Kerstin Lindblad-Toh

Summary

Publications

  1. pmc An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts
    Marc P Hoeppner
    Science for Life Laboratories, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    PLoS ONE 9:e91172. 2014
  2. pmc The ESR1 gene is associated with risk for canine mammary tumours
    Kaja Sverdrup Borge
    Section of Genetics, Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, P, O Box 8146 Dep, 0033 Oslo, Norway
    BMC Vet Res 9:69. 2013
  3. pmc Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica
    Radhika Das
    Department of Radiation Oncology, Duke University Medical Center, Box 3433, Durham, NC 27710, USA
    BMC Genomics 13:394. 2012
  4. pmc Mutation discovery in mice by whole exome sequencing
    Heather Fairfield
    The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
    Genome Biol 12:R86. 2011
  5. pmc Comparison of buccal and blood-derived canine DNA, either native or whole genome amplified, for array-based genome-wide association studies
    Gonzalo Rincon
    Department of Animal Science, University of California, Davis, CA 95616, USA
    BMC Res Notes 4:226. 2011
  6. pmc A high-resolution map of human evolutionary constraint using 29 mammals
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 478:476-82. 2011
  7. ncbi Genome sequence, comparative analysis and haplotype structure of the domestic dog
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 438:803-19. 2005
  8. pmc Thorough investigation of a canine autoinflammatory disease (AID) confirms one main risk locus and suggests a modifier locus for amyloidosis
    Mia Olsson
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    PLoS ONE 8:e75242. 2013
  9. pmc The genome of the green anole lizard and a comparative analysis with birds and mammals
    Jessica Alföldi
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 477:587-91. 2011
  10. pmc Unsupervised genome-wide recognition of local relationship patterns
    Neda Zamani
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    BMC Genomics 14:347. 2013

