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Zhang S, Xu N, Fu L, Yang X, Li Y, Yang Z, Feng Y, Ma K, Jiang X, Han J, Hu R, Zhang L, de Gennaro L, Ryabov F, Meng D, He Y, Wu D, Yang C, Paparella A, Mao Y, Bian X, Lu Y, Antonacci F, Ventura M, Shepelev VA, Miga KH, Alexandrov IA, Logsdon GA, Phillippy AM, Su B, Zhang G, Eichler EE, Lu Q, Shi Y, Sun Q, Mao Y. Comparative genomics of macaques and integrated insights into genetic variation and population history. bioRxiv 2024:2024.04.07.588379. [PMID: 38645259 PMCID: PMC11030432 DOI: 10.1101/2024.04.07.588379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The crab-eating macaques ( Macaca fascicularis ) and rhesus macaques ( M. mulatta ) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is ∼42% lower, while centromeres are ∼3.7 times longer than those in humans. The characterization of ∼2 Mbp fixed genetic variants and ∼240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g., CYP2C76 and EHBP1L1 ). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g., PNPO ). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g., FOLH1 and PIEZO2 ). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g., STAB1 , SEMA3F , and HOXD13 ). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.
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Riviello FN, Daponte A, Ponzi E, Ficarella R, Orsini P, Bucci R, Ventura M, Antonacci F, Catacchio CR, Gentile M. A Rare Case of Concurrent 2q34q36 Duplication and 2q37 Deletion in a Neonate with Syndromic Features. Genes (Basel) 2023; 14:2194. [PMID: 38137016 PMCID: PMC10742419 DOI: 10.3390/genes14122194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Large-scale genomic structural variations can have significant clinical implications, depending on the specific altered genomic region. Briefly, 2q37 microdeletion syndrome is a prevalent subtelomeric deletion disorder characterized by variable-sized deletions. Affected patients exhibit a wide range of clinical manifestations, including short stature, facial dysmorphism, and features of autism spectrum disorder, among others. Conversely, isolated duplications of proximal chromosome 2q are rare and lack a distinct phenotype. In this report, we provide an extensive molecular analysis of a 15-day-old newborn referred for syndromic features. Our analysis reveals an 8.5 Mb microdeletion at 2q37.1, which extends to the telomere, in conjunction with an 8.6 Mb interstitial microduplication at 2q34q36.1. Our findings underscore the prominence of 2q37 terminal deletions as commonly reported genomic anomalies. We compare our patient's phenotype with previously reported cases in the literature to contribute to a more refined classification of 2q37 microdeletion syndrome and assess the potential impact of 2q34q36.1 microduplication. We also investigate multiple hypotheses to clarify the genetic mechanisms responsible for the observed genomic rearrangement.
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Affiliation(s)
- Francesco Nicola Riviello
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Alessia Daponte
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Emanuela Ponzi
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Romina Ficarella
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Paola Orsini
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Roberta Bucci
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Mario Ventura
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Francesca Antonacci
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Claudia Rita Catacchio
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Mattia Gentile
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
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3
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Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJ, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PG, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O’Neill RJ, Eichler E, Phillippy AM. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. bioRxiv 2023:2023.11.30.569198. [PMID: 38077089 PMCID: PMC10705393 DOI: 10.1101/2023.11.30.569198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Apes possess two sex chromosomes-the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and cognition. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosome structure and evolution. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the state-of-the-art experimental and computational methods developed for the telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies completely resolved ampliconic, palindromic, and satellite sequences, including the entire centromeres, allowing us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the X, ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions and palindromes (which are shared more broadly among species on the X) and from the abundance of transposable elements and satellites (which have a lower representation on the X). Our analysis of Y chromosome genes revealed lineage-specific expansions of multi-copy gene families and signatures of purifying selection. In summary, the Y exhibits dynamic evolution, while the X is more stable. Finally, mapping short-read sequencing data from >100 great ape individuals revealed the patterns of diversity and selection on their sex chromosomes, demonstrating the utility of these reference assemblies for studies of great ape evolution. These complete sex chromosome assemblies are expected to further inform conservation genetics of nonhuman apes, all of which are endangered species.
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Affiliation(s)
| | - Brandon D. Pickett
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Monika Cechova
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Karol Pal
- Penn State University, University Park, PA, USA
| | - Sergey Nurk
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - DongAhn Yoo
- University of Washington School of Medicine, Seattle, WA, USA
| | - Qiuhui Li
- Johns Hopkins University, Baltimore, MD, USA
| | - Prajna Hebbar
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | | | | | - Erich Bomberg
- University of Münster, Münster, Germany
- MPI for Developmental Biology, Tübingen, Germany
| | - Gerard G. Bouffard
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shelise Y. Brooks
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lucia Carbone
- Oregon Health & Science University, Portland, OR, USA
- Oregon National Primate Research Center, Hillsboro, OR, USA
| | - Laura Carrel
- Penn State University School of Medicine, Hershey, PA, USA
| | | | | | - Chen-Shan Chin
- Foundation of Biological Data Sciences, Belmont, CA, USA
| | | | | | | | - Mark Diekhans
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Amalia Dutra
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gage H. Garcia
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Glenn Hickey
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - David A. Hillis
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | - Hyeonsoo Jeong
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | | | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Karen H. Miga
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Evgenia Pak
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benedict Paten
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Arang Rhie
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | | | - Samuel Sacco
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | - Steven J. Solar
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Sweetalana
- Penn State University, University Park, PA, USA
| | - Alex Sweeten
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | | | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Alice C. Young
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xinru Zhang
- Penn State University, University Park, PA, USA
| | | | | | | | - Soojin V. Yi
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | | | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Evan Eichler
- University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Adam M. Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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4
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Paparella A, L’Abbate A, Palmisano D, Chirico G, Porubsky D, Catacchio CR, Ventura M, Eichler EE, Maggiolini FAM, Antonacci F. Structural Variation Evolution at the 15q11-q13 Disease-Associated Locus. Int J Mol Sci 2023; 24:15818. [PMID: 37958807 PMCID: PMC10648317 DOI: 10.3390/ijms242115818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The impact of segmental duplications on human evolution and disease is only just starting to unfold, thanks to advancements in sequencing technologies that allow for their discovery and precise genotyping. The 15q11-q13 locus is a hotspot of recurrent copy number variation associated with Prader-Willi/Angelman syndromes, developmental delay, autism, and epilepsy and is mediated by complex segmental duplications, many of which arose recently during evolution. To gain insight into the instability of this region, we characterized its architecture in human and nonhuman primates, reconstructing the evolutionary history of five different inversions that rearranged the region in different species primarily by accumulation of segmental duplications. Comparative analysis of human and nonhuman primate duplication structures suggests a human-specific gain of directly oriented duplications in the regions flanking the GOLGA cores and HERC segmental duplications, representing potential genomic drivers for the human-specific expansions. The increasing complexity of segmental duplication organization over the course of evolution underlies its association with human susceptibility to recurrent disease-associated rearrangements.
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Affiliation(s)
- Annalisa Paparella
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Alberto L’Abbate
- Institute of Biomembranes, Bioenergetics, and Molecular Biotechnology (IBIOM), 70125 Bari, Italy
| | - Donato Palmisano
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Gerardina Chirico
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Claudia R. Catacchio
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Mario Ventura
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute (HHMI), University of Washington, Seattle, WA 98195, USA
| | - Flavia A. M. Maggiolini
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA), 70010 Bari, Italy
| | - Francesca Antonacci
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
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5
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De Angelis S, De Sanctis MC, Altieri F, Ferrari M, Ammannito E, Novi S, Dami M, Antonacci F, Villa F, Meini M, Ruggiero F, Fonte S, Formisano M, Frigeri A, Tinivelli P, Giardino M, Mugnuolo R, Pirrotta S. The pre-launch on-ground characterization of Ma_MISS spectrometer for ExoMars-Rosalind Franklin Rover mission. II. Radiometric calibration. Rev Sci Instrum 2023; 94:094501. [PMID: 37655988 DOI: 10.1063/5.0152205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/06/2023] [Indexed: 09/02/2023]
Abstract
The Ma_MISS miniaturized spectrometer is integrated within the Drilling System of the ExoMars Rosalind Franklin Rover for Mars exploration. Here we focus on the on ground calibration campaign to obtain radiometric and linearity calibrations of the Ma_MISS instrument, while the first paper dealt with the spectral calibration [De Angelis et al., Rev. Sci. Instrum. 93, 123704 (2022)]. The experimental setup used to carry out radiometric calibration is described, as are the methods used for data processing and key parameter retrieval. In particular, the Spectrometer Transfer Function (Responsivity), Signal-to-Noise Ratio, and detector linearity are determined. In a third paper [De Sanctis et al., Planet. Sci. J. 3, 142 (2022)], validation of the Ma_MISS calibration results through spectral measurements performed on rock and synthetic targets during the radiometric calibration campaign is described.
