1
|
Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Yoo D, Gordon DS, Fair T, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Mao Y, Shi Y, Sun Q, Lu Q, Paten B, Bakken TE, Pollen AA, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Structurally divergent and recurrently mutated regions of primate genomes. Cell 2024; 187:1547-1562.e13. [PMID: 38428424 PMCID: PMC10947866 DOI: 10.1016/j.cell.2024.01.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 11/26/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.
Collapse
Affiliation(s)
- Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
| | - William T Harvey
- 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
| | - Katherine M Munson
- 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
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Allison Rozanski
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xiangyu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - 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
| | - Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaoxi Wei
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ricardo Del Rosario
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vanessa L Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Will T Fattor
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Gregory K Wilkerson
- Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX, USA; Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Yuxiang Mao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China; Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Qiang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Wesley C Warren
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA; Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - 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.
| |
Collapse
|
2
|
Soto DC, Uribe-Salazar JM, Shew CJ, Sekar A, McGinty SP, Dennis MY. Genomic structural variation: A complex but important driver of human evolution. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 36794631 DOI: 10.1002/ajpa.24713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 01/21/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023]
Abstract
Structural variants (SVs)-including duplications, deletions, and inversions of DNA-can have significant genomic and functional impacts but are technically difficult to identify and assay compared with single-nucleotide variants. With the aid of new genomic technologies, it has become clear that SVs account for significant differences across and within species. This phenomenon is particularly well-documented for humans and other primates due to the wealth of sequence data available. In great apes, SVs affect a larger number of nucleotides than single-nucleotide variants, with many identified SVs exhibiting population and species specificity. In this review, we highlight the importance of SVs in human evolution by (1) how they have shaped great ape genomes resulting in sensitized regions associated with traits and diseases, (2) their impact on gene functions and regulation, which subsequently has played a role in natural selection, and (3) the role of gene duplications in human brain evolution. We further discuss how to incorporate SVs in research, including the strengths and limitations of various genomic approaches. Finally, we propose future considerations in integrating existing data and biospecimens with the ever-expanding SV compendium propelled by biotechnology advancements.
Collapse
Affiliation(s)
- Daniela C Soto
- Genome Center, MIND Institute, Department of Biochemstry & Molecular Medicine, University of California, Davis, California, USA.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA
| | - José M Uribe-Salazar
- Genome Center, MIND Institute, Department of Biochemstry & Molecular Medicine, University of California, Davis, California, USA.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA
| | - Colin J Shew
- Genome Center, MIND Institute, Department of Biochemstry & Molecular Medicine, University of California, Davis, California, USA.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA
| | - Aarthi Sekar
- Genome Center, MIND Institute, Department of Biochemstry & Molecular Medicine, University of California, Davis, California, USA.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA
| | - Sean P McGinty
- Genome Center, MIND Institute, Department of Biochemstry & Molecular Medicine, University of California, Davis, California, USA.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA
| | - Megan Y Dennis
- Genome Center, MIND Institute, Department of Biochemstry & Molecular Medicine, University of California, Davis, California, USA.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA
| |
Collapse
|
3
|
Sánchez S, Juárez U, Domínguez J, Molina B, Barrientos R, Martínez-Hernández A, Carnevale A, Grether-González P, Mayen DG, Villarroel C, Lieberman E, Yokoyama E, Del Castillo V, Torres L, Frias S. Frequent copy number variants in a cohort of Mexican-Mestizo individuals. Mol Cytogenet 2023; 16:2. [PMID: 36631885 PMCID: PMC9835318 DOI: 10.1186/s13039-022-00631-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The human genome presents variation at distinct levels, copy number variants (CNVs) are DNA segments of variable lengths that range from several base pairs to megabases and are present at a variable number of copies in human genomes. Common CNVs have no apparent influence on the phenotype; however, some rare CNVs have been associated with phenotypic traits, depending on their size and gene content. CNVs are detected by microarrays of different densities and are generally visualized, and their frequencies analysed using the HapMap as default reference population. Nevertheless, this default reference is inadequate when the samples analysed are from people from Mexico, since population with a Hispanic genetic background are minimally represented. In this work, we describe the variation in the frequencies of four common CNVs in Mexican-Mestizo individuals. RESULTS In a cohort of 147 unrelated Mexican-Mestizo individuals, we found that the common CNVs 2p11.2 (99.6%), 8p11.22 (54.5%), 14q32.33 (100%), and 15q11.2 (71.1%) appeared with unexpectedly high frequencies when contrasted with the HapMap reference (ChAS). Yet, while when comparing to an ethnically related reference population, these differences were significantly reduced or even disappeared. CONCLUSION The findings in this work contribute to (1) a better description of the CNVs characteristics of the Mexican Mestizo population and enhance the knowledge of genome variation in different ethnic groups. (2) emphasize the importance of contrasting CNVs identified in studied individuals against a reference group that-as best as possible-share the same ethnicity while keeping this relevant information in mind when conducting CNV studies at the population or clinical level.
Collapse
Affiliation(s)
- Silvia Sánchez
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México ,grid.9486.30000 0001 2159 0001Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ulises Juárez
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Julieta Domínguez
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Bertha Molina
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Rehotbevely Barrientos
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Angélica Martínez-Hernández
- grid.452651.10000 0004 0627 7633Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, México
| | - Alessandra Carnevale
- grid.452651.10000 0004 0627 7633Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, México
| | - Patricia Grether-González
- grid.419218.70000 0004 1773 5302Departamento de Genética y Genómica Humana, Instituto Nacional de Perinatología, Ciudad de Mexico, México ,grid.413678.fPresent Address: Centro Médico ABC, Campus Santa Fe, Ciudad de Mexico, México
| | - Dora Gilda Mayen
- Unidad de Genética Aplicada. Hospital Ángeles Lomas, Huixquilucan, Edo. de México México
| | - Camilo Villarroel
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Esther Lieberman
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Emiy Yokoyama
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Victoria Del Castillo
- grid.419216.90000 0004 1773 4473Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - Leda Torres
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México
| | - Sara Frias
- grid.419216.90000 0004 1773 4473Laboratorio de Citogenética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C Insurgentes Cuicuilco, P01090 Ciudad de Mexico, México ,grid.9486.30000 0001 2159 0001Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| |
Collapse
|
4
|
Auwerx C, Lepamets M, Sadler MC, Patxot M, Stojanov M, Baud D, Mägi R, Porcu E, Reymond A, Kutalik Z, Metspalu A, Milani L, Mägi R, Nelis M. The individual and global impact of copy-number variants on complex human traits. Am J Hum Genet 2022; 109:647-668. [PMID: 35240056 PMCID: PMC9069145 DOI: 10.1016/j.ajhg.2022.02.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/09/2022] [Indexed: 12/25/2022] Open
Abstract
The impact of copy-number variations (CNVs) on complex human traits remains understudied. We called CNVs in 331,522 UK Biobank participants and performed genome-wide association studies (GWASs) between the copy number of CNV-proxy probes and 57 continuous traits, revealing 131 signals spanning 47 phenotypes. Our analysis recapitulated well-known associations (e.g., 1q21 and height), revealed the pleiotropy of recurrent CNVs (e.g., 26 and 16 traits for 16p11.2-BP4-BP5 and 22q11.21, respectively), and suggested gene functionalities (e.g., MARF1 in female reproduction). Forty-eight CNV signals (38%) overlapped with single-nucleotide polymorphism (SNP)-GWASs signals for the same trait. For instance, deletion of PDZK1, which encodes a urate transporter scaffold protein, decreased serum urate levels, while deletion of RHD, which encodes the Rhesus blood group D antigen, associated with hematological traits. Other signals overlapped Mendelian disorder regions, suggesting variable expressivity and broad impact of these loci, as illustrated by signals mapping to Rotor syndrome (SLCO1B1/3), renal cysts and diabetes syndrome (HNF1B), or Charcot-Marie-Tooth (PMP22) loci. Total CNV burden negatively impacted 35 traits, leading to increased adiposity, liver/kidney damage, and decreased intelligence and physical capacity. Thirty traits remained burden associated after correcting for CNV-GWAS signals, pointing to a polygenic CNV architecture. The burden negatively correlated with socio-economic indicators, parental lifespan, and age (survivorship proxy), suggesting a contribution to decreased longevity. Together, our results showcase how studying CNVs can expand biological insights, emphasizing the critical role of this mutational class in shaping human traits and arguing in favor of a continuum between Mendelian and complex diseases.
Collapse
Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; University Center for Primary Care and Public Health, Lausanne 1010, Switzerland
| | - Maarja Lepamets
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia; Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Marie C Sadler
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; University Center for Primary Care and Public Health, Lausanne 1010, Switzerland
| | - Marion Patxot
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Miloš Stojanov
- Materno-fetal and Obstetrics Research Unit, Department Woman-Mother-Child, CHUV, Lausanne 1011, Switzerland
| | - David Baud
- Materno-fetal and Obstetrics Research Unit, Department Woman-Mother-Child, CHUV, Lausanne 1011, Switzerland
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | -
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Eleonora Porcu
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; University Center for Primary Care and Public Health, Lausanne 1010, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland.
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; University Center for Primary Care and Public Health, Lausanne 1010, Switzerland.
| | | | | | | | | |
Collapse
|
5
|
Quantitative assessment reveals the dominance of duplicated sequences in germline-derived extrachromosomal circular DNA. Proc Natl Acad Sci U S A 2021; 118:2102842118. [PMID: 34789574 PMCID: PMC8617514 DOI: 10.1073/pnas.2102842118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 01/08/2023] Open
Abstract
Extrachromosomal circular DNA (eccDNA) plays a role in human diseases such as cancer, but little is known about the impact of eccDNA in healthy human biology. Since eccDNA is a tiny fraction of nuclear DNA, artificial amplification has been employed to increase eccDNA amounts, resulting in the loss of native compositions. We developed an approach to enrich eccDNA populations at the native state (naïve small circular DNA, nscDNA) and investigated their origins in the human genome. We found that, in human sperm, the vast majority of nscDNA came from high-copy genomic regions, including the most variable regions between individuals. Because eccDNA can be incorporated back into chromosomes, eccDNA may promote human genetic variation. Extrachromosomal circular DNA (eccDNA) originates from linear chromosomal DNA in various human tissues under physiological and disease conditions. The genomic origins of eccDNA have largely been investigated using in vitro–amplified DNA. However, in vitro amplification obscures quantitative information by skewing the total population stoichiometry. In addition, the analyses have focused on eccDNA stemming from single-copy genomic regions, leaving eccDNA from multicopy regions unexamined. To address these issues, we isolated eccDNA without in vitro amplification (naïve small circular DNA, nscDNA) and assessed the populations quantitatively by integrated genomic, molecular, and cytogenetic approaches. nscDNA of up to tens of kilobases were successfully enriched by our approach and were predominantly derived from multicopy genomic regions including segmental duplications (SDs). SDs, which account for 5% of the human genome and are hotspots for copy number variations, were significantly overrepresented in sperm nscDNA, with three times more sequencing reads derived from SDs than from the entire single-copy regions. SDs were also overrepresented in mouse sperm nscDNA, which we estimated to comprise 0.2% of nuclear DNA. Considering that eccDNA can be integrated into chromosomes, germline-derived nscDNA may be a mediator of genome diversity.
Collapse
|
6
|
El Bitar F, Al Sudairy N, Qadi N, Al Rajeh S, Alghamdi F, Al Amari H, Al Dawsari G, Alsubaie S, Al Sudairi M, Abdulaziz S, Al Tassan N. A Comprehensive Analysis of Unique and Recurrent Copy Number Variations in Alzheimer's Disease and its Related Disorders. Curr Alzheimer Res 2020; 17:926-938. [PMID: 33256577 DOI: 10.2174/1567205017666201130111424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/20/2020] [Accepted: 10/29/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Copy number variations (CNVs) play an important role in the genetic etiology of various neurological disorders, including Alzheimer's disease (AD). Type 2 diabetes mellitus (T2DM) and major depressive disorder (MDD) were shown to have share mechanisms and signaling pathways with AD. OBJECTIVE We aimed to assess CNVs regions that may harbor genes contributing to AD, T2DM, and MDD in 67 Saudi familial and sporadic AD patients, with no alterations in the known genes of AD and genotyped previously for APOE. METHODS DNA was analyzed using the CytoScan-HD array. Two layers of filtering criteria were applied. All the identified CNVs were checked in the Database of Genomic Variants (DGV). RESULTS A total of 1086 CNVs (565 gains and 521 losses) were identified in our study. We found 73 CNVs harboring genes that may be associated with AD, T2DM or MDD. Nineteen CNVs were novel. Most importantly, 42 CNVs were unique in our studied cohort existing only in one patient. Two large gains on chromosomes 1 and 13 harbored genes implicated in the studied disorders. We identified CNVs in genes that encode proteins involved in the metabolism of amyloid-β peptide (AGRN, APBA2, CR1, CR2, IGF2R, KIAA0125, MBP, RER1, RTN4R, VDR and WISPI) or Tau proteins (CACNAIC, CELF2, DUSP22, HTRA1 and SLC2A14). CONCLUSION The present work provided information on the presence of CNVs related to AD, T2DM, and MDD in Saudi Alzheimer's patients.
