Patologia Endocrina e Metabolica, Rome, Italy
    PLoS Genet 3:e115. 2007
    ..These changes could have a significant impact on the risk of obesity-related morbidity in the general population...
  69. pmc Genome-wide detection and characterization of positive selection in human populations
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nature 449:913-8. 2007
    ....
  70. ncbi A trisomic transmission disequilibrium test
    Zhiying Xu
    Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
    Genet Epidemiol 26:125-31. 2004
    ..We demonstrate the method on a dataset of parent-child trios in which the child has Down syndrome...
  71. ncbi Positional identification of hypertension susceptibility genes on chromosome 2
    Ruth Ann Barkley
    Human Genetics Center and Institute of Molecular Medicine, of Texas Health Science Center at Houston, USA
    Hypertension 43:477-82. 2004
    ..Moreover, the present study validates previous evidence for one or more genes on chromosome 2 that influence hypertension-related phenotypes in the population-at-large...
  72. doi Association between microdeletion and microduplication at 16p11.2 and autism
    Lauren A Weiss
    Autism Consortium, Boston, USA
    N Engl J Med 358:667-75. 2008
    ..Autism spectrum disorder is a heritable developmental disorder in which chromosomal abnormalities are thought to play a role...
  73. ncbi High incidence of deafness from three frequent connexin 26 mutations in an isolated community
    Joel Zlotogora
    Department of Genetic Community, Public Health Services, Health Ministry Israel and Hebrew University, Jerusalem, Israel
    Genet Test 10:40-3. 2006
    ..4%), or V37I (4.8%). The three mutations appeared in the village approximately 100-150 years ago. The question of why three distinct mutations of similar age are observed at high frequency within a genetic isolate is discussed...
  74. ncbi Planning the genome institute's future
    Wendy R Uhlmann
    Science 299:1515; author reply 1515. 2003
  75. ncbi Cloning of rat thymic stromal lymphopoietin receptor (TSLPR) and characterization of genomic structure of murine Tslpr gene
    Blagoy Blagoev
    Protein Interaction Laboratory, Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, M, DK 5230, Odense, Denmark
    Gene 284:161-8. 2002
    ..Finally, using linkage analysis, we mapped the murine Tslpr gene to mouse chromosome 5 between the Ecm2 and Pxn genes...
  76. ncbi Segregation analysis of blood pressure and body mass index in a rural US community
    Swapan K Nath
    Arthritis and Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, USA
    Hum Biol 74:11-23. 2002
    ..Our analysis results support the segregation of a major gene for BMI, but not for SBP or DBP. A recessive locus effect provided the best explanation for BMI where approximately 43% of the variance of BMI was due to this gene...
  77. ncbi Segregation at three loci explains familial and population risk in Hirschsprung disease
    Stacey B Gabriel
    Department of Genetics and Center for Human Genetics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
    Nat Genet 31:89-93. 2002
    ..This study demonstrates by a complete genetic dissection why the inheritance pattern of S-HSCR is nonmendelian...
  78. pmc Human embryonic stem cells have a unique epigenetic signature
    Marina Bibikova
    Illumina, Inc, San Diego, California 92121, USA
    Genome Res 16:1075-83. 2006
    ..Our results indicate that hES cells have a unique epigenetic signature that may contribute to their developmental potential...
  79. ncbi An investigation of genome-wide associations of hypertension with microsatellite markers in the family blood pressure program (FBPP)
    C Charles Gu
    Division of Biostatistics, Washington University School of Medicine, 660 S Euclid Avenue, Campus Box 8067, St Louis, MO 63110, USA
    Hum Genet 121:577-90. 2007
    ....
  80. pmc An ancestral variant of Secretogranin II confers regulation by PHOX2 transcription factors and association with hypertension
    Gen Wen
    Department of Medicine, Moores UCSD Cancer Center, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Hum Mol Genet 16:1752-64. 2007
    ..These results identify a common regulatory variation in SCG2 and implicate granin gene expression in the control of human blood pressure and susceptibility to hypertension...
  81. ncbi A genome-wide scan for obesity in African-Americans
    Xiaofeng Zhu
    Department of Preventive Medicine and Epidemiology, Loyola University Medical School, Maywood, Illinois 60153, USA
    Diabetes 51:541-4. 2002
    ..The replication of linkage evidence using different ethnic groups reinforces the potential significance of this latter candidate region...
  82. ncbi Future of genetics of mood disorders research
    Kathleen R Merikangas
    National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
    Biol Psychiatry 52:457-77. 2002
    ..To prepare for shifts to more complex genetic models, the committee recommended that the NIMH develop new interdisciplinary training strategies to prepare for the next generation of genetics research...
  83. ncbi Finding needles in haystacks--IRF6 gene variants in isolated cleft lip or cleft palate
    Aravinda Chakravarti
    N Engl J Med 351:822-4. 2004
  84. pmc A second generation human haplotype map of over 3.1 million SNPs
    Kelly A Frazer
    The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
    Nature 449:851-61. 2007
    ..Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations...