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Affiliation(s)
- S De Angelis
- INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome, Italy
| | - M C De Sanctis
- INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome, Italy
| | - F Altieri
- INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome, Italy
| | - M Ferrari
- INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome, Italy
| | - E Ammannito
- ASI-Italian Space Agency, Via del Politecnico snc, 00133 Rome, Italy
| | - S Novi
- Sitael, Via Alessandro Gherardesca, 5, 56121 Pisa, Italy
| | - M Dami
- Leonardo Company Finmeccanica, V. Delle Officine Galileo, 1, 50013 Campi Bisenzio FI, Italy
| | - F Antonacci
- Leonardo Company Finmeccanica, V. Delle Officine Galileo, 1, 50013 Campi Bisenzio FI, Italy
| | - F Villa
- Leonardo Company Finmeccanica, V. Delle Officine Galileo, 1, 50013 Campi Bisenzio FI, Italy
| | - M Meini
- Sitael, Via Alessandro Gherardesca, 5, 56121 Pisa, Italy
| | - F Ruggiero
- Leonardo Company Finmeccanica, V. Delle Officine Galileo, 1, 50013 Campi Bisenzio FI, Italy
| | - S Fonte
- INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome, Italy
| | - M Formisano
- INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome, Italy
| | - A Frigeri
- INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome, Italy
| | - P Tinivelli
- University of Perugia, Piazza Università, 1, 06123 Perugia, Italy
| | - M Giardino
- ASI-Italian Space Agency, Via del Politecnico snc, 00133 Rome, Italy
| | - R Mugnuolo
- ASI-Italian Space Agency, Centro di Geodesia Spaziale, 75100 Matera, Italy
| | - S Pirrotta
- ASI-Italian Space Agency, Via del Politecnico snc, 00133 Rome, Italy
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6
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De Angelis S, De Sanctis MC, Altieri F, Ferrari M, Ammannito E, Novi S, Dami M, Barbis A, Antonacci F, Villa F, Ruggiero F, Fonte S, Formisano M, Tinivelli P, Giardino M, Mugnuolo R, Pirrotta S. The pre-launch on-ground characterization of Mars Multispectral Imager for Subsurface Studies (Ma_MISS) spectrometer for ExoMars rover mission: Spectral calibration. Rev Sci Instrum 2022; 93:123704. [PMID: 36586927 DOI: 10.1063/5.0102386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/16/2022] [Indexed: 06/17/2023]
Abstract
The Ma_MISS spectrometer is integrated within the drilling system of the Rosalind Franklin ExoMars rover. This paper reports the on-ground calibration campaign performed on the spectrometer. Here, we focus on the spectral calibration of the instrument. The experimental setup used to carry out calibration is described, and the methods used for data processing and key parameters retrieval are explained. In particular, the spectral parameters such as (i) pixel central wavelengths, (ii) spectral response function, (iii) spectral resolution, (iv) sampling, and (v) range are determined. In a follow-up paper, the linearity and radiometric calibrations are described, while in De Sanctis et al. [Planet. Sci. J. 3, 142 (2022)], the validation of spectral measurements performed on synthetic and natural rock targets is presented.
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Affiliation(s)
- S De Angelis
- INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome, Italy
| | - M C De Sanctis
- INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome, Italy
| | - F Altieri
- INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome, Italy
| | - M Ferrari
- INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome, Italy
| | - E Ammannito
- ASI - Italian Space Agency, Via del Politecnico snc, 00133 Rome, Italy
| | - S Novi
- Sitael, Via Alessandro Gherardesca, 5, 56121 Pisa (PI), Italy
| | - M Dami
- Leonardo Company Finmeccanica, V. Delle Officine Galileo, 1, 50013 Campi Bisenzio (FI), Italy
| | - A Barbis
- Leonardo Company Finmeccanica, V. Delle Officine Galileo, 1, 50013 Campi Bisenzio (FI), Italy
| | - F Antonacci
- Leonardo Company Finmeccanica, V. Delle Officine Galileo, 1, 50013 Campi Bisenzio (FI), Italy
| | - F Villa
- Leonardo Company Finmeccanica, V. Delle Officine Galileo, 1, 50013 Campi Bisenzio (FI), Italy
| | - F Ruggiero
- Leonardo Company Finmeccanica, V. Delle Officine Galileo, 1, 50013 Campi Bisenzio (FI), Italy
| | - S Fonte
- INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome, Italy
| | - M Formisano
- INAF-IAPS, Via Fosso del Cavaliere, 100, 00133 Rome, Italy
| | - P Tinivelli
- University of Perugia, Piazza Università, 1, 06123 Perugia, Italy
| | - M Giardino
- ASI - Italian Space Agency, Via del Politecnico snc, 00133 Rome, Italy
| | - R Mugnuolo
- ASI - Italian Space Agency, Centro di Geodesia Spaziale, 75100 Matera, Italy
| | - S Pirrotta
- ASI - Italian Space Agency, Via del Politecnico snc, 00133 Rome, Italy
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7
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Mercuri L, Palmisano D, L'Abbate A, D'Addabbo P, Montinaro F, Catacchio CR, Hasenfeld P, Ventura M, Korbel JO, Sanders AD, Maggiolini FAM, Antonacci F. A high-resolution map of small-scale inversions in the gibbon genome. Genome Res 2022; 32:1941-1951. [PMID: 36180231 PMCID: PMC9712629 DOI: 10.1101/gr.276960.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022]
Abstract
Gibbons are the most speciose family of living apes, characterized by a strikingly diverse chromosome number and rapid rate of large-scale rearrangements. Here we performed single-cell template strand sequencing (Strand-seq), molecular cytogenetics and deep in silico analysis of a southern white-cheeked gibbon genome providing the first comprehensive map of 238 previously hidden small-scale inversions. We determined that more than half are gibbon-specific, at least 5-fold higher than shown for other primate lineage specific inversions, with a significant high number of small heterozygous inversions, suggesting that accelerated evolution of inversions may have played a role in the high sympatric diversity of gibbons. Although the precise mechanisms underlying these inversions are not yet understood, it is clear that segmental duplication-mediated NAHR only accounts for a small fraction of events. Several genomic features including gene density and repeat (e.g. LINE1) content might render these regions more break-prone and susceptible to inversion formation. In the attempt to characterize interspecific variation between southern and northern white-cheeked gibbons, we identify several large assembly errors in the current GGSC Nleu3.0/nomLeu3 reference genome comprising over 49 megabases of DNA. Finally, we provide a list of 182 candidate genes potentially involved in gibbons diversification and speciation.
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Affiliation(s)
| | | | | | | | - Francesco Montinaro
- Universita' degli Studi di Bari Aldo Moro, Estonian Biocentre, Institute of Genomics, University of Tartu
| | | | | | | | | | - Ashley D Sanders
- Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association, Berlin Institute of Health (BIH), Charite-Universitatsmedizin Berlin
| | - Flavia Angela Maria Maggiolini
- Universita' degli Studi di Bari Aldo Moro, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-Centro di Ricerca Viticoltura ed Enologia (CREA-VE)
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8
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Porubsky D, Höps W, Ashraf H, Hsieh P, Rodriguez-Martin B, Yilmaz F, Ebler J, Hallast P, Maria Maggiolini FA, Harvey WT, Henning B, Audano PA, Gordon DS, Ebert P, Hasenfeld P, Benito E, Zhu Q, Lee C, Antonacci F, Steinrücken M, Beck CR, Sanders AD, Marschall T, Eichler EE, Korbel JO. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell 2022; 185:1986-2005.e26. [PMID: 35525246 PMCID: PMC9563103 DOI: 10.1016/j.cell.2022.04.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/14/2022] [Accepted: 04/08/2022] [Indexed: 12/13/2022]
Abstract
Unlike copy number variants (CNVs), inversions remain an underexplored genetic variation class. By integrating multiple genomic technologies, we discover 729 inversions in 41 human genomes. Approximately 85% of inversions <2 kbp form by twin-priming during L1 retrotransposition; 80% of the larger inversions are balanced and affect twice as many nucleotides as CNVs. Balanced inversions show an excess of common variants, and 72% are flanked by segmental duplications (SDs) or retrotransposons. Since flanking repeats promote non-allelic homologous recombination, we developed complementary approaches to identify recurrent inversion formation. We describe 40 recurrent inversions encompassing 0.6% of the genome, showing inversion rates up to 2.7 × 10-4 per locus per generation. Recurrent inversions exhibit a sex-chromosomal bias and co-localize with genomic disorder critical regions. We propose that inversion recurrence results in an elevated number of heterozygous carriers and structural SD diversity, which increases mutability in the population and predisposes specific haplotypes to disease-causing CNVs.
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9
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Magnani I, Dardi F, Palazzini M, Zuffa E, Guarino D, Daddi N, Dolci G, Antonacci F, Solli P, Paganelli GM, De Lorenzis A, Rotunno M, Ballerini A, Manes A, Galie N. Survival of patients with pulmonary arterial hypertension and chronic thromboembolic pulmonary hypertension listed for lung transplantation. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.1946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Lung transplantation (LT) still remains a treatment option for patients with pulmonary arterial hypertension (PAH) and not operable chronic thromboembolic pulmonary hypertension patients (CTEPH).