Collapse
Affiliation(s)
- Fadia El Bitar
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nourah Al Sudairy
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Najeeb Qadi
- Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | - Fatimah Alghamdi
- Institute of Biology and Environmental Research, National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hala Al Amari
- Institute of Biology and Environmental Research, National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Ghadeer Al Dawsari
- Institute of Biology and Environmental Research, National Center for Genomics Technology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Sahar Alsubaie
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mishael Al Sudairi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sara Abdulaziz
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nada Al Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| |
Collapse
|
7
|
Zmienko A, Marszalek-Zenczak M, Wojciechowski P, Samelak-Czajka A, Luczak M, Kozlowski P, Karlowski WM, Figlerowicz M. AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome. THE PLANT CELL 2020; 32:1797-1819. [PMID: 32265262 PMCID: PMC7268809 DOI: 10.1105/tpc.19.00640] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 03/09/2020] [Accepted: 03/30/2020] [Indexed: 05/13/2023]
Abstract
Copy number variations (CNVs) greatly contribute to intraspecies genetic polymorphism and phenotypic diversity. Recent analyses of sequencing data for >1000 Arabidopsis (Arabidopsis thaliana) accessions focused on small variations and did not include CNVs. Here, we performed genome-wide analysis and identified large indels (50 to 499 bp) and CNVs (500 bp and larger) in these accessions. The CNVs fully overlap with 18.3% of protein-coding genes, with enrichment for evolutionarily young genes and genes involved in stress and defense. By combining analysis of both genes and transposable elements (TEs) affected by CNVs, we revealed that the variation statuses of genes and TEs are tightly linked and jointly contribute to the unequal distribution of these elements in the genome. We also determined the gene copy numbers in a set of 1060 accessions and experimentally validated the accuracy of our predictions by multiplex ligation-dependent probe amplification assays. We then successfully used the CNVs as markers to analyze population structure and migration patterns. Finally, we examined the impact of gene dosage variation triggered by a CNV spanning the SEC10 gene on SEC10 expression at both the transcript and protein levels. The catalog of CNVs, CNV-overlapping genes, and their genotypes in a top model dicot will stimulate the exploration of the genetic basis of phenotypic variation.
Collapse
Affiliation(s)
- Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
| | | | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Luczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
| |
Collapse
|
8
|
Abstract
Background Recent advances in whole-genome sequencing and SNP array technology have led to the generation of a large amount of genotype data. Large volumes of genotype data will require faster and more efficient methods for storing and searching the data. Positional Burrows-Wheeler Transform (PBWT) provides an appropriate data structure for bi-allelic data. With the increasing sample sizes, more multi-allelic sites are expected to be observed. Hence, there is a necessity to handle multi-allelic genotype data. Results In this paper, we introduce a multi-allelic version of the Positional Burrows-Wheeler Transform (mPBWT) based on the bi-allelic version for compression and searching. The time-complexity for constructing the data structure and searching within a panel containing t-allelic sites increases by a factor of t. Conclusion Considering the small value for the possible alleles t, the time increase for the multi-allelic PBWT will be negligible and comparable to the bi-allelic version of PBWT.
Collapse
Affiliation(s)
- Ardalan Naseri
- Department of Computer Science, University of Central Florida, Orlando, FL, 32816, USA
| | - Degui Zhi
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL, 32816, USA.
| |
Collapse
|
9
|
Deletions and loss-of-function variants in TP63 associated with orofacial clefting. Eur J Hum Genet 2019; 27:1101-1112. [PMID: 30850703 DOI: 10.1038/s41431-019-0370-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 02/04/2019] [Accepted: 02/12/2019] [Indexed: 11/08/2022] Open
Abstract
We aimed to identify novel deletions and variants of TP63 associated with orofacial clefting (OFC). Copy number variants were assessed in three OFC families using microarray analysis. Subsequently, we analyzed TP63 in a cohort of 1072 individuals affected with OFC and 706 population-based controls using molecular inversion probes (MIPs). We identified partial deletions of TP63 in individuals from three families affected with OFC. In the OFC cohort, we identified several TP63 variants predicting to cause loss-of-function alleles, including a frameshift variant c.569_576del (p.(Ala190Aspfs*5)) and a nonsense variant c.997C>T (p.(Gln333*)) that introduces a premature stop codon in the DNA-binding domain. In addition, we identified the first missense variants in the oligomerization domain c.1213G>A (p.(Val405Met)), which occurred in individuals with OFC. This variant was shown to abrogate oligomerization of mutant p63 protein into oligomeric complexes, and therefore likely represents a loss-of-function allele rather than a dominant-negative. All of these variants were inherited from an unaffected parent, suggesting reduced penetrance of such loss-of-function alleles. Our data indicate that loss-of-function alleles in TP63 can also give rise to OFC as the main phenotype. We have uncovered the dosage-dependent functions of p63, which were previously rejected.
Collapse
|
10
|
Zhang H, Roe D, Kuang R. Detecting Population-Differentiation Copy Number Variants in Human Population Tree by Sparse Group Selection. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:538-549. [PMID: 29990238 DOI: 10.1109/tcbb.2017.2779481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Copy-number variants (CNVs) account for a substantial proportion of human genetic variations. Understanding the CNV diversities across populations is a computational challenge because CNV patterns are often present in several related populations and only occur in a subgroup of individuals within each of the population. This paper introduces a tree-guided sparse group selection algorithm (treeSGS) to detect population-differentiation CNV markers of subgroups across populations organized by a phylogenetic tree of human populations. The treeSGS algorithm detects CNV markers of populations associated with nodes from all levels of the tree such that the evolutionary relations among the populations are incorporated for more accurate detection of population-differentiation CNVs. We applied treeSGS algorithm to study the 1,179 samples from the 11 populations in Hapmap3 CNV data. The treeSGS algorithm accurately identifies CNV markers of each population and the collection of populations organized under the branches of the human population tree, validated by consistency among family trios and SNP characterizations of the CNV regions. Further comparison between the detected CNV markers and other population-differentiation CNVs reported in 1,000 genome data and other recent studies also shows that treeSGS can significantly improve the current annotations of population-differentiation CNV markers. TreeSGS package is available at https://github.com/kuanglab/treeSGS.
Collapse
|
11
|
Gennarino VA, Palmer EE, McDonell LM, Wang L, Adamski CJ, Koire A, See L, Chen CA, Schaaf CP, Rosenfeld JA, Panzer JA, Moog U, Hao S, Bye A, Kirk EP, Stankiewicz P, Breman AM, McBride A, Kandula T, Dubbs HA, Macintosh R, Cardamone M, Zhu Y, Ying K, Dias KR, Cho MT, Henderson LB, Baskin B, Morris P, Tao J, Cowley MJ, Dinger ME, Roscioli T, Caluseriu O, Suchowersky O, Sachdev RK, Lichtarge O, Tang J, Boycott KM, Holder JL, Zoghbi HY. A Mild PUM1 Mutation Is Associated with Adult-Onset Ataxia, whereas Haploinsufficiency Causes Developmental Delay and Seizures. Cell 2019; 172:924-936.e11. [PMID: 29474920 DOI: 10.1016/j.cell.2018.02.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 08/23/2017] [Accepted: 02/01/2018] [Indexed: 02/06/2023]
Abstract
Certain mutations can cause proteins to accumulate in neurons, leading to neurodegeneration. We recently showed, however, that upregulation of a wild-type protein, Ataxin1, caused by haploinsufficiency of its repressor, the RNA-binding protein Pumilio1 (PUM1), also causes neurodegeneration in mice. We therefore searched for human patients with PUM1 mutations. We identified eleven individuals with either PUM1 deletions or de novo missense variants who suffer a developmental syndrome (Pumilio1-associated developmental disability, ataxia, and seizure; PADDAS). We also identified a milder missense mutation in a family with adult-onset ataxia with incomplete penetrance (Pumilio1-related cerebellar ataxia, PRCA). Studies in patient-derived cells revealed that the missense mutations reduced PUM1 protein levels by ∼25% in the adult-onset cases and by ∼50% in the infantile-onset cases; levels of known PUM1 targets increased accordingly. Changes in protein levels thus track with phenotypic severity, and identifying posttranscriptional modulators of protein expression should identify new candidate disease genes.
Collapse
Affiliation(s)
- Vincenzo A Gennarino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.
| | - Elizabeth E Palmer
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia; Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | - Laura M McDonell
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Li Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Carolyn J Adamski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amanda Koire
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lauren See
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jessica A Panzer
- Department of Pediatrics, Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany
| | - Shuang Hao
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ann Bye
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia
| | - Edwin P Kirk
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia; Genetics Laboratory, NSW Health Pathology East Randwick, Sydney, NSW, Australia
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arran McBride
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Tejaswi Kandula
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia
| | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Michael Cardamone
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia
| | - Ying Zhu
- Genetics Laboratory, NSW Health Pathology East Randwick, Sydney, NSW, Australia
| | - Kevin Ying
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Kerith-Rae Dias
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Megan T Cho
- GeneDx, 207 Perry Pkwy Gaithersburg, MD 20877, USA
| | | | | | - Paula Morris
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Jiang Tao
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Tony Roscioli
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; Genetics Laboratory, NSW Health Pathology East Randwick, Sydney, NSW, Australia; Neuroscience Research Australia and Prince of Wales Clinical School, University of New South Wales, Randwick, NSW 2031, Australia
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, AB T6G 2H7, Canada
| | - Oksana Suchowersky
- Department of Medical Genetics, University of Alberta, AB T6G 2H7, Canada; Departments of Medicine (Neurology) and Pediatrics, University of Alberta, AB, Canada
| | - Rani K Sachdev
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianrong Tang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - J Lloyd Holder
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huda Y Zoghbi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
12
|
Effector variation at tandem gene arrays in tissue-dwelling coccidia: who needs antigenic variation anyway? Curr Opin Microbiol 2018; 46:86-92. [PMID: 30317151 DOI: 10.1016/j.mib.2018.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/28/2018] [Accepted: 09/24/2018] [Indexed: 11/20/2022]
Abstract
Locus expansion and diversification is pervasive in apicomplexan genomes and is predominantly found in loci encoding secreted proteins that interact with factors outside of the parasite. Key for understanding the impact of each of these loci on the host requires identification and functional characterization of their protein products, but these repetitive loci often are refractory to genome assembly. In this review we focus on Toxoplasma gondii and its nearest relatives to highlight the known impact of duplicated and diversified loci on our understanding of the host-pathogen molecular arms race. We describe current tools used for the identification and characterization of these loci, and review the most recent examples of how gene-expansion driven diversification can lead to novel gene functions.
Collapse
|
13
|
Pierce MD, Dzama K, Muchadeyi FC. Genetic Diversity of Seven Cattle Breeds Inferred Using Copy Number Variations. Front Genet 2018; 9:163. [PMID: 29868114 PMCID: PMC5962699 DOI: 10.3389/fgene.2018.00163] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/23/2018] [Indexed: 11/25/2022] Open
Abstract
Copy number variations (CNVs) comprise deletions, duplications, and insertions found within the genome larger than 50 bp in size. CNVs are thought to be primary role-players in breed formation and adaptation. South Africa boasts a diverse ecology with harsh environmental conditions and a broad spectrum of parasites and diseases that pose challenges to livestock production. This has led to the development of composite cattle breeds which combine the hardiness of Sanga breeds and the production potential of the Taurine breeds. The prevalence of CNVs within these respective breeds of cattle and the prevalence of CNV regions (CNVRs) in their diversity, adaptation and production is however not understood. This study therefore aimed to ascertain the prevalence, diversity, and correlations of CNVRs within cattle breeds used in South Africa. Illumina Bovine SNP50 data and PennCNV were utilized to identify CNVRs within the genome of 287 animals from seven cattle breeds representing Sanga, Taurine, Composite, and cross breeds. Three hundred and fifty six CNVRs of between 36 kb to 4.1 Mb in size were identified. The null hypothesis that one CNVR loci is independent of another was tested using the GENEPOP software. One hunded and two and seven of the CNVRs in the Taurine and Sanga/Composite cattle breeds demonstrated a significant (p ≤ 0.05) association. PANTHER overrepresentation analyses of correlated CNVRs demonstrated significant enrichment of a number of biological processes, molecular functions, cellular components, and protein classes. CNVR genetic variation between and within breed group was measured using phiPT which allows intra-individual variation to be suppressed and hence proved suitable for measuring binary CNVR presence/absence data. Estimate PhiPT within and between breed variance was 2.722 and 0.518 respectively. Pairwise population PhiPT values corresponded with breed type, with Taurine Holstein and Angus breeds demonstrating no between breed CNVR variation. Phylogenetic trees were drawn. CNVRs primarily clustered animals of the same breed type together. This study successfully identified, characterized, and analyzed 356 CNVRs within seven cattle breeds. CNVR correlations were evident, with many more correlations being present among the exotic Taurine breeds. CNVR genetic diversity of Sanga, Taurine and Composite breeds was ascertained with breed types exposed to similar selection pressures demonstrating analogous incidences of CNVRs.
