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Kang Y, Nam SH, Park KS, Kim Y, Kim JW, Lee E, Ko JM, Lee KA, Park I. DeviCNV: detection and visualization of exon-level copy number variants in targeted next-generation sequencing data. BMC Bioinformatics 2018; 19:381. [PMID: 30326846 PMCID: PMC6192323 DOI: 10.1186/s12859-018-2409-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/04/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Targeted next-generation sequencing (NGS) is increasingly being adopted in clinical laboratories for genomic diagnostic tests. RESULTS We developed a new computational method, DeviCNV, intended for the detection of exon-level copy number variants (CNVs) in targeted NGS data. DeviCNV builds linear regression models with bootstrapping for every probe to capture the relationship between read depth of an individual probe and the median of read depth values of all probes in the sample. From the regression models, it estimates the read depth ratio of the observed and predicted read depth with confidence interval for each probe which is applied to a circular binary segmentation (CBS) algorithm to obtain CNV candidates. Then, it assigns confidence scores to those candidates based on the reliability and strength of the CNV signals inferred from the read depth ratios of the probes within them. Finally, it also provides gene-centric plots with confidence levels of CNV candidates for visual inspection. We applied DeviCNV to targeted NGS data generated for newborn screening and demonstrated its ability to detect novel pathogenic CNVs from clinical samples. CONCLUSIONS We propose a new pragmatic method for detecting CNVs in targeted NGS data with an intuitive visualization and a systematic method to assign confidence scores for candidate CNVs. Since DeviCNV was developed for use in clinical diagnosis, sensitivity is increased by the detection of exon-level CNVs.
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Affiliation(s)
- Yeeok Kang
- SD Genomics Co., Ltd., 11F, Seoul Gangnam Post Office, 619 Gaepo-ro, Gangnam-gu, Seoul, 06336, Republic of Korea.,Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Seong-Hyeuk Nam
- SD Genomics Co., Ltd., 11F, Seoul Gangnam Post Office, 619 Gaepo-ro, Gangnam-gu, Seoul, 06336, Republic of Korea
| | - Kyung Sun Park
- SD Genomics Co., Ltd., 11F, Seoul Gangnam Post Office, 619 Gaepo-ro, Gangnam-gu, Seoul, 06336, Republic of Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, 211 Eonjuro, Gangnam-gu, Seoul, 06273, Republic of Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eunjung Lee
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, USA
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, 211 Eonjuro, Gangnam-gu, Seoul, 06273, Republic of Korea.
| | - Inho Park
- SD Genomics Co., Ltd., 11F, Seoul Gangnam Post Office, 619 Gaepo-ro, Gangnam-gu, Seoul, 06336, Republic of Korea.
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Fernández Asensio A, Iglesias T, Cotarelo A, Espina M, Blanco-González E, Sierra L, Montes-Bayón M. Multiplex polymerase chain reaction in combination with gel electrophoresis-inductively coupled plasma mass spectrometry: A powerful tool for the determination of gene copy number variations and gene expression changes. Anal Chim Acta 2018; 1023:64-73. [DOI: 10.1016/j.aca.2018.03.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 03/09/2018] [Accepted: 03/10/2018] [Indexed: 12/14/2022]
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Mable BK, Brysting AK, Jørgensen MH, Carbonell AKZ, Kiefer C, Ruiz-Duarte P, Lagesen K, Koch MA. Adding Complexity to Complexity: Gene Family Evolution in Polyploids. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Schurink A, da Silva VH, Velie BD, Dibbits BW, Crooijmans RPMA, Franҫois L, Janssens S, Stinckens A, Blott S, Buys N, Lindgren G, Ducro BJ. Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity. BMC Genet 2018; 19:49. [PMID: 30060732 PMCID: PMC6065148 DOI: 10.1186/s12863-018-0657-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 07/19/2018] [Indexed: 12/04/2022] Open
Abstract
Background Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. Results Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. Conclusions CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture. Electronic supplementary material The online version of this article (10.1186/s12863-018-0657-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anouk Schurink
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands.
| | - Vinicius H da Silva
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden.,Department of Animal Ecology, Netherlands Institute of Ecology, NIOO-KNAW, 6708, PB, Wageningen, the Netherlands
| | - Brandon D Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden
| | - Bert W Dibbits
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands
| | - Richard P M A Crooijmans
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands
| | - Liesbeth Franҫois
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Steven Janssens
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Anneleen Stinckens
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Sarah Blott
- Reproductive Biology, Faculty of Medicine and Health Sciences, The University of Nottingham, Leicestershire, LE12 5RD, UK
| | - Nadine Buys
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden
| | - Bart J Ducro
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands
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56
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Moreno-Grau S, Hernández I, Heilmann-Heimbach S, Ruiz S, Rosende-Roca M, Mauleón A, Vargas L, Rodríguez-Gómez O, Alegret M, Espinosa A, Ortega G, Aguilera N, Abdelnour C, Neuroimaging Initiative AD, Gil S, Maier W, Sotolongo-Grau O, Tárraga L, Ramirez A, López-Arrrieta J, Antúnez C, Serrano-Ríos M, Boada M, Ruiz A. Genome-wide significant risk factors on chromosome 19 and the APOE locus. Oncotarget 2018; 9:24590-24600. [PMID: 29872490 PMCID: PMC5973862 DOI: 10.18632/oncotarget.25083] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/22/2018] [Indexed: 12/30/2022] Open
Abstract
The apolipoprotein E (APOE) gene on chromosome 19q13.32, was the first, and remains the strongest, genetic risk factor for Alzheimer’s disease (AD). Additional signals associated with AD have been located in chromosome 19, including ABCA7 (19p13.3) and CD33 (19q13.41). The ABCA7 gene has been replicated in most populations. However, the contribution to AD of other signals close to APOE gene remains controversial. Possible explanations for inconsistency between reports include long range linkage disequilibrium (LRLD). We analysed the contribution of ABCA7 and CD33 loci to AD risk and explore LRLD patterns across APOE region. To evaluate AD risk conferred by ABCA7 rs4147929:G>A and CD33 rs3865444:C>A, we used a large Spanish population (1796 AD cases, 2642 controls). The ABCA7 rs4147929:G>A SNP effect was nominally replicated in the Spanish cohort and reached genome-wide significance after meta-analysis (odds ratio (OR)=1.15, 95% confidence interval (95% CI)=1.12–1.19; P = 1.60 x 10-19). CD33 rs3865444:C>A was not associated with AD in the dataset. The meta-analysis was also negative (OR=0.98, 95% CI=0.93–1.04; P=0.48). After exploring LRLD patterns between APOE and CD33 in several datasets, we found significant LD (D’ >0.20; P <0.030) between APOE-Ɛ2 and CD33 rs3865444C>A in two of five datasets, suggesting the presence of a non-universal long range interaction between these loci affecting to some populations. In conclusion, we provide here evidence of genetic association of the ABCA7 locus in the Spanish population and also propose a plausible explanation for the controversy on the contribution of CD33 to AD susceptibility.
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Affiliation(s)
- Sonia Moreno-Grau
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Isabel Hernández
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Susana Ruiz
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Maitée Rosende-Roca
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Ana Mauleón
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Liliana Vargas
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Octavio Rodríguez-Gómez
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Montserrat Alegret
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Ana Espinosa
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Gemma Ortega
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Nuria Aguilera
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Carla Abdelnour
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Alzheimer's Disease Neuroimaging Initiative
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain.,Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases, DZNE, Bonn, Germany.,Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany.,Memory Unit, University Hospital La Paz-Cantoblanco, Madrid, Spain.,Dementia Unit, University Hospital Virgen de la Arrixaca, Murcia, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, CIBERDEM, Spain, Hospital Clínico San Carlos, Madrid, Spain
| | - Silvia Gil
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Wolfgang Maier
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases, DZNE, Bonn, Germany
| | - Oscar Sotolongo-Grau
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Lluís Tárraga
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Alfredo Ramirez
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany.,Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | | | - Carmen Antúnez
- Dementia Unit, University Hospital Virgen de la Arrixaca, Murcia, Spain
| | - Manuel Serrano-Ríos
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, CIBERDEM, Spain, Hospital Clínico San Carlos, Madrid, Spain
| | - Mercè Boada
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
| | - Agustín Ruiz
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain
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Cosemans N, Claes P, Brison N, Vermeesch JR, Peeters H. Noise-robust assessment of SNP array based CNV calls through local noise estimation of log R ratios. Stat Appl Genet Mol Biol 2018; 17:sagmb-2017-0026. [PMID: 29708886 DOI: 10.1515/sagmb-2017-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Arrays based on single nucleotide polymorphisms (SNPs) have been successful for the large scale discovery of copy number variants (CNVs). However, current CNV calling algorithms still have limitations in detecting CNVs with high specificity and sensitivity, especially in case of small (<100 kb) CNVs. Therefore, this study presents a simple statistical analysis to evaluate CNV calls from SNP arrays in order to improve the noise-robustness of existing CNV calling algorithms. The proposed approach estimates local noise of log R ratios and returns the probability that a certain observation is different from this log R ratio noise level. This probability can be triggered at different thresholds to tailor specificity and/or sensitivity in a flexible way. Moreover, a comparison based on qPCR experiments showed that the proposed noise-robust CNV calls outperformed original ones for multiple threshold values.
