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Ngo C, Baluyot M, Bennetts B, Carmichael J, Clark A, Darmanian A, Gayagay T, Jones L, Nash B, Clark M, Jose N, Robinson S, St Heaps L, Wright D. SNP chromosome microarray genotyping for detection of uniparental disomy in the clinical diagnostic laboratory. Pathology 2023; 55:818-826. [PMID: 37414616 DOI: 10.1016/j.pathol.2023.04.004] [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] [Received: 08/28/2022] [Revised: 01/21/2023] [Accepted: 04/17/2023] [Indexed: 07/08/2023]
Abstract
Single nucleotide polymorphism (SNP) chromosome microarray is well established for investigation of children with intellectual deficit/development delay and prenatal diagnosis of fetal malformation but has also emerged for uniparental disomy (UPD) genotyping. Despite published guidelines on clinical indications for testing there are no laboratory guidelines published for performing SNP microarray UPD genotyping. We evaluated SNP microarray UPD genotyping using Illumina beadchips on family trios/duos within a clinical cohort (n=98) and then explored our findings in a post-study audit (n=123). UPD occurred in 18.6% and 19.5% cases, respectively, with chromosome 15 most frequent (62.5% and 25.0%). UPD was predominantly maternal in origin (87.5% and 79.2%), highest in suspected genomic imprinting disorder cases (56.3% and 41.7%) but absent amongst children of translocation carriers. We assessed regions of homozygosity among UPD cases. The smallest interstitial and terminal regions were 2.5 Mb and 9.3 Mb, respectively. We found regions of homozygosity confounded genotyping in a consanguineous case with UPD15 and another with segmental UPD due to non-informative probes. In a unique case with chromosome 15q UPD mosaicism, we established the detection limit of mosaicism as ∼5%. From the benefits and pitfalls identified in this study, we propose a testing model and recommendations for UPD genotyping by SNP microarray.
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Affiliation(s)
- Con Ngo
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia.
| | - Maria Baluyot
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Bruce Bennetts
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Sydney Genome Diagnostics, Molecular Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Johanna Carmichael
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Alissa Clark
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Artur Darmanian
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Thet Gayagay
- Sydney Genome Diagnostics, Molecular Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Luke Jones
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Benjamin Nash
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Melanie Clark
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Ngaire Jose
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Samantha Robinson
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Luke St Heaps
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Dale Wright
- Sydney Genome Diagnostics, Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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Ozcan Z, San Lucas FA, Wong JW, Chang K, Stopsack KH, Fowler J, Jakubek YA, Scheet P. Chromosomal imbalances detected via RNA-sequencing in 28 cancers. Bioinformatics 2022; 38:1483-1490. [PMID: 34999743 PMCID: PMC8896613 DOI: 10.1093/bioinformatics/btab861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/05/2021] [Accepted: 01/03/2022] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION RNA-sequencing (RNA-seq) of tumor tissue is typically only used to measure gene expression. Here, we present a statistical approach that leverages existing RNA-seq data to also detect somatic copy number alterations (SCNAs), a pervasive phenomenon in human cancers, without a need to sequence the corresponding DNA. RESULTS We present an analysis of 4942 participant samples from 28 cancers in The Cancer Genome Atlas (TCGA), demonstrating robust detection of SCNAs from RNA-seq. Using genotype imputation and haplotype information, our RNA-based method had a median sensitivity of 85% to detect SCNAs defined by DNA analysis, at high specificity (∼95%). As an example of translational potential, we successfully replicated SCNA features associated with breast cancer subtypes. Our results credential haplotype-based inference based on RNA-seq to detect SCNAs in clinical and population-based settings. AVAILABILITY AND IMPLEMENTATION The analyses presented use the data publicly available from TCGA Research Network (http://cancergenome.nih.gov/). See Methods for details regarding data downloads. hapLOHseq software is freely available under The MIT license and can be downloaded from http://scheet.org/software.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zuhal Ozcan
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Francis A San Lucas
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Justin W Wong
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kyle Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Konrad H Stopsack
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jerry Fowler
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yasminka A Jakubek
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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Balagué-Dobón L, Cáceres A, González JR. Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure. Brief Bioinform 2022; 23:6535682. [PMID: 35211719 PMCID: PMC8921734 DOI: 10.1093/bib/bbac043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation and the most accessible to genotype in large cohorts. However, they individually explain a small proportion of phenotypic differences between individuals. Ancestry, collective SNP effects, structural variants, somatic mutations or even differences in historic recombination can potentially explain a high percentage of genomic divergence. These genetic differences can be infrequent or laborious to characterize; however, many of them leave distinctive marks on the SNPs across the genome allowing their study in large population samples. Consequently, several methods have been developed over the last decade to detect and analyze different genomic structures using SNP arrays, to complement genome-wide association studies and determine the contribution of these structures to explain the phenotypic differences between individuals. We present an up-to-date collection of available bioinformatics tools that can be used to extract relevant genomic information from SNP array data including population structure and ancestry; polygenic risk scores; identity-by-descent fragments; linkage disequilibrium; heritability and structural variants such as inversions, copy number variants, genetic mosaicisms and recombination histories. From a systematic review of recently published applications of the methods, we describe the main characteristics of R packages, command-line tools and desktop applications, both free and commercial, to help make the most of a large amount of publicly available SNP data.