Collapse
Affiliation(s)
- Magretha D Pierce
- Animal Production, Agricultural Research Council, Pretoria, South Africa
| | - Kennedy Dzama
- Department of Animal Sciences, University of Stellenbosch, Stellenbosch, South Africa
| | - Farai C Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| |
Collapse
|
14
|
Yang L, Xu L, Zhou Y, Liu M, Wang L, Kijas JW, Zhang H, Li L, Liu GE. Diversity of copy number variation in a worldwide population of sheep. Genomics 2018; 110:143-148. [DOI: 10.1016/j.ygeno.2017.09.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/24/2017] [Accepted: 09/11/2017] [Indexed: 01/14/2023]
|
15
|
Ahn J, Conkright B, Boca SM, Madhavan S. POPSTR: Inference of Admixed Population Structure Based on Single-Nucleotide Polymorphisms and Copy Number Variations. J Comput Biol 2018; 25:417-429. [PMID: 29293371 DOI: 10.1089/cmb.2017.0127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Statistical approaches for population structure estimation have been predominantly driven by a particular data type, single-nucleotide polymorphisms (SNPs). However, in the presence of weak identifiability in SNPs, population structure estimation can suffer from undesirable accuracy loss. Copy number variations (CNVs) are genomic structural variants with loci that are commonly shared within a specific population and thus provide valuable information for estimation of the ancestry of sampled populations. We develop a Bayesian joint modeling framework of SNPs and CNVs, called POPSTR, to better understand population structure than approaches that use SNPs solely. To deal with the increased data volume, we use the Metropolis Adjusted Langevin algorithm (MALA) that guides the target distribution in a computationally efficient way. We illustrate applications of our approach using the HapMap 2005 project data. We carry out simulation studies and show that the performance of our approach is comparable or better than that of popular benchmarks, STRUCTURE and ADMIXTURE. We also observe that using only CNVs can be remarkably efficient if SNP data are not available.
Collapse
Affiliation(s)
- Jaeil Ahn
- 1 Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University , Washington, District of Columbia
| | - Brian Conkright
- 2 Innovation Center for Biomedical Informatics, Georgetown University , Washington, District of Columbia
| | - Simina M Boca
- 1 Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University , Washington, District of Columbia.,2 Innovation Center for Biomedical Informatics, Georgetown University , Washington, District of Columbia.,3 Department of Oncology, Georgetown University , Washington, District of Columbia
| | - Subha Madhavan
- 2 Innovation Center for Biomedical Informatics, Georgetown University , Washington, District of Columbia.,3 Department of Oncology, Georgetown University , Washington, District of Columbia
| |
Collapse
|
16
|
Xu L, Yang L, Bickhart DM, Li J, Liu GE. Analysis of Population-Genetic Properties of Copy Number Variations. Methods Mol Biol 2018; 1833:179-186. [PMID: 30039373 DOI: 10.1007/978-1-4939-8666-8_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
While single nucleotide polymorphisms (SNPs) are typically the variant of choice for population genetics, copy number variations (CNVs) which comprise insertions, deletions and duplications of genomic sequences, is also an informative type of genetic variation. CNVs have been shown to be both common in mammals and important for understanding the relationship between genotype and phenotype. Moreover, population-specific CNVs are candidate regions under selection and are potentially responsible for diverse phenotypes.
Collapse
Affiliation(s)
- Lingyang Xu
- Institute of Animal Science, Beijing, China.
| | - Liu Yang
- Institute of Animal Science, Beijing, China
| | - Derek M Bickhart
- Research Microbiologist/Bioinformatician, USDA ARS DFRC, Madison, WI, USA
| | - JunYa Li
- Institute of Animal Science, Beijing, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, USDA ARS, Beltsville, MD, USA
| |
Collapse
|
17
|
Jenkinson EM, Livingston JH, O'Driscoll MC, Desguerre I, Nabbout R, Boddaert N, Soares G, Gonçalves da Rocha M, D'Arrigo S, Rice GI, Crow YJ. Comprehensive molecular screening strategy of OCLN in band-like calcification with simplified gyration and polymicrogyria. Clin Genet 2017; 93:228-234. [PMID: 28386946 DOI: 10.1111/cge.13025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/08/2017] [Accepted: 03/28/2017] [Indexed: 11/29/2022]
Abstract
Occludin (OCLN) is an important component of the tight junction complex, providing apical intercellular connections between adjacent cells in endothelial and epithelial tissue. In 2010 O'Driscoll et al reported mutations in OCLN to cause band-like calcification with simplified gyration and polymicrogyria (BLC-PMG). BLC-PMG is a rare autosomal recessive syndrome, characterized by early onset seizures, progressive microcephaly, severe developmental delay and deep cortical gray matter and basal ganglia calcification with symmetrical, predominantly fronto-parietal, polymicrogyria. Here we report 4 additional cases of BLC-PMG with novel OCLN mutations, and provide a summary of the published mutational spectrum. More generally, we describe a comprehensive molecular screening strategy taking into account the technical challenges associated with the genetic architecture of OCLN, which include the presence of a pseudo-gene and copy number variants.
Collapse
Affiliation(s)
- E M Jenkinson
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, Manchester, UK
| | - J H Livingston
- Department of Paediatric Neurology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - M C O'Driscoll
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's Hospital NHS Foundation Trust, Birmingham, UK
| | - I Desguerre
- Department of Paediatric Neurology, Paris Descartes University, Sorbonne-Paris-Cité, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - R Nabbout
- Department of Paediatric Neurology, Paris Descartes University, Sorbonne-Paris-Cité, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - N Boddaert
- Department of Pediatric Radiology, Hôpital Necker Enfants Malades, AP-HP, PRES Sorbonne Paris Cité, INSERM U1000 and UMR 1163, Institut Imagine, University René Descartes, Paris, France
| | - G Soares
- Medical Genetics, Porto Hospital Center, Porto, Portugal
| | - M Gonçalves da Rocha
- Centro Genética Médica, Porto, Portugal.,Medical Genetics Unit, Hospital de Braga, Braga, Portugal
| | - S D'Arrigo
- Development Neurology Department, Fondazione IRCCS Istituto Neurologico "C. Besta,", Milan, Italy
| | - G I Rice
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, Manchester, UK
| | - Y J Crow
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, Manchester, UK.,Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR 1163, Paris, France.,Institut Imagine, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris Descartes University, Sorbonne-Paris-Cité, Paris, France
| |
Collapse
|
18
|
Zhang C, Lu J, Lou H, Du R, Xu S, Shen Y, Zhang F, Jin L. CNVbase: Batch identification of novel and rare copy number variations based on multi-ethnic population data. J Genet Genomics 2017; 44:367-370. [PMID: 28739046 DOI: 10.1016/j.jgg.2017.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 07/05/2017] [Accepted: 07/10/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Cheng Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200438, China; Key Laboratory of Reproduction Regulation of NPFPC, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China; Departments of Laboratory Medicine and Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jianqi Lu
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200438, China; Key Laboratory of Reproduction Regulation of NPFPC, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China
| | - Haiyi Lou
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Renqian Du
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yiping Shen
- Departments of Laboratory Medicine and Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Genetic Metabolism, Children's Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China; Department of Medical Genetics, Shanghai Children's Medical Center, Shanghai 200127, China
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200438, China; Key Laboratory of Reproduction Regulation of NPFPC, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China.
| | - Li Jin
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai 200438, China.
| |
Collapse
|
19
|
Mihaylova M, Staneva R, Toncheva D, Pancheva M, Hadjidekova S. Benign, Pathogenic and Copy Number Variations of Unknown Clinical Significance in Patients with Congenital Malformations and Developmental Delay. Balkan J Med Genet 2017; 20:5-12. [PMID: 28924535 PMCID: PMC5596816 DOI: 10.1515/bjmg-2017-0010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The high frequency (3.0-5.0%) of congenital anomalies (CA) and intellectual disabilities (IDs), make them a serious problem, responsible for a high percentage (33.0%) of neonatal mortality. The genetic cause remains unclear in 40.0% of cases. Recently, molecular karyotyping has become the most powerful method for detection of pathogenic imbalances in patients with multiple CAs and IDs. This method is with high resolution and gives us the opportunity to investigate and identify candidate genes that could explain the genotype-phenotype correlations. This article describes the results from analysis of 81 patients with congenital malformations (CMs), developmental delay (DD) and ID, in which we utilized the CytoChip ISCA oligo microarray, 4 × 44 k, covering the whole genome with a resolution of 70 kb. In the selected group of patients with CAs, 280 copy number variations (CNVs) have been proven, 41 were pathogenic, 118 benign and 121 of unknown clinical significance (average number of variations 3.5). In six patients with established pathogenic variations, our data revealed eight pathogenic aberrations associated with the corresponding phenotype. The interpretation of the other CNVs was made on the basis of their frequency in the investigated group, the size of the variation, content of genes in the region and the type of the CNVs (deletion or duplication).
Collapse
Affiliation(s)
- M Mihaylova
- Department of Medical Genetics, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - R Staneva
- Department of Medical Genetics, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria.,Woman Health Hospital "Nadezhda", Sofia, Bulgaria
| | - D Toncheva
- Department of Medical Genetics, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - M Pancheva
- Department of Medical Genetics, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria.,Woman Health Hospital "Nadezhda", Sofia, Bulgaria
| | - S Hadjidekova
- Department of Medical Genetics, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria.,Woman Health Hospital "Nadezhda", Sofia, Bulgaria
| |
Collapse
|
20
|
Werdyani S, Yu Y, Skardasi G, Xu J, Shestopaloff K, Xu W, Dicks E, Green J, Parfrey P, Yilmaz YE, Savas S. Germline INDELs and CNVs in a cohort of colorectal cancer patients: their characteristics, associations with relapse-free survival time, and potential time-varying effects on the risk of relapse. Cancer Med 2017; 6:1220-1232. [PMID: 28544645 PMCID: PMC5463068 DOI: 10.1002/cam4.1074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/13/2017] [Accepted: 03/16/2017] [Indexed: 12/24/2022] Open
Abstract
INDELs and CNVs are structural variations that may play roles in cancer susceptibility and patient outcomes. Our objectives were a) to computationally detect and examine the genome‐wide INDEL/CNV profiles in a cohort of colorectal cancer patients, and b) to examine the associations of frequent INDELs/CNVs with relapse‐free survival time. We also identified unique variants in 13 Familial Colorectal Cancer Type X (FCCX) cases. The study cohort consisted of 495 colorectal cancer patients. QuantiSNP and PennCNV algorithms were utilized to predict the INDELs/CNVs using genome‐wide signal intensity data. Duplex PCR was used to validate predictions for 10 variants. Multivariable Cox regression models were used to test the associations of 106 common variants with relapse‐free survival time. Score test and the multivariable Cox proportional hazards models with time‐varying coefficients were applied to identify the variants with time‐varying effects on the relapse‐free survival time. A total of 3486 distinct INDELs/CNVs were identified in the patient cohort. The majority of these variants were rare (83%) and deletion variants (81%). The results of the computational predictions and duplex PCR results were highly concordant (93–100%). We identified four promising variants significantly associated with relapse‐free survival time (P < 0.05) in the multivariable Cox proportional hazards regression models after adjustment for clinical factors. More importantly, two additional variants were identified to have time‐varying effects on the risk of relapse. Finally, 58 rare variants were identified unique to the FCCX cases; none of them were detected in more than one patient. This is one of the first genome‐wide analyses that identified the germline INDEL/CNV profiles in colorectal cancer patients. Our analyses identified novel variants and genes that can biologically affect the risk of relapse in colorectal cancer patients. Additionally, for the first time, we identified germline variants that can potentially be early‐relapse markers in colorectal cancer.
