Steven A McCarroll

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. ncbi request reprint Copy-number variation and association studies of human disease
    Steven A McCarroll
    Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Genet 39:S37-42. 2007
  2. doi request reprint Extending genome-wide association studies to copy-number variation
    Steven A McCarroll
    Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Hum Mol Genet 17:R135-42. 2008
  3. pmc Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs
    Joshua M Korn
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nat Genet 40:1253-60. 2008
  4. pmc A polygenic burden of rare disruptive mutations in schizophrenia
    SHAUN M PURCELL
    1 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA 2 Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA 3 Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA 4 Analytic and Translational Genetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA 5 Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 506:185-90. 2014
  5. pmc Mapping the human reference genome's missing sequence by three-way admixture in Latino genomes
    Giulio Genovese
    Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Am J Hum Genet 93:411-21. 2013
  6. pmc Structural haplotypes and recent evolution of the human 17q21.31 region
    Linda M Boettger
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 44:881-5. 2012
  7. pmc No evidence for rare recessive and compound heterozygous disruptive variants in schizophrenia
    Douglas M Ruderfer
    1 Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA 2 Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA 3 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Eur J Hum Genet 23:555-7. 2015
  8. doi request reprint Copy number variation and human genome maps
    Steven A McCarroll
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 42:365-6. 2010
  9. doi request reprint Discovery and genotyping of genome structural polymorphism by sequencing on a population scale
    Robert E Handsaker
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 43:269-76. 2011
  10. pmc De novo mutations in schizophrenia implicate synaptic networks
    Menachem Fromer
    1 Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA 2 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 506:179-84. 2014

Detail Information

Publications38

  1. ncbi request reprint Copy-number variation and association studies of human disease
    Steven A McCarroll
    Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Genet 39:S37-42. 2007
    ..Critical needs are high-resolution maps of common CNPs and techniques that accurately determine the allelic state of affected individuals...
  2. doi request reprint Extending genome-wide association studies to copy-number variation
    Steven A McCarroll
    Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Hum Mol Genet 17:R135-42. 2008
    ..This review will discuss new approaches, recent findings and the analytical challenges involved in expanding GWAS to appreciate the contribution of CNV to human phenotypes...
  3. pmc Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs
    Joshua M Korn
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nat Genet 40:1253-60. 2008
    ..The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype...
  4. pmc A polygenic burden of rare disruptive mutations in schizophrenia
    SHAUN M PURCELL
    1 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA 2 Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA 3 Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA 4 Analytic and Translational Genetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA 5 Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 506:185-90. 2014
    ..5 to 1 per cent) and moderately large effect. Taken together, these data suggest that population-based exome sequencing can discover risk alleles and complements established gene-mapping paradigms in neuropsychiatric disease. ..
  5. pmc Mapping the human reference genome's missing sequence by three-way admixture in Latino genomes
    Giulio Genovese
    Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Am J Hum Genet 93:411-21. 2013
    ..Genome assembly efforts and future builds of the human genome reference will be strongly informed by this localization of genes and other euchromatic sequences that are embedded within highly repetitive pericentromeric regions. ..
  6. pmc Structural haplotypes and recent evolution of the human 17q21.31 region
    Linda M Boettger
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 44:881-5. 2012
    ..An older H2 form lacking such a duplication is present at low frequency in European and central African hunter-gatherer populations. We further show that complex genome structures can be analyzed by imputation from SNPs...
  7. pmc No evidence for rare recessive and compound heterozygous disruptive variants in schizophrenia
    Douglas M Ruderfer
    1 Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA 2 Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA 3 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Eur J Hum Genet 23:555-7. 2015
    ..We do not find evidence for association with SCZ, either genome wide or at specific loci. However, we note the possible impact of sample size and population genetic factors on the power to detect and quantify any burden that may exist. ..
  8. doi request reprint Copy number variation and human genome maps
    Steven A McCarroll
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 42:365-6. 2010
    ..Maps of human genome copy number variation (CNV) are maturing into useful resources for complex disease genetics. Four new studies increase the resolution of CNV maps and seek to locate human phenotypic variation on these maps...