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Glessner JT, Chang X, Liu Y, Li J, Khan M, Wei Z, Sleiman PMA, Hakonarson H. MONTAGE: a new tool for high-throughput detection of mosaic copy number variation. BMC Genomics 2021; 22:133. [PMID: 33627065 PMCID: PMC7905641 DOI: 10.1186/s12864-021-07395-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/19/2021] [Indexed: 01/21/2023] Open
Abstract
Background Not all cells in a given individual are identical in their genomic makeup. Mosaicism describes such a phenomenon where a mixture of genotypic states in certain genomic segments exists within the same individual. Mosaicism is a prevalent and impactful class of non-integer state copy number variation (CNV). Mosaicism implies that certain cell types or subset of cells contain a CNV in a segment of the genome while other cells in the same individual do not. Several studies have investigated the impact of mosaicism in single patients or small cohorts but no comprehensive scan of mosaic CNVs has been undertaken to accurately detect such variants and interpret their impact on human health and disease. Results We developed a tool called Montage to improve the accuracy of detection of mosaic copy number variants in a high throughput fashion. Montage directly interfaces with ParseCNV2 algorithm to establish disease phenotype genome-wide association and determine which genomic ranges had more or less than expected frequency of mosaic events. We screened for mosaic events in over 350,000 samples using 1% allele frequency as the detection limit. Additionally, we uncovered disease associations of multiple phenotypes with mosaic CNVs at several genomic loci. We additionally investigated the allele imbalance observations genome-wide to define non-diploid and non-integer copy number states. Conclusions Our novel algorithm presents an efficient tool with fast computational runtime and high levels of accuracy of mosaic CNV detection. A curated mosaic CNV callset of 3716 events in 2269 samples is presented with comparability to previous reports and disease phenotype associations. The new algorithm can be freely accessed via: https://github.com/CAG-CNV/MONTAGE. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07395-7.
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Affiliation(s)
- Joseph T Glessner
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Xiao Chang
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Yichuan Liu
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Jin Li
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Munir Khan
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Zhi Wei
- New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Patrick M A Sleiman
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
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Reilly J, Gallagher L, Chen JL, Leader G, Shen S. Bio-collections in autism research. Mol Autism 2017; 8:34. [PMID: 28702161 PMCID: PMC5504648 DOI: 10.1186/s13229-017-0154-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/23/2017] [Indexed: 01/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a group of complex neurodevelopmental disorders with diverse clinical manifestations and symptoms. In the last 10 years, there have been significant advances in understanding the genetic basis for ASD, critically supported through the establishment of ASD bio-collections and application in research. Here, we summarise a selection of major ASD bio-collections and their associated findings. Collectively, these include mapping ASD candidate genes, assessing the nature and frequency of gene mutations and their association with ASD clinical subgroups, insights into related molecular pathways such as the synapses, chromatin remodelling, transcription and ASD-related brain regions. We also briefly review emerging studies on the use of induced pluripotent stem cells (iPSCs) to potentially model ASD in culture. These provide deeper insight into ASD progression during development and could generate human cell models for drug screening. Finally, we provide perspectives concerning the utilities of ASD bio-collections and limitations, and highlight considerations in setting up a new bio-collection for ASD research.