Collapse
Affiliation(s)
- Salem Werdyani
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Georgia Skardasi
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Jingxiong Xu
- Department of Biostatistics, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada
| | | | - Wei Xu
- Department of Biostatistics, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Jane Green
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Yildiz E Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| |
Collapse
|
21
|
Gao Y, Jiang J, Yang S, Hou Y, Liu GE, Zhang S, Zhang Q, Sun D. CNV discovery for milk composition traits in dairy cattle using whole genome resequencing. BMC Genomics 2017; 18:265. [PMID: 28356085 PMCID: PMC5371188 DOI: 10.1186/s12864-017-3636-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 03/17/2017] [Indexed: 01/08/2023] Open
Abstract
Background Copy number variations (CNVs) are important and widely distributed in the genome. CNV detection opens a new avenue for exploring genes associated with complex traits in humans, animals and plants. Herein, we present a genome-wide assessment of CNVs that are potentially associated with milk composition traits in dairy cattle. Results In this study, CNVs were detected based on whole genome re-sequencing data of eight Holstein bulls from four half- and/or full-sib families, with extremely high and low estimated breeding values (EBVs) of milk protein percentage and fat percentage. The range of coverage depth per individual was 8.2–11.9×. Using CNVnator, we identified a total of 14,821 CNVs, including 5025 duplications and 9796 deletions. Among them, 487 differential CNV regions (CNVRs) comprising ~8.23 Mb of the cattle genome were observed between the high and low groups. Annotation of these differential CNVRs were performed based on the cattle genome reference assembly (UMD3.1) and totally 235 functional genes were found within the CNVRs. By Gene Ontology and KEGG pathway analyses, we found that genes were significantly enriched for specific biological functions related to protein and lipid metabolism, insulin/IGF pathway-protein kinase B signaling cascade, prolactin signaling pathway and AMPK signaling pathways. These genes included INS, IGF2, FOXO3, TH, SCD5, GALNT18, GALNT16, ART3, SNCA and WNT7A, implying their potential association with milk protein and fat traits. In addition, 95 CNVRs were overlapped with 75 known QTLs that are associated with milk protein and fat traits of dairy cattle (Cattle QTLdb). Conclusions In conclusion, based on NGS of 8 Holstein bulls with extremely high and low EBVs for milk PP and FP, we identified a total of 14,821 CNVs, 487 differential CNVRs between groups, and 10 genes, which were suggested as promising candidate genes for milk protein and fat traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3636-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yahui Gao
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianping Jiang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shaohua Yang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yali Hou
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Md, 20705, USA
| | - Shengli Zhang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dongxiao Sun
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
22
|
Copy Number Variations in Candidate Genes and Intergenic Regions Affect Body Mass Index and Abdominal Obesity in Mexican Children. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2432957. [PMID: 28428959 PMCID: PMC5385910 DOI: 10.1155/2017/2432957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 01/26/2017] [Accepted: 02/06/2017] [Indexed: 01/11/2023]
Abstract
Introduction. Increase in body weight is a gradual process that usually begins in childhood and in adolescence as a result of multiple interactions among environmental and genetic factors. This study aimed to analyze the relationship between copy number variants (CNVs) in five genes and four intergenic regions with obesity in Mexican children. Methods. We studied 1423 children aged 6–12 years. Anthropometric measurements and blood levels of biochemical parameters were obtained. Identification of CNVs was performed by real-time PCR. The effect of CNVs on obesity or body composition was assessed using regression models adjusted for age, gender, and family history of obesity. Results. Gains in copy numbers of LEPR and NEGR1 were associated with decreased body mass index (BMI), waist circumference (WC), and risk of abdominal obesity, whereas gain in ARHGEF4 and CPXCR1 and the intergenic regions 12q15c, 15q21.1a, and 22q11.21d and losses in INS were associated with increased BMI and WC. Conclusion. Our results indicate a possible contribution of CNVs in LEPR, NEGR1, ARHGEF4, and CPXCR1 and the intergenic regions 12q15c, 15q21.1a, and 22q11.21d to the development of obesity, particularly abdominal obesity in Mexican children.
Collapse
|
23
|
Dennis MY, Eichler EE. Human adaptation and evolution by segmental duplication. Curr Opin Genet Dev 2016; 41:44-52. [PMID: 27584858 DOI: 10.1016/j.gde.2016.08.001] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/02/2016] [Accepted: 08/02/2016] [Indexed: 12/29/2022]
Abstract
Duplications are the primary force by which new gene functions arise and provide a substrate for large-scale structural variation. Analysis of thousands of genomes shows that humans and great apes have more genetic differences in content and structure over recent segmental duplications than any other euchromatic region. Novel human-specific duplicated genes, ARHGAP11B and SRGAP2C, have recently been described with a potential role in neocortical expansion and increased neuronal spine density. Large segmental duplications and the structural variants they promote are also frequently stratified between human populations with a subset being subjected to positive selection. The impact of recent duplications on human evolution and adaptation is only beginning to be realized as new technologies enhance their discovery and accurate genotyping.
Collapse
Affiliation(s)
- Megan Y Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, 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.
| |
Collapse
|
24
|
Chen J, Calhoun VD, Perrone-Bizzozero NI, Pearlson GD, Sui J, Du Y, Liu J. A pilot study on commonality and specificity of copy number variants in schizophrenia and bipolar disorder. Transl Psychiatry 2016; 6:e824. [PMID: 27244233 PMCID: PMC5545651 DOI: 10.1038/tp.2016.96] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia (SZ) and bipolar disorder (BD) are known to share genetic risks. In this work, we conducted whole-genome scanning to identify cross-disorder and disorder-specific copy number variants (CNVs) for these two disorders. The Database of Genotypes and Phenotypes (dbGaP) data were used for discovery, deriving from 2416 SZ patients, 592 BD patients and 2393 controls of European Ancestry, as well as 998 SZ patients, 121 BD patients and 822 controls of African Ancestry. PennCNV and Birdsuite detected high-confidence CNVs that were aggregated into CNV regions (CNVRs) and compared with the database of genomic variants for confirmation. Then, large (size⩾500 kb) and small common CNVRs (size <500 kb, frequency⩾1%) were examined for their associations with SZ and BD. Particularly for the European Ancestry samples, the dbGaP findings were further evaluated in the Wellcome Trust Case Control Consortium (WTCCC) data set for replication. Previously implicated variants (1q21.1, 15q13.3, 16p11.2 and 22q11.21) were replicated. Some cross-disorder variants were noted to differentially affect SZ and BD, including CNVRs in chromosomal regions encoding immunoglobulins and T-cell receptors that were associated more with SZ, and the 10q11.21 small CNVR (GPRIN2) associated more with BD. Disorder-specific CNVRs were also found. The 22q11.21 CNVR (COMT) and small CNVRs in 11p15.4 (TRIM5) and 15q13.2 (ARHGAP11B and FAN1) appeared to be SZ-specific. CNVRs in 17q21.2, 9p21.3 and 9q21.13 might be BD-specific. Overall, our primary findings in individual disorders largely echo previous reports. In addition, the comparison between SZ and BD reveals both specific and common risk CNVs. Particularly for the latter, differential involvement is noted, motivating further comparative studies and quantitative models.
Collapse
Affiliation(s)
- J Chen
- The Mind Research Network, Albuquerque, NM, USA
| | - V D Calhoun
- The Mind Research Network, Albuquerque, NM, USA
- Department of Electrical Engineering, University of New Mexico, Albuquerque, NM, USA
| | - N I Perrone-Bizzozero
- Departments of Neurosciences and Psychiatry, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - G D Pearlson
- Olin Neuropsychiatry Research Center, Institute of Living, Hartford, CT, USA
- Departments of Psychiatry and Neurobiology, Yale University, New Haven, CT, USA
| | - J Sui
- The Mind Research Network, Albuquerque, NM, USA
- Brainnetome Center and National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Y Du
- The Mind Research Network, Albuquerque, NM, USA
| | - J Liu
- The Mind Research Network, Albuquerque, NM, USA
- Department of Electrical Engineering, University of New Mexico, Albuquerque, NM, USA
| |
Collapse
|
25
|
Priest JR, Osoegawa K, Mohammed N, Nanda V, Kundu R, Schultz K, Lammer EJ, Girirajan S, Scheetz T, Waggott D, Haddad F, Reddy S, Bernstein D, Burns T, Steimle JD, Yang XH, Moskowitz IP, Hurles M, Lifton RP, Nickerson D, Bamshad M, Eichler EE, Mital S, Sheffield V, Quertermous T, Gelb BD, Portman M, Ashley EA. De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects. PLoS Genet 2016; 12:e1005963. [PMID: 27058611 PMCID: PMC4825975 DOI: 10.1371/journal.pgen.1005963] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
Congenital heart disease (CHD) has a complex genetic etiology, and recent studies suggest that high penetrance de novo mutations may account for only a small fraction of disease. In a multi-institutional cohort surveyed by exome sequencing, combining analysis of 987 individuals (discovery cohort of 59 affected trios and 59 control trios, and a replication cohort of 100 affected singletons and 533 unaffected singletons) we observe variation at novel and known loci related to a specific cardiac malformation the atrioventricular septal defect (AVSD). In a primary analysis, by combining developmental coexpression networks with inheritance modeling, we identify a de novo mutation in the DNA binding domain of NR1D2 (p.R175W). We show that p.R175W changes the transcriptional activity of Nr1d2 using an in vitro transactivation model in HUVEC cells. Finally, we demonstrate previously unrecognized cardiovascular malformations in the Nr1d2tm1-Dgen knockout mouse. In secondary analyses we map genetic variation to protein-interaction networks suggesting a role for two collagen genes in AVSD, which we corroborate by burden testing in a second replication cohort of 100 AVSDs and 533 controls (p = 8.37e-08). Finally, we apply a rare-disease inheritance model to identify variation in genes previously associated with CHD (ZFPM2, NSD1, NOTCH1, VCAN, and MYH6), cardiac malformations in mouse models (ADAM17, CHRD, IFT140, PTPRJ, RYR1 and ATE1), and hypomorphic alleles of genes causing syndromic CHD (EHMT1, SRCAP, BBS2, NOTCH2, and KMT2D) in 14 of 59 trios, greatly exceeding variation in control trios without CHD (p = 9.60e-06). In total, 32% of trios carried at least one putatively disease-associated variant across 19 loci,suggesting that inherited and de novo variation across a heterogeneous group of loci may contribute to disease risk.
Collapse
Affiliation(s)
- James R. Priest
- Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Kazutoyo Osoegawa
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Nebil Mohammed
- University of California San Francisco Benioff Children’s Hospital Oakland, University of California San Francisco, San Francisco, California, United States of America
| | - Vivek Nanda
- Department of Vascular Surgery, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Ramendra Kundu
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Kathleen Schultz
- University of California San Francisco Benioff Children’s Hospital Oakland, University of California San Francisco, San Francisco, California, United States of America
| | - Edward J. Lammer
- University of California San Francisco Benioff Children’s Hospital Oakland, University of California San Francisco, San Francisco, California, United States of America
| | - Santhosh Girirajan
- Departments of Biochemistry, Molecular Biology, and Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Todd Scheetz
- College of Engineering, University of Iowa, Iowa City, Iowa, United States of America
| | - Daryl Waggott
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Francois Haddad
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Sushma Reddy
- Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Daniel Bernstein
- Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Trudy Burns
- College of Public Health, University of Iowa, Iowa City, Iowa, United States of America
| | - Jeffrey D. Steimle
- Department of Pathology, University of Chicago, Chicago, Illinois, United States of America
| | - Xinan H. Yang
- Department of Pathology, University of Chicago, Chicago, Illinois, United States of America
| | - Ivan P. Moskowitz
- Department of Pathology, University of Chicago, Chicago, Illinois, United States of America
| | - Matthew Hurles
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Richard P. Lifton
- Department of Genetics, Yale University, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Debbie Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Michael Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Evan E. Eichler
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Seema Mital
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Val Sheffield
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Division of Medical Genetics, University of Iowa Carver College of Medicine, Iowa City, Iowa, United States of America
| | - Thomas Quertermous
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mt. Sinai, New York, New York, United States of America
| | - Michael Portman
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Euan A. Ashley
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| |
Collapse
|
26
|
Xu L, Hou Y, Bickhart DM, Zhou Y, Hay EHA, Song J, Sonstegard TS, Van Tassell CP, Liu GE. Population-genetic properties of differentiated copy number variations in cattle. Sci Rep 2016; 6:23161. [PMID: 27005566 PMCID: PMC4804293 DOI: 10.1038/srep23161] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 02/25/2016] [Indexed: 01/24/2023] Open
Abstract
While single nucleotide polymorphism (SNP) is typically the variant of choice for population genetics, copy number variation (CNV) which comprises insertion, deletion and duplication of genomic sequence, is an informative type of genetic variation. CNVs have been shown to be both common in mammals and important for understanding the relationship between genotype and phenotype. However, CNV differentiation, selection and its population genetic properties are not well understood across diverse populations. We performed a population genetics survey based on CNVs derived from the BovineHD SNP array data of eight distinct cattle breeds. We generated high resolution results that show geographical patterns of variations and genome-wide admixture proportions within and among breeds. Similar to the previous SNP-based studies, our CNV-based results displayed a strong correlation of population structure and geographical location. By conducting three pairwise comparisons among European taurine, African taurine, and indicine groups, we further identified 78 unique CNV regions that were highly differentiated, some of which might be due to selection. These CNV regions overlapped with genes involved in traits related to parasite resistance, immunity response, body size, fertility, and milk production. Our results characterize CNV diversity among cattle populations and provide a list of lineage-differentiated CNVs.