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Affiliation(s)
- Nele Cosemans
- Center for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Peter Claes
- Medical Image Computing, ESAT/PSI, Department of Electrical Engineering, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
| | - Nathalie Brison
- Center for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | | | - Hilde Peeters
- Center for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
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58
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Abstract
PURPOSE OF REVIEW DNA copy number variations (CNVs) are quantitative structural rearrangements that include deletions, duplications, and higher order amplifications. Because of technical limitations, the contribution of this common form of genetic variation to regulation of lipid metabolism and dyslipidemia has been underestimated. RECENT FINDINGS Recent literature involving CNVs and dyslipidemias has focused mainly on rare CNVs causing familial hypercholesterolemia, and a common CNV polymorphism as the major determinant of lipoprotein(a) plasma concentrations. Additionally, there is tantalizing evidence of largely uninvestigated but plausible presence of CNVs underlying other dyslipidemias. We also discuss the future role of improved technologies in facilitating more economic, routine CNV assessment in dyslipidemias. SUMMARY CNVs account for large proportion of human genetic variation and are already known to contribute to susceptibility of dyslipidemias, particularly in about 10% of familial hypercholesterolemia patients. Increasing availability of clinical next-generation sequencing and bioinformatics presents a cost-effective opportunity for novel CNV discoveries in dyslipidemias.
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Eisfeldt J, Nilsson D, Andersson-Assarsson JC, Lindstrand A. AMYCNE: Confident copy number assessment using whole genome sequencing data. PLoS One 2018; 13:e0189710. [PMID: 29579039 PMCID: PMC5868770 DOI: 10.1371/journal.pone.0189710] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/30/2017] [Indexed: 11/18/2022] Open
Abstract
Copy number variations (CNVs) within the human genome have been linked to a diversity of inherited diseases and phenotypic traits. The currently used methodology to measure copy numbers has limited resolution and/or precision, especially for regions with more than 4 copies. Whole genome sequencing (WGS) offers an alternative data source to allow for the detection and characterization of the copy number across different genomic regions in a single experiment. A plethora of tools have been developed to utilize WGS data for CNV detection. None of these tools are designed specifically to accurately estimate copy numbers of complex regions in a small cohort or clinical setting. Herein, we present AMYCNE (automatic modeling functionality for copy number estimation), a CNV analysis tool using WGS data. AMYCNE is multifunctional and performs copy number estimation of complex regions, annotation of VCF files, and CNV detection on individual samples. The performance of AMYCNE was evaluated using AMY1A ddPCR measurements from 86 unrelated individuals. In addition, we validated the accuracy of AMYCNE copy number predictions on two additional genes (FCGR3A and FCGR3B) using datasets available through the 1000 genomes consortium. Finally, we simulated levels of mosaic loss and gain of chromosome X and used this dataset for benchmarking AMYCNE. The results show a high concordance between AMYCNE and ddPCR, validating the use of AMYCNE to measure tandem AMY1 repeats with high accuracy. This opens up new possibilities for the use of WGS for accurate copy number determination of other complex regions in the genome in small cohorts or single individuals.
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Affiliation(s)
- Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
- * E-mail:
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | | | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Li W, Bickhart DM, Ramunno L, Iamartino D, Williams JL, Liu GE. Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle. Genomics 2018; 111:418-425. [PMID: 29501677 DOI: 10.1016/j.ygeno.2018.02.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/12/2018] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Abstract
This study sought to characterize differences in gene content, regulation and structure between taurine cattle and river buffalo (one subspecies of domestic water buffalo) using the extensively annotated UMD3.1 cattle reference genome as a basis for comparisons. We identified 127 deletion CNV regions in river buffalo representing 5 annotated cattle genes. We also characterized 583 merged mobile element insertion (MEI) events within the upstream regions of annotated cattle genes. Transcriptome analysis in various tissue types on river buffalo confirmed the absence of four cattle genes. Four genes which may be related to phenotypic differences in meat quality and color, had upstream MEI predictions and were found to have significantly elevated expression in river buffalo compared with cattle. Our comparative alignment approach and gene expression analyses suggested a functional role for many genomic structural variations, which may contribute to the unique phenotypes of river buffalo.
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Affiliation(s)
- Wenli Li
- The Cell Wall Utilization and Biology Laboratory, US Dairy Forage Research Center, USDA ARS, Madison, WI 53706, USA
| | - Derek M Bickhart
- The Cell Wall Utilization and Biology Laboratory, US Dairy Forage Research Center, USDA ARS, Madison, WI 53706, USA
| | - Luigi Ramunno
- Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", via Università 100, 80055 Portici (NA), Italy
| | - Daniela Iamartino
- AIA-LGS, Associazione Italiana Allevatori - Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 Cremona (CR), Italy; Parco Tecnologico Padano, Via Einstein, 26500 Lodi, Italy
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - George E Liu
- The Animal Genomics and Improvement Laboratory, USDA ARS, Beltsville, MD, USA.
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Dosage-Dependent Expression Variation Suppressed on the Drosophila Male X Chromosome. G3-GENES GENOMES GENETICS 2018; 8:587-598. [PMID: 29242386 PMCID: PMC5919722 DOI: 10.1534/g3.117.300400] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA copy number variation is associated with many high phenotypic heterogeneity disorders. We systematically examined the impact of Drosophila melanogaster deletions on gene expression profiles to ask whether increased expression variability owing to reduced gene dose might underlie this phenotypic heterogeneity. Indeed, we found that one-dose genes have higher gene expression variability relative to two-dose genes. We then asked whether this increase in variability could be explained by intrinsic noise within cells due to stochastic biochemical events, or whether expression variability is due to extrinsic noise arising from more complex interactions. Our modeling showed that intrinsic gene expression noise averages at the organism level and thus cannot explain increased variation in one-dose gene expression. Interestingly, expression variability was related to the magnitude of expression compensation, suggesting that regulation, induced by gene dose reduction, is noisy. In a remarkable exception to this rule, the single X chromosome of males showed reduced expression variability, even compared with two-dose genes. Analysis of sex-transformed flies indicates that X expression variability is independent of the male differentiation program. Instead, we uncovered a correlation between occupancy of the chromatin-modifying protein encoded by males absent on the first (mof) and expression variability, linking noise suppression to the specialized X chromosome dosage compensation system. MOF occupancy on autosomes in both sexes also lowered transcriptional noise. Our results demonstrate that gene dose reduction can lead to heterogeneous responses, which are often noisy. This has implications for understanding gene network regulatory interactions and phenotypic heterogeneity. Additionally, chromatin modification appears to play a role in dampening transcriptional noise.
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Lin S, Lin X, Zhang Z, Jiang M, Rao Y, Nie Q, Zhang X. Copy Number Variation in SOX6 Contributes to Chicken Muscle Development. Genes (Basel) 2018; 9:genes9010042. [PMID: 29342086 PMCID: PMC5793193 DOI: 10.3390/genes9010042] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 11/16/2022] Open
Abstract
Copy number variations (CNVs), which cover many functional genes, are associated with complex diseases, phenotypic diversity and traits that are economically important to raising chickens. The sex-determining region Y-box 6 (Sox6) plays a key role in fast-twitch muscle fiber differentiation of zebrafish and mice, but it is still unknown whether SOX6 plays a role in chicken skeletal muscle development. We identified two copy number polymorphisms (CNPs) which were significantly related to different traits on the genome level in chickens by AccuCopy® and CNVplex® analyses. Notably, five white recessive rock (CN = 1, CN = 3) variant individuals and two Xinghua (CN = 3) variant individuals contain a CNP13 (chromosome5: 10,500,294-10,675,531) which overlaps with SOX6. There is a disordered region in SOX6 proteins 265-579 aa coded by a partial CNV overlapping region. A quantitative real-time polymerase chain reaction showed that the expression level of SOX6 mRNA was positively associated with CNV and highly expressed during the skeletal muscle cell differentiation in chickens. After the knockdown of the SOX6, the expression levels of IGFIR1, MYF6, SOX9, SHOX and CCND1 were significantly down-regulated. All of them directly linked to muscle development. These results suggest that the number of CNVs in the CNP13 is positively associated with the expression level of SOX6, which promotes the proliferation and differentiation of skeletal muscle cells by up-regulating the expression levels of the muscle-growth-related genes in chickens as in other animal species.
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Affiliation(s)
- Shudai Lin
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, China.
| | - Xiran Lin
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, China.
| | - Zihao Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, China.
| | - Mingya Jiang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, China.
| | - Yousheng Rao
- Department of Biological Technology, Nanchang Normal University, Nanchang 330029, China.
| | - Qinghua Nie
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, China.
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, China.
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63
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Li L, Bai H, Yang J, Cao D, Shen K. Genome-wide DNA copy number analysis in clonally expanded human ovarian cancer cells with distinct invasive/migratory capacities. Oncotarget 2017; 8:15136-15148. [PMID: 28122348 PMCID: PMC5362473 DOI: 10.18632/oncotarget.14767] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/10/2017] [Indexed: 01/26/2023] Open
Abstract
Ovarian cancer has the worst prognosis of any gynecological malignancy, and generally presents with metastasis at advanced stages. Copy number variation (CNV) frequently contributes to the alteration of oncogenic drivers. In this study, we sought to identify genetic targets in heterogeneous clones from human ovarian cancers cells. We used array-based technology to systematically assess all the genes with CNVs in cell models clonally expanded from A2780 and SKOV3 ovarian cancer cell lines with distinct highly and minimally invasive/migratory capacities. We found that copy number alterations differed between matched highly and minimally invasive/migratory subclones, differentially affecting specific functional processes including immune response processes, DNA damage repair, cell cycle and cell proliferation. We also identified seven genes as strong candidates, including DDB1, ERCC1, ERCC2, PRPF19, BCAT1, CDKN1B and MARK4, by integrating the above data with gene expression and clinical outcome data. Thus, by determining the molecular signatures of heterogeneous invasive/migratory ovarian cancer cells, we identified genes that could be specifically targeted for the treatment and prognosis of advanced ovarian cancers.
