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Sehgal A, Ziaei Jam H, Shen A, Gymrek M. Genome-wide detection of somatic mosaicism at short tandem repeats. Bioinformatics 2024; 40:btae485. [PMID: 39078205 PMCID: PMC11319640 DOI: 10.1093/bioinformatics/btae485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 06/30/2024] [Accepted: 07/29/2024] [Indexed: 07/31/2024] Open
Abstract
MOTIVATION Somatic mosaicism has been implicated in several developmental disorders, cancers, and other diseases. Short tandem repeats (STRs) consist of repeated sequences of 1-6 bp and comprise >1 million loci in the human genome. Somatic mosaicism at STRs is known to play a key role in the pathogenicity of loci implicated in repeat expansion disorders and is highly prevalent in cancers exhibiting microsatellite instability. While a variety of tools have been developed to genotype germline variation at STRs, a method for systematically identifying mosaic STRs is lacking. RESULTS We introduce prancSTR, a novel method for detecting mosaic STRs from individual high-throughput sequencing datasets. prancSTR is designed to detect loci characterized by a single high-frequency mosaic allele, but can also detect loci with multiple mosaic alleles. Unlike many existing mosaicism detection methods for other variant types, prancSTR does not require a matched control sample as input. We show that prancSTR accurately identifies mosaic STRs in simulated data, demonstrate its feasibility by identifying candidate mosaic STRs in Illumina whole genome sequencing data derived from lymphoblastoid cell lines for individuals sequenced by the 1000 Genomes Project, and evaluate the use of prancSTR on Element and PacBio data. In addition to prancSTR, we present simTR, a novel simulation framework which simulates raw sequencing reads with realistic error profiles at STRs. AVAILABILITY AND IMPLEMENTATION prancSTR and simTR are freely available at https://github.com/gymrek-lab/trtools. Detailed documentation is available at https://trtools.readthedocs.io/.
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Affiliation(s)
- Aarushi Sehgal
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, United States
| | - Helyaneh Ziaei Jam
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, United States
| | - Andrew Shen
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, United States
| | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, United States
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, United States
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2
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Militaru MS, Babliuc IM, Bloaje-Florică VL, Danci VA, Filip-Deac I, Kutasi E, Simon V, Militaru M, Cătană A. The Impact of Chromosomal Mosaicisms on Prenatal Diagnosis and Genetic Counseling-A Narrative Review. J Pers Med 2024; 14:774. [PMID: 39064028 PMCID: PMC11277968 DOI: 10.3390/jpm14070774] [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: 06/14/2024] [Revised: 07/13/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Genetic disorders represent a high-impact diagnosis for both patients and their families. Prenatal screening methods and, when recommended, genetic testing allow parents to make informed decisions about the course a pregnancy is going to take. Although offering certainty about the potential evolution and prognosis of the pregnancy, and then the newborn, is usually not possible, genetic counseling can offer valuable insights into genetic disorders. Chromosomal mosaicisms are genetic anomalies that affect only some cell lines in either the fetus or the placenta or both. They can affect autosomal or heterosomal chromosomes, and they can be either numerical or structural. The prognosis seems to be more severe if the genetic alterations are accompanied by malformations visible in ultrasounds. Several genetic techniques can be used to diagnose certain mosaicisms, depending on their nature. A novel approach in prenatal care is non-invasive prenatal screening (NIPS), also known as non-invasive prenatal testing (NIPT), which, although it does not always have diagnostic value, can provide valuable information about potential genetic anomalies, especially numerical, with high sensitivity (Se).
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Affiliation(s)
- Mariela Sanda Militaru
- Department of Molecular Sciences, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hatieganu”, 400012 Cluj-Napoca, Romania; (M.S.M.); (A.C.)
- Regional Laboratory Cluj-Napoca, Department of Medical Genetics, Regina Maria Health Network, 400363 Cluj-Napoca, Romania
| | - Ioana-Mădălina Babliuc
- Department for Mother and Child Health, Pediatric 1, Emergency County Hospital, No. 68 Motilor Street, 400394 Cluj-Napoca, Romania; (I.-M.B.); (V.-A.D.); (V.S.)
| | | | - Valentin-Adrian Danci
- Department for Mother and Child Health, Pediatric 1, Emergency County Hospital, No. 68 Motilor Street, 400394 Cluj-Napoca, Romania; (I.-M.B.); (V.-A.D.); (V.S.)
| | - Iulia Filip-Deac
- County Emergency Clinical Hospital, 50 Dr. Gheorghe Marinescu Street, 540136 Târgu Mureș, Romania;
| | - Enikő Kutasi
- Department of Molecular Sciences, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hatieganu”, 400012 Cluj-Napoca, Romania; (M.S.M.); (A.C.)