Collapse
Affiliation(s)
- Lingyang Xu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA.,Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
| | - Yali Hou
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Yang Zhou
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA.,College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi, 712100, China
| | - El Hamidi Abdel Hay
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| |
Collapse
|
27
|
Alves JM, Lima AC, Pais IA, Amir N, Celestino R, Piras G, Monne M, Comas D, Heutink P, Chikhi L, Amorim A, Lopes AM. Reassessing the Evolutionary History of the 17q21 Inversion Polymorphism. Genome Biol Evol 2015; 7:3239-48. [PMID: 26560338 PMCID: PMC4700947 DOI: 10.1093/gbe/evv214] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A polymorphic inversion that lies on chromosome 17q21 comprises two major haplotype families (H1 and H2) that not only differ in orientation but also in copy-number. Although the processes driving the spread of the inversion-associated lineage (H2) in humans remain unclear, a selective advantage has been proposed for one of its subtypes. Here, we genotyped a large panel of individuals from previously overlooked populations using a custom array with a unique panel of H2-specific single nucleotide polymorphisms and found a patchy distribution of H2 haplotypes in Africa, with North Africans displaying a higher frequency of inverted subtypes, when compared with Sub-Saharan groups. Interestingly, North African H2s were found to be closer to "non-African" chromosomes further supporting that these populations may have diverged more recently from groups outside Africa. Our results uncovered higher diversity within the H2 family than previously described, weakening the hypothesis of a strong selective sweep on all inverted chromosomes and suggesting a rather complex evolutionary history at this locus.
Collapse
Affiliation(s)
- Joao M Alves
- Doctoral Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Portugal Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal Instituto de Patologia e Imunologia Molecular da Universidade do Porto-IPATIMUP, Portugal Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal Present address: Department of Biochemistry, Genetics and Immunology and Institute of Biomedical Research of Vigo (IBIV), University of Vigo, Vigo, Spain
| | - Ana C Lima
- Doctoral Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Portugal Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal Instituto de Patologia e Imunologia Molecular da Universidade do Porto-IPATIMUP, Portugal Department of Genetics, Washington University School of Medicine, St. Louis
| | - Isa A Pais
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
| | - Nadir Amir
- Laboratoire de Biochimie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université Abedrrahmane Mira de Bejaia, Algerie
| | - Ricardo Celestino
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal Instituto de Patologia e Imunologia Molecular da Universidade do Porto-IPATIMUP, Portugal School of Allied Health Technologies, Polytechnic of Porto, Porto, Portugal
| | - Giovanna Piras
- Department of Hematology, Centro di Diagnostica Biomoleculare et Citogenetica Emato-Oncologica, San Francesco Hospital-ASL, Nuoro, Italy
| | - Maria Monne
- Department of Hematology, Centro di Diagnostica Biomoleculare et Citogenetica Emato-Oncologica, San Francesco Hospital-ASL, Nuoro, Italy
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal CNRS (Centre National de la Recherche Scientifique), Université Paul Sabatier, École Nationale de Formation Agronomique, Unité Mixte de Recherche 5174 EDB (Laboratoire Évolution & Diversit Biologique), Toulouse, France
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal Instituto de Patologia e Imunologia Molecular da Universidade do Porto-IPATIMUP, Portugal Faculdade de Ciências da Universidade do Porto, Portugal
| | - Alexandra M Lopes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal Instituto de Patologia e Imunologia Molecular da Universidade do Porto-IPATIMUP, Portugal
| |
Collapse
|
28
|
Bachère E, Rosa RD, Schmitt P, Poirier AC, Merou N, Charrière GM, Destoumieux-Garzón D. The new insights into the oyster antimicrobial defense: Cellular, molecular and genetic view. FISH & SHELLFISH IMMUNOLOGY 2015; 46:50-64. [PMID: 25753917 DOI: 10.1016/j.fsi.2015.02.040] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/24/2015] [Accepted: 02/26/2015] [Indexed: 06/04/2023]
Abstract
Oysters are sessile filter feeders that live in close association with abundant and diverse communities of microorganisms that form the oyster microbiota. In such an association, cellular and molecular mechanisms have evolved to maintain oyster homeostasis upon stressful conditions including infection and changing environments. We give here cellular and molecular insights into the Crassostrea gigas antimicrobial defense system with focus on antimicrobial peptides and proteins (AMPs). This review highlights the central role of the hemocytes in the modulation and control of oyster antimicrobial response. As vehicles for AMPs and other antimicrobial effectors, including reactive oxygen species (ROS), and together with epithelia, hemocytes provide the oyster with local defense reactions instead of systemic humoral ones. These reactions are largely based on phagocytosis but also, as recently described, on the extracellular release of antimicrobial histones (ETosis) which is triggered by ROS. Thus, ROS can signal danger and activate cellular responses in the oyster. From the current literature, AMP production/release could serve similar functions. We provide also new lights on the oyster genetic background that underlies a great diversity of AMP sequences but also an extraordinary individual polymorphism of AMP gene expression. We discuss here how this polymorphism could generate new immune functions, new pathogen resistances or support individual adaptation to environmental stresses.
Collapse
Affiliation(s)
- Evelyne Bachère
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France.
| | - Rafael Diego Rosa
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France; Laboratory of Immunology Applied to Aquaculture, Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina, 88040-900 Florianópolis, SC, Brazil
| | - Paulina Schmitt
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France; Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad, Católica de Valparaíso, Avenida Universidad 330, 2373223 Valparaíso, Chile
| | - Aurore C Poirier
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France
| | - Nicolas Merou
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France
| | - Guillaume M Charrière
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France
| | - Delphine Destoumieux-Garzón
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France
| |
Collapse
|
29
|
Gennarino VA, Alcott CE, Chen CA, Chaudhury A, Gillentine MA, Rosenfeld JA, Parikh S, Wheless JW, Roeder ER, Horovitz DDG, Roney EK, Smith JL, Cheung SW, Li W, Neilson JR, Schaaf CP, Zoghbi HY. NUDT21-spanning CNVs lead to neuropsychiatric disease and altered MeCP2 abundance via alternative polyadenylation. eLife 2015; 4. [PMID: 26312503 PMCID: PMC4586391 DOI: 10.7554/elife.10782] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 08/26/2015] [Indexed: 01/27/2023] Open
Abstract
The brain is sensitive to the dose of MeCP2 such that small fluctuations in protein quantity lead to neuropsychiatric disease. Despite the importance of MeCP2 levels to brain function, little is known about its regulation. In this study, we report eleven individuals with neuropsychiatric disease and copy-number variations spanning NUDT21, which encodes a subunit of pre-mRNA cleavage factor Im. Investigations of MECP2 mRNA and protein abundance in patient-derived lymphoblastoid cells from one NUDT21 deletion and three duplication cases show that NUDT21 regulates MeCP2 protein quantity. Elevated NUDT21 increases usage of the distal polyadenylation site in the MECP2 3′ UTR, resulting in an enrichment of inefficiently translated long mRNA isoforms. Furthermore, normalization of NUDT21 via siRNA-mediated knockdown in duplication patient lymphoblasts restores MeCP2 to normal levels. Ultimately, we identify NUDT21 as a novel candidate for intellectual disability and neuropsychiatric disease, and elucidate a mechanism of pathogenesis by MeCP2 dysregulation via altered alternative polyadenylation. DOI:http://dx.doi.org/10.7554/eLife.10782.001 The X-chromosome carries a number of genes that are involved in a child's intellectual development. One of these genes encodes a protein called MeCP2, which is important for brain function after birth. Mutations in the MECP2 gene cause a disorder known as Rett syndrome. At around 18 months of age, affected children begin to lose the cognitive and motor skills that they had previously acquired. Individuals with extra copies of this gene also show cognitive impairments. For both diseases, individuals with levels of the MeCP2 protein that are the most different from those found in healthy individuals also show the most severe symptoms. To produce the protein that is encoded by a particular gene, enzymes inside the cell must first make a copy of that gene using a molecule called messenger ribonucleic acid (or mRNA). This mRNA is then used as a template to assemble the protein itself. In the case of MECP2, two different mRNA templates are produced: a long version and a short version. A gene called NUDT21 makes a protein that regulates whether the long or short version of MECP2 mRNA is made. Gennarino, Alcott et al. have now discovered that people with too many, or too few, copies of the NUDT21 gene have intellectual disabilities and altered levels of MeCP2 protein. Specifically, individuals with extra copies of NUDT21—and thus higher levels of the corresponding protein—produce more of the long MECP2 mRNA. The production of proteins from this long mRNA is less efficient than from the short mRNA; therefore, these individuals have lower levels of MeCP2 protein. The opposite is true for individuals who lack a copy of the NUDT21 gene. To confirm these data, Gennarino, Alcott et al. grew cells in the laboratory from patients with extra copies of the NUDT21 gene and found that reducing the production of its protein returned the levels of the MeCP2 protein back to normal. These findings show that alterations in the NUDT21 gene cause changes in the level of MeCP2 protein in cells and leads to neuropsychiatric diseases. DOI:http://dx.doi.org/10.7554/eLife.10782.002
Collapse
Affiliation(s)
- Vincenzo A Gennarino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Callison E Alcott
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States
| | - Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Arindam Chaudhury
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, United States
| | - Madelyn A Gillentine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Sumit Parikh
- Center for Child Neurology, Cleveland Clinic Children's Hospital, Cleveland, United States
| | - James W Wheless
- Department of Pediatric Neurology, Neuroscience Institute and Tuberous Sclerosis Clinic, Le Bonheur Children's Hospital, University of Tennessee Health Science Center, Memphis, United States
| | - Elizabeth R Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Dafne D G Horovitz
- Depto de Genetica Medica, Instituto Nacional de Saude da Mulher, da Criança e do Adolescente Fernandes Figueira, Rio de Janeiro, Brazil
| | - Erin K Roney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Sau W Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Wei Li
- Division of Biostatistics, Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, United States
| | - Joel R Neilson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, United States
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Huda Y Zoghbi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| |
Collapse
|
30
|
Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, Coe BP, Baker C, Nordenfelt S, Bamshad M, Jorde LB, Posukh OL, Sahakyan H, Watkins WS, Yepiskoposyan L, Abdullah MS, Bravi CM, Capelli C, Hervig T, Wee JTS, Tyler-Smith C, van Driem G, Romero IG, Jha AR, Karachanak-Yankova S, Toncheva D, Comas D, Henn B, Kivisild T, Ruiz-Linares A, Sajantila A, Metspalu E, Parik J, Villems R, Starikovskaya EB, Ayodo G, Beall CM, Di Rienzo A, Hammer MF, Khusainova R, Khusnutdinova E, Klitz W, Winkler C, Labuda D, Metspalu M, Tishkoff SA, Dryomov S, Sukernik R, Patterson N, Reich D, Eichler EE. Global diversity, population stratification, and selection of human copy-number variation. Science 2015; 349:aab3761. [PMID: 26249230 DOI: 10.1126/science.aab3761] [Citation(s) in RCA: 255] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 07/29/2015] [Indexed: 12/14/2022]
Abstract
In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.