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Affiliation(s)
- Lei Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Huimin Bai
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiaxin Yang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dongyan Cao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Keng Shen
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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64
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McNew SM, Beck D, Sadler-Riggleman I, Knutie SA, Koop JAH, Clayton DH, Skinner MK. Epigenetic variation between urban and rural populations of Darwin's finches. BMC Evol Biol 2017; 17:183. [PMID: 28835203 PMCID: PMC5569522 DOI: 10.1186/s12862-017-1025-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 07/26/2017] [Indexed: 11/10/2022] Open
Abstract
Background The molecular basis of evolutionary change is assumed to be genetic variation. However, growing evidence suggests that epigenetic mechanisms, such as DNA methylation, may also be involved in rapid adaptation to new environments. An important first step in evaluating this hypothesis is to test for the presence of epigenetic variation between natural populations living under different environmental conditions. Results In the current study we explored variation between populations of Darwin’s finches, which comprise one of the best-studied examples of adaptive radiation. We tested for morphological, genetic, and epigenetic differences between adjacent “urban” and “rural” populations of each of two species of ground finches, Geospiza fortis and G. fuliginosa, on Santa Cruz Island in the Galápagos. Using data collected from more than 1000 birds, we found significant morphological differences between populations of G. fortis, but not G. fuliginosa. We did not find large size copy number variation (CNV) genetic differences between populations of either species. However, other genetic variants were not investigated. In contrast, we did find dramatic epigenetic differences between the urban and rural populations of both species, based on DNA methylation analysis. We explored genomic features and gene associations of the differentially DNA methylated regions (DMR), as well as their possible functional significance. Conclusions In summary, our study documents local population epigenetic variation within each of two species of Darwin’s finches. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1025-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sabrina M McNew
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Sarah A Knutie
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
| | - Jennifer A H Koop
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
| | - Dale H Clayton
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
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65
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Rabbani B, Nakaoka H, Akhondzadeh S, Tekin M, Mahdieh N. Next generation sequencing: implications in personalized medicine and pharmacogenomics. MOLECULAR BIOSYSTEMS 2017; 12:1818-30. [PMID: 27066891 DOI: 10.1039/c6mb00115g] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A breakthrough in next generation sequencing (NGS) in the last decade provided an unprecedented opportunity to investigate genetic variations in humans and their roles in health and disease. NGS offers regional genomic sequencing such as whole exome sequencing of coding regions of all genes, as well as whole genome sequencing. RNA-seq offers sequencing of the entire transcriptome and ChIP-seq allows for sequencing the epigenetic architecture of the genome. Identifying genetic variations in individuals can be used to predict disease risk, with the potential to halt or retard disease progression. NGS can also be used to predict the response to or adverse effects of drugs or to calculate appropriate drug dosage. Such a personalized medicine also provides the possibility to treat diseases based on the genetic makeup of the patient. Here, we review the basics of NGS technologies and their application in human diseases to foster human healthcare and personalized medicine.
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Affiliation(s)
- Bahareh Rabbani
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Niayesh-Vali asr Intersection, Tehran, Iran.
| | - Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Shahin Akhondzadeh
- Psychiatric Research Center, Roozbeh Psychiatric Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mustafa Tekin
- John P Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Nejat Mahdieh
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Niayesh-Vali asr Intersection, Tehran, Iran.
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66
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Fukami M, Miyado M. Next generation sequencing and array-based comparative genomic hybridization for molecular diagnosis of pediatric endocrine disorders. Ann Pediatr Endocrinol Metab 2017; 22:90-94. [PMID: 28690986 PMCID: PMC5495984 DOI: 10.6065/apem.2017.22.2.90] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/17/2017] [Indexed: 11/20/2022] Open
Abstract
Next-generation sequencing (NGS) and array-based comparative genomic hybridization (array CGH) have enabled us to perform high-throughput mutation screening and genome-wide copy number analysis, respectively. These methods can be used for molecular diagnosis of pediatric endocrine disorders. NGS has determined the frequency and phenotypic variation of mutations in several disease-associated genes. Furthermore, whole exome analysis using NGS has successfully identified several novel causative genes for endocrine disorders. Array CGH is currently used as the standard procedure for molecular cytogenetic analysis. Array CGH can detect various submicroscopic genomic rearrangements involving exons or enhancers of disease-associated genes. This review introduces some examples of the use of NGS and array CGH for the molecular diagnosis of pediatric endocrine disorders.
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Affiliation(s)
- Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Mami Miyado
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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67
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CRISPR/Cas9-mediated correction of human genetic disease. SCIENCE CHINA-LIFE SCIENCES 2017; 60:447-457. [DOI: 10.1007/s11427-017-9032-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 03/05/2017] [Indexed: 12/21/2022]
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68
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He Z, Wang L, Harper AL, Havlickova L, Pradhan AK, Parkin IAP, Bancroft I. Extensive homoeologous genome exchanges in allopolyploid crops revealed by mRNAseq-based visualization. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:594-604. [PMID: 27808473 PMCID: PMC5399007 DOI: 10.1111/pbi.12657] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/25/2016] [Accepted: 10/28/2016] [Indexed: 05/21/2023]
Abstract
Polyploidy, the possession of multiple sets of chromosomes, has been a predominant factor in the evolution and success of the angiosperms. Although artificially formed allopolyploids show a high rate of genome rearrangement, the genomes of cultivars and germplasm used for crop breeding were assumed stable and genome structural variation under the artificial selection process of commercial breeding has remained little studied. Here, we show, using a repurposed visualization method based on transcriptome sequence data, that genome structural rearrangement occurs frequently in varieties of three polyploid crops (oilseed rape, mustard rape and bread wheat), meaning that the extent of genome structural variation present in commercial crops is much higher than expected. Exchanges were found to occur most frequently where homoeologous chromosome segments are collinear to telomeres and in material produced as doubled haploids. The new insights into genome structural evolution enable us to reinterpret the results of recent studies and implicate homoeologous exchanges, not deletions, as being responsible for variation controlling important seed quality traits in rapeseed. Having begun to identify the extent of genome structural variation in polyploid crops, we can envisage new strategies for the global challenge of broadening crop genetic diversity and accelerating adaptation, such as the molecular identification and selection of genome deletions or duplications encompassing genes with trait-controlling dosage effects.
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Affiliation(s)
- Zhesi He
- Department of BiologyUniversity of YorkHeslingtonYorkUK
| | - Lihong Wang
- Department of BiologyUniversity of YorkHeslingtonYorkUK
| | | | | | - Akshay K. Pradhan
- Department of Genetics and Centre for Genetic Manipulation of Crop PlantsUniversity of DelhiNew DelhiIndia
| | | | - Ian Bancroft
- Department of BiologyUniversity of YorkHeslingtonYorkUK
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69
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Graffelman J, Jain D, Weir B. A genome-wide study of Hardy-Weinberg equilibrium with next generation sequence data. Hum Genet 2017; 136:727-741. [PMID: 28374190 PMCID: PMC5429372 DOI: 10.1007/s00439-017-1786-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/22/2017] [Indexed: 12/03/2022]
Abstract
Statistical tests for Hardy–Weinberg equilibrium have been an important tool for detecting genotyping errors in the past, and remain important in the quality control of next generation sequence data. In this paper, we analyze complete chromosomes of the 1000 genomes project by using exact test procedures for autosomal and X-chromosomal variants. We find that the rate of disequilibrium largely exceeds what might be expected by chance alone for all chromosomes. Observed disequilibrium is, in about 60% of the cases, due to heterozygote excess. We suggest that most excess disequilibrium can be explained by sequencing problems, and hypothesize mechanisms that can explain exceptional heterozygosities. We report higher rates of disequilibrium for the MHC region on chromosome 6, regions flanking centromeres and p-arms of acrocentric chromosomes. We also detected long-range haplotypes and areas with incidental high disequilibrium. We report disequilibrium to be related to read depth, with variants having extreme read depths being more likely to be out of equilibrium. Disequilibrium rates were found to be 11 times higher in segmental duplications and simple tandem repeat regions. The variants with significant disequilibrium are seen to be concentrated in these areas. For next generation sequence data, Hardy–Weinberg disequilibrium seems to be a major indicator for copy number variation.