Detail Information

Publications39

  1. pmc An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts
    Marc P Hoeppner
    Science for Life Laboratories, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    PLoS ONE 9:e91172. 2014
    ..All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts. ..
  2. pmc The ESR1 gene is associated with risk for canine mammary tumours
    Kaja Sverdrup Borge
    Section of Genetics, Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, P, O Box 8146 Dep, 0033 Oslo, Norway
    BMC Vet Res 9:69. 2013
    ..ESS is a dog breed known to be at increased risk of developing CMTs. In the second dataset, dogs from breeds known to have a high frequency of CMTs were compared to dogs from breeds with a lower occurrence of these tumours...
  3. pmc Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica
    Radhika Das
    Department of Radiation Oncology, Duke University Medical Center, Box 3433, Durham, NC 27710, USA
    BMC Genomics 13:394. 2012
    ..It is postulated to have evolved in placental mammals to modulate intrauterine resource allocation to the offspring. In this study, we determined the imprint status of metatherian orthologues of eutherian imprinted genes...
  4. pmc Mutation discovery in mice by whole exome sequencing
    Heather Fairfield
    The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
    Genome Biol 12:R86. 2011
    ..We found strong candidate mutations for the majority of mutant exomes sequenced, including new models of orofacial clefting, urogenital dysmorphology, kyphosis and autoimmune hepatitis...
  5. pmc Comparison of buccal and blood-derived canine DNA, either native or whole genome amplified, for array-based genome-wide association studies
    Gonzalo Rincon
    Department of Animal Science, University of California, Davis, CA 95616, USA
    BMC Res Notes 4:226. 2011
    ..abstract:..
  6. pmc A high-resolution map of human evolutionary constraint using 29 mammals
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 478:476-82. 2011
    ..Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease...
  7. ncbi Genome sequence, comparative analysis and haplotype structure of the domestic dog
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 438:803-19. 2005
    ..The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health...
  8. pmc Thorough investigation of a canine autoinflammatory disease (AID) confirms one main risk locus and suggests a modifier locus for amyloidosis
    Mia Olsson
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    PLoS ONE 8:e75242. 2013
    ....
  9. pmc The genome of the green anole lizard and a comparative analysis with birds and mammals
    Jessica Alföldi
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 477:587-91. 2011
    ..Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations...
  10. pmc Unsupervised genome-wide recognition of local relationship patterns
    Neda Zamani
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    BMC Genomics 14:347. 2013
    ..In order to assess the possible biological roles for these subdivisions, they must first be identified and characterised, preferably on a large scale and in an automated fashion...
  11. pmc Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
    Xiaohui Xie
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Nature 434:338-45. 2005
    ..The overall results provide a systematic view of gene regulation in the human, which will be refined as additional mammalian genomes become available...
  12. ncbi The dog as a genetic model for immunoglobulin A (IgA) deficiency: Identification of several breeds with low serum IgA concentrations
    Mia Olsson
    Division of Clinical Immunology F79, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital, SE 14186 Huddinge, Sweden Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE 75123 Uppsala, Sweden Electronic address
    Vet Immunol Immunopathol 160:255-9. 2014
    ..In addition, we discovered low IgA concentrations to be significantly associated with canine atopic dermatitis (CAD, p<0.0001) and pancreatic acinar atrophy (PAA, p=0.04) in German shepherds. ..
  13. pmc Whole-genome sequence assembly for mammalian genomes: Arachne 2
    David B Jaffe
    Whitehead Institute MIT Center for Genome Research, Cambridge, Massachusetts 02141, USA
    Genome Res 13:91-6. 2003
    ..The outcome of this mouse assembly and its analysis are described in (Mouse Genome Sequencing Consortium 2002)...
  14. pmc Genome-wide synteny through highly sensitive sequence alignment: Satsuma
    Manfred G Grabherr
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Bioinformatics 26:1145-51. 2010
    ..From an engineering perspective, the problem here is to provide maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accommodate the billions of base pairs of vertebrate genomes)...
  15. pmc A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs
    Mia Olsson
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    PLoS Genet 7:e1001332. 2011
    ..The identification of HA as a major risk factor for this canine disease raises the potential of this glycosaminoglycan as a risk factor for human periodic fevers and as an important driver of chronic inflammation...
  16. doi Whole-genome resequencing reveals loci under selection during chicken domestication
    Carl Johan Rubin
    Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE 75123 Uppsala, Sweden
    Nature 464:587-91. 2010
    ..This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research...
  17. doi The genomic signature of dog domestication reveals adaptation to a starch-rich diet
    Erik Axelsson
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75237 Uppsala, Sweden
    Nature 495:360-4. 2013
    ..Our results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in the early domestication of dogs...
  18. pmc Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites
    Xiaohui Xie
    Broad Institute of MIT and Harvard, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 104:7145-50. 2007
    ..These sites may thus partition the human genome into domains of expression...
  19. pmc Genome-wide analysis in German shepherd dogs reveals association of a locus on CFA 27 with atopic dermatitis
    Katarina Tengvall
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    PLoS Genet 9:e1003475. 2013
    ..Our results may yield further insight into the genetics behind both canine and human AD...
  20. pmc DLA class II alleles are associated with risk for canine symmetrical lupoid onychodystrophy [corrected](SLO)
    Maria Wilbe
    Department of Animal Breeding and Genetics, Biomedical Centre, Swedish University of Agricultural Sciences SLU, Uppsala, Sweden