- Department for Mother and Child Health, Pediatric 1, Emergency County Hospital, No. 68 Motilor Street, 400394 Cluj-Napoca, Romania; (I.-M.B.); (V.-A.D.); (V.S.)
| | - Vasile Simon
- Department for Mother and Child Health, Pediatric 1, Emergency County Hospital, No. 68 Motilor Street, 400394 Cluj-Napoca, Romania; (I.-M.B.); (V.-A.D.); (V.S.)
- Department of Urology, University of Medicine and Pharmacy “Iuliu Hatieganu”, 11 Tăbăcarilor Street, 400139 Cluj-Napoca, Romania
| | - Mihai Militaru
- Pediatric 2 Discipline, University of Medicine and Pharmacy “Iuliu Hatieganu”, Emergency County Hospital, No. 3-5 Clinicilor Street, 400535 Cluj-Napoca, Romania;
| | - Andreea Cătană
- Department of Molecular Sciences, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hatieganu”, 400012 Cluj-Napoca, Romania; (M.S.M.); (A.C.)
- Regional Laboratory Cluj-Napoca, Department of Medical Genetics, Regina Maria Health Network, 400363 Cluj-Napoca, Romania
- Department of Oncogenetics, Institute of Oncology, “Prof. Dr. I. Chiricuță”, 400015 Cluj-Napoca, Romania
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3
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Liou JJ, Lou J, Nakagiri J, Yong W, Hom CL, Doran EW, Totoiu M, Lott I, Mapstone M, Keator DB, Brickman AM, Wright S, Nelson B, Lai F, Xicota L, Dang LHT, Li J, Santini T, Mettenburg JM, Ikonomovic MD, Kofler J, Ibrahim T, Head E. A Neuropathology Case Report of a Woman with Down Syndrome who Remained Cognitively Stable. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.01.24308050. [PMID: 38883742 PMCID: PMC11177914 DOI: 10.1101/2024.06.01.24308050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
In this neuropathology case report, we present findings from an individual with Down syndrome (DS) who remained cognitively stable despite Alzheimer's disease (AD) neuropathology. Clinical assessments, fluid biomarkers, neuroimaging, and neuropathological examinations were conducted to characterize her condition. Notably, her ApoE genotype was E2/3, which is associated with a decreased risk of dementia. Neuroimaging revealed stable yet elevated amyloid profiles and moderately elevated tau levels, while neuropathology indicated intermediate AD neuropathologic change with Lewy body pathology and cerebrovascular pathology. Despite the presence of AD pathology, the participant demonstrated intact cognitive functioning, potentially attributed to factors such as genetic variations, cognitive resilience, and environmental enrichment. The findings suggest a dissociation between clinical symptoms and neuropathological changes, emphasizing the complexity of AD progression in DS. Further investigation into factors influencing cognitive resilience in individuals with DS, including comorbidities and social functioning, is warranted. Understanding the mechanisms underlying cognitive stability in DS could offer insights into resilience to AD neuropathology in people with DS and in the general population and inform future interventions.
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Waldvogel SM, Posey JE, Goodell MA. Human embryonic genetic mosaicism and its effects on development and disease. Nat Rev Genet 2024:10.1038/s41576-024-00715-z. [PMID: 38605218 DOI: 10.1038/s41576-024-00715-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
Nearly every mammalian cell division is accompanied by a mutational event that becomes fixed in a daughter cell. When carried forward to additional cell progeny, a clone of variant cells can emerge. As a result, mammals are complex mosaics of clones that are genetically distinct from one another. Recent high-throughput sequencing studies have revealed that mosaicism is common, clone sizes often increase with age and specific variants can affect tissue function and disease development. Variants that are acquired during early embryogenesis are shared by multiple cell types and can affect numerous tissues. Within tissues, variant clones compete, which can result in their expansion or elimination. Embryonic mosaicism has clinical implications for genetic disease severity and transmission but is likely an under-recognized phenomenon. To better understand its implications for mosaic individuals, it is essential to leverage research tools that can elucidate the mechanisms by which expanded embryonic variants influence development and disease.