Purpose
The study is intended to compare the survival of transplant recipients (TR) and the survival of not-transplanted (NT) patients since listing.
Methods
We included all patients with PAH and not-operable CTEPH listed for LT. The survival of NT, TR and of all listed patients was evaluated starting from the date of listing (patients were censored as alive at the time of LT). The survival of TR was also evaluated starting from the date of the LT.
Results
125 patients were included (112, 90% had PAH). Fifty-eight (46%) patients were transplanted, after a mean waiting time of 1.5±1.3 years. Forty-one patients (33%) died while on the list and 25 (20%) patients were alive on the list on December 2019. The survival of NT patients at 1, 3 and 5 years after listing was 74%, 42%, 33%, respectively. The survival of TR patients at 1, 3 and 5 years after listing was 90%, 70%, 63%, respectively. The survival of all patients since listing (intention to treat analysis) at 1, 3 and 5 years was 85%, 59%, 48% respectively. The survival of TR at 1, 3 and 5 years since transplantation was 63%, 61%, 59%, respectively.
Conclusions
Despite biases in the comparison of non-randomized groups, the data confirm a better long-term survival since listing of TR as compared with NT PAH or not-operable CTEPH patients.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- I Magnani
- University of Bologna, Department of Specialized, Diagnostic and Experimental Medicine – DIMES - Bologna/IT, Bologna, Italy
| | - F Dardi
- University of Bologna, Department of Specialized, Diagnostic and Experimental Medicine – DIMES - Bologna/IT, Bologna, Italy
| | - M Palazzini
- University of Bologna, Department of Specialized, Diagnostic and Experimental Medicine – DIMES - Bologna/IT, Bologna, Italy
| | - E Zuffa
- University of Bologna, Department of Specialized, Diagnostic and Experimental Medicine – DIMES - Bologna/IT, Bologna, Italy
| | - D Guarino
- University of Bologna, Department of Specialized, Diagnostic and Experimental Medicine – DIMES - Bologna/IT, Bologna, Italy
| | - N Daddi
- University of Bologna, Department of Specialized, Diagnostic and Experimental Medicine – DIMES - Bologna/IT, Bologna, Italy
| | - G Dolci
- Universitary Hospital Sant'orsola Malpighi, Cardio-thoracic-vascular Department, Thoracic surgery, Bologna, Italy
| | - F Antonacci
- Universitary Hospital Sant'orsola Malpighi, Cardio-thoracic-vascular Department, Thoracic surgery, Bologna, Italy
| | - P Solli
- Maggiore Hospital, Bellaria Hospital, Presidio Ospedaliero Bellaria-Maggiore, Thoracic Surgery, Bologna, Italy, Bologna, Italy
| | - G M Paganelli
- Policlinico S. Orsola-Malpighi, Universitary Hospital Sant'orsola Malpighi, Cardio-thoracic-vascular Department, Pulmonology, Bologna, Italy
| | - A De Lorenzis
- University of Bologna, Department of Specialized, Diagnostic and Experimental Medicine – DIMES - Bologna/IT, Bologna, Italy
| | - M Rotunno
- University of Bologna, Department of Specialized, Diagnostic and Experimental Medicine – DIMES - Bologna/IT, Bologna, Italy
| | - A Ballerini
- University of Bologna, Department of Specialized, Diagnostic and Experimental Medicine – DIMES - Bologna/IT, Bologna, Italy
| | - A Manes
- University of Bologna, Department of Specialized, Diagnostic and Experimental Medicine – DIMES - Bologna/IT, Bologna, Italy
| | - N Galie
- University of Bologna, Department of Specialized, Diagnostic and Experimental Medicine – DIMES - Bologna/IT, Bologna, Italy
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10
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Ricciardi S, Daddi N, Tallini G, Dolci G, Antonacci F, Salvaterra E, Parisi C, Pantaleo M, Solli P. P36.02 A Case of Recurrent Giant Malignant Solitary Fibrous Tumour of the Pleura: An Elephant in the Room? J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Ventura M, Antonacci F. Special Issue: A Tale of Genes and Genomes. Genes (Basel) 2021; 12:genes12050774. [PMID: 34069634 PMCID: PMC8161243 DOI: 10.3390/genes12050774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 11/16/2022] Open
Abstract
Variability is the source on which selective pressure acts, allowing genome evolution and adaptation [...].
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12
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Mao Y, Catacchio CR, Hillier LW, Porubsky D, Li R, Sulovari A, Fernandes JD, Montinaro F, Gordon DS, Storer JM, Haukness M, Fiddes IT, Murali SC, Dishuck PC, Hsieh P, Harvey WT, Audano PA, Mercuri L, Piccolo I, Antonacci F, Munson KM, Lewis AP, Baker C, Underwood JG, Hoekzema K, Huang TH, Sorensen M, Walker JA, Hoffman J, Thibaud-Nissen F, Salama SR, Pang AWC, Lee J, Hastie AR, Paten B, Batzer MA, Diekhans M, Ventura M, Eichler EE. A high-quality bonobo genome refines the analysis of hominid evolution. Nature 2021; 594:77-81. [PMID: 33953399 PMCID: PMC8172381 DOI: 10.1038/s41586-021-03519-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/07/2021] [Indexed: 12/17/2022]
Abstract
The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation1,2. Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes1,3–5 and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome. A high-quality bonobo genome assembly provides insights into incomplete lineage sorting in hominids and its relevance to gene evolution and the genetic relationship among living hominids.
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Affiliation(s)
- Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - LaDeana W Hillier
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ruiyang Li
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jason D Fernandes
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Francesco Montinaro
- Department of Biology, University of Bari, Bari, Italy.,Estonian Biocentre, Institute of Genomics, Tartu, Estonia
| | - David S Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | | | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ian T Fiddes
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Shwetha Canchi Murali
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | | | | | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Tzu-Hsueh Huang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Melanie Sorensen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Sofie R Salama
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | | | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Mario Ventura
- Department of Biology, University of Bari, Bari, Italy.
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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13
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Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, Munson KM, DeVogelaere E, Armstrong J, Diekhans M, Walker JA, Tomlinson C, Graves-Lindsay TA, Kremitzki M, Salama SR, Audano PA, Escalona M, Maurer NW, Antonacci F, Mercuri L, Maggiolini FAM, Catacchio CR, Underwood JG, O'Connor DH, Sanders AD, Korbel JO, Ferguson B, Kubisch HM, Picker L, Kalin NH, Rosene D, Levine J, Abbott DH, Gray SB, Sanchez MM, Kovacs-Balint ZA, Kemnitz JW, Thomasy SM, Roberts JA, Kinnally EL, Capitanio JP, Skene JHP, Platt M, Cole SA, Green RE, Ventura M, Wiseman RW, Paten B, Batzer MA, Rogers J, Eichler EE. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science 2021; 370:370/6523/eabc6617. [PMID: 33335035 DOI: 10.1126/science.abc6617] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/29/2020] [Indexed: 12/15/2022]
Abstract
The rhesus macaque (Macaca mulatta) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Whole-genome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.
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Affiliation(s)
- Wesley C Warren
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA. .,Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65211, USA.,Institute of Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marina Haukness
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Shwetha C Murali
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Jason Fernandes
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jessica M Storer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.,Institue for Systems Biology, Seattle, WA 98109, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - LaDeana W Hillier
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Yafei Mao
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - David Gordon
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth DeVogelaere
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Joel Armstrong
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA
| | | | - Milinn Kremitzki
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA
| | - Sofie R Salama
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nicholas W Maurer
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Ludovica Mercuri
- Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy
| | | | | | | | - David H O'Connor
- Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Ashley D Sanders
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Betsy Ferguson
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | | | - Louis Picker
- Oregon National Primate Research Center and Vaccine and Gene Therapy Institute, Oregon Health Sciences University, Beaverton, OR 97006, USA
| | - Ned H Kalin
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53719, USA
| | - Douglas Rosene
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jon Levine
- Department of Neuroscience, University of Wisconsin, Madison, WI 53175, USA.,Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA
| | - David H Abbott
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA.,Department of Obstetrics and Gynecology, Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA
| | - Stanton B Gray
- The University of Texas MD Anderson Cancer Center, Michale E. Keeling Center for Comparative Medicine and Research, Bastrop, TX 78602, USA
| | - Mar M Sanchez
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA.,Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
| | | | - Joseph W Kemnitz
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA.,Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA
| | - Sara M Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.,Department of Ophthalmology and Vision Science, School of Medicine, University of California-Davis, Davis, CA 95817, USA
| | | | - Erin L Kinnally
- California National Primate Research Center, Davis, CA 95616, USA.,Department of Psychology, University of California, Davis, CA 95616, USA
| | - John P Capitanio
- California National Primate Research Center, Davis, CA 95616, USA.,Department of Psychology, University of California, Davis, CA 95616, USA
| | - J H Pate Skene
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Michael Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute and Southwest National Primate Research Center, San Antonio, TX 78227, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mario Ventura
- Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Benedict Paten
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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14
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Hsieh P, Vollger MR, Dang V, Porubsky D, Baker C, Cantsilieris S, Hoekzema K, Lewis AP, Munson KM, Sorensen M, Kronenberg ZN, Murali S, Nelson BJ, Chiatante G, Maggiolini FAM, Blanché H, Underwood JG, Antonacci F, Deleuze JF, Eichler EE. Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes. Science 2020; 366:366/6463/eaax2083. [PMID: 31624180 DOI: 10.1126/science.aax2083] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 07/05/2019] [Accepted: 09/12/2019] [Indexed: 01/01/2023]
Abstract
Copy number variants (CNVs) are subject to stronger selective pressure than single-nucleotide variants, but their roles in archaic introgression and adaptation have not been systematically investigated. We show that stratified CNVs are significantly associated with signatures of positive selection in Melanesians and provide evidence for adaptive introgression of large CNVs at chromosomes 16p11.2 and 8p21.3 from Denisovans and Neanderthals, respectively. Using long-read sequence data, we reconstruct the structure and complex evolutionary history of these polymorphisms and show that both encode positively selected genes absent from most human populations. Our results collectively suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation.