  85. ncbi A BDNF coding variant is associated with the NEO personality inventory domain neuroticism, a risk factor for depression
    Srijan Sen
    Neuroscience Program, University of Michigan, Ann Arbor, MI, USA
    Neuropsychopharmacology 28:397-401. 2003
  86. pmc Sequence variations in the public human genome data reflect a bottlenecked population history
    Gabor Marth
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Proc Natl Acad Sci U S A 100:376-81. 2003
    ..The inferred times of collapse and recovery are Upper Paleolithic, in agreement with archaeological evidence of the initial modern human colonization of Europe...

Research Grants19

  1. GENETIC ANALYSIS OF HIRSCHSPRUNG DISEASE
    Aravinda Chakravarti; Fiscal Year: 2000
    ..More generally, the aim is to develop a paradigm for the genetic and molecular analysis of complex, multifactorial human diseases. ..
  2. Genome-Wide Association Analysis in Essential Hypertension (FEHGAS study)
    Aravinda Chakravarti; Fiscal Year: 2009
    ..The long-term goal of this study is to enable a molecular understanding of the genetic basis of essential hypertension and provide a paradigm for SNP-based gene discovery in complex human disease. ..
  3. Human Genomic Polymorphism in Autism
    Aravinda Chakravarti; Fiscal Year: 2006
    ..In this proposal, we carry on the tradition from the previous funding cycle of developing novel genomic technologies that are of direct relevance to the genetic dissection of complex neuropsychiatric traits. ..
  4. GENETIC ANALYSIS OF HIRSCHSPRUNG DISEASE
    Aravinda Chakravarti; Fiscal Year: 2007
    ..The long-term objective of this study is to understand the molecular genetic basis of HSCR. More generally, our aim is to develop a paradigm for sequence-based biology in complex, human diseases. ..
  5. GENETIC ANALYSIS OF HIRSCHSPRUNG DISEASE
    Aravinda Chakravarti; Fiscal Year: 2006
    ..The long-term objective of this study is to understand the molecular genetic basis of HSCR. More generally, our aim is to develop a paradigm for sequence-based biology in complex, human diseases. ..
  6. Human Genomic Polymorphism in Autism
    Aravinda Chakravarti; Fiscal Year: 2005
    ..In this proposal, we carry on the tradition from the previous funding cycle of developing novel genomic technologies that are of direct relevance to the genetic dissection of complex neuropsychiatric traits. ..
  7. Human Genomic Polymorphisms And Haplotypes
    Aravinda Chakravarti; Fiscal Year: 2004
    ..They have demonstrated experience and expertise in genomic variation technology and their applications to human disease and population genetics and DNA chip technology. ..
  8. GENETIC ANALYSIS OF HIRSCHSPRUNG DISEASE
    Aravinda Chakravarti; Fiscal Year: 2005
    ..The long-term objective of this study is to understand the molecular genetic basis of HSCR. More generally, our aim is to develop a paradigm for sequence-based biology in complex, human diseases. ..
  9. HUMAN GENOMIC POLYMORPHISMS
    Aravinda Chakravarti; Fiscal Year: 2000
    ..The second aim will allow us to accurately estimate the density of SNPs needed to efficiently develop haplotypes across the entire human genome for disease association studies. ..
  10. GENETIC ANALYSIS OF HIRSCHSPRUNG DISEASE
    Aravinda Chakravarti; Fiscal Year: 2000
    ..More generally, the aim is to develop a paradigm for the genetic and molecular analysis of complex, multifactorial human diseases. ..
  11. GENETIC ANALYSIS OF HIRSCHSPRUNG DISEASE
    Aravinda Chakravarti; Fiscal Year: 2001
    ..More generally, the aim is to develop a paradigm for the genetic and molecular analysis of complex, multifactorial human diseases. ..
  12. GENETIC ANALYSIS OF HIRSCHSPRUNG DISEASE
    Aravinda Chakravarti; Fiscal Year: 2004
    ..The long-term objective of this study is to understand the molecular genetic basis of HSCR. More generally, our aim is to develop a paradigm for sequence-based biology in complex, human diseases. ..
  13. GENETIC EPIDEMIOLOGY OF HYPERTENSION: GENOMIC CORES
    Aravinda Chakravarti; Fiscal Year: 2004
    ..The resulting synthesis of ideas and amassed data permits rigorous hypothesis testing not otherwise possible and will hasten understanding of the previously elusive genetic variation responsible for disease risk. ..
  14. Human Genomic Polymorphism in Autism
    Aravinda Chakravarti; Fiscal Year: 2004
    ..In this proposal, we carry on the tradition from the previous funding cycle of developing novel genomic technologies that are of direct relevance to the genetic dissection of complex neuropsychiatric traits. ..
  15. Genome-Wide Association Analysis in Essential Hypertension (FEHGAS study)
    Aravinda Chakravarti; Fiscal Year: 2007
    ..The long-term goal of this study is to enable a molecular understanding of the genetic basis of essential hypertension and provide a paradigm for SNP-based gene discovery in complex human disease. ..