Collapse
Affiliation(s)
- Peter H Sudmant
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Swapan Mallick
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Niklas Krumm
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Bradley P Coe
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Susanne Nordenfelt
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98119, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Olga L Posukh
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Novosibirsk State University, Novosibirsk 630090, Russia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia
| | - W Scott Watkins
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia
| | - M Syafiq Abdullah
- Raja Isteri Pengiran Anak Saleha (RIPAS) Hospital, Bandar Seri Begawan, Brunei Darussalam
| | - Claudio M Bravi
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), Centro Científico y Tecnológico-Consejo Nacional de Investigaciones Científicas y Técnicas (CCT-CONICET) and Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), La Plata B1906APO, Argentina
| | | | - Tor Hervig
- Department of Clinical Science, University of Bergen, Bergen 5021, Norway
| | | | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - George van Driem
- Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland
| | | | - Aashish R Jha
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Sena Karachanak-Yankova
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - David Comas
- Institut de Biologia Evolutiva [Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra (CSIC-UPF)], Departament de Ciències Experimentals i de la Salut, UPF, Barcelona 08003, Spain
| | - Brenna Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Toomas Kivisild
- Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London, WC1E 6BT, UK
| | - Antti Sajantila
- University of Helsinki, Department of Forensic Medicine, Helsinki 00014, Finland
| | - Ene Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. University of Tartu, Department of Evolutionary Biology, Tartu 5101, Estonia
| | - Jüri Parik
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia
| | - Richard Villems
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia
| | - Elena B Starikovskaya
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - George Ayodo
- Center for Global Health and Child Development, Kisumu 40100, Kenya
| | - Cynthia M Beall
- Department of Anthropology, Case Western Reserve University, Cleveland, OH 44106-7125, USA
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Michael F Hammer
- Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
| | - Rita Khusainova
- Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia
| | - William Klitz
- Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Cheryl Winkler
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Incorporated, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Damian Labuda
- Centre Hospitalier Universitaire (CHU) Sainte-Justine, Département de Pédiatrie, Université de Montréal, QC H3T 1C5, Canada
| | - Mait Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia
| | - Sarah A Tishkoff
- Departments of Biology and Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stanislav Dryomov
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Department of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Rem Sukernik
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Altai State University, Barnaul 656000, Russia
| | - Nick Patterson
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - David Reich
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, 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.
| |
Collapse
|
31
|
Chen MJ, Wei SY, Yang WS, Wu TT, Li HY, Ho HN, Yang YS, Chen PL. Concurrent exome-targeted next-generation sequencing and single nucleotide polymorphism array to identify the causative genetic aberrations of isolated Mayer-Rokitansky-Küster-Hauser syndrome. Hum Reprod 2015; 30:1732-42. [PMID: 25924657 DOI: 10.1093/humrep/dev095] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/09/2015] [Indexed: 12/30/2022] Open
Abstract
STUDY QUESTION Can the use of whole-exome sequencing (WES) together with single nucleotide polymorphism (SNP) array help to identify novel causative genes of isolated Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome? SUMMARY ANSWER OR4M2 (olfactory receptor, family 4, subfamily M, member 2) and PDE11A (phosphodiesterase 11A) gene loss-of-function variants as well as deletions at 15q11.2, 19q13.31, 1p36.21, and 1q44 were identified as possible commonly altered regions in patients with type 1 MRKH. WHAT IS KNOWN ALREADY The isolated form of Müllerian aplasia is the most common subtype of MRKH syndrome, which invariably leads to difficulties producing offspring in affected women. However, there is little information currently available to allow for genetic testing and counseling to be performed for those affected by this syndrome. STUDY DESIGN, SIZE AND DURATION This was a case-series genetic study. A total of seven consecutive unrelated women with type 1 MRKH were enrolled. The enrollment and experimental procedures were performed over a 2-year period. PARTICIPANTS/MATERIALS, SETTING, METHODS Whole exome-targeted next-generation sequencing and SNP array (Affymetrix Genome-Wide Human SNP Array 6.0) were performed on the first five unrelated women with type 1 MRKH syndrome. The data were combined, and the '3-hit principal' was applied on a genome-wide scale to search for the common causative genes. Quantitative PCR (qPCR) and Sanger sequencing were used to validate the identified genomic copy number losses and variants. Replication tests using direct Sanger sequencing and qPCR were performed on the remaining two women with type 1 MRKH syndrome to support the credibility of the potential candidate genes and deletions. MAIN RESULTS AND THE ROLE OF CHANCE A total of 3443 damaging variants based on WES were shown to intersect with 1336 copy number variations (deletions) derived from the SNP array. Four highly recurrent deletions at 15q11.2 (80%), 19q13.31 (40%), 1p36.21 (40%) and 1q44 (40%) were identified in the first five women with type 1 MRKH syndrome and were considered to be novel candidate aberrations. A previously reported 1q21.1 deletion was also recurrent in two of the first five women with type 1 MRKH syndrome. The 1q44 and 19q13.31 deletions were present in at least one of the two additional patients. Damaging variants were detected in HNRNPCL1 (heterogeneous nuclear ribonucleoprotein C-like 1), OR2T2 (olfactory receptor, family 2, subfamily T, member 2), OR4M2, ZNF816 (zinc finger protein 816), and PDE11A in several of the initial five patients. Among these, the damaging variants of OR4M2 (located at 15q11.2) and PDE11A were found in at least one of the two additional patients with type 1 MRKH. LIMITATIONS, REASONS FOR CAUTION In this study, we only searched for the deletions or damaging variants causing loss-of-function of genes in at least three of the initial five patients (3-hit criteria). Therefore, the study was designed to only detect common causative genes. Genomic duplications and/or rare individual mutations that may have also contributed to MRKH syndrome were not investigated. WIDER IMPLICATIONS OF THE FINDINGS This study demonstrated the feasibility of the use of combined data from both WES and SNP arrays for the identification of possible common causative genetic aberrations in patients with type 1 MRKH syndrome on a genome-wide scale. Further validation of our found causative genes is required before applying on genetic testing and counseling. STUDY FUNDING/COMPETING INTERESTS The study was supported by grants from the National Science Council of Taiwan (NSC98-2314-B002-105-MY3 and NSC 100-2314-B002-027-MY3). The funding sources had no involvement in the design or analysis of the study. The authors have no competing interests to declare. TRIAL REGISTRATION NUMBER Not applicable.
Collapse
Affiliation(s)
- Mei-Jou Chen
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Shin-Yi Wei
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Wei-Shiung Yang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Tsai-Tzu Wu
- Graduate Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Huei-Ying Li
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Hong-Nerng Ho
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Yu-Shih Yang
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Pei-Lung Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei 100, Taiwan Department of Medical Genetics, National Taiwan University Hospital, Taipei 100, Taiwan Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| |
Collapse
|
32
|
Zarrei M, MacDonald JR, Merico D, Scherer SW. A copy number variation map of the human genome. Nat Rev Genet 2015; 16:172-83. [DOI: 10.1038/nrg3871] [Citation(s) in RCA: 565] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
33
|
Abstract
PURPOSE OF REVIEW Recent studies clearly demonstrate that copy number variations (CNVs) are widespread in our genome and play an important role in human genetic variation, accounting for both human population diversity and human genetic disease. This review will discuss the most current knowledge regarding our understanding of the biology of CNVs in relation to human genetic disease. RECENT FINDINGS CNVs associated with human genetic disease can be either recurrent, with a common size and breakpoint clustering, or nonrecurrent, with different sizes and variable breakpoints. Two types of recurrent CNVs have been distinguished, including the syndromic forms in which the phenotypic features are relatively consistent, and those in which the same recurrent CNV can be associated with a diverse set of diagnoses. Recently, the 'Two-hit model' was used to explain the phenotypic variability associated with the latter group of recurrent CNVs. Nonrecurrent CNVs, on the contrary, occur at a relatively lower frequency at the individual locus level but collectively they are as common as recurrent CNVs. Finally, the study of CNV burden in different diseases demonstrated a clear trend of an increasing CNV burden in diseases with more severe phenotypes. SUMMARY In spite of the advances in the study of the CNV landscape associated with human genetic disease, there still remain many unexplored questions especially regarding the role of CNVs in the pathogenesis of complex human genetic diseases.
Collapse
|
34
|
Yi G, Qu L, Liu J, Yan Y, Xu G, Yang N. Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing. BMC Genomics 2014; 15:962. [PMID: 25378104 PMCID: PMC4239369 DOI: 10.1186/1471-2164-15-962] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 10/13/2014] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we performed a genome-wide CNV analysis in 12 diversified chicken genomes based on whole genome sequencing. RESULTS A total of 8,840 CNV regions (CNVRs) covering 98.2 Mb and representing 9.4% of the chicken genome were identified, ranging in size from 1.1 to 268.8 kb with an average of 11.1 kb. Sequencing-based predictions were confirmed at a high validation rate by two independent approaches, including array comparative genomic hybridization (aCGH) and quantitative PCR (qPCR). The Pearson's correlation coefficients between sequencing and aCGH results ranged from 0.435 to 0.755, and qPCR experiments revealed a positive validation rate of 91.71% and a false negative rate of 22.43%. In total, 2,214 (25.0%) predicted CNVRs span 2,216 (36.4%) RefSeq genes associated with specific biological functions. Besides two previously reported copy number variable genes EDN3 and PRLR, we also found some promising genes with potential in phenotypic variation. Two genes, FZD6 and LIMS1, related to disease susceptibility/resistance are covered by CNVRs. The highly duplicated SOCS2 may lead to higher bone mineral density. Entire or partial duplication of some genes like POPDC3 may have great economic importance in poultry breeding. CONCLUSIONS Our results based on extensive genetic diversity provide a more refined chicken CNV map and genome-wide gene copy number estimates, and warrant future CNV association studies for important traits in chickens.
Collapse
Affiliation(s)
| | | | | | | | | | - Ning Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
| |
Collapse
|
35
|
McCole RB, Fonseka CY, Koren A, Wu CT. Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells. PLoS Genet 2014; 10:e1004646. [PMID: 25340765 PMCID: PMC4207606 DOI: 10.1371/journal.pgen.1004646] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 08/04/2014] [Indexed: 12/17/2022] Open
Abstract
Ultraconserved elements (UCEs) are strongly depleted from segmental duplications and copy number variations (CNVs) in the human genome, suggesting that deletion or duplication of a UCE can be deleterious to the mammalian cell. Here we address the process by which CNVs become depleted of UCEs. We begin by showing that depletion for UCEs characterizes the most recent large-scale human CNV datasets and then find that even newly formed de novo CNVs, which have passed through meiosis at most once, are significantly depleted for UCEs. In striking contrast, CNVs arising specifically in cancer cells are, as a rule, not depleted for UCEs and can even become significantly enriched. This observation raises the possibility that CNVs that arise somatically and are relatively newly formed are less likely to have established a CNV profile that is depleted for UCEs. Alternatively, lack of depletion for UCEs from cancer CNVs may reflect the diseased state. In support of this latter explanation, somatic CNVs that are not associated with disease are depleted for UCEs. Finally, we show that it is possible to observe the CNVs of induced pluripotent stem (iPS) cells become depleted of UCEs over time, suggesting that depletion may be established through selection against UCE-disrupting CNVs without the requirement for meiotic divisions.
Collapse
Affiliation(s)
- Ruth B. McCole
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chamith Y. Fonseka
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Biological and Biomedical Sciences PhD program, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Amnon Koren
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - C.-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| |
Collapse
|
36
|
Campbell CD, Mohajeri K, Malig M, Hormozdiari F, Nelson B, Du G, Patterson KM, Eng C, Torgerson DG, Hu D, Herman C, Chong JX, Ko A, O'Roak BJ, Krumm N, Vives L, Lee C, Roth LA, Rodriguez-Cintron W, Rodriguez-Santana J, Brigino-Buenaventura E, Davis A, Meade K, LeNoir MA, Thyne S, Jackson DJ, Gern JE, Lemanske RF, Shendure J, Abney M, Burchard EG, Ober C, Eichler EE. Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma. PLoS One 2014; 9:e104396. [PMID: 25116239 PMCID: PMC4130548 DOI: 10.1371/journal.pone.0104396] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/12/2014] [Indexed: 12/30/2022] Open
Abstract
Asthma is a complex genetic disease caused by a combination of genetic and environmental risk factors. We sought to test classes of genetic variants largely missed by genome-wide association studies (GWAS), including copy number variants (CNVs) and low-frequency variants, by performing whole-genome sequencing (WGS) on 16 individuals from asthma-enriched and asthma-depleted families. The samples were obtained from an extended 13-generation Hutterite pedigree with reduced genetic heterogeneity due to a small founding gene pool and reduced environmental heterogeneity as a result of a communal lifestyle. We sequenced each individual to an average depth of 13-fold, generated a comprehensive catalog of genetic variants, and tested the most severe mutations for association with asthma. We identified and validated 1960 CNVs, 19 nonsense or splice-site single nucleotide variants (SNVs), and 18 insertions or deletions that were out of frame. As follow-up, we performed targeted sequencing of 16 genes in 837 cases and 540 controls of Puerto Rican ancestry and found that controls carry a significantly higher burden of mutations in IL27RA (2.0% of controls; 0.23% of cases; nominal p = 0.004; Bonferroni p = 0.21). We also genotyped 593 CNVs in 1199 Hutterite individuals. We identified a nominally significant association (p = 0.03; Odds ratio (OR) = 3.13) between a 6 kbp deletion in an intron of NEDD4L and increased risk of asthma. We genotyped this deletion in an additional 4787 non-Hutterite individuals (nominal p = 0.056; OR = 1.69). NEDD4L is expressed in bronchial epithelial cells, and conditional knockout of this gene in the lung in mice leads to severe inflammation and mucus accumulation. Our study represents one of the early instances of applying WGS to complex disease with a large environmental component and demonstrates how WGS can identify risk variants, including CNVs and low-frequency variants, largely untested in GWAS.