    PLoS ONE 5:e12332. 2010
    ....
  21. pmc Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses
    Elisabeth Sundström
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
    BMC Genomics 13:365. 2012
    ..The aims of this study were to investigate if the duplication in Grey horses shows copy number variation and to exclude that any other polymorphism is uniquely associated with the Grey mutation...
  22. ncbi Genomic maps and comparative analysis of histone modifications in human and mouse
    Bradley E Bernstein
    Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Cell 120:169-81. 2005
    ..This suggests that the DNA elements that direct the methylation represent only a small fraction of the region or lie at some distance from the site...
  23. pmc A Simple Repeat Polymorphism in the MITF-M Promoter Is a Key Regulator of White Spotting in Dogs
    Izabella Baranowska Körberg
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
    PLoS ONE 9:e104363. 2014
    ..Thus, both genetic and functional evidence show that the simple repeat polymorphism is a key regulator of white spotting in dogs. ..
  24. doi Leader of the pack: gene mapping in dogs and other model organisms
    Elinor K Karlsson
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge Center, 02142, USA
    Nat Rev Genet 9:713-25. 2008
    ..Here, we review the different trait-mapping strategies, some key biological findings emerging from recent studies and the implications for human health. We also discuss the development of similar resources for other vertebrate organisms...
  25. pmc Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome
    Erik Axelsson
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75237 Uppsala, Sweden
    Genome Res 22:51-63. 2012
    ..The genetic determinants of recombination hotspots in the dog genome may thus reflect a fundamental process of relevance to diverse animal species...
  26. doi Mammary tumor development in dogs is associated with BRCA1 and BRCA2
    Patricio Rivera
    Department of Clinical Sciences, Division of Small Animal Clinical Sciences, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
    Cancer Res 69:8770-4. 2009
    ..Both BRCA1 and BRCA2 showed odds ratios of approximately 4. In conclusion, this study indicates that BRCA1 and BRCA2 contribute to the risk of CMT in ESS, suggesting that dogs may serve as a good model for human breast cancer...
  27. ncbi Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 447:167-77. 2007
    ..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation...
  28. pmc Human immunodeficiency virus type 1 V1-to-V5 envelope variants from the chronic phase of infection use CCR5 and fuse more efficiently than those from early after infection
    Behzad Etemad
    Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, Cambridge, Massachusetts 02139, USA
    J Virol 83:9694-708. 2009
    ..Thus, envelope modifications over time within a host potentially enhance replication capacity...
  29. doi Genome-wide association mapping identifies multiple loci for a canine SLE-related disease complex
    Maria Wilbe
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Biomedical Centre, Uppsala, Sweden
    Nat Genet 42:250-4. 2010
    ....
  30. pmc ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth
    Ellen Markljung
    Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    PLoS Biol 7:e1000256. 2009
    ....
  31. pmc Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing
    Andrew Kirby
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
    Nat Genet 45:299-303. 2013
    ..These results provide a cautionary tale about the challenges in identifying the genes responsible for mendelian, let alone more complex, disorders through massively parallel sequencing...
  32. pmc Full-length transcriptome assembly from RNA-Seq data without a reference genome
    Manfred G Grabherr
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:644-52. 2011
    ..Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome...
  33. pmc Distinguishing protein-coding and noncoding genes in the human genome
    Michele Clamp
    Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 104:19428-33. 2007
    ..It also provides a principled methodology for evaluating future proposed additions to the human gene catalog. Finally, the results indicate that there has been relatively little true innovation in mammalian protein-coding genes...
  34. pmc Comparative genomics as a tool to understand evolution and disease
    Jessica Alföldi
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Genome Res 23:1063-8. 2013
    ..Furthermore, we anticipate discoveries related to evolutionary mechanisms, adaptation, and disease to quickly accelerate in the coming years. ..
  35. pmc Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array
    Anna Maja Molin
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
    BMC Genomics 15:210. 2014
    ..The hitherto largest dataset in canine CNV discovery was assessed, 351 dogs from 30 different breeds, enabling identification of novel CNVs and a thorough characterisation of breed-specific CNVs...
  36. pmc Assisted assembly: how to improve a de novo genome assembly by using related species
    Sante Gnerre
    Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, Massachusetts 02142, USA
    Genome Biol 10:R88. 2009
    ..We show that the information provided by aligning the whole-genome shotgun reads of the target against a reference genome can be used to substantially improve the quality of the resulting assembly...
  37. ncbi Heart development in fibronectin-null mice is governed by a genetic modifier on chromosome four
    Sophie Astrof
    Howard Hughes Medical Institute, Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Mech Dev 124:551-8. 2007
    ..Identification of the modifier would significantly enhance our understanding of the molecular underpinning of heart development and disease...
  38. ncbi Efficient mapping of mendelian traits in dogs through genome-wide association
    Elinor K Karlsson
    Broad Institute of Harvard and Massachusetts Institute of Technology MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 39:1321-8. 2007
    ....
  39. pmc Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection, and these modifications affect antibody neutralization sensitivity
    Manish Sagar
    Department of Medicine, Brigham and Women s Hospital, Cambridge, Massachusetts 02139, USA
    J Virol 80:9586-98. 2006
    ..These studies suggest that changes within the V1-V2 envelope domains over the course of an infection influence sensitivity to autologous neutralizing antibodies and may also impact host receptor/coreceptor interactions...