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Affiliation(s)
- Jamie Reilly
- Regenerative Medicine Institute, School of Medicine, BioMedical Sciences Building, National University of Ireland (NUI), Galway, Ireland
| | - Louise Gallagher
- Trinity Translational Medicine Institute and Department of Psychiatry, Trinity Centre for Health Sciences, St. James Hospital Street, Dublin 8, Ireland
| | - June L Chen
- Department of Special Education, Faculty of Education, East China Normal University, Shanghai, 200062 China
| | - Geraldine Leader
- Irish Centre for Autism and Neurodevelopmental Research (ICAN), Department of Psychology, National University of Ireland Galway, University Road, Galway, Ireland
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, BioMedical Sciences Building, National University of Ireland (NUI), Galway, Ireland
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Kadara H, Scheet P, Wistuba II, Spira AE. Early Events in the Molecular Pathogenesis of Lung Cancer. Cancer Prev Res (Phila) 2016; 9:518-27. [PMID: 27006378 DOI: 10.1158/1940-6207.capr-15-0400] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/01/2016] [Indexed: 11/16/2022]
Abstract
The majority of cancer-related deaths in the United States and worldwide are attributed to lung cancer. There are more than 90 million smokers in the United States who represent a significant population at elevated risk for lung malignancy. In other epithelial tumors, it has been shown that if neoplastic lesions can be detected and treated at their intraepithelial stage, patient prognosis is significantly improved. Thus, new strategies to detect and treat lung preinvasive lesions are urgently needed in order to decrease the overwhelming public health burden of lung cancer. Limiting these advances is a poor knowledge of the earliest events that underlie lung cancer development and that would constitute markers and targets for early detection and prevention. This review summarizes the state of knowledge of human lung cancer pathogenesis and the molecular pathology of premalignant lung lesions, with a focus on the molecular premalignant field that associates with lung cancer development. Lastly, we highlight new approaches and models to study genome-wide alterations in human lung premalignancy in order to facilitate the discovery of new markers for early detection and prevention of this fatal disease. Cancer Prev Res; 9(7); 518-27. ©2016 AACR.
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Affiliation(s)
- Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas. The University of Texas Graduate School of Biomedical Sciences, Houston, Texas.
| | - Paul Scheet
- The University of Texas Graduate School of Biomedical Sciences, Houston, Texas. Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Avrum E Spira
- Section of Computational Biomedicine, Boston University School of Medicine, Boston University, Boston, Massachusetts
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7
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Extensive Hidden Genomic Mosaicism Revealed in Normal Tissue. Am J Hum Genet 2016; 98:571-578. [PMID: 26942289 DOI: 10.1016/j.ajhg.2016.02.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/03/2016] [Indexed: 01/10/2023] Open
Abstract
Genomic mosaicism arising from post-zygotic mutation has recently been demonstrated to occur in normal tissue of individuals ascertained with varied phenotypes, indicating that detectable mosaicism may be less an exception than a rule in the general population. A challenge to comprehensive cataloging of mosaic mutations and their consequences is the presence of heterogeneous mixtures of cells, rendering low-frequency clones difficult to discern. Here we applied a computational method using estimated haplotypes to characterize mosaic megabase-scale structural mutations in 31,100 GWA study subjects. We provide in silico validation of 293 previously identified somatic mutations and identify an additional 794 novel mutations, most of which exist at lower aberrant cell fractions than have been demonstrated in previous surveys. These mutations occurred across the genome but in a nonrandom manner, and several chromosomes and loci showed unusual levels of mutation. Our analysis supports recent findings about the relationship between clonal mosaicism and old age. Finally, our results, in which we demonstrate a nearly 3-fold higher rate of clonal mosaicism, suggest that SNP-based population surveys of mosaic structural mutations should be conducted with haplotypes for optimal discovery.
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8
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Unrevealed mosaicism in the next-generation sequencing era. Mol Genet Genomics 2015; 291:513-30. [PMID: 26481646 PMCID: PMC4819561 DOI: 10.1007/s00438-015-1130-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/07/2015] [Indexed: 12/19/2022]
Abstract
Mosaicism refers to the presence in an individual of normal and abnormal cells that are genotypically distinct and are derived from a single zygote. The incidence of mosaicism events in the human body is underestimated as the genotypes in the mosaic ratio, especially in the low-grade mosaicism, stay unrevealed. This review summarizes various research outcomes and diagnostic questions in relation to different types of mosaicism. The impact of both tested biological material and applied method on the mosaicism detection rate is especially highlighted. As next-generation sequencing technologies constitute a promising methodological solution in mosaicism detection in the coming years, revisions in current diagnostic protocols are necessary to increase the detection rate of the unrevealed mosaicism events. Since mosaicism identification is a complex process, numerous examples of multistep mosaicism investigations are presented and discussed.