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Affiliation(s)
- Jan Graffelman
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Avinguda Diagonal 647, 08028, Barcelona, Spain. .,Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA, 98105-9461, USA.
| | - Deepti Jain
- Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA, 98105-9461, USA
| | - Bruce Weir
- Department of Biostatistics, University of Washington, University Tower, 15th Floor, 4333 Brooklyn Avenue, Seattle, WA, 98105-9461, USA
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70
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Chen Y, Zhao L, Wang Y, Cao M, Gelowani V, Xu M, Agrawal SA, Li Y, Daiger SP, Gibbs R, Wang F, Chen R. SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data. BMC Bioinformatics 2017; 18:147. [PMID: 28253855 PMCID: PMC5335817 DOI: 10.1186/s12859-017-1566-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 02/24/2017] [Indexed: 12/15/2022] Open
Abstract
Background Targeted next-generation sequencing (NGS) has been widely used as a cost-effective way to identify the genetic basis of human disorders. Copy number variations (CNVs) contribute significantly to human genomic variability, some of which can lead to disease. However, effective detection of CNVs from targeted capture sequencing data remains challenging. Results Here we present SeqCNV, a novel CNV calling method designed to use capture NGS data. SeqCNV extracts the read depth information and utilizes the maximum penalized likelihood estimation (MPLE) model to identify the copy number ratio and CNV boundary. We applied SeqCNV to both bacterial artificial clone (BAC) and human patient NGS data to identify CNVs. These CNVs were validated by array comparative genomic hybridization (aCGH). Conclusions SeqCNV is able to robustly identify CNVs of different size using capture NGS data. Compared with other CNV-calling methods, SeqCNV shows a significant improvement in both sensitivity and specificity. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1566-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yong Chen
- Shanghai Key Lab of Intelligent Information Processing, Shanghai, China.,School of Computer Science and Technology, Fudan University, Shanghai, China
| | - Li Zhao
- Structural and Computational Biology & Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Yi Wang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Ming Cao
- University of Texas Health Science Center, Houston, TX, USA
| | - Violet Gelowani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mingchu Xu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Smriti A Agrawal
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Stephen P Daiger
- Department of Ophthalmology and Visual Sciences, University of Texas Health Science Center, Houston, TX, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Fei Wang
- Shanghai Key Lab of Intelligent Information Processing, Shanghai, China. .,School of Computer Science and Technology, Fudan University, Shanghai, China.
| | - Rui Chen
- Structural and Computational Biology & Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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71
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Skryabin NA, Vasilyev SA, Lebedev IN. Epigenetic silencing of genomic structural variations. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417100106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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72
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Hu XS, Yeh FC, Hu Y, Deng LT, Ennos RA, Chen X. High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens. Sci Rep 2017; 7:43178. [PMID: 28225073 PMCID: PMC5320550 DOI: 10.1038/srep43178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/19/2017] [Indexed: 11/09/2022] Open
Abstract
Copy-number-variable (CNV) loci differ from single nucleotide polymorphic (SNP) sites in size, mutation rate, and mechanisms of maintenance in natural populations. It is therefore hypothesized that population genetic divergence at CNV loci will differ from that found at SNP sites. Here, we test this hypothesis by analysing 856 CNV loci from the genomes of 1184 healthy individuals from 11 HapMap populations with a wide range of ancestry. The results show that population genetic divergence at the CNV loci is generally more than three times lower than at genome-wide SNP sites. Populations generally exhibit very small genetic divergence (Gst = 0.05 ± 0.049). The smallest divergence is among African populations (Gst = 0.0081 ± 0.0025), with increased divergence among non-African populations (Gst = 0.0217 ± 0.0109) and then among African and non-African populations (Gst = 0.0324 ± 0.0064). Genetic diversity is high in African populations (~0.13), low in Asian populations (~0.11), and intermediate in the remaining 11 populations. Few significant linkage disequilibria (LDs) occur between the genome-wide CNV loci. Patterns of gametic and zygotic LDs indicate the absence of epistasis among CNV loci. Mutation rate is about twice as large as the migration rate in the non-African populations, suggesting that the high mutation rates play dominant roles in producing the low population genetic divergence at CNV loci.
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Affiliation(s)
- Xin-Sheng Hu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong 510642, China
| | - Francis C Yeh
- Department of Renewable Resources, 751 General Service Building, University of Alberta, Edmonton, AB T6G 2H1, Canada
| | - Yang Hu
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2S4, Canada
| | - Li-Ting Deng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong 510642, China
| | - Richard A Ennos
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH 9 3JT, United Kingdom
| | - Xiaoyang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong 510642, China
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73
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Li BJ, Li HL, Meng Z, Zhang Y, Lin H, Yue GH, Xia JH. Copy Number Variations in Tilapia Genomes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:11-21. [PMID: 28168542 DOI: 10.1007/s10126-017-9733-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/23/2016] [Indexed: 06/06/2023]
Abstract
Discovering the nature and pattern of genome variation is fundamental in understanding phenotypic diversity among populations. Although several millions of single nucleotide polymorphisms (SNPs) have been discovered in tilapia, the genome-wide characterization of larger structural variants, such as copy number variation (CNV) regions has not been carried out yet. We conducted a genome-wide scan for CNVs in 47 individuals from three tilapia populations. Based on 254 Gb of high-quality paired-end sequencing reads, we identified 4642 distinct high-confidence CNVs. These CNVs account for 1.9% (12.411 Mb) of the used Nile tilapia reference genome. A total of 1100 predicted CNVs were found overlapping with exon regions of protein genes. Further association analysis based on linear model regression found 85 CNVs ranging between 300 and 27,000 base pairs significantly associated to population types (R 2 > 0.9 and P > 0.001). Our study sheds first insights on genome-wide CNVs in tilapia. These CNVs among and within tilapia populations may have functional effects on phenotypes and specific adaptation to particular environments.
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Affiliation(s)
- Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hong Lian Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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74
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Liu Z, Yin N, Gong L, Tan Z, Yin B, Yang Y, Luo C. Microduplication of 7q36.3 encompassing the SHH long‑range regulator (ZRS) in a patient with triphalangeal thumb‑polysyndactyly syndrome and congenital heart disease. Mol Med Rep 2016; 15:793-797. [PMID: 28035386 PMCID: PMC5364826 DOI: 10.3892/mmr.2016.6092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 11/26/2016] [Indexed: 12/12/2022] Open
Abstract
Triphalangeal thumb‑polysyndactyly syndrome (TPT‑PS) is an autosomal dominant disorder with complete penetrance and a variable expression consisting of opposable triphalangeal thumbs, duplication of the distal thumb phalanx, pre‑axial polydactyly and duplication of the big toes (hallux). The causative gene of TPT‑PS has been mapped to 7q36.3. Sonic hedgehog (SHH) expressed in the zone of polarizing activity (ZPA) has an important role in defining the anterior‑posterior axis and numbers of digits in limb bud development. Point mutation or duplication in the ZPA regulatory sequence (ZRS), a cis‑regulator of SHH, will lead to TPT‑PS. The present study describes a 1‑year‑old female congenital heart disease (CHD) patient with TPT‑PS phenotype. In this Han Chinese family with TPT‑PS, high resolution single nucleotide polymorphism array technology identified a novel 0.29 Mb duplication comprising ZRS at 7q36.3 where LMBR1 is located. Additionally, a novel deletion of 22q11.21 was detected in the proband with Tetralogy of Fallot. However, the parents and other relatives of the patient did not harbor this genomic lesion nor CHD. The findings supported the hypothesis that an increased copy number variation of ZRS is the genetic mechanism underlying the phenotype of TPT‑PS, and corroborated that 22q11.21 deletion is a genetic cause of CHD.
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Affiliation(s)
- Zhenghua Liu
- Department of Cardiothoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Ni Yin
- Department of Cardiothoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Lianghui Gong
- Department of Cardiothoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Zhiping Tan
- Department of Cardiothoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Bangliang Yin
- Department of Cardiothoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Yifeng Yang
- Department of Cardiothoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Cheng Luo
- Department of Cardiothoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
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75
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Liu L, Wang HD, Cui CY, Wu D, Li T, Fan TB, Peng BT, Zhang LZ, Wang CZ. Application of array-comparative genomic hybridization in tetralogy of Fallot. Medicine (Baltimore) 2016; 95:e5552. [PMID: 27930557 PMCID: PMC5266029 DOI: 10.1097/md.0000000000005552] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
To explore the underlying pathogenesis and provide references for genetic counseling and prenatal gene diagnosis, we analyzed the chromosome karyotypes and genome-wide copy number variations (CNVs) in 86 patients with tetralogy of Fallot (TOF) by G-banding karyotype analysis and array-comparative genomic hybridization (aCGH), respectively. And then quantitative polymerase chain reaction was used to validate these candidate CNVs. Based on their different properties, CNVs were categorized into benign CNVs, suspiciously pathogenic CNVs, and indefinite CNVs. Data analysis was based on public databases such as UCSC, DECIPHER, DGV, ISCA, and OMIM.The karyotype was normal in all the 86 patients with TOF. CNVs were detected in 11 patients by aCGH and quantitative polymerase chain reaction. Patient no. 0001, 0010, and 0029 had 2.52-Mb deletion in the chromosome 22q11.21 region; patient no. 0008 had both 595- and 428-kb duplications, respectively, in 12p12.3p12.2 and 14q23.2q23.3 regions; patient no. 0009 had 1.46-Mb duplication in the 1q21.1q21.2 region; patient no. 0016 had 513-kb duplication in the 1q42.13 region; patient no. 0024 had 292-kb duplication in the 16q11.2 region; patient no. 0026 had 270-kb duplication in the 16q24.1 region; patient no. 0028 had 222-kb deletion in the 7q31.1 region; patient no. 0033 had 1.73-Mb duplication in the 17q12 region; and patient no. 0061 had 5.79-Mb deletion in the 1p36.33p36.31 region.aCGH can accurately detect CNVs in the patients with TOF. This is conducive to genetic counseling and prenatal diagnosis for TOF and provides a new clue and theoretical basis for exploring the pathogenesis of congenital heart disease.