  9. doi request reprint Discovery and genotyping of genome structural polymorphism by sequencing on a population scale
    Robert E Handsaker
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 43:269-76. 2011
    ..These methods offer a way to relate genome structural polymorphism to complex disease in populations...
  10. pmc De novo mutations in schizophrenia implicate synaptic networks
    Menachem Fromer
    1 Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA 2 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 506:179-84. 2014
    ..Aligning our findings with a parallel case-control study, we demonstrate reproducible insights into aetiological mechanisms for schizophrenia and reveal pathophysiology shared with other neurodevelopmental disorders. ..
  11. pmc Accurately assessing the risk of schizophrenia conferred by rare copy-number variation affecting genes with brain function
    Soumya Raychaudhuri
    Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
    PLoS Genet 6:e1001097. 2010
    ..Our method is implemented in the PLINK software package...
  12. doi request reprint Integrated detection and population-genetic analysis of SNPs and copy number variation
    Steven A McCarroll
    Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nat Genet 40:1166-74. 2008
    ..Most common, diallelic CNPs were in strong linkage disequilibrium with SNPs, and most low-frequency CNVs segregated on specific SNP haplotypes...
  13. pmc New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk
    Josee Dupuis
    Department of Biostatistics, Boston University School of Public Health, Massachusetts, USA
    Nat Genet 42:105-16. 2010
    ....
  14. pmc Large multiallelic copy number variations in humans
    Robert E Handsaker
    1 Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 2 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 3 Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 47:296-303. 2015
    ..We also describe partially successful initial strategies for analyzing mCNVs via imputation and provide an initial data resource to support such analyses. ..
  15. pmc Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index
    Elizabeth K Speliotes
    Metabolism Initiative and Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
    Nat Genet 42:937-48. 2010
    ..Furthermore, genes in other newly associated loci may provide new insights into human body weight regulation...
  16. ncbi request reprint Evaluation of common variants in the six known maturity-onset diabetes of the young (MODY) genes for association with type 2 diabetes
    Wendy Winckler
    Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
    Diabetes 56:685-93. 2007
    ..We conclude that although rare variants in these six genes explain most cases of MODY, common variants in these same genes contribute very modestly, if at all, to the common form of type 2 diabetes...
  17. pmc De novo copy number variants identify new genes and loci in isolated sporadic tetralogy of Fallot
    Steven C Greenway
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 41:931-5. 2009
    ..Our findings predict that at least 10% (4.5-15.5%, 95% confidence interval) of sporadic nonsyndromic TOF cases result from de novo CNVs and suggest that mutations within these loci might be etiologic in other cases of TOF...
  18. pmc Recurring exon deletions in the HP (haptoglobin) gene contribute to lower blood cholesterol levels
    Linda M Boettger
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 48:359-66. 2016
    ..Recurring exonic deletions in HP likely enhance human health by lowering cholesterol levels in the blood. ..
  19. pmc Structural forms of the human amylase locus and their relationships to SNPs, haplotypes and obesity
    Christina L Usher
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 47:921-5. 2015
    ..We measured amylase gene copy number in 1,000 obese or lean Estonians and in 2 other cohorts totaling ∼3,500 individuals. We had 99% power to detect the lower bound of the reported effects on BMI, yet found no association. ..
  20. pmc Genome-scale neurogenetics: methodology and meaning
    Steven A McCarroll
    1 Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA 2 Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Neurosci 17:756-63. 2014
    ..Here we describe early results from genome-scale studies of large numbers of subjects and the emerging significance of these results for neurobiology. ..
  21. pmc Genome-wide association analysis identifies 13 new risk loci for schizophrenia
    Stephan Ripke
    1 Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA 2 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 3
    Nat Genet 45:1150-9. 2013
    ..Common genetic variation has an important role in the etiology of schizophrenia, and larger studies will allow more detailed understanding of this disorder. ..
  22. 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
    ....
  23. pmc Using population admixture to help complete maps of the human genome
    Giulio Genovese
    Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Genet 45:406-14, 414e1-2. 2013
    ..We describe how knowledge of the locations of these sequences can inform disease association and genome biology studies...