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Affiliation(s)
- PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Vy Dang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Melanie Sorensen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Shwetha Murali
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Giorgia Chiatante
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari, Italy
| | | | - Hélène Blanché
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris, France
| | - Jason G Underwood
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Pacific Biosciences (PacBio) of California, Inc., Menlo Park, CA, USA
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari, Italy
| | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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15
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Maggiolini FAM, Cantsilieris S, D’Addabbo P, Manganelli M, Coe BP, Dumont BL, Sanders AD, Pang AWC, Vollger MR, Palumbo O, Palumbo P, Accadia M, Carella M, Eichler EE, Antonacci F. Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus. PLoS Genet 2019; 15:e1008075. [PMID: 30917130 PMCID: PMC6436712 DOI: 10.1371/journal.pgen.1008075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/07/2019] [Indexed: 11/19/2022] Open
Abstract
Human chromosome 15q25 is involved in several disease-associated structural rearrangements, including microdeletions and chromosomal markers with inverted duplications. Using comparative fluorescence in situ hybridization, strand-sequencing, single-molecule, real-time sequencing and Bionano optical mapping analyses, we investigated the organization of the 15q25 region in human and nonhuman primates. We found that two independent inversions occurred in this region after the fission event that gave rise to phylogenetic chromosomes XIV and XV in humans and great apes. One of these inversions is still polymorphic in the human population today and may confer differential susceptibility to 15q25 microdeletions and inverted duplications. The inversion breakpoints map within segmental duplications containing core duplicons of the GOLGA gene family and correspond to the site of an ancestral centromere, which became inactivated about 25 million years ago. The inactivation of this centromere likely released segmental duplications from recombination repression typical of centromeric regions. We hypothesize that this increased the frequency of ectopic recombination creating a hotspot of hominid inversions where dispersed GOLGA core elements now predispose this region to recurrent genomic rearrangements associated with disease.
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Affiliation(s)
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Pietro D’Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Michele Manganelli
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Beth L. Dumont
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - Ashley D. Sanders
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, Heidelberg, Germany
| | | | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Orazio Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Pietro Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital “Cardinale G. Panico”, Via San Pio X n°4, Tricase, LE, Italy
| | - Massimo Carella
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States of America
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
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16
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Catacchio CR, Maggiolini FAM, D'Addabbo P, Bitonto M, Capozzi O, Lepore Signorile M, Miroballo M, Archidiacono N, Eichler EE, Ventura M, Antonacci F. Inversion variants in human and primate genomes. Genome Res 2018; 28:910-920. [PMID: 29776991 PMCID: PMC5991517 DOI: 10.1101/gr.234831.118] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/26/2018] [Indexed: 02/06/2023]
Abstract
For many years, inversions have been proposed to be a direct driving force in speciation since they suppress recombination when heterozygous. Inversions are the most common large-scale differences among humans and great apes. Nevertheless, they represent large events easily distinguishable by classical cytogenetics, whose resolution, however, is limited. Here, we performed a genome-wide comparison between human, great ape, and macaque genomes using the net alignments for the most recent releases of genome assemblies. We identified a total of 156 putative inversions, between 103 kb and 91 Mb, corresponding to 136 human loci. Combining literature, sequence, and experimental analyses, we analyzed 109 of these loci and found 67 regions inverted in one or multiple primates, including 28 newly identified inversions. These events overlap with 81 human genes at their breakpoints, and seven correspond to sites of recurrent rearrangements associated with human disease. This work doubles the number of validated primate inversions larger than 100 kb, beyond what was previously documented. We identified 74 sites of errors, where the sequence has been assembled in the wrong orientation, in the reference genomes analyzed. Our data serve two purposes: First, we generated a map of evolutionary inversions in these genomes representing a resource for interrogating differences among these species at a functional level; second, we provide a list of misassembled regions in these primate genomes, involving over 300 Mb of DNA and 1978 human genes. Accurately annotating these regions in the genome references has immediate applications for evolutionary and biomedical studies on primates.
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Affiliation(s)
| | | | - Pietro D'Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | - Miriana Bitonto
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | - Oronzo Capozzi
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | | | - Mattia Miroballo
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Mario Ventura
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
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17
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Dougherty ML, Nuttle X, Penn O, Nelson BJ, Huddleston J, Baker C, Harshman L, Duyzend MH, Ventura M, Antonacci F, Sandstrom R, Dennis MY, Eichler EE. The birth of a human-specific neural gene by incomplete duplication and gene fusion. Genome Biol 2017; 18:49. [PMID: 28279197 PMCID: PMC5345166 DOI: 10.1186/s13059-017-1163-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/27/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks. The human-specific gene hydrocephalus-inducing 2, HYDIN2, was generated by a 364 kbp duplication of 79 internal exons of the large ciliary gene HYDIN from chromosome 16q22.2 to chromosome 1q21.1. Because the HYDIN2 locus lacks the ancestral promoter and seven terminal exons of the progenitor gene, we sought to characterize transcription at this locus by coupling reverse transcription polymerase chain reaction and long-read sequencing. RESULTS 5' RACE indicates a transcription start site for HYDIN2 outside of the duplication and we observe fusion transcripts spanning both the 5' and 3' breakpoints. We observe extensive splicing diversity leading to the formation of altered open reading frames (ORFs) that appear to be under relaxed selection. We show that HYDIN2 adopted a new promoter that drives an altered pattern of expression, with highest levels in neural tissues. We estimate that the HYDIN duplication occurred ~3.2 million years ago and find that it is nearly fixed (99.9%) for diploid copy number in contemporary humans. Examination of 73 chromosome 1q21 rearrangement patients reveals that HYDIN2 is deleted or duplicated in most cases. CONCLUSIONS Together, these data support a model of rapid gene innovation by fusion of incomplete segmental duplications, altered tissue expression, and potential subfunctionalization or neofunctionalization of HYDIN2 early in the evolution of the Homo lineage.
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Affiliation(s)
- Max L Dougherty
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Xander Nuttle
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Osnat Penn
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Lana Harshman
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Michael H Duyzend
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Mario Ventura
- Department of Biology, University of Bari, Bari, 70121, Italy
| | | | | | - Megan Y Dennis
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, 95616, CA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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18
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Dennis MY, Harshman L, Nelson BJ, Penn O, Cantsilieris S, Huddleston J, Antonacci F, Penewit K, Denman L, Raja A, Baker C, Mark K, Malig M, Janke N, Espinoza C, Stessman HAF, Nuttle X, Hoekzema K, Lindsay-Graves TA, Wilson RK, Eichler EE. The evolution and population diversity of human-specific segmental duplications. Nat Ecol Evol 2017; 1:69. [PMID: 28580430 PMCID: PMC5450946 DOI: 10.1038/s41559-016-0069] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (n=80 genes/33 gene families). We show that HSDs are non-randomly organized, associate preferentially with ancestral ape duplications termed “core duplicons”, and evolved primarily in an interspersed inverted orientation. In addition to Homo sapiens-specific gene expansions (e.g., TCAF1/2), we highlight ten gene families (e.g., ARHGAP11B and SRGAP2C) where copy number never returns to the ancestral state, there is evidence of mRNA splicing, and no common gene-disruptive mutations are observed in the general population. Such duplicates are candidates for the evolution of human-specific adaptive traits.