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King DA, Jones WD, Crow YJ, Dominiczak AF, Foster NA, Gaunt TR, Harris J, Hellens SW, Homfray T, Innes J, Jones EA, Joss S, Kulkarni A, Mansour S, Morris AD, Parker MJ, Porteous DJ, Shihab HA, Smith BH, Tatton-Brown K, Tolmie JL, Trzaskowski M, Vasudevan PC, Wakeling E, Wright M, Plomin R, Timpson NJ, Hurles ME. Mosaic structural variation in children with developmental disorders. Hum Mol Genet 2015; 24:2733-45. [PMID: 25634561 PMCID: PMC4406290 DOI: 10.1093/hmg/ddv033] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/27/2015] [Indexed: 01/01/2023] Open
Abstract
Delineating the genetic causes of developmental disorders is an area of active investigation. Mosaic structural abnormalities, defined as copy number or loss of heterozygosity events that are large and present in only a subset of cells, have been detected in 0.2–1.0% of children ascertained for clinical genetic testing. However, the frequency among healthy children in the community is not well characterized, which, if known, could inform better interpretation of the pathogenic burden of this mutational category in children with developmental disorders. In a case–control analysis, we compared the rate of large-scale mosaicism between 1303 children with developmental disorders and 5094 children lacking developmental disorders, using an analytical pipeline we developed, and identified a substantial enrichment in cases (odds ratio = 39.4, P-value 1.073e − 6). A meta-analysis that included frequency estimates among an additional 7000 children with congenital diseases yielded an even stronger statistical enrichment (P-value 1.784e − 11). In addition, to maximize the detection of low-clonality events in probands, we applied a trio-based mosaic detection algorithm, which detected two additional events in probands, including an individual with genome-wide suspected chimerism. In total, we detected 12 structural mosaic abnormalities among 1303 children (0.9%). Given the burden of mosaicism detected in cases, we suspected that many of the events detected in probands were pathogenic. Scrutiny of the genotypic–phenotypic relationship of each detected variant assessed that the majority of events are very likely pathogenic. This work quantifies the burden of structural mosaicism as a cause of developmental disorders.
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Affiliation(s)
- Daniel A King
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Wendy D Jones
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Yanick J Crow
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals, NHS Foundation Trust, Manchester Academic Health Science Centre (MAHSC), Manchester M13 9WL, UK
| | - Anna F Dominiczak
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Nicola A Foster
- University Hospitals of Leicester, NHS Trust, Leicester Royal Infirmary, Leicester LE1 5WW, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Jade Harris
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals, NHS Foundation Trust, Manchester Academic Health Science Centre (MAHSC), Manchester M13 9WL, UK
| | - Stephen W Hellens
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE1 3BZ, UK
| | - Tessa Homfray
- Southwest Thames Regional Genetics Centre, St George's Healthcare NHS Trust, London SW17 0RE, UK
| | - Josie Innes
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals, NHS Foundation Trust, Manchester Academic Health Science Centre (MAHSC), Manchester M13 9WL, UK
| | - Elizabeth A Jones
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals, NHS Foundation Trust, Manchester Academic Health Science Centre (MAHSC), Manchester M13 9WL, UK, Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, MAHSC, Manchester M13 9WL, UK
| | - Shelagh Joss
- West of Scotland Clinical Genetics Service, Southern General Hospital, Glasgow DD1 9SY, UK
| | - Abhijit Kulkarni
- Southwest Thames Regional Genetics Centre, St George's Healthcare NHS Trust, London SW17 0RE, UK
| | - Sahar Mansour
- Southwest Thames Regional Genetics Centre, St George's Healthcare NHS Trust, London SW17 0RE, UK
| | - Andrew D Morris
- School of Molecular, Genetic and Population Health Sciences, University of Edinburgh Medical School, Teviot Place, Edinburgh EH8 9AG, UK
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield, UK
| | - David J Porteous
- Medical Genetics Section, Molecular Medicine Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Hashem A Shihab
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Blair H Smith
- School of Medicine, Dundee University, Mackenzie Building, Kirsty Semple Way, Ninewells Hospital and Medical School, Dundee DD2 4RB, UK
| | - Katrina Tatton-Brown
- Southwest Thames Regional Genetics Centre, St George's Healthcare NHS Trust, London SW17 0RE, UK
| | - John L Tolmie
- West of Scotland Clinical Genetics Service, Southern General Hospital, Glasgow DD1 9SY, UK
