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Morozova I, Flegontov P, Mikheyev AS, Bruskin S, Asgharian H, Ponomarenko P, Klyuchnikov V, ArunKumar G, Prokhortchouk E, Gankin Y, Rogaev E, Nikolsky Y, Baranova A, Elhaik E, Tatarinova TV. Toward high-resolution population genomics using archaeological samples. DNA Res 2016; 23:295-310. [PMID: 27436340 PMCID: PMC4991838 DOI: 10.1093/dnares/dsw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 05/22/2016] [Indexed: 12/30/2022] Open
Abstract
The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.
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Affiliation(s)
- Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Sergey Bruskin
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Hosseinali Asgharian
- Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Petr Ponomarenko
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
| | | | | | - Egor Prokhortchouk
- Research Center of Biotechnology RAS, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Russia
| | | | - Evgeny Rogaev
- Vavilov Institute of General Genetics RAS, Moscow, Russia University of Massachusetts Medical School, Worcester, MA, USA
| | - Yuri Nikolsky
- Vavilov Institute of General Genetics RAS, Moscow, Russia F1 Genomics, San Diego, CA, USA School of Systems Biology, George Mason University, VA, USA
| | - Ancha Baranova
- School of Systems Biology, George Mason University, VA, USA Research Centre for Medical Genetics, Moscow, Russia Atlas Biomed Group, Moscow, Russia
| | - Eran Elhaik
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK
| | - Tatiana V Tatarinova
- Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
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Sohn KA, Ho JWK, Djordjevic D, Jeong HH, Park PJ, Kim JH. hiHMM: Bayesian non-parametric joint inference of chromatin state maps. ACTA ACUST UNITED AC 2015; 31:2066-74. [PMID: 25725496 PMCID: PMC4481846 DOI: 10.1093/bioinformatics/btv117] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 02/19/2015] [Indexed: 12/19/2022]
Abstract
MOTIVATION Genome-wide mapping of chromatin states is essential for defining regulatory elements and inferring their activities in eukaryotic genomes. A number of hidden Markov model (HMM)-based methods have been developed to infer chromatin state maps from genome-wide histone modification data for an individual genome. To perform a principled comparison of evolutionarily distant epigenomes, we must consider species-specific biases such as differences in genome size, strength of signal enrichment and co-occurrence patterns of histone modifications. RESULTS Here, we present a new Bayesian non-parametric method called hierarchically linked infinite HMM (hiHMM) to jointly infer chromatin state maps in multiple genomes (different species, cell types and developmental stages) using genome-wide histone modification data. This flexible framework provides a new way to learn a consistent definition of chromatin states across multiple genomes, thus facilitating a direct comparison among them. We demonstrate the utility of this method using synthetic data as well as multiple modENCODE ChIP-seq datasets. CONCLUSION The hierarchical and Bayesian non-parametric formulation in our approach is an important extension to the current set of methodologies for comparative chromatin landscape analysis. AVAILABILITY AND IMPLEMENTATION Source codes are available at https://github.com/kasohn/hiHMM. Chromatin data are available at http://encode-x.med.harvard.edu/data_sets/chromatin/.
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Affiliation(s)
- Kyung-Ah Sohn
- Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department o
| | - Joshua W K Ho
- Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department o
| | - Djordje Djordjevic
- Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hyun-Hwan Jeong
- Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Park
- Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ju Han Kim
- Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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