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Affiliation(s)
- Lin Liu
- Department of Cardiovascular Ultrasound
| | | | | | - Dong Wu
- Institute of Medical Genetics
| | - Tao Li
- Institute of Medical Genetics
| | - Tai-Bing Fan
- Children's Heart Center, Henan Provincial People's Hospital, Zhengzhou University People's Hospital
| | - Bang-Tian Peng
- Children's Heart Center, Henan Provincial People's Hospital, Zhengzhou University People's Hospital
| | | | - Cheng-Zeng Wang
- Department of Ultrasound, Affiliated Cancer Hospital, Zhengzhou University, Zhengzhou 450008, China
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76
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Liang KH, Lin CL, Hsu CW, Lai MW, Chien RN, Yeh CT. UGT2B28 genomic variation is associated with hepatitis B e-antigen seroconversion in response to antiviral therapy. Sci Rep 2016; 6:34088. [PMID: 27665939 PMCID: PMC5036189 DOI: 10.1038/srep34088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/05/2016] [Indexed: 02/07/2023] Open
Abstract
Seroconversion of hepatitis B virus (HBV) e-antigen (HBeAg) is a critical but often-missed therapeutic goal in standard antiviral treatments. An extreme-phenotype genome-wide association study was performed, comparing untreated spontaneous recoverers (with seroconversion of HBV surface antigen) versus entecavir-treated patients failing to achieve HBeAg seroconversion. A single-nucleotide-polymorphism rs2132039 on the UGT2B28 gene, alongside an adjacent copy number polymorphism (CNP605), manifested the strongest clinical associations (P = 3.4 × 10-8 and 0.001, respectively). Multivariate analysis showed that rs2132039-TT genotypes, but not CNP605 copy numbers, remained associated to spontaneous recoverers (P = 0.009). The clinical association of rs2132039 was validated successfully in an independent cohort (n = 302; P = 0.002). Longitudinal case-only analyses revealed that the rs2132039-TT genotype predicted shorter time-to-HBeAg-seroconversion in all antiviral-treated patients (n = 380, P = 0.012), as well as the peginterferon-treated subgroup (n = 123; P = 0.024, Hazard ratio [HR] = 2.104, Confidence interval [CI] = 1.105-4.007). In the entecavir-treated subgroup, the predictive effect was restricted by pretreatment alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, with effective prediction observed in patients with ALT < 200 IU/ml and ALT/AST ratio <2 (n = 132; P = 0.013, HR = 10.538, CI = 1.420-78.196).
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Affiliation(s)
- Kung-Hao Liang
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Lang Lin
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Liver Research Unit, Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
- Chang Gung University, College of Medicine, Taiwan
| | - Chao-Wei Hsu
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Chang Gung University, College of Medicine, Taiwan
| | - Ming-Wei Lai
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Chang Gung University, College of Medicine, Taiwan
| | - Rong-Nan Chien
- Liver Research Unit, Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Chau-Ting Yeh
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Chang Gung University, College of Medicine, Taiwan
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77
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Bar-Ziv R, Voichek Y, Barkai N. Dealing with Gene-Dosage Imbalance during S Phase. Trends Genet 2016; 32:717-723. [PMID: 27575299 DOI: 10.1016/j.tig.2016.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/09/2016] [Accepted: 08/12/2016] [Indexed: 12/01/2022]
Abstract
DNA replication perturbs the dosage balance between genes that replicate early during S phase and those that replicate late. If propagated to influence protein content, this dosage imbalance could influence cellular functions. In bacteria, mechanisms have evolved to use this imbalance to tune certain processes with the rate of cell growth. By contrast, eukaryotes buffer this dosage imbalance to ensure gene expression homeostasis also during S phase. Here, we outline classical and more recent studies describing how different organisms deal with this replication-dependent dosage imbalance, and describe recent results linking the eukaryotic buffering mechanism to replication-dependent histone acetylation. Finally, we discuss the possible implications of this buffering mechanism and speculate why it is specific to eukaryote cells.
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Affiliation(s)
- Raz Bar-Ziv
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Voichek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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78
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Hu XS, Hu Y, Chen X. Testing neutrality at copy-number-variable loci under the finite-allele and finite-site models. Theor Popul Biol 2016; 112:1-13. [PMID: 27423854 DOI: 10.1016/j.tpb.2016.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 02/01/2023]
Abstract
Copy-number variation (CNV) is an important form of DNA structural variation because a certain proportion of genomes in many eukaryotic species can contribute to such variations. Owing to the differences between CNVs and single nucleotide polymorphisms (SNPs) in size, mutation rate and maintaining mechanism, it is more realistic to characterize CNV evolution under the finite-allele and finite-site models. Here, we propose a method to test multiple CNVs neutrality under the finite-allele and finite-site models and the assumption of mutation-drift process. The statistical property of the method is evaluated through Monte Carlo simulations under the effects of the sample size, the scaled mutation rates, the number of CNVs, the population demographic change, and selection. Different from Tajima's D test, a bootstrap or a permutation approach is suggested to conduct a neutrality test. Application of this method is illustrated using the diploid CNV genotypes measured in discrete copy numbers in 11 HapMap phase III populations. The results show that the mutation-drift process can explain the variation of genome-wide CNVs among 1184 individuals (856 CNVs, ∼0.02Mb on average in size), irrespective of the historical demographic changes. Patterns from allele-frequency-spectrum analysis also support the hypothesis of neutral CNVs. Our results suggest that most human chromosomal changes in healthy individuals via unbalanced rearrangements of the segments with certain sizes are neutral.
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Affiliation(s)
- Xin-Sheng Hu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong 510642, China; Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX13RB, United Kingdom.
| | - Yang Hu
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2S4, Canada
| | - Xiaoyang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong 510642, China.
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79
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Pelleri MC, Cicchini E, Locatelli C, Vitale L, Caracausi M, Piovesan A, Rocca A, Poletti G, Seri M, Strippoli P, Cocchi G. Systematic reanalysis of partial trisomy 21 cases with or without Down syndrome suggests a small region on 21q22.13 as critical to the phenotype. Hum Mol Genet 2016; 25:2525-2538. [PMID: 27106104 PMCID: PMC5181629 DOI: 10.1093/hmg/ddw116] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/12/2016] [Accepted: 04/12/2016] [Indexed: 01/13/2023] Open
Abstract
A 'Down Syndrome critical region' (DSCR) sufficient to induce the most constant phenotypes of Down syndrome (DS) had been identified by studying partial (segmental) trisomy 21 (PT21) as an interval of 0.6-8.3 Mb within human chromosome 21 (Hsa21), although its existence was later questioned. We propose an innovative, systematic reanalysis of all described PT21 cases (from 1973 to 2015). In particular, we built an integrated, comparative map from 125 cases with or without DS fulfilling stringent cytogenetic and clinical criteria. The map allowed to define or exclude as candidates for DS fine Hsa21 sequence intervals, also integrating duplication copy number variants (CNVs) data. A highly restricted DSCR (HR-DSCR) of only 34 kb on distal 21q22.13 has been identified as the minimal region whose duplication is shared by all DS subjects and is absent in all non-DS subjects. Also being spared by any duplication CNV in healthy subjects, HR-DSCR is proposed as a candidate for the typical DS features, the intellectual disability and some facial phenotypes. HR-DSCR contains no known gene and has relevant homology only to the chimpanzee genome. Searching for HR-DSCR functional loci might become a priority for understanding the fundamental genotype-phenotype relationships in DS.
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Affiliation(s)
- Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, Italy
| | - Elena Cicchini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, Italy
| | - Chiara Locatelli
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138 Bologna, BO, Italy
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, Italy
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, Italy
| | - Alessandro Rocca
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138 Bologna, BO, Italy
| | - Giulia Poletti
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Via Massarenti 9, 40138 Bologna, BO, Italy
| | | | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, BO, Italy
| | - Guido Cocchi
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via Massarenti 9, 40138 Bologna, BO, Italy
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80
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Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression. PLoS Comput Biol 2016; 12:e1004871. [PMID: 27177143 PMCID: PMC4866742 DOI: 10.1371/journal.pcbi.1004871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/14/2016] [Indexed: 11/22/2022] Open
Abstract
By integrating Haar wavelets with Hidden Markov Models, we achieve drastically reduced running times for Bayesian inference using Forward-Backward Gibbs sampling. We show that this improves detection of genomic copy number variants (CNV) in array CGH experiments compared to the state-of-the-art, including standard Gibbs sampling. The method concentrates computational effort on chromosomal segments which are difficult to call, by dynamically and adaptively recomputing consecutive blocks of observations likely to share a copy number. This makes routine diagnostic use and re-analysis of legacy data collections feasible; to this end, we also propose an effective automatic prior. An open source software implementation of our method is available at http://schlieplab.org/Software/HaMMLET/ (DOI: 10.5281/zenodo.46262). This paper was selected for oral presentation at RECOMB 2016, and an abstract is published in the conference proceedings.