  24. pmc Mapping copy number variation by population-scale genome sequencing
    Ryan E Mills
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
    Nature 470:59-65. 2011
    ..Our analytical framework and SV map serves as a resource for sequencing-based association studies...
  25. pmc Genetic variation in human DNA replication timing
    Amnon Koren
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 159:1015-26. 2014
    ..Our results show replication timing to be shaped by genetic polymorphism and identify a means by which inherited polymorphism regulates the mutability of nearby sequences. ..
  26. pmc Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
    Evan Z Macosko
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA Electronic address
    Cell 161:1202-14. 2015
    ..Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution. VIDEO ABSTRACT...
  27. pmc Analysis of copy number variations at 15 schizophrenia-associated loci
    Elliott Rees
    Elliott Rees, MRes, James T R Walters, PhD, MRCPsych, Lyudmila Georgieva, PhD, Anthony R Isles, PhD, MRC, Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK Kimberly D Chambert, MS, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachuetts, USA Alexander L Richards, PhD, Gerwyn Mahoney Davies, Bsc, Sophie E Legge, Bsc, Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK Jennifer L Moran, PhD, Steven A McCarroll, PhD, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge
    Br J Psychiatry 204:108-14. 2014
    ..A number of copy number variants (CNVs) have been suggested as susceptibility factors for schizophrenia. For some of these the data remain equivocal, and the frequency in individuals with schizophrenia is uncertain...
  28. pmc Differential relationship of DNA replication timing to different forms of human mutation and variation
    Amnon Koren
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 91:1033-40. 2012
    ..These results indicate differential and sex-specific relationship of DNA replication timing to different forms of mutation and recombination...
  29. pmc Donor-recipient mismatch for common gene deletion polymorphisms in graft-versus-host disease
    Steven A McCarroll
    Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
    Nat Genet 41:1341-4. 2009
    ..Human genome structural variation merits investigation as a potential mechanism in diseases of alloimmunity...
  30. pmc Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome
    Devin P Locke
    Department of Genome Sciences, University of Washington and Howard Hughes Medical Institute, Seattle, WA 98195, USA
    Am J Hum Genet 79:275-90. 2006
    ..Our results underscore the need for complete maps of genetic variation in duplication-rich regions of the genome...
  31. ncbi request reprint Copy number variation: new insights in genome diversity
    Jennifer L Freeman
    Department of Pathology, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Genome Res 16:949-61. 2006
    ..Current efforts are directed toward a more comprehensive cataloging and characterization of CNVs that will provide the basis for determining how genomic diversity impacts biological function, evolution, and common human diseases...
  32. ncbi request reprint Common deletion polymorphisms in the human genome
    Steven A McCarroll
    Department of Molecular Biology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA
    Nat Genet 38:86-92. 2006
    ....
  33. pmc Improved detection of global copy number variation using high density, non-polymorphic oligonucleotide probes
    Fan Shen
    Affymetrix, Inc, 3420 Central Expressway Santa Clara, CA 95051, USA
    BMC Genet 9:27. 2008
    ....
  34. pmc Mapping and sequencing of structural variation from eight human genomes
    Jeffrey M Kidd
    Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
    Nature 453:56-64. 2008
    ..These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects...
  35. ncbi request reprint New insights into the biological basis of genomic disorders
    Simon R Myers
    Nat Genet 38:1363-4. 2006
  36. ncbi request reprint Copy-number analysis goes more than skin deep
    Steven A McCarroll
    Nat Genet 40:5-6. 2008
  37. ncbi request reprint Comparing genomic expression patterns across species identifies shared transcriptional profile in aging
    Steven A McCarroll
    Program in Neuroscience, University of California, San Francisco, California 94143, USA
    Nat Genet 36:197-204. 2004
    ..Using this approach to search databases of gene expression data, we found conserved transcriptional signatures in larval development, embryogenesis, gametogenesis and mRNA degradation...
  38. ncbi request reprint Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans
    Coleen T Murphy
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143 2200, USA
    Nature 424:277-83. 2003
    ....