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Affiliation(s)
- Megan Y Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA.,Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Lana Harshman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Osnat Penn
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Bari 70125, Italy
| | - Kelsi Penewit
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Laura Denman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Archana Raja
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kenneth Mark
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Maika Malig
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Nicolette Janke
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Claudia Espinoza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Holly A F Stessman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Xander Nuttle
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Tina A Lindsay-Graves
- McDonnell Genome Institute at Washington University, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Richard K Wilson
- McDonnell Genome Institute at Washington University, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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19
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Eslami Rasekh M, Chiatante G, Miroballo M, Tang J, Ventura M, Amemiya CT, Eichler EE, Antonacci F, Alkan C. Discovery of large genomic inversions using long range information. BMC Genomics 2017; 18:65. [PMID: 28073353 PMCID: PMC5223412 DOI: 10.1186/s12864-016-3444-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/19/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Although many algorithms are now available that aim to characterize different classes of structural variation, discovery of balanced rearrangements such as inversions remains an open problem. This is mainly due to the fact that breakpoints of such events typically lie within segmental duplications or common repeats, which reduces the mappability of short reads. The algorithms developed within the 1000 Genomes Project to identify inversions are limited to relatively short inversions, and there are currently no available algorithms to discover large inversions using high throughput sequencing technologies. RESULTS Here we propose a novel algorithm, VALOR, to discover large inversions using new sequencing methods that provide long range information such as 10X Genomics linked-read sequencing, pooled clone sequencing, or other similar technologies that we commonly refer to as long range sequencing. We demonstrate the utility of VALOR using both pooled clone sequencing and 10X Genomics linked-read sequencing generated from the genome of an individual from the HapMap project (NA12878). We also provide a comprehensive comparison of VALOR against several state-of-the-art structural variation discovery algorithms that use whole genome shotgun sequencing data. CONCLUSIONS In this paper, we show that VALOR is able to accurately discover all previously identified and experimentally validated large inversions in the same genome with a low false discovery rate. Using VALOR, we also predicted a novel inversion, which we validated using fluorescent in situ hybridization. VALOR is available at https://github.com/BilkentCompGen/VALOR.
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Affiliation(s)
- Marzieh Eslami Rasekh
- Department of Computer Engineering, Bilkent University, Bilkent, 06800, Ankara, Turkey
| | - Giorgia Chiatante
- Department of Biology, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | - Mattia Miroballo
- Department of Biology, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | - Joyce Tang
- Benaroya Research Institute, 1201 Ninth Avenue, 98101, Seattle, WA, USA
| | - Mario Ventura
- Department of Biology, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | - Chris T Amemiya
- Benaroya Research Institute, 1201 Ninth Avenue, 98101, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, 3720 15th Avenue NE, 98195, Seattle, WA, USA
| | - Francesca Antonacci
- Department of Biology, University of Bari, Via Orabona 4, 70125, Bari, Italy.
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Bilkent, 06800, Ankara, Turkey.
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20
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Nuttle X, Giannuzzi G, Duyzend MH, Schraiber JG, Narvaiza I, Sudmant PH, Penn O, Chiatante G, Malig M, Huddleston J, Benner C, Camponeschi F, Ciofi-Baffoni S, Stessman HA, Marchetto MCN, Denman L, Harshman L, Baker C, Raja A, Penewit K, Janke N, Tang WJ, Ventura M, Banci L, Antonacci F, Akey JM, Amemiya CT, Gage FH, Reymond A, Eichler EE. Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility. Nature 2016; 536:205-9. [PMID: 27487209 PMCID: PMC4988886 DOI: 10.1038/nature19075] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 07/02/2016] [Indexed: 12/31/2022]
Abstract
Genetic differences that specify unique aspects of human evolution have typically been identified by comparative analyses between the genomes of humans and closely related primates, including more recently the genomes of archaic hominins. Not all regions of the genome, however, are equally amenable to such study. Recurrent copy number variation (CNV) at chromosome 16p11.2 accounts for approximately 1% of cases of autism and is mediated by a complex set of segmental duplications, many of which arose recently during human evolution. Here we reconstruct the evolutionary history of the locus and identify bolA family member 2 (BOLA2) as a gene duplicated exclusively in Homo sapiens. We estimate that a 95-kilobase-pair segment containing BOLA2 duplicated across the critical region approximately 282 thousand years ago (ka), one of the latest among a series of genomic changes that dramatically restructured the locus during hominid evolution. All humans examined carried one or more copies of the duplication, which nearly fixed early in the human lineage--a pattern unlikely to have arisen so rapidly in the absence of selection (P < 0.0097). We show that the duplication of BOLA2 led to a novel, human-specific in-frame fusion transcript and that BOLA2 copy number correlates with both RNA expression (r = 0.36) and protein level (r = 0.65), with the greatest expression difference between human and chimpanzee in experimentally derived stem cells. Analyses of 152 patients carrying a chromosome 16p11. rearrangement show that more than 96% of breakpoints occur within the H. sapiens-specific duplication. In summary, the duplicative transposition of BOLA2 at the root of the H. sapiens lineage about 282 ka simultaneously increased copy number of a gene associated with iron homeostasis and predisposed our species to recurrent rearrangements associated with disease.
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Affiliation(s)
- Xander Nuttle
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Giuliana Giannuzzi
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Michael H. Duyzend
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Joshua G. Schraiber
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Iñigo Narvaiza
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter H. Sudmant
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Osnat Penn
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Maika Malig
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Chris Benner
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Francesca Camponeschi
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Simone Ciofi-Baffoni
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Holly A.F. Stessman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Maria C. N. Marchetto
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Laura Denman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Lana Harshman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Archana Raja
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Kelsi Penewit
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Nicolette Janke
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - W. Joyce Tang
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Mario Ventura
- Department of Biology, University of Bari, Bari, Italy
| | - Lucia Banci
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | | | - Joshua M. Akey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Chris T. Amemiya
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Fred H. Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
- Center for Academic Research and Training in Anthropogeny (CARTA), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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21
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Piloni D, Morosini M, Magni S, Balderacchi A, Scudeller L, Cova E, Oggionni T, Stella G, Tinelli C, Antonacci F, Meloni F. Role of CD4+CD25highCD127- Treg Cells in Long Term Outcome of Lung Recipients. J Heart Lung Transplant 2016. [DOI: 10.1016/j.healun.2016.01.635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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22
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Chaisson MJP, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M, Landolin JM, Stamatoyannopoulos JA, Hunkapiller MW, Korlach J, Eichler EE. Resolving the complexity of the human genome using single-molecule sequencing. Nature 2014; 517:608-11. [PMID: 25383537 DOI: 10.1038/nature13907] [Citation(s) in RCA: 505] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/30/2014] [Indexed: 12/11/2022]
Abstract
The human genome is arguably the most complete mammalian reference assembly, yet more than 160 euchromatic gaps remain and aspects of its structural variation remain poorly understood ten years after its completion. To identify missing sequence and genetic variation, here we sequence and analyse a haploid human genome (CHM1) using single-molecule, real-time DNA sequencing. We close or extend 55% of the remaining interstitial gaps in the human GRCh37 reference genome--78% of which carried long runs of degenerate short tandem repeats, often several kilobases in length, embedded within (G+C)-rich genomic regions. We resolve the complete sequence of 26,079 euchromatic structural variants at the base-pair level, including inversions, complex insertions and long tracts of tandem repeats. Most have not been previously reported, with the greatest increases in sensitivity occurring for events less than 5 kilobases in size. Compared to the human reference, we find a significant insertional bias (3:1) in regions corresponding to complex insertions and long short tandem repeats. Our results suggest a greater complexity of the human genome in the form of variation of longer and more complex repetitive DNA that can now be largely resolved with the application of this longer-read sequencing technology.
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Affiliation(s)
- Mark J P Chaisson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - John Huddleston
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Megan Y Dennis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Peter H Sudmant
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Maika Malig
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Fereydoun Hormozdiari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari 70125, Italy
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Matthew Boitano
- Pacific Biosciences of California, Inc., Menlo Park, California 94025, USA
| | - Jane M Landolin
- Pacific Biosciences of California, Inc., Menlo Park, California 94025, USA
| | - John A Stamatoyannopoulos
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | | | - Jonas Korlach
- Pacific Biosciences of California, Inc., Menlo Park, California 94025, USA
| | - Evan E Eichler
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
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23
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Giannuzzi G, Pazienza M, Huddleston J, Antonacci F, Malig M, Vives L, Eichler EE, Ventura M. Hominoid fission of chromosome 14/15 and the role of segmental duplications. Genome Res 2013; 23:1763-73. [PMID: 24077392 PMCID: PMC3814877 DOI: 10.1101/gr.156240.113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ape chromosomes homologous to human chromosomes 14 and 15 were generated by a fission event of an ancestral submetacentric chromosome, where the two chromosomes were joined head-to-tail. The hominoid ancestral chromosome most closely resembles the macaque chromosome 7. In this work, we provide insights into the evolution of human chromosomes 14 and 15, performing a comparative study between macaque boundary region 14/15 and the orthologous human regions. We construct a 1.6-Mb contig of macaque BAC clones in the region orthologous to the ancestral hominoid fission site and use it to define the structural changes that occurred on human 14q pericentromeric and 15q subtelomeric regions. We characterize the novel euchromatin–heterochromatin transition region (∼20 Mb) acquired during the neocentromere establishment on chromosome 14, and find it was mainly derived through pericentromeric duplications from ancestral hominoid chromosomes homologous to human 2q14–qter and 10. Further, we show a relationship between evolutionary hotspots and low-copy repeat loci for chromosome 15, revealing a possible role of segmental duplications not only in mediating but also in “stitching” together rearrangement breakpoints.