Collapse
Affiliation(s)
- Catarina D. Campbell
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kiana Mohajeri
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Maika Malig
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Fereydoun Hormozdiari
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Benjamin Nelson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Gaixin Du
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Kristen M. Patterson
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Dara G. Torgerson
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Catherine Herman
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jessica X. Chong
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Arthur Ko
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Brian J. O'Roak
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Niklas Krumm
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Laura Vives
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Lindsey A. Roth
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | | | | | - Emerita Brigino-Buenaventura
- Department of Allergy & Immunology, Kaiser Permanente-Vallejo Medical Center, Vallejo, California, United States of America
| | - Adam Davis
- Children's Hospital and Research Center Oakland, Oakland, California, United States of America
| | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, California, United States of America
| | | | - Shannon Thyne
- San Francisco General Hospital, San Francisco, California, and the Department of Pediatrics, University of California San Francisco, San Francisco, California, United States of America
| | - Daniel J. Jackson
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Robert F. Lemanske
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Mark Abney
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Esteban G. Burchard
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, 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
| |
Collapse
|
37
|
Nguyen HT, Merriman TR, Black MA. The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data. Front Genet 2014; 5:248. [PMID: 25136349 PMCID: PMC4117933 DOI: 10.3389/fgene.2014.00248] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/09/2014] [Indexed: 11/15/2022] Open
Abstract
Recent advances in high-throughout sequencing technologies have made it possible to accurately assign copy number (CN) at CN variable loci. However, current analytic methods often perform poorly in regions in which complex CN variation is observed. Here we report the development of a read depth-based approach, CNVrd2, for investigation of CN variation using high-throughput sequencing data. This methodology was developed using data from the 1000 Genomes Project from the CCL3L1 locus, and tested using data from the DEFB103A locus. In both cases, samples were selected for which paralog ratio test data were also available for comparison. The CNVrd2 method first uses observed read-count ratios to refine segmentation results in one population. Then a linear regression model is applied to adjust the results across multiple populations, in combination with a Bayesian normal mixture model to cluster segmentation scores into groups for individual CN counts. The performance of CNVrd2 was compared to that of two other read depth-based methods (CNVnator, cn.mops) at the CCL3L1 and DEFB103A loci. The highest concordance with the paralog ratio test method was observed for CNVrd2 (77.8/90.4% for CNVrd2, 36.7/4.8% for cn.mops and 7.2/1% for CNVnator at CCL3L1 and DEF103A). CNVrd2 is available as an R package as part of the Bioconductor project: http://www.bioconductor.org/packages/release/bioc/html/CNVrd2.html.
Collapse
Affiliation(s)
- Hoang T Nguyen
- Department of Biochemistry, University of Otago Dunedin, New Zealand ; Department of Mathematics and Statistics, University of Otago Dunedin, New Zealand ; Department of Biochemistry, Virtual Institute of Statistical Genetics, University of Otago Dunedin, New Zealand
| | - Tony R Merriman
- Department of Biochemistry, University of Otago Dunedin, New Zealand ; Department of Biochemistry, Virtual Institute of Statistical Genetics, University of Otago Dunedin, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago Dunedin, New Zealand ; Department of Biochemistry, Virtual Institute of Statistical Genetics, University of Otago Dunedin, New Zealand
| |
Collapse
|
38
|
Tessereau C, Lesecque Y, Monnet N, Buisson M, Barjhoux L, Léoné M, Feng B, Goldgar DE, Sinilnikova OM, Mousset S, Duret L, Mazoyer S. Estimation of the RNU2 macrosatellite mutation rate by BRCA1 mutation tracing. Nucleic Acids Res 2014; 42:9121-30. [PMID: 25034697 PMCID: PMC4132748 DOI: 10.1093/nar/gku639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Large tandem repeat sequences have been poorly investigated as severe technical limitations and their frequent absence from the genome reference hinder their analysis. Extensive allelotyping of this class of variation has not been possible until now and their mutational dynamics are still poorly known. In order to estimate the mutation rate of a macrosatellite, we analysed in detail the RNU2 locus, which displays at least 50 different alleles containing 5-82 copies of a 6.1 kb repeat unit. Mining data from the 1000 Genomes Project allowed us to precisely estimate copy numbers of the RNU2 repeat unit using read depth of coverage. This further revealed significantly different mean values in various recent modern human populations, favoring a scenario of fast evolution of this locus. Its proximity to a disease gene with numerous founder mutations, BRCA1, within the same linkage disequilibrium block, offered the unique opportunity to trace RNU2 arrays over a large timescale. Analysis of the transmission of RNU2 arrays associated with one ‘private’ mutation in an extended kindred and four founder mutations in multiple kindreds gave an estimation by maximum likelihood of 5 × 10−3 mutations per generation, which is close to that of microsatellites.
Collapse
Affiliation(s)
- Chloé Tessereau
- Genetics of Breast Cancer Team, Cancer Research Centre of Lyon, CNRS UMR5286, Inserm U1052, Université Lyon 1, Centre Léon Bérard, Lyon, France Genomic Vision, Bagneux, Paris, France
| | - Yann Lesecque
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, France
| | - Nastasia Monnet
- Genetics of Breast Cancer Team, Cancer Research Centre of Lyon, CNRS UMR5286, Inserm U1052, Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Monique Buisson
- Genetics of Breast Cancer Team, Cancer Research Centre of Lyon, CNRS UMR5286, Inserm U1052, Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Laure Barjhoux
- Genetics of Breast Cancer Team, Cancer Research Centre of Lyon, CNRS UMR5286, Inserm U1052, Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Mélanie Léoné
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | - Bingjian Feng
- Department of Dermatology and Huntsman Cancer Institute University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - David E Goldgar
- Department of Dermatology and Huntsman Cancer Institute University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Olga M Sinilnikova
- Genetics of Breast Cancer Team, Cancer Research Centre of Lyon, CNRS UMR5286, Inserm U1052, Université Lyon 1, Centre Léon Bérard, Lyon, France Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | - Sylvain Mousset
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, France
| | - Laurent Duret
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, France
| | - Sylvie Mazoyer
- Genetics of Breast Cancer Team, Cancer Research Centre of Lyon, CNRS UMR5286, Inserm U1052, Université Lyon 1, Centre Léon Bérard, Lyon, France
| |
Collapse
|
39
|
Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome. Proc Natl Acad Sci U S A 2014; 111:8131-6. [PMID: 24847061 DOI: 10.1073/pnas.1401532111] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Insertions of the human-specific subfamily of LINE-1 (L1) retrotransposon are highly polymorphic across individuals and can critically influence the human transcriptome. We hypothesized that L1 insertions could represent genetic variants determining important human phenotypic traits, and performed an integrated analysis of L1 elements and single nucleotide polymorphisms (SNPs) in several human populations. We found that a large fraction of L1s were in high linkage disequilibrium with their surrounding genomic regions and that they were well tagged by SNPs. However, L1 variants were only partially captured by SNPs on standard SNP arrays, so that their potential phenotypic impact would be frequently missed by SNP array-based genome-wide association studies. We next identified potential phenotypic effects of L1s by looking for signatures of natural selection linked to L1 insertions; significant extended haplotype homozygosity was detected around several L1 insertions. This finding suggests that some of these L1 insertions may have been the target of recent positive selection.
Collapse
|
40
|
Zhao Q, Han MJ, Sun W, Zhang Z. Copy number variations among silkworms. BMC Genomics 2014; 15:251. [PMID: 24684762 PMCID: PMC3997817 DOI: 10.1186/1471-2164-15-251] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 03/25/2014] [Indexed: 11/10/2022] Open
Abstract
Background Copy number variations (CNVs), which are important source for genetic and phenotypic variation, have been shown to be associated with disease as well as important QTLs, especially in domesticated animals. However, little is known about the CNVs in silkworm. Results In this study, we have constructed the first CNVs map based on genome-wide analysis of CNVs in domesticated silkworm. Using next-generation sequencing as well as quantitative PCR (qPCR), we identified ~319 CNVs in total and almost half of them (~ 49%) were distributed on uncharacterized chromosome. The CNVs covered 10.8 Mb, which is about 2.3% of the entire silkworm genome. Furthermore, approximately 61% of CNVs directly overlapped with SDs in silkworm. The genes in CNVs are mainly related to reproduction, immunity, detoxification and signal recognition, which is consistent with the observations in mammals. Conclusions An initial CNVs map for silkworm has been described in this study. And this map provides new information for genetic variations in silkworm. Furthermore, the silkworm CNVs may play important roles in reproduction, immunity, detoxification and signal recognition. This study provided insight into the evolution of the silkworm genome and an invaluable resource for insect genomics research.
Collapse
Affiliation(s)
| | | | | | - Ze Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 400044, China.
| |
Collapse
|
41
|
Polimanti R, Piacentini S, Iorio A, De Angelis F, Kozlov A, Novelletto A, Fuciarelli M. Haplotype differences for copy number variants in the 22q11.23 region among human populations: a pigmentation-based model for selective pressure. Eur J Hum Genet 2014; 23:116-23. [PMID: 24667780 DOI: 10.1038/ejhg.2014.47] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 02/13/2014] [Accepted: 02/19/2014] [Indexed: 12/17/2022] Open
Abstract
Two gene clusters are tightly linked in a narrow region of chromosome 22q11.23: the macrophage migration inhibitory factor (MIF) gene family and the glutathione S-transferase theta class. Within 120 kb in this region, two 30-kb deletions reach high frequencies in human populations. This gives rise to four haplotypic arrangements, which modulate the number of genes in both families. The variable patterns of linkage disequilibrium (LD) between these copy number variants (CNVs) in diverse human populations remain poorly understood. We analyzed 2469 individuals belonging to 27 human populations with different ethnic origins. Then we correlated the genetic variability of 22q11.23 CNVs with environmental variables. We confirmed an increasing strength of LD from Africa to Asia and to Europe. Further, we highlighted strongly significant correlations between the frequency of one of the haplotypes and pigmentation-related variables: skin color (R(2)=0.675, P<0.001), distance from the equator (R(2)=0.454, P<0.001), UVA radiation (R(2)=0.439, P<0.001), and UVB radiation (R(2)=0.313, P=0.002). The fact that all MIF-related genes are retained on this haplotype and the evidences gleaned from experimental systems seem to agree with the role of MIF-related genes in melanogenesis. As such, we propose a model that explains the geographic and ethnic distribution of 22q11.23 CNVs among human populations, assuming that MIF-related gene dosage could be associated with adaptation to low UV radiation.
Collapse
Affiliation(s)
- Renato Polimanti
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Sara Piacentini
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Andrea Iorio
- Clinical Pathophysiology Center, AFaR - 'San Giovanni Calibita' Fatebenefratelli Hospital, Rome, Italy
| | - Flavio De Angelis
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Andrey Kozlov
- Institute and Museum of Anthropology, M. Lomonosov State University, Moscow, Russia
| | - Andrea Novelletto
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Maria Fuciarelli
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| |
Collapse
|
42
|
Liu G, Zou Y, Cheng Q, Zeng Y, Gu X, Su Z. Age distribution patterns of human gene families: divergent for Gene Ontology categories and concordant between different subcellular localizations. Mol Genet Genomics 2013; 289:137-47. [PMID: 24322347 DOI: 10.1007/s00438-013-0799-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/03/2013] [Indexed: 12/13/2022]
Abstract
The age distribution of gene duplication events within the human genome exhibits two waves of duplications along with an ancient component. However, because of functional constraint differences, genes in different functional categories might show dissimilar retention patterns after duplication. It is known that genes in some functional categories are highly duplicated in the early stage of vertebrate evolution. However, the correlations of the age distribution pattern of gene duplication between the different functional categories are still unknown. To investigate this issue, we developed a robust pipeline to date the gene duplication events in the human genome. We successfully estimated about three-quarters of the duplication events within the human genome, along with the age distribution pattern in each Gene Ontology (GO) slim category. We found that some GO slim categories show different distribution patterns when compared to the whole genome. Further hierarchical clustering of the GO slim functional categories enabled grouping into two main clusters. We found that human genes located in the duplicated copy number variant regions, whose duplicate genes have not been fixed in the human population, were mainly enriched in the groups with a high proportion of recently duplicated genes. Moreover, we used a phylogenetic tree-based method to date the age of duplications in three signaling-related gene superfamilies: transcription factors, protein kinases and G-protein coupled receptors. These superfamilies were expressed in different subcellular localizations. They showed a similar age distribution as the signaling-related GO slim categories. We also compared the differences between the age distributions of gene duplications in multiple subcellular localizations. We found that the distribution patterns of the major subcellular localizations were similar to that of the whole genome. This study revealed the whole picture of the evolution patterns of gene functional categories in the human genome.