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81
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Ferguson LR, De Caterina R, Görman U, Allayee H, Kohlmeier M, Prasad C, Choi MS, Curi R, de Luis DA, Gil Á, Kang JX, Martin RL, Milagro FI, Nicoletti CF, Nonino CB, Ordovas JM, Parslow VR, Portillo MP, Santos JL, Serhan CN, Simopoulos AP, Velázquez-Arellano A, Zulet MA, Martinez JA. Guide and Position of the International Society of Nutrigenetics/Nutrigenomics on Personalised Nutrition: Part 1 - Fields of Precision Nutrition. Lifestyle Genom 2016; 9:12-27. [DOI: 10.1159/000445350] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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82
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Rao YS, Li J, Zhang R, Lin XR, Xu JG, Xie L, Xu ZQ, Wang L, Gan JK, Xie XJ, He J, Zhang XQ. Copy number variation identification and analysis of the chicken genome using a 60K SNP BeadChip. Poult Sci 2016; 95:1750-6. [PMID: 27118864 DOI: 10.3382/ps/pew136] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2016] [Indexed: 12/24/2022] Open
Abstract
Copy number variation (CNV) is an important source of genetic variation in organisms and a main factor that affects phenotypic variation. A comprehensive study of chicken CNV can provide valuable information on genetic diversity and facilitate future analyses of associations between CNV and economically important traits in chickens. In the present study, an F2 full-sib chicken population (554 individuals), established from a cross between Xinghua and White Recessive Rock chickens, was used to explore CNV in the chicken genome. Genotyping was performed using a chicken 60K SNP BeadChip. A total of 1,875 CNV were detected with the PennCNV algorithm, and the average number of CNV was 3.42 per individual. The CNV were distributed across 383 independent CNV regions (CNVR) and covered 41 megabases (3.97%) of the chicken genome. Seven CNVR in 108 individuals were validated by quantitative real-time PCR, and 81 of these individuals (75%) also were detected with the PennCNV algorithm. In total, 274 CNVR (71.54%) identified in the current study were previously reported. Of these, 147 (38.38%) were reported in at least 2 studies. Additionally, 109 of the CNVR (28.46%) discovered here are novel. A total of 709 genes within or overlapping with the CNVR was retrieved. Out of the 2,742 quantitative trait loci (QTL) collected in the chicken QTL database, 43 QTL had confidence intervals overlapping with the CNVR, and 32 CNVR encompassed one or more functional genes. The functional genes located in the CNVR are likely to be the QTG that are associated with underlying economic traits. This study considerably expands our insight into the structural variation in the genome of chickens and provides an important resource for genomic variation, especially for genomic structural variation related to economic traits in chickens.
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Affiliation(s)
- Y S Rao
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou 510642, Guangdong, China Department of Biological Technology, Nanchang Normal University, Nanchang 330029, Jiangxi, China
| | - J Li
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou 510642, Guangdong, China Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - R Zhang
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou 510642, Guangdong, China Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - X R Lin
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou 510642, Guangdong, China Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - J G Xu
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou 510642, Guangdong, China Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China Department of Biological Technology, Nanchang Normal University, Nanchang 330029, Jiangxi, China
| | - L Xie
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou 510642, Guangdong, China
| | - Z Q Xu
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou 510642, Guangdong, China Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - L Wang
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou 510642, Guangdong, China Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - J K Gan
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou 510642, Guangdong, China Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - X J Xie
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou 510642, Guangdong, China Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - J He
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou 510642, Guangdong, China Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - X Q Zhang
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou 510642, Guangdong, China Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
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83
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Huang MC, Chuang TP, Chen CH, Wu JY, Chen YT, Li LH, Yang HC. An integrated analysis tool for analyzing hybridization intensities and genotypes using new-generation population-optimized human arrays. BMC Genomics 2016; 17:266. [PMID: 27029637 PMCID: PMC4815280 DOI: 10.1186/s12864-016-2478-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/16/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Affymetrix Axiom single nucleotide polymorphism (SNP) arrays provide a cost-effective, high-density, and high-throughput genotyping solution for population-optimized analyses. However, no public software is available for the integrated genomic analysis of hybridization intensities and genotypes for this new-generation population-optimized genotyping platform. RESULTS A set of statistical methods was developed for an integrated analysis of allele frequency (AF), allelic imbalance (AI), loss of heterozygosity (LOH), long contiguous stretch of homozygosity (LCSH), and copy number variation or alteration (CNV/CNA) on the basis of SNP probe hybridization intensities and genotypes. This study analyzed 3,236 samples that were genotyped using different SNP platforms. The proposed AF adjustment method considerably increased the accuracy of AF estimation. The proposed quick circular binary segmentation algorithm for segmenting copy number reduced the computation time of the original segmentation method by 30-67 %. The proposed CNV/CNA detection, which integrates AI and LOH/LCSH detection, had a promising true positive rate and well-controlled false positive rate in simulation studies. Moreover, our real-time quantitative polymerase chain reaction experiments successfully validated the CNVs/CNAs that were identified in the Axiom data analyses using the proposed methods; some of the validated CNVs/CNAs were not detected in the Affymetrix Array 6.0 data analysis using the Affymetrix Genotyping Console. All the analysis functions are packaged into the ALICE (AF/LOH/LCSH/AI/CNV/CNA Enterprise) software. CONCLUSIONS ALICE and the used genomic reference databases, which can be downloaded from http://hcyang.stat.sinica.edu.tw/software/ALICE.html , are useful resources for analyzing genomic data from the Axiom and other SNP arrays.
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Affiliation(s)
- Mei-Chu Huang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan.,Institute of Statistical Science, Academia Sinica, No 128, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, 112, Taiwan
| | - Tzu-Po Chuang
- Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan
| | - Ling-Hui Li
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan.
| | - Hsin-Chou Yang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan. .,Institute of Statistical Science, Academia Sinica, No 128, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan. .,Institute of Public Health, National Yang Ming University, Taipei, 112, Taiwan. .,Department of Statistics, National Cheng Kung University, Tainan, 701, Taiwan. .,Institute of Statistics, National Tsing Hua University, Hsinchu, 300, Taiwan. .,School of Public Health, National Defense Medical Center, Taipei, 114, Taiwan.
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84
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Ghosh S, Das PJ, McQueen CM, Gerber V, Swiderski CE, Lavoie JP, Chowdhary BP, Raudsepp T. Analysis of genomic copy number variation in equine recurrent airway obstruction (heaves). Anim Genet 2016; 47:334-44. [PMID: 26932307 DOI: 10.1111/age.12426] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2016] [Indexed: 12/18/2022]
Abstract
We explored the involvement of genomic copy number variants (CNVs) in susceptibility to recurrent airway obstruction (RAO), or heaves-an asthmalike inflammatory disease in horses. Analysis of 16 RAO-susceptible (cases) and six RAO-resistant (control) horses on a custom-made whole-genome 400K equine tiling array identified 245 CNV regions (CNVRs), 197 previously known and 48 new, distributed on all horse autosomes and the X chromosome. Among the new CNVRs, 30 were exclusively found in RAO cases and were further analyzed by quantitative PCR, including additional cases and controls. Suggestive association (P = 0.03; corrected P = 0.06) was found between RAO and a loss on chromosome 5 involving NME7, a gene necessary for ciliary functions in lungs and involved in primary ciliary dyskinesia in humans. The CNVR could be a potential marker for RAO susceptibility but needs further study in additional RAO cohorts. Other CNVRs were not associated with RAO, although several involved genes of interest, such as SPI2/SERPINA1 from the serpin gene family, which are associated with chronic obstructive pulmonary disease and asthma in humans. The SPI2/SERPINA1 CNVR showed striking variation among horses, but it was not significantly different between RAO cases and controls. The findings provide baseline information on the relationship between CNVs and RAO susceptibility. Discovery of new CNVs and the use of a larger population of RAO-affected and control horses are needed to shed more light on their significance in modulating this complex and heterogeneous disease.
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Affiliation(s)
- S Ghosh
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - P J Das
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA.,National Research Centre on Yak (ICAR), Dirang, Arunachal Pradesh, 790101, India
| | - C M McQueen
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - V Gerber
- Department of Veterinary Medicine, University of Bern, Bern, Switzerland
| | - C E Swiderski
- Department of Clinical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - J-P Lavoie
- Department of Clinical Sciences, University of Montreal, Montreal, QC, J2S 7C6, Canada
| | - B P Chowdhary
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA.,New Research Complex, Qatar University, Doha, 2713, Qatar
| | - T Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
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85
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GARTON FLEURC, NORTH KATHRYNN. The Effect of Heterozygosity for the ACTN3 Null Allele on Human Muscle Performance. Med Sci Sports Exerc 2016; 48:509-20. [DOI: 10.1249/mss.0000000000000784] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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86
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Enhancing ergosterol production in Pichia pastoris GS115 by overexpressing squalene synthase gene from Glycyrrhiza uralensis. Chin J Nat Med 2016; 13:338-45. [PMID: 25986282 PMCID: PMC7128851 DOI: 10.1016/s1875-5364(15)30024-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The present study was designed to determine the effects of copy number variations (CNVs) of squalene synthase 1(SQS1) gene on the mevalonate (MVA) pathway. SQS1 gene from G. uralensis (GuSQS1) was cloned and over-expressed in Pichia pastoris GS115. Six recombinant P. pastoris strains containing different copy number of GuSQS1 were constructed. HPLC was used to assay the level of ergosterol in all transgenic P. pastoris strains containing GuSQS1. HPLC analysis showed that the contents of ergosterol in all of the transgenic P. pastoris containing GuSQS1 were higher than that in the negative control. And with the increase of copy number of GuSQS1, the content of ergosterol showed an increasing-decreasing-increasing pattern. The contents of ergosterol in 10-copy-GuSQS1 P. pastoris and 47-copy-GuSQS1 P. pastoris were significantly higher than that in the rest recombinant P. pastoris strains. In conclusion, the CNVs of GuSQS1 influence the content of secondary metabolites in the MVA pathway. The present study provides a basis for over-expressing GuSQS1 and increasing the content of glycyrrhizin in G. uralensis cultivars.