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Affiliation(s)
- Giuliana Giannuzzi
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
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25
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Chen YZ, Matsushita MM, Robertson P, Rieder M, Girirajan S, Antonacci F, Lipe H, Eichler EE, Nickerson DA, Bird TD, Raskind WH. Autosomal dominant familial dyskinesia and facial myokymia: single exome sequencing identifies a mutation in adenylyl cyclase 5. ACTA ACUST UNITED AC 2012; 69:630-5. [PMID: 22782511 DOI: 10.1001/archneurol.2012.54] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
BACKGROUND Familial dyskinesia with facial myokymia (FDFM) is an autosomal dominant disorder that is exacerbated by anxiety. In a 5-generation family of German ancestry, we previously mapped FDFM to chromosome band 3p21-3q21. The 72.5-Mb linkage region was too large for traditional positional mutation identification. OBJECTIVE To identify the gene responsible for FDFM by exome resequencing of a single affected individual. PARTICIPANTS We performed whole exome sequencing in 1 affected individual and used a series of bioinformatic filters, including functional significance and presence in dbSNP or the 1000 Genomes Project, to reduce the number of candidate variants. Co-segregation analysis was performed in 15 additional individuals in 3 generations. MAIN OUTCOME MEASURES Unique DNA variants in the linkage region that co-segregate with FDFM. RESULTS The exome contained 23 428 single-nucleotide variants, of which 9391 were missense, nonsense, or splice site alterations. The critical region contained 323 variants, 5 of which were not present in 1 of the sequence databases. Adenylyl cyclase 5 (ADCY5) was the only gene in which the variant (c.2176G>A) was co-transmitted perfectly with disease status and was not present in 3510 control white exomes. This residue is highly conserved, and the change is nonconservative and predicted to be damaging. CONCLUSIONS ADCY5 is highly expressed in striatum. Mice deficient in Adcy5 develop a movement disorder that is worsened by stress. We conclude that FDFM likely results from a missense mutation in ADCY5. This study demonstrates the power of a single exome sequence combined with linkage information to identify causative genes for rare autosomal dominant mendelian diseases.
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Affiliation(s)
- Ying-Zhang Chen
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA 98195, USA
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Compagnoni M, Bestagini P, Antonacci F, Sarti A, Tubaro S. Localization of Acoustic Sources Through the Fitting of Propagation Cones Using Multiple Independent Arrays. ACTA ACUST UNITED AC 2012. [DOI: 10.1109/tasl.2012.2191958] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Steinberg KM, Antonacci F, Sudmant PH, Kidd JM, Campbell CD, Vives L, Malig M, Scheinfeldt L, Beggs W, Ibrahim M, Lema G, Nyambo TB, Omar SA, Bodo JM, Froment A, Donnelly MP, Kidd KK, Tishkoff SA, Eichler EE. Structural diversity and African origin of the 17q21.31 inversion polymorphism. Nat Genet 2012; 44:872-80. [PMID: 22751100 PMCID: PMC3408829 DOI: 10.1038/ng.2335] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 06/01/2012] [Indexed: 12/12/2022]
Abstract
The 17q21.31 inversion polymorphism exists either as direct (H1) or inverted (H2) haplotypes with differential predispositions to disease and selection. We investigated its genetic diversity in 2,700 individuals, with an emphasis on African populations. We characterize eight structural haplotypes due to complex rearrangements that vary in size from 1.08-1.49 Mb and provide evidence for a 30-kb H1-H2 double recombination event. We show that recurrent partial duplications of the KANSL1 gene have occurred on both the H1 and H2 haplotypes and have risen to high frequency in European populations. We identify a likely ancestral H2 haplotype (H2') lacking these duplications that is enriched among African hunter-gatherer groups yet essentially absent from West African populations. Whereas H1 and H2 segmental duplications arose independently and before human migration out of Africa, they have reached high frequencies recently among Europeans, either because of extraordinary genetic drift or selective sweeps.
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Dennis MY, Nuttle X, Sudmant PH, Antonacci F, Graves TA, Nefedov M, Rosenfeld JA, Sajjadian S, Malig M, Kotkiewicz H, Curry CJ, Shafer S, Shaffer LG, de Jong PJ, Wilson RK, Eichler EE. Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell 2012; 149:912-22. [PMID: 22559943 DOI: 10.1016/j.cell.2012.03.033] [Citation(s) in RCA: 242] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/17/2012] [Accepted: 03/01/2012] [Indexed: 10/28/2022]
Abstract
Gene duplication is an important source of phenotypic change and adaptive evolution. We leverage a haploid hydatidiform mole to identify highly identical sequences missing from the reference genome, confirming that the cortical development gene Slit-Robo Rho GTPase-activating protein 2 (SRGAP2) duplicated three times exclusively in humans. We show that the promoter and first nine exons of SRGAP2 duplicated from 1q32.1 (SRGAP2A) to 1q21.1 (SRGAP2B) ∼3.4 million years ago (mya). Two larger duplications later copied SRGAP2B to chromosome 1p12 (SRGAP2C) and to proximal 1q21.1 (SRGAP2D) ∼2.4 and ∼1 mya, respectively. Sequence and expression analyses show that SRGAP2C is the most likely duplicate to encode a functional protein and is among the most fixed human-specific duplicate genes. Our data suggest a mechanism where incomplete duplication created a novel gene function-antagonizing parental SRGAP2 function-immediately "at birth" 2-3 mya, which is a time corresponding to the transition from Australopithecus to Homo and the beginning of neocortex expansion.
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Affiliation(s)
- Megan Y Dennis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, 98195, USA
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Fieuw A, Kumps C, Schramm A, Pattyn F, Menten B, Antonacci F, Sudmant P, Schulte JH, Van Roy N, Vergult S, Buckley PG, De Paepe A, Noguera R, Versteeg R, Stallings R, Eggert A, Vandesompele J, De Preter K, Speleman F. Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas. Int J Cancer 2011; 130:2599-606. [PMID: 21796619 DOI: 10.1002/ijc.26317] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 07/12/2011] [Indexed: 01/04/2023]
Abstract
Neuroblastoma is an aggressive embryonal tumor that accounts for ∼15% of childhood cancer deaths. Hitherto, despite the availability of comprehensive genomic data on DNA copy number changes in neuroblastoma, relatively little is known about the genes driving neuroblastoma tumorigenesis. In this study, high resolution array comparative genome hybridization (CGH) was performed on 188 primary neuroblastoma tumors and 33 neuroblastoma cell lines to search for previously undetected recurrent DNA copy number gains and losses. A new recurrent distal chromosome 1q deletion (del(1)(q42.2qter)) was detected in seven cases. Further analysis of available array CGH datasets revealed 13 additional similar distal 1q deletions. The majority of all detected 1q deletions was found in high risk 11q deleted tumors without MYCN amplification (Fisher exact test p = 5.61 × 10(-5) ). Using ultra-high resolution (∼115 bp resolution) custom arrays covering the breakpoints on 1q for 11 samples, clustering of nine breakpoints was observed within a 12.5-kb region, of which eight were found in a 7-kb copy number variable region, whereas the remaining two breakpoints were colocated 1.4-Mb proximal. The commonly deleted region contains one miRNA (hsa-mir-1537), four transcribed ultra conserved region elements (uc.43-uc.46) and 130 protein coding genes including at least two bona fide tumor suppressor genes, EGLN1 (or PHD2) and FH. This finding further contributes to the delineation of the genomic profile of aggressive neuroblastoma, offers perspectives for the identification of genes contributing to the disease phenotype and may be relevant in the light of assessment of response to new molecular treatments.
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Affiliation(s)
- Annelies Fieuw
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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Hurle B, Marques-Bonet T, Antonacci F, Hughes I, Ryan JF, Eichler EE, Ornitz DM, Green ED. Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses. BMC Evol Biol 2011; 11:23. [PMID: 21261979 PMCID: PMC3038909 DOI: 10.1186/1471-2148-11-23] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 01/24/2011] [Indexed: 11/19/2022] Open
Abstract
Background Mutations in the Otopetrin 1 gene (Otop1) in mice and fish produce an unusual bilateral vestibular pathology that involves the absence of otoconia without hearing impairment. The encoded protein, Otop1, is the only functionally characterized member of the Otopetrin Domain Protein (ODP) family; the extended sequence and structural preservation of ODP proteins in metazoans suggest a conserved functional role. Here, we use the tools of sequence- and cytogenetic-based comparative genomics to study the Otop1 and the Otop2-Otop3 genes and to establish their genomic context in 25 vertebrates. We extend our evolutionary study to include the gene mutated in Usher syndrome (USH) subtype 1G (Ush1g), both because of the head-to-tail clustering of Ush1g with Otop2 and because Otop1 and Ush1g mutations result in inner ear phenotypes. Results We established that OTOP1 is the boundary gene of an inversion polymorphism on human chromosome 4p16 that originated in the common human-chimpanzee lineage more than 6 million years ago. Other lineage-specific evolutionary events included a three-fold expansion of the Otop genes in Xenopus tropicalis and of Ush1g in teleostei fish. The tight physical linkage between Otop2 and Ush1g is conserved in all vertebrates. To further understand the functional organization of the Ushg1-Otop2 locus, we deduced a putative map of binding sites for CCCTC-binding factor (CTCF), a mammalian insulator transcription factor, from genome-wide chromatin immunoprecipitation-sequencing (ChIP-seq) data in mouse and human embryonic stem (ES) cells combined with detection of CTCF-binding motifs. Conclusions The results presented here clarify the evolutionary history of the vertebrate Otop and Ush1g families, and establish a framework for studying the possible interaction(s) of Ush1g and Otop in developmental pathways.