| | - Maciej Trzaskowski
- King's College London, MRC Social, Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London SE5 8AF, UK and
| | - Pradeep C Vasudevan
- University Hospitals of Leicester, NHS Trust, Leicester Royal Infirmary, Leicester LE1 5WW, UK
| | - Emma Wakeling
- North West Thames Regional Genetics Service, North West London Hospitals NHS Trust, Watford Rd, Harrow HA1 3UJ, UK
| | - Michael Wright
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE1 3BZ, UK
| | - Robert Plomin
- King's College London, MRC Social, Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London SE5 8AF, UK and
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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Somatic mosaicism in the human genome. Genes (Basel) 2014; 5:1064-94. [PMID: 25513881 PMCID: PMC4276927 DOI: 10.3390/genes5041064] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/26/2014] [Accepted: 11/28/2014] [Indexed: 12/17/2022] Open
Abstract
Somatic mosaicism refers to the occurrence of two genetically distinct populations of cells within an individual, derived from a postzygotic mutation. In contrast to inherited mutations, somatic mosaic mutations may affect only a portion of the body and are not transmitted to progeny. These mutations affect varying genomic sizes ranging from single nucleotides to entire chromosomes and have been implicated in disease, most prominently cancer. The phenotypic consequences of somatic mosaicism are dependent upon many factors including the developmental time at which the mutation occurs, the areas of the body that are affected, and the pathophysiological effect(s) of the mutation. The advent of second-generation sequencing technologies has augmented existing array-based and cytogenetic approaches for the identification of somatic mutations. We outline the strengths and weaknesses of these techniques and highlight recent insights into the role of somatic mosaicism in causing cancer, neurodegenerative, monogenic, and complex disease.
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11
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Xia R, Vattathil S, Scheet P. Identification of allelic imbalance with a statistical model for subtle genomic mosaicism. PLoS Comput Biol 2014; 10:e1003765. [PMID: 25166618 PMCID: PMC4148184 DOI: 10.1371/journal.pcbi.1003765] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/22/2014] [Indexed: 11/18/2022] Open
Abstract
Genetic heterogeneity in a mixed sample of tumor and normal DNA can confound characterization of the tumor genome. Numerous computational methods have been proposed to detect aberrations in DNA samples from tumor and normal tissue mixtures. Most of these require tumor purities to be at least 10-15%. Here, we present a statistical model to capture information, contained in the individual's germline haplotypes, about expected patterns in the B allele frequencies from SNP microarrays while fully modeling their magnitude, the first such model for SNP microarray data. Our model consists of a pair of hidden Markov models--one for the germline and one for the tumor genome--which, conditional on the observed array data and patterns of population haplotype variation, have a dependence structure induced by the relative imbalance of an individual's inherited haplotypes. Together, these hidden Markov models offer a powerful approach for dealing with mixtures of DNA where the main component represents the germline, thus suggesting natural applications for the characterization of primary clones when stromal contamination is extremely high, and for identifying lesions in rare subclones of a tumor when tumor purity is sufficient to characterize the primary lesions. Our joint model for germline haplotypes and acquired DNA aberration is flexible, allowing a large number of chromosomal alterations, including balanced and imbalanced losses and gains, copy-neutral loss-of-heterozygosity (LOH) and tetraploidy. We found our model (which we term J-LOH) to be superior for localizing rare aberrations in a simulated 3% mixture sample. More generally, our model provides a framework for full integration of the germline and tumor genomes to deal more effectively with missing or uncertain features, and thus extract maximal information from difficult scenarios where existing methods fail.
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Affiliation(s)
- Rui Xia
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, United States of America
| | - Selina Vattathil
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Human & Molecular Genetics Program, The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, United States of America
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, United States of America
- Human & Molecular Genetics Program, The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, United States of America
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