Collapse
Affiliation(s)
- Gangbiao Liu
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Biology Building II 113, Shanghai, 200433, China
| | | | | | | | | | | |
Collapse
|
43
|
Khan FF, Carpenter D, Mitchell L, Mansouri O, Black HA, Tyson J, Armour JAL. Accurate measurement of gene copy number for human alpha-defensin DEFA1A3. BMC Genomics 2013; 14:719. [PMID: 24138543 PMCID: PMC4046698 DOI: 10.1186/1471-2164-14-719] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/19/2013] [Indexed: 01/01/2023] Open
Abstract
Background Multi-allelic copy number variants include examples of extensive variation between individuals in the copy number of important genes, most notably genes involved in immune function. The definition of this variation, and analysis of its impact on function, has been hampered by the technical difficulty of large-scale but accurate typing of genomic copy number. The copy-variable alpha-defensin locus DEFA1A3 on human chromosome 8 commonly varies between 4 and 10 copies per diploid genome, and presents considerable challenges for accurate high-throughput typing. Results In this study, we developed two paralogue ratio tests and three allelic ratio measurements that, in combination, provide an accurate and scalable method for measurement of DEFA1A3 gene number. We combined information from different measurements in a maximum-likelihood framework which suggests that most samples can be assigned to an integer copy number with high confidence, and applied it to typing 589 unrelated European DNA samples. Typing the members of three-generation pedigrees provided further reassurance that correct integer copy numbers had been assigned. Our results have allowed us to discover that the SNP rs4300027 is strongly associated with DEFA1A3 gene copy number in European samples. Conclusions We have developed an accurate and robust method for measurement of DEFA1A3 copy number. Interrogation of rs4300027 and associated SNPs in Genome-Wide Association Study SNP data provides no evidence that alpha-defensin copy number is a strong risk factor for phenotypes such as Crohn’s disease, type I diabetes, HIV progression and multiple sclerosis. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-719) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | | | - John A L Armour
- School of Biology, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| |
Collapse
|
44
|
Campbell CD, Eichler EE. Properties and rates of germline mutations in humans. Trends Genet 2013; 29:575-84. [PMID: 23684843 PMCID: PMC3785239 DOI: 10.1016/j.tig.2013.04.005] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/05/2013] [Accepted: 04/18/2013] [Indexed: 11/25/2022]
Abstract
All genetic variation arises via new mutations; therefore, determining the rate and biases for different classes of mutation is essential for understanding the genetics of human disease and evolution. Decades of mutation rate analyses have focused on a relatively small number of loci because of technical limitations. However, advances in sequencing technology have allowed for empirical assessments of genome-wide rates of mutation. Recent studies have shown that 76% of new mutations originate in the paternal lineage and provide unequivocal evidence for an increase in mutation with paternal age. Although most analyses have focused on single nucleotide variants (SNVs), studies have begun to provide insight into the mutation rate for other classes of variation, including copy number variants (CNVs), microsatellites, and mobile element insertions (MEIs). Here, we review the genome-wide analyses for the mutation rate of several types of variants and suggest areas for future research.
Collapse
Affiliation(s)
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, Seattle, WA 98195
| |
Collapse
|
45
|
Rapid and accurate large-scale genotyping of duplicated genes and discovery of interlocus gene conversions. Nat Methods 2013; 10:903-9. [PMID: 23892896 PMCID: PMC3985568 DOI: 10.1038/nmeth.2572] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 06/06/2013] [Indexed: 01/17/2023]
Abstract
Over 900 genes have been annotated within duplicated regions of the human genome, yet their functions and potential roles in disease remain largely unknown. One major obstacle has been the inability to accurately and comprehensively assay genetic variation for these genes in a high-throughput manner. We developed a sequencing-based method for rapid and high-throughput genotyping of duplicated genes using molecular inversion probes designed to target unique paralogous sequence variants. We applied this method to genotype all members of two gene families, SRGAP2 and RH, among a diversity panel of 1,056 humans. The approach could accurately distinguish copy number in paralogs having up to ∼99.6% sequence identity, identify small gene-disruptive deletions, detect single-nucleotide variants, define breakpoints of unequal crossover and discover regions of interlocus gene conversion. The ability to rapidly and accurately genotype multiple gene families in thousands of individuals at low cost enables the development of genome-wide gene conversion maps and 'unlocks' many previously inaccessible duplicated genes for association with human traits.
Collapse
|
46
|
Alonso A, Marsal S, Tortosa R, Canela-Xandri O, Julià A. GStream: improving SNP and CNV coverage on genome-wide association studies. PLoS One 2013; 8:e68822. [PMID: 23844243 PMCID: PMC3700900 DOI: 10.1371/journal.pone.0068822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 06/03/2013] [Indexed: 11/22/2022] Open
Abstract
We present GStream, a method that combines genome-wide SNP and CNV genotyping in the Illumina microarray platform with unprecedented accuracy. This new method outperforms previous well-established SNP genotyping software. More importantly, the CNV calling algorithm of GStream dramatically improves the results obtained by previous state-of-the-art methods and yields an accuracy that is close to that obtained by purely CNV-oriented technologies like Comparative Genomic Hybridization (CGH). We demonstrate the superior performance of GStream using microarray data generated from HapMap samples. Using the reference CNV calls generated by the 1000 Genomes Project (1KGP) and well-known studies on whole genome CNV characterization based either on CGH or genotyping microarray technologies, we show that GStream can increase the number of reliably detected variants up to 25% compared to previously developed methods. Furthermore, the increased genome coverage provided by GStream allows the discovery of CNVs in close linkage disequilibrium with SNPs, previously associated with disease risk in published Genome-Wide Association Studies (GWAS). These results could provide important insights into the biological mechanism underlying the detected disease risk association. With GStream, large-scale GWAS will not only benefit from the combined genotyping of SNPs and CNVs at an unprecedented accuracy, but will also take advantage of the computational efficiency of the method.
Collapse
Affiliation(s)
- Arnald Alonso
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
- Department of ESAII, Polytechnical University of Catalonia, Barcelona, Spain
| | - Sara Marsal
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| | - Raül Tortosa
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| | - Oriol Canela-Xandri
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| |
Collapse
|
47
|
Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data. MICROARRAYS 2013; 2:171-85. [PMID: 27605188 PMCID: PMC5003459 DOI: 10.3390/microarrays2030171] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/04/2013] [Accepted: 06/05/2013] [Indexed: 11/23/2022]
Abstract
Copy number variations (CNVs) are gains and losses of genomic sequence between two individuals of a species when compared to a reference genome. The data from single nucleotide polymorphism (SNP) microarrays are now routinely used for genotyping, but they also can be utilized for copy number detection. Substantial progress has been made in array design and CNV calling algorithms and at least 10 comparison studies in humans have been published to assess them. In this review, we first survey the literature on existing microarray platforms and CNV calling algorithms. We then examine a number of CNV calling tools to evaluate their impacts using bovine high-density SNP data. Large incongruities in the results from different CNV calling tools highlight the need for standardizing array data collection, quality assessment and experimental validation. Only after careful experimental design and rigorous data filtering can the impacts of CNVs on both normal phenotypic variability and disease susceptibility be fully revealed.
Collapse
|
48
|
Bánlaki Z, Szabó JA, Szilágyi Á, Patócs A, Prohászka Z, Füst G, Doleschall M. Intraspecific evolution of human RCCX copy number variation traced by haplotypes of the CYP21A2 gene. Genome Biol Evol 2013; 5:98-112. [PMID: 23241443 PMCID: PMC3595039 DOI: 10.1093/gbe/evs121] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The RCCX region is a complex, multiallelic, tandem copy number variation (CNV). Two complete genes, complement component 4 (C4) and steroid 21-hydroxylase (CYP21A2, formerly CYP21B), reside in its variable region. RCCX is prone to nonallelic homologous recombination (NAHR) such as unequal crossover, generating duplications and deletions of RCCX modules, and gene conversion. A series of allele-specific long-range polymerase chain reaction coupled to the whole-gene sequencing of CYP21A2 was developed for molecular haplotyping. By means of the developed techniques, 35 different kinds of CYP21A2 haplotype variant were experimentally determined from 112 unrelated European subjects. The number of the resolved CYP21A2 haplotype variants was increased to 61 by bioinformatic haplotype reconstruction. The CYP21A2 haplotype variants could be assigned to the haplotypic RCCX CNV structures (the copy number of RCCX modules) in most cases. The genealogy network constructed from the CYP21A2 haplotype variants delineated the origin of RCCX structures. The different RCCX structures were located in tight groups. The minority of groups with identical RCCX structure occurred once in the network, implying monophyletic origin, but the majority of groups occurred several times and in different locations, indicating polyphyletic origin. The monophyletic groups were often created by single unequal crossover, whereas recurrent unequal crossover events generated some of the polyphyletic groups. As a result of recurrent NAHR events, more CYP21A2 haplotype variants with different allele patterns belonged to the same RCCX structure. The intraspecific evolution of RCCX CNV described here has provided a reasonable expectation for that of complex, multiallelic, tandem CNVs in humans.
Collapse
Affiliation(s)
- Zsófia Bánlaki
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | | | | | | | | | | | | |
Collapse
|
49
|
Vogiatzi P, Perdigones N, Mason PJ, Wilson DB, Bessler M. A family with Hoyeraal-Hreidarsson syndrome and four variants in two genes of the telomerase core complex. Pediatr Blood Cancer 2013; 60:E4-6. [PMID: 23335200 PMCID: PMC3860171 DOI: 10.1002/pbc.24389] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 10/09/2012] [Indexed: 11/07/2022]
Abstract
We describe an African American family with Hoyeraal-Hreidarrson syndrome (HHS) in which 2 TERT mutations (causing P530L and A880T amino acid changes) and two in the DKC1 variants (G486R and A487A) were segregating. Both genes are associated with dyskeratosis congenita and HHS. It was important to determine the importance of these mutations in disease pathogenesis to counsel family members. From genetic analysis of family members, telomere length and X-inactivation studies we concluded that compound heterozygosity for the TERT mutations was the major cause of HHS and the DKC1 G486R variant is a rare African variant unlikely to cause disease.
Collapse
Affiliation(s)
- Paraskevi Vogiatzi
- Division of Hematology, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Nieves Perdigones
- Division of Hematology, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Philip J. Mason
- Division of Hematology, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - David B. Wilson
- Department of Pediatrics, Washington University, St. Louis Children’s Hospital, St. Louis, MO, USA
| | - Monica Bessler
- Division of Hematology, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA,Division of Hematology/Oncology, Department of Internal Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
50
|
Kim JH, Jung SH, Bae JS, Lee HS, Yim SH, Park SY, Bang SY, Hu HJ, Shin HD, Bae SC, Chung YJ. Deletion variants of RABGAP1L, 10q21.3, and C4 are associated with the risk of systemic lupus erythematosus in Korean women. ACTA ACUST UNITED AC 2013; 65:1055-63. [PMID: 23335107 DOI: 10.1002/art.37854] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 12/27/2012] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Several copy number variations (CNVs) have been found to be associated with systemic lupus erythematosus (SLE) through the target gene approach. However, genome-wide features of CNVs and their role in the risk of SLE remain unknown. The aim of this study was to identify SLE-associated CNVs in Korean women. METHODS Genome-wide assessments of CNVs were performed in 382 SLE patients and 191 control subjects, using an Illumina HumanHap610 BeadChip genotyping platform. SLE-associated CNV regions that were identified by genome-wide association study (GWAS) were replicated in quantitative polymerase chain reaction (PCR) and deletion-typing PCR analyses in an independent sample set comprising 564 SLE patients and 511 control subjects. RESULTS Of 144 common CNV regions, 3 deletion-type CNV regions in 1q25.1, 8q23.3, and 10q21.3 were found to be significantly associated with SLE by GWAS analysis. In the independent replication, the CNV regions in 1q25.1 (RABGAP1L) and 10q21.3 were successfully replicated (odds ratio [OR] 1.30, P=0.038 and OR 1.90, P=3.6×10(-5), respectively), and the associations were confirmed again by deletion-typing PCR. The CNV region in the C4 gene, which showed a potential association in the discovery stage, was included in the replication analysis and was found to be significantly associated with the risk of SLE (OR 1.88, P=0.01). Through deletion-typing PCR, the exact sizes and breakpoint sequences of the deletions were defined. Individuals with the deletions in all 3 loci (RABGAP1L, 10q21.3, and C4) had a much higher risk of SLE than did those without any deletions in the 3 loci (OR 5.52, P=3.9×10(-4)). CONCLUSION These CNV regions can be useful to identify the pathogenic mechanisms of SLE, and might be used to more accurately predict the risk of SLE by taking into consideration their synergistic effects on disease susceptibility.
Collapse
Affiliation(s)
- Ji-Hong Kim
- Catholic University of Korea, and Department of Rheumatology, Hanyang University Hospital of Rheumatic Diseases, Haengdang-dong, Seongdong-gu, Seoul, Republic of Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|