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Affiliation(s)
- Belen Hurle
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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31
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Mefford HC, Shafer N, Antonacci F, Tsai JM, Park SS, Hing AV, Rieder MJ, Smyth MD, Speltz ML, Eichler EE, Cunningham ML. Copy number variation analysis in single-suture craniosynostosis: multiple rare variants including RUNX2 duplication in two cousins with metopic craniosynostosis. Am J Med Genet A 2010; 152A:2203-10. [PMID: 20683987 PMCID: PMC3104131 DOI: 10.1002/ajmg.a.33557] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Little is known about genes that underlie isolated single-suture craniosynostosis. In this study, we hypothesize that rare copy number variants (CNV) in patients with isolated single-suture craniosynostosis contain genes important for cranial development. Using whole genome array comparative genomic hybridization (CGH), we evaluated DNA from 186 individuals with single-suture craniosynostosis for submicroscopic deletions and duplications. We identified a 1.1 Mb duplication encompassing RUNX2 in two affected cousins with metopic synostosis and hypodontia. Given that RUNX2 is required as a master switch for osteoblast differentiation and interacts with TWIST1, mutations in which also cause craniosynostosis, we conclude that the duplication in this family is pathogenic, albeit with reduced penetrance. In addition, we find that a total of 7.5% of individuals with single-suture synostosis in our series have at least one rare deletion or duplication that contains genes and that has not been previously reported in unaffected individuals. The genes within and disrupted by CNVs in this cohort are potential novel candidate genes for craniosynostosis. © 2010 Wiley-Liss, Inc.
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Affiliation(s)
- Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
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Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Eichler EE. Diversity of human copy number variation and multicopy genes. Science 2010; 330:641-6. [PMID: 21030649 DOI: 10.1126/science.1197005] [Citation(s) in RCA: 492] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.
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Affiliation(s)
- Peter H Sudmant
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
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Alkan C, Cardone MF, Catacchio CR, Antonacci F, O'Brien SJ, Ryder OA, Purgato S, Zoli M, Della Valle G, Eichler EE, Ventura M. Genome-wide characterization of centromeric satellites from multiple mammalian genomes. Genome Res 2010; 21:137-45. [PMID: 21081712 DOI: 10.1101/gr.111278.110] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.
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Affiliation(s)
- Can Alkan
- Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington 98195, USA
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Girirajan S, Rosenfeld JA, Cooper GM, Antonacci F, Siswara P, Itsara A, Vives L, Walsh T, McCarthy SE, Baker C, Mefford HC, Kidd JM, Browning SR, Browning BL, Dickel DE, Levy DL, Ballif BC, Platky K, Farber DM, Gowans GC, Wetherbee JJ, Asamoah A, Weaver DD, Mark PR, Dickerson J, Garg BP, Ellingwood SA, Smith R, Banks VC, Smith W, McDonald MT, Hoo JJ, French BN, Hudson C, Johnson JP, Ozmore JR, Moeschler JB, Surti U, Escobar LF, El-Khechen D, Gorski JL, Kussmann J, Salbert B, Lacassie Y, Biser A, McDonald-McGinn DM, Zackai EH, Deardorff MA, Shaikh TH, Haan E, Friend KL, Fichera M, Romano C, Gécz J, DeLisi LE, Sebat J, King MC, Shaffer LG, Eichler EE. A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nat Genet 2010; 42:203-9. [PMID: 20154674 PMCID: PMC2847896 DOI: 10.1038/ng.534] [Citation(s) in RCA: 454] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 01/15/2010] [Indexed: 02/06/2023]
Abstract
We report the identification of a recurrent 520-kbp 16p12.1 microdeletion significantly associated with childhood developmental delay. The microdeletion was detected in 20/11,873 cases vs. 2/8,540 controls (p=0.0009, OR=7.2) and replicated in a second series of 22/9,254 cases vs. 6/6,299 controls (p=0.028, OR=2.5). Most deletions were inherited with carrier parents likely to manifest neuropsychiatric phenotypes (p=0.037, OR=6). Probands were more likely to carry an additional large CNV when compared to matched controls (10/42 cases, p=5.7×10-5, OR=6.65). Clinical features of cases with two mutations were distinct from and/or more severe than clinical features of patients carrying only the co-occurring mutation. Our data suggest a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity suggests that this two-hit model may be more generally applicable to neuropsychiatric disease.
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Affiliation(s)
- Santhosh Girirajan
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
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Cellamare A, Catacchio CR, Alkan C, Giannuzzi G, Antonacci F, Cardone MF, Della Valle G, Malig M, Rocchi M, Eichler EE, Ventura M. New insights into centromere organization and evolution from the white-cheeked gibbon and marmoset. Mol Biol Evol 2009; 26:1889-900. [PMID: 19429672 DOI: 10.1093/molbev/msp101] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The evolutionary history of alpha-satellite DNA, the major component of primate centromeres, is hardly defined because of the difficulty in its sequence assembly and its rapid evolution when compared with most genomic sequences. By using several approaches, we have cloned, sequenced, and characterized alpha-satellite sequences from two species representing critical nodes in the primate phylogeny: the white-cheeked gibbon, a lesser ape, and marmoset, a New World monkey. Sequence analyses demonstrate that white-cheeked gibbon and marmoset alpha-satellite sequences are formed by units of approximately 171 and approximately 342 bp, respectively, and they both lack the high-order structure found in humans and great apes. Fluorescent in situ hybridization characterization shows a broad dispersal of alpha-satellite in the white-cheeked gibbon genome including centromeric, telomeric, and chromosomal interstitial localizations. On the other hand, centromeres in marmoset appear organized in highly divergent dimers roughly of 342 bp that show a similarity between monomers much lower than previously reported dimers, thus representing an ancient dimeric structure. All these data shed light on the evolution of the centromeric sequences in Primates. Our results suggest radical differences in the structure, organization, and evolution of alpha-satellite DNA among different primate species, supporting the notion that 1) all the centromeric sequence in Primates evolved by genomic amplification, unequal crossover, and sequence homogenization using a 171 bp monomer as the basic seeding unit and 2) centromeric function is linked to relatively short repeated elements, more than higher-order structure. Moreover, our data indicate that complex higher-order repeat structures are a peculiarity of the hominid lineage, showing the more complex organization in humans.
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Affiliation(s)
- A Cellamare
- Department of Genetics and Microbiology, University of Bari, Bari, Italy
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Antonacci F, Kidd JM, Marques-Bonet T, Ventura M, Siswara P, Jiang Z, Eichler EE. Characterization of six human disease-associated inversion polymorphisms. Hum Mol Genet 2009; 18:2555-66. [PMID: 19383631 PMCID: PMC2701327 DOI: 10.1093/hmg/ddp187] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The human genome is a highly dynamic structure that shows a wide range of genetic polymorphic variation. Unlike other types of structural variation, little is known about inversion variants within normal individuals because such events are typically balanced and are difficult to detect and analyze by standard molecular approaches. Using sequence-based, cytogenetic and genotyping approaches, we characterized six large inversion polymorphisms that map to regions associated with genomic disorders with complex segmental duplications mapping at the breakpoints. We developed a metaphase FISH-based assay to genotype inversions and analyzed the chromosomes of 27 individuals from three HapMap populations. In this subset, we find that these inversions are less frequent or absent in Asians when compared with European and Yoruban populations. Analyzing multiple individuals from outgroup species of great apes, we show that most of these large inversion polymorphisms are specific to the human lineage with two exceptions, 17q21.31 and 8p23 inversions, which are found to be similarly polymorphic in other great ape species and where the inverted allele represents the ancestral state. Investigating linkage disequilibrium relationships with genotyped SNPs, we provide evidence that most of these inversions appear to have arisen on at least two different haplotype backgrounds. In these cases, discovery and genotyping methods based on SNPs may be confounded and molecular cytogenetics remains the only method to genotype these inversions.