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87
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Wang MD, Dzama K, Rees DJG, Muchadeyi FC. Tropically adapted cattle of Africa: perspectives on potential role of copy number variations. Anim Genet 2015; 47:154-64. [DOI: 10.1111/age.12391] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2015] [Indexed: 12/12/2022]
Affiliation(s)
- M. D. Wang
- Department of Animal Sciences; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
| | - K. Dzama
- Department of Animal Sciences; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
| | - D. J. G. Rees
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
| | - F. C. Muchadeyi
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
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88
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Beckmann JS. Can we afford to sequence every newborn baby's genome? Hum Mutat 2015; 36:283-6. [PMID: 25546530 DOI: 10.1002/humu.22748] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/17/2014] [Indexed: 01/19/2023]
Abstract
Whole-exome sequencing and whole-genome sequencing are gradually entering into the clinical arena. Drops in sequencing prices have led some to suggest that these analyses could be extended to the screening of whole populations or subsets thereof. Herein, we argue that this optimism is presently still unfounded. While cost estimates take into account the generation of sequence data, they fail to properly evaluate both the price of accurate and efficient interpretation and of the proper return of genomic information to the consulting individuals. Thus, short of inventing new, cost-effective ways of achieving these goals, the latter are likely to ruin our healthcare systems. We posit that due to lack of available resources, generalization of this practice remains, for the time being, unrealistic.
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Affiliation(s)
- Jacques S Beckmann
- Clinical Bioinformatics, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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89
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Shi T, Xu Y, Yang M, Huang Y, Lan X, Lei C, Qi X, Yang X, Chen H. Copy number variations atLEPRgene locus associated with gene expression and phenotypic traits in Chinese cattle. Anim Sci J 2015; 87:336-43. [DOI: 10.1111/asj.12531] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/11/2015] [Accepted: 07/29/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Tao Shi
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Yao Xu
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Mingjuan Yang
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Yongzhen Huang
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Xianyong Lan
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Chuzhao Lei
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Xinglei Qi
- Biyang Bureau of Animal Husbandry of Biyang County; Biyang Henan China
| | - Xiaoming Yang
- Institute of Animal Husbandry and Veterinary; Shanxi Academy of Agricultural Sciences; Taiyuan Shanxi China
| | - Hong Chen
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
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90
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Noninvasive detection of fetal subchromosomal abnormalities by semiconductor sequencing of maternal plasma DNA. Proc Natl Acad Sci U S A 2015; 112:14670-5. [PMID: 26554006 DOI: 10.1073/pnas.1518151112] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Noninvasive prenatal testing (NIPT) using sequencing of fetal cell-free DNA from maternal plasma has enabled accurate prenatal diagnosis of aneuploidy and become increasingly accepted in clinical practice. We investigated whether NIPT using semiconductor sequencing platform (SSP) could reliably detect subchromosomal deletions/duplications in women carrying high-risk fetuses. We first showed that increasing concentration of abnormal DNA and sequencing depth improved detection. Subsequently, we analyzed plasma from 1,456 pregnant women to develop a method for estimating fetal DNA concentration based on the size distribution of DNA fragments. Finally, we collected plasma from 1,476 pregnant women with fetal structural abnormalities detected on ultrasound who also underwent an invasive diagnostic procedure. We used SSP of maternal plasma DNA to detect subchromosomal abnormalities and validated our results with array comparative genomic hybridization (aCGH). With 3.5 million reads, SSP detected 56 of 78 (71.8%) subchromosomal abnormalities detected by aCGH. With increased sequencing depth up to 10 million reads and restriction of the size of abnormalities to more than 1 Mb, sensitivity improved to 69 of 73 (94.5%). Of 55 false-positive samples, 35 were caused by deletions/duplications present in maternal DNA, indicating the necessity of a validation test to exclude maternal karyotype abnormalities. This study shows that detection of fetal subchromosomal abnormalities is a viable extension of NIPT based on SSP. Although we focused on the application of cell-free DNA sequencing for NIPT, we believe that this method has broader applications for genetic diagnosis, such as analysis of circulating tumor DNA for detection of cancer.
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91
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Plengvidhya N, Chanprasert K, Tangjittipokin W, Thongnoppakhun W, Yenchitsomanus PT. Detection of CAPN10 copy number variation in Thai patients with type 2 diabetes by denaturing high performance liquid chromatography and real-time quantitative polymerase chain reaction. J Diabetes Investig 2015; 6:632-9. [PMID: 26543536 PMCID: PMC4627539 DOI: 10.1111/jdi.12341] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 02/11/2015] [Accepted: 02/16/2015] [Indexed: 11/30/2022] Open
Abstract
Aims/Introduction A combination of multiple genetic and environmental factors contribute to the pathogenesis of type 2 diabetes. Copy number variations (CNVs) are associated with complex human diseases. However, CNVs can cause genotype deviation from the Hardy–Weinberg equilibrium (HWE). A genetic case–control association study in 216 Thai diabetic patients and 192 non-diabetic controls found that, after excluding genotyping errors, genotype distribution of calpain 10 (CAPN10) SNP44 (rs2975760) deviated from HWE. Here, we aimed to detect CNV within the CAPN10 SNP44 region. Materials and Methods CNV within the CAPN10 SNP44 region was detected using denaturing high-performance liquid chromatography, and the results confirmed by real-time quantitative polymerase chain reaction with SYBR Green I. Results Both methods successfully identified CNV in the CAPN10 SNP44 region, obtaining concordant results. Correction of genotype calling based on the status of identified CNVs showed that the CAPN10 SNP44 genotype is in good agreement with HWE (P > 0.05). However, no association between CNV genotypes and risk of type 2 diabetes was observed. Conclusions Identified CNVs for CAPN10 SNP44 genotypes lead to deviation from HWE. Furthermore, both denaturing high-performance liquid chromatography and real-time quantitative polymerase chain reaction are useful for detecting CNVs.
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Affiliation(s)
- Nattachet Plengvidhya
- Division of Endocrinology and Metabolism, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University Bangkok, Thailand
| | - Kanjana Chanprasert
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University Bangkok, Thailand
| | - Watip Tangjittipokin
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University Bangkok, Thailand
| | - Wanna Thongnoppakhun
- Division of Molecular Genetics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University Bangkok, Thailand
| | - Pa-Thai Yenchitsomanus
- Division of Molecular Medicine, Departments of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University Bangkok, Thailand
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92
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Affiliation(s)
- Mario Cáceres
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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93
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Nakai N, Otsuka S, Myung J, Takumi T. Autism spectrum disorder model mice: Focus on copy number variation and epigenetics. SCIENCE CHINA-LIFE SCIENCES 2015; 58:976-84. [DOI: 10.1007/s11427-015-4891-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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94
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Zain SM, Mohamed Z, Pirmohamed M, Tan HL, Alshawsh MA, Mahadeva S, Chan WK, Mustapha NRN, Mohamed R. Copy number variation in exportin-4 (XPO4) gene and its association with histological severity of non-alcoholic fatty liver disease. Sci Rep 2015; 5:13306. [PMID: 26293807 PMCID: PMC4543956 DOI: 10.1038/srep13306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/26/2015] [Indexed: 12/17/2022] Open
Abstract
A recent genome-wide copy number (CNV) scan identified a 13q12.11 duplication in the exportin-4 (XPO4) gene to be associated with non-alcoholic steatohepatitis (NASH). We sought to confirm the finding in a larger cohort and to assess the serum XPO4 pattern in a broad spectrum of non-alcoholic fatty liver disease (NAFLD) cases. We analysed 249 NAFLD patients and 232 matched controls using TaqMan assay and serum XPO4 was measured. Copy number distribution was as follows: copy number neutral (NAFLD: 53.8%, controls: 68.6%), copy number losses (NAFLD: 13.3%, controls: 12.9%), copy number gains (NAFLD: 32.9%, controls: 18.5%). CNV gain was significantly associated with a greater risk of NAFLD (adjusted OR 2.22, 95% CI 1.42–3.46, P = 0.0004) and NASH (adjusted OR 2.33, 95% CI 1.47–3.68, P = 0.0003). Interestingly, subjects carrying extra copy number showed significantly higher serum ALT and triglyceride (P < 0.05). Serum XPO4 levels progressively declined (P = 0.043) from controls (24.6 ng/mL) to simple steatosis (20.8 ng/mL) to NASH (13.8 ng/mL). In conclusion, XPO4 CNV duplication was associated with histological severity of NAFLD, and accompanied by changes in serum XPO4 levels providing insights into NAFLD pathogenesis, and has the potential for biomarker development.
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Affiliation(s)
- Shamsul Mohd Zain
- The Pharmacogenomics Laboratory, Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Zahurin Mohamed
- The Pharmacogenomics Laboratory, Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Munir Pirmohamed
- The Wolfson Centre for Personalised Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Hwa Li Tan
- The Pharmacogenomics Laboratory, Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Sanjiv Mahadeva
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Wah-Kheong Chan
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Rosmawati Mohamed
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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95
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Copy number variations and gene polymorphisms of complement components in ocular Behcet's disease and Vogt-Koyanagi-Harada syndrome. Sci Rep 2015; 5:12989. [PMID: 26269006 PMCID: PMC4534762 DOI: 10.1038/srep12989] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/01/2015] [Indexed: 01/30/2023] Open
Abstract
Complement is involved in many immune-mediated diseases. However, the association of its copy number variations (CNVs) and polymorphisms with Behcet’s disease (BD) and Vogt-Koyanagi-Harada syndrome (VKH) is unknown. We examined copy number and mRNA expression by real-time PCR. Cytokine production by stimulated peripheral blood mononuclear cells (PBMCs) in genotyped individuals was measured by ELISA. The frequencies of having more than two copies of C3 were significantly increased in BD and VKH, whereas CNV of C5 was only associated with BD. Increased frequencies of the GG genotype of C3 rs408290 and C5 rs2269067 were found in BD. No association was observed between C3 and C5 SNPs and VKH. mRNA expression in the high CNV group and GG cases of C3 and C5 was significantly higher compared to other genotypes. Increased interleukin-17 and IFN-γ was observed in the high CNV group and GG genotype cases of C3. Interleukin-17 but not IFN-γ was increased in the high CNV group and GG genotype cases of C5. No effect of C3 or C5 genetic variants was seen on the production of TNF-α, IL-10, IL-1β, MCP-1, IL-6 and IL-8. Our study thus provides further evidence for a role of complement in the pathogenesis of uveitis.
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96
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Dillon LW, Kumar P, Shibata Y, Wang YH, Willcox S, Griffith JD, Pommier Y, Takeda S, Dutta A. Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity. Cell Rep 2015; 11:1749-59. [PMID: 26051933 DOI: 10.1016/j.celrep.2015.05.020] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/20/2015] [Accepted: 05/11/2015] [Indexed: 12/15/2022] Open
Abstract
MicroDNAs are <400-base extrachromosomal circles found in mammalian cells. Tens of thousands of microDNAs have been found in all tissue types, including sperm. MicroDNAs arise preferentially from areas with high gene density, GC content, and exon density from promoters with activating chromatin modifications and in sperm from the 5'-UTR of full-length LINE-1 elements, but are depleted from lamin-associated heterochromatin. Analysis of microDNAs from a set of human cancer cell lines revealed lineage-specific patterns of microDNA origins. A survey of microDNAs from chicken cells defective in various DNA repair proteins reveals that homologous recombination and non-homologous end joining repair pathways are not required for microDNA production. Deletion of the MSH3 DNA mismatch repair protein results in a significant decrease in microDNA abundance, specifically from non-CpG genomic regions. Thus, microDNAs arise as part of normal cellular physiology—either from DNA breaks associated with RNA metabolism or from replication slippage followed by mismatch repair.
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Affiliation(s)
- Laura W Dillon
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yoshiyuki Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology and Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA
| | - Shunichi Takeda
- CREST Research Project, Japan Science and Technology Corporation, Radiation Genetics, Faculty of Medicine, Kyoto University, Konoe Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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97
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Schilter KF, Reis LM, Sorokina EA, Semina EV. Identification of an Alu-repeat-mediated deletion of OPTN upstream region in a patient with a complex ocular phenotype. Mol Genet Genomic Med 2015; 3:490-9. [PMID: 26740941 PMCID: PMC4694134 DOI: 10.1002/mgg3.159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/05/2015] [Accepted: 05/08/2015] [Indexed: 12/14/2022] Open
Abstract
Genetic causes of ocular conditions remain largely unknown. To reveal the molecular basis for a congenital ocular phenotype associated with glaucoma we performed whole‐exome sequencing (WES) and whole‐genome copy number analyses of patient DNA. WES did not identify a causative variant. Copy number variation analysis identified a deletion of 10p13 in the patient and his unaffected father; the deletion breakpoint contained a single 37‐bp sequence that is normally present in two distinct Alu repeats separated by ~181 kb. The deletion removed part of the upstream region of optineurin (OPTN) as well as the upstream sequence and two coding exons of coiled‐coil domain containing 3 (CCDC3); analysis of the patient's second allele showed normal OPTN and CCDC3 sequences. Studies of zebrafish orthologs identified expression in the developing eye for both genes. OPTN is a known factor in dominant adult‐onset glaucoma and Amyotrophic Lateral Sclerosis (ALS). The deletion eliminates 98 kb of the OPTN upstream sequence leaving only ~1 kb of the proximal promoter region. Comparison of transcriptional activation capability of the 3 kb normal and the rearranged del(10)(p13) OPTN promoter sequences demonstrated a statistically significant decrease for the deleted allele; sequence analysis of the entire deleted region identified multiple conserved elements with possible cis‐regulatory activity. Additional screening of CCDC3 indicated that heterozygous loss‐of‐function alleles are unlikely to cause congenital ocular disease. In summary, we report the first regulatory region deletion involving OPTN, caused by Alu‐mediated nonallelic homologous recombination and possibly contributing to the patient's ocular phenotype. In addition, our data indicate that Alu‐mediated rearrangements of the OPTN upstream region may represent a new source of affected alleles in human conditions. Evaluation of the upstream OPTN sequences in additional ocular and ALS patients may help to determine the role of this region, if any, in human disease.
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Affiliation(s)
- Kala F Schilter
- Department of Pediatrics and Children's Research InstituteMedical College of WisconsinMilwaukeeWisconsin53226; Department of Cell Biology, Neurobiology and AnatomyMedical College of WisconsinMilwaukeeWisconsin53226
| | - Linda M Reis
- Department of Pediatrics and Children's Research Institute Medical College of Wisconsin Milwaukee Wisconsin 53226
| | - Elena A Sorokina
- Department of Pediatrics and Children's Research Institute Medical College of Wisconsin Milwaukee Wisconsin 53226
| | - Elena V Semina
- Department of Pediatrics and Children's Research InstituteMedical College of WisconsinMilwaukeeWisconsin53226; Department of Cell Biology, Neurobiology and AnatomyMedical College of WisconsinMilwaukeeWisconsin53226
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98
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Bhatt AB, Foster E, Kuehl K, Alpert J, Brabeck S, Crumb S, Davidson WR, Earing MG, Ghoshhajra BB, Karamlou T, Mital S, Ting J, Tseng ZH. Congenital Heart Disease in the Older Adult. Circulation 2015; 131:1884-931. [DOI: 10.1161/cir.0000000000000204] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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99
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Meechan DW, Maynard TM, Tucker ES, Fernandez A, Karpinski BA, Rothblat LA, LaMantia AS. Modeling a model: Mouse genetics, 22q11.2 Deletion Syndrome, and disorders of cortical circuit development. Prog Neurobiol 2015; 130:1-28. [PMID: 25866365 DOI: 10.1016/j.pneurobio.2015.03.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/24/2015] [Accepted: 03/29/2015] [Indexed: 12/21/2022]
Abstract
Understanding the developmental etiology of autistic spectrum disorders, attention deficit/hyperactivity disorder and schizophrenia remains a major challenge for establishing new diagnostic and therapeutic approaches to these common, difficult-to-treat diseases that compromise neural circuits in the cerebral cortex. One aspect of this challenge is the breadth and overlap of ASD, ADHD, and SCZ deficits; another is the complexity of mutations associated with each, and a third is the difficulty of analyzing disrupted development in at-risk or affected human fetuses. The identification of distinct genetic syndromes that include behavioral deficits similar to those in ASD, ADHC and SCZ provides a critical starting point for meeting this challenge. We summarize clinical and behavioral impairments in children and adults with one such genetic syndrome, the 22q11.2 Deletion Syndrome, routinely called 22q11DS, caused by micro-deletions of between 1.5 and 3.0 MB on human chromosome 22. Among many syndromic features, including cardiovascular and craniofacial anomalies, 22q11DS patients have a high incidence of brain structural, functional, and behavioral deficits that reflect cerebral cortical dysfunction and fall within the spectrum that defines ASD, ADHD, and SCZ. We show that developmental pathogenesis underlying this apparent genetic "model" syndrome in patients can be defined and analyzed mechanistically using genomically accurate mouse models of the deletion that causes 22q11DS. We conclude that "modeling a model", in this case 22q11DS as a model for idiopathic ASD, ADHD and SCZ, as well as other behavioral disorders like anxiety frequently seen in 22q11DS patients, in genetically engineered mice provides a foundation for understanding the causes and improving diagnosis and therapy for these disorders of cortical circuit development.
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Affiliation(s)
- Daniel W Meechan
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States
| | - Thomas M Maynard
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States
| | - Eric S Tucker
- Department of Neurobiology and Anatomy, Neuroscience Graduate Program, and Center for Neuroscience, West Virginia University School of Medicine, Morgantown, West Virginia
| | - Alejandra Fernandez
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States
| | - Beverly A Karpinski
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States
| | - Lawrence A Rothblat
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States; Department of Psychology, The George Washington University, Washington, DC, United States
| | - Anthony-S LaMantia
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States.
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100
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Decoding the complex genetic causes of heart diseases using systems biology. Biophys Rev 2015; 7:141-159. [PMID: 28509974 DOI: 10.1007/s12551-014-0145-3] [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: 09/09/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022] Open
Abstract
The pace of disease gene discovery is still much slower than expected, even with the use of cost-effective DNA sequencing and genotyping technologies. It is increasingly clear that many inherited heart diseases have a more complex polygenic aetiology than previously thought. Understanding the role of gene-gene interactions, epigenetics, and non-coding regulatory regions is becoming increasingly critical in predicting the functional consequences of genetic mutations identified by genome-wide association studies and whole-genome or exome sequencing. A systems biology approach is now being widely employed to systematically discover genes that are involved in heart diseases in humans or relevant animal models through bioinformatics. The overarching premise is that the integration of high-quality causal gene regulatory networks (GRNs), genomics, epigenomics, transcriptomics and other genome-wide data will greatly accelerate the discovery of the complex genetic causes of congenital and complex heart diseases. This review summarises state-of-the-art genomic and bioinformatics techniques that are used in accelerating the pace of disease gene discovery in heart diseases. Accompanying this review, we provide an interactive web-resource for systems biology analysis of mammalian heart development and diseases, CardiacCode ( http://CardiacCode.victorchang.edu.au/ ). CardiacCode features a dataset of over 700 pieces of manually curated genetic or molecular perturbation data, which enables the inference of a cardiac-specific GRN of 280 regulatory relationships between 33 regulator genes and 129 target genes. We believe this growing resource will fill an urgent unmet need to fully realise the true potential of predictive and personalised genomic medicine in tackling human heart disease.
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