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Affiliation(s)
- Francesca Antonacci
- Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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Bekpen C, Marques-Bonet T, Alkan C, Antonacci F, Leogrande MB, Ventura M, Kidd JM, Siswara P, Howard JC, Eichler EE. Death and resurrection of the human IRGM gene. PLoS Genet 2009; 5:e1000403. [PMID: 19266026 PMCID: PMC2644816 DOI: 10.1371/journal.pgen.1000403] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 01/20/2009] [Indexed: 01/25/2023] Open
Abstract
Immunity-related GTPases (IRG) play an important role in defense against intracellular pathogens. One member of this gene family in humans, IRGM, has been recently implicated as a risk factor for Crohn's disease. We analyzed the detailed structure of this gene family among primates and showed that most of the IRG gene cluster was deleted early in primate evolution, after the divergence of the anthropoids from prosimians ( about 50 million years ago). Comparative sequence analysis of New World and Old World monkey species shows that the single-copy IRGM gene became pseudogenized as a result of an Alu retrotransposition event in the anthropoid common ancestor that disrupted the open reading frame (ORF). We find that the ORF was reestablished as a part of a polymorphic stop codon in the common ancestor of humans and great apes. Expression analysis suggests that this change occurred in conjunction with the insertion of an endogenous retrovirus, which altered the transcription initiation, splicing, and expression profile of IRGM. These data argue that the gene became pseudogenized and was then resurrected through a series of complex structural events and suggest remarkable functional plasticity where alleles experience diverse evolutionary pressures over time. Such dynamism in structure and evolution may be critical for a gene family locked in an arms race with an ever-changing repertoire of intracellular parasites. The IRG gene family plays an important role in defense against intracellular bacteria, and genome-wide association studies have implicated structural variants of the single-copy human IRGM locus as a risk factor for Crohn's disease. We reconstruct the evolutionary history of this region among primates and show that the ancestral tandem gene family contracted to a single pseudogene within the ancestral lineage of apes and monkeys. Phylogenetic analyses support a model where the gene has been “dead” for at least 25 million years of human primate evolution but whose ORF became restored in all human and great ape lineages. We suggest that the rebirth or restoration of the gene coincided with the insertion of an endogenous retrovirus, which now serves as the functional promoter driving human gene expression. We suggest that either the gene is not functional in humans or this represents one of the first documented examples of gene death and rebirth.
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Affiliation(s)
- Cemalettin Bekpen
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
| | - Tomas Marques-Bonet
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Institut de Biologia Evolutiva (UPF-CSIC), Barcelona, Spain
| | - Can Alkan
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
| | - Francesca Antonacci
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | | | | | - Jeffrey M. Kidd
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Priscillia Siswara
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | | | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
- * E-mail:
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Zody MC, Jiang Z, Fung HC, Antonacci F, Hillier LW, Cardone MF, Graves TA, Kidd JM, Cheng Z, Abouelleil A, Chen L, Wallis J, Glasscock J, Wilson RK, Reily AD, Duckworth J, Ventura M, Hardy J, Warren WC, Eichler EE. Evolutionary toggling of the MAPT 17q21.31 inversion region. Nat Genet 2009; 40:1076-83. [PMID: 19165922 DOI: 10.1038/ng.193] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Using comparative sequencing approaches, we investigated the evolutionary history of the European-enriched 17q21.31 MAPT inversion polymorphism. We present a detailed, BAC-based sequence assembly of the inverted human H2 haplotype and compare it to the sequence structure and genetic variation of the corresponding 1.5-Mb region for the noninverted H1 human haplotype and that of chimpanzee and orangutan. We found that inversion of the MAPT region is similarly polymorphic in other great ape species, and we present evidence that the inversions occurred independently in chimpanzees and humans. In humans, the inversion breakpoints correspond to core duplications with the LRRC37 gene family. Our analysis favors the H2 configuration and sequence haplotype as the likely great ape and human ancestral state, with inversion recurrences during primate evolution. We show that the H2 architecture has evolved more extensive sequence homology, perhaps explaining its tendency to undergo microdeletion associated with mental retardation in European populations.
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Affiliation(s)
- Michael C Zody
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
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Buysse K, Antonacci F, Callewaert B, Loeys B, Fränkel U, Siu V, Mortier G, Speleman F, Menten B. Unusual 8p inverted duplication deletion with telomere capture from 8q. Eur J Med Genet 2009; 52:31-6. [DOI: 10.1016/j.ejmg.2008.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 10/28/2008] [Indexed: 11/25/2022]
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Buysse K, Crepel A, Menten B, Pattyn F, Antonacci F, Veltman JA, Larsen LA, Tümer Z, de Klein A, van de Laar I, Devriendt K, Mortier G, Speleman F. Mapping of 5q35 chromosomal rearrangements within a genomically unstable region. J Med Genet 2008; 45:672-8. [PMID: 18628311 DOI: 10.1136/jmg.2008.058883] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Recent molecular studies of breakpoints of recurrent chromosome rearrangements revealed the role of genomic architecture in their formation. In particular, segmental duplications representing blocks of >1 kb with >90% sequence homology were shown to mediate non-allelic homologous recombination (NAHR). However, the occurrence of the majority of newly detected submicroscopic imbalances cannot be explained by the presence of segmental duplications. Therefore, further studies are needed to investigate whether architectural features other than segmental duplications mediate these rearrangements. METHODS We analysed a series of patients with breakpoints clustering within chromosome band 5q35. Using high density arrays and subsequent quantitative polymerase chain reaction (qPCR), we characterised the breakpoints of four interstitial deletions (including one associated with an unbalanced paracentric inversion), a duplication and a familial reciprocal t(5;18)(q35;q22) translocation. RESULTS AND CONCLUSION Five of the breakpoints were located within an interval of approximately 265 kb encompassing the RANBP17 and TLX3 genes. This region is also targeted by the recurrent cryptic t(5;14)(q35;q32) translocation, which occurs in approximately 20% of childhood T cell acute lymphoblastic leukaemia (T-ALL). In silico analysis indicated the architectural features most likely to contribute to the genomic instability of this region, which was supported by our molecular data. Of further interest, in two patients and the familial translocation, the delineated breakpoint regions encompassed highly homologous LINEs (long interspersed nuclear elements), suggesting that NAHR between these LINEs may have mediated these rearrangements.
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Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tüzün E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, Smith JD, Korn JM, McCarroll SA, Altshuler DA, Peiffer DA, Dorschner M, Stamatoyannopoulos J, Schwartz D, Nickerson DA, Mullikin JC, Wilson RK, Bruhn L, Olson MV, Kaul R, Smith DR, Eichler EE. Mapping and sequencing of structural variation from eight human genomes. Nature 2008; 453:56-64. [PMID: 18451855 PMCID: PMC2424287 DOI: 10.1038/nature06862] [Citation(s) in RCA: 877] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 02/15/2008] [Indexed: 11/08/2022]
Abstract
Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. 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.
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Affiliation(s)
- Jeffrey M Kidd
- Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
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Vandesompele J, Michels E, De Preter K, Menten B, Schramm A, Eggert A, Ambros PF, Combaret V, Francotte N, Antonacci F, De Paepe A, Laureys G, Speleman F, Van Roy N. Identification of 2 putative critical segments of 17q gain in neuroblastoma through integrative genomics. Int J Cancer 2008; 122:1177-82. [PMID: 17973261 DOI: 10.1002/ijc.23156] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Partial gain of chromosome arm 17q is the most frequent genetic change in neuroblastoma (NB) and constitutes the strongest independent genetic factor for adverse prognosis. It is assumed that 1 or more genes on 17q contribute to NB pathogenesis by a gene dosage effect. In the present study, we applied chromosome 17 tiling path BAC arrays on a panel of 69 primary tumors and 28 NB cell lines in order to reduce the current smallest region of gain and facilitate identification of candidate dosage sensitive genes. In all tumors and cell lines with 17q gain, large distal segments were consistently present in extra copies and no interstitial gains were observed. In addition to these large regions of distal gain with breakpoints proximal to coordinate 44.3 Mb (17q21.32), smaller regions of gain (distal to coordinate 60 Mb at 17q24.1) were found superimposed on the larger region in a minority of cases. Positional gene enrichment analysis for 17q genes overexpressed in NB showed that dosage sensitive NB oncogenes are most likely located in the gained region immediately distal to the most distal breakpoint of the 2 breakpoint regions. Interestingly, comparison of gene expression profiles between primary tumors and normal fetal adrenal neuroblasts revealed 2 gene clusters on chromosome 17q that are overexpressed in NB, i.e. a region on 17q21.32 immediately distal to the most distal breakpoint (in cases with single regions of gain) and 17q24.1, a region coinciding with breakpoints leading to superimposed gain.
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Affiliation(s)
- Jo Vandesompele
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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Ventura M, Antonacci F, Cardone MF, Stanyon R, D'Addabbo P, Cellamare A, Sprague LJ, Eichler EE, Archidiacono N, Rocchi M. Evolutionary Formation of New Centromeres in Macaque. Science 2007; 316:243-6. [PMID: 17431171 DOI: 10.1126/science.1140615] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A systematic fluorescence in situ hybridization comparison of macaque and human synteny organization disclosed five additional macaque evolutionary new centromeres (ENCs) for a total of nine ENCs. To understand the dynamics of ENC formation and progression, we compared the ENC of macaque chromosome 4 with the human orthologous region, at 6q24.3, that conserves the ancestral genomic organization. A 250-kilobase segment was extensively duplicated around the macaque centromere. These duplications were strictly intrachromosomal. Our results suggest that novel centromeres may trigger only local duplication activity and that the absence of genes in the seeding region may have been important in ENC maintenance and progression.
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Affiliation(s)
- Mario Ventura
- Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
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Ventura M, Cardone MF, Antonacci F, Misceo D, D. Addabbo P, Archidiacono N, Rocchi M. O14: Evolutionary centromere repositioning. Eur J Med Genet 2005. [DOI: 10.1016/j.ejmg.2005.10.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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