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Affiliation(s)
- Sarah M Waldvogel
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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Brlek P, Bulić L, Bračić M, Projić P, Škaro V, Shah N, Shah P, Primorac D. Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives. Cells 2024; 13:504. [PMID: 38534348 DOI: 10.3390/cells13060504] [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: 02/06/2024] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The integration of whole genome sequencing (WGS) into all aspects of modern medicine represents the next step in the evolution of healthcare. Using this technology, scientists and physicians can observe the entire human genome comprehensively, generating a plethora of new sequencing data. Modern computational analysis entails advanced algorithms for variant detection, as well as complex models for classification. Data science and machine learning play a crucial role in the processing and interpretation of results, using enormous databases and statistics to discover new and support current genotype-phenotype correlations. In clinical practice, this technology has greatly enabled the development of personalized medicine, approaching each patient individually and in accordance with their genetic and biochemical profile. The most propulsive areas include rare disease genomics, oncogenomics, pharmacogenomics, neonatal screening, and infectious disease genomics. Another crucial application of WGS lies in the field of multi-omics, working towards the complete integration of human biomolecular data. Further technological development of sequencing technologies has led to the birth of third and fourth-generation sequencing, which include long-read sequencing, single-cell genomics, and nanopore sequencing. These technologies, alongside their continued implementation into medical research and practice, show great promise for the future of the field of medicine.
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Affiliation(s)
- Petar Brlek
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Luka Bulić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Matea Bračić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Petar Projić
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
| | | | - Nidhi Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Parth Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Dragan Primorac
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Split, 21000 Split, Croatia
- Eberly College of Science, The Pennsylvania State University, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- REGIOMED Kliniken, 96450 Coburg, Germany
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- National Forensic Sciences University, Gujarat 382007, India
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6
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Sehgal A, Ziaei-Jam H, Shen A, Gymrek M. Genome-wide detection of somatic mosaicism at short tandem repeats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568371. [PMID: 38045311 PMCID: PMC10690266 DOI: 10.1101/2023.11.22.568371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Motivation Somatic mosaicism, in which a mutation occurs post-zygotically, has been implicated in several developmental disorders, cancers, and other diseases. Short tandem repeats (STRs) consist of repeated sequences of 1-6bp and comprise more than 1 million loci in the human genome. Somatic mosaicism at STRs is known to play a key role in the pathogenicity of loci implicated in repeat expansion disorders and is highly prevalent in cancers exhibiting microsatellite instability. While a variety of tools have been developed to genotype germline variation at STRs, a method for systematically identifying mosaic STRs (mSTRs) is lacking. Results We introduce prancSTR, a novel method for detecting mSTRs from individual high-throughput sequencing datasets. Unlike many existing mosaicism detection methods for other variant types, prancSTR does not require a matched control sample as input. We show that prancSTR accurately identifies mSTRs in simulated data and demonstrate its feasibility by identifying candidate mSTRs in whole genome sequencing (WGS) data derived from lymphoblastoid cell lines for individuals sequenced by the 1000 Genomes Project. Our analysis identified an average of 76 and 577 non-homopolymer and homopolymer mSTRs respectively per cell line as well as multiple cell lines with outlier mSTR counts more than 6 times the population average, suggesting a subset of cell lines have particularly high STR instability rates. Availability prancSTR is freely available at https://github.com/gymrek-lab/trtools. Documentation Detailed documentation is available at https://trtools.readthedocs.io/.
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Affiliation(s)
- Aarushi Sehgal
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, USA
| | - Helyaneh Ziaei-Jam
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, USA
| | - Andrew Shen
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, USA
| | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, USA
- Department of Medicine, University of California San Diego, La Jolla, USA
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7
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Lim J, Chin V, Fairfax K, Moutinho C, Suan D, Ji H, Powell JE. Transitioning single-cell genomics into the clinic. Nat Rev Genet 2023:10.1038/s41576-023-00613-w. [PMID: 37258725 DOI: 10.1038/s41576-023-00613-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 06/02/2023]
Abstract
The use of genomics is firmly established in clinical practice, resulting in innovations across a wide range of disciplines such as genetic screening, rare disease diagnosis and molecularly guided therapy choice. This new field of genomic medicine has led to improvements in patient outcomes. However, most clinical applications of genomics rely on information generated from bulk approaches, which do not directly capture the genomic variation that underlies cellular heterogeneity. With the advent of single-cell technologies, research is rapidly uncovering how genomic data at cellular resolution can be used to understand disease pathology and mechanisms. Both DNA-based and RNA-based single-cell technologies have the potential to improve existing clinical applications and open new application spaces for genomics in clinical practice, with oncology, immunology and haematology poised for initial adoption. However, challenges in translating cellular genomics from research to a clinical setting must first be overcome.
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Affiliation(s)
- Jennifer Lim
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Department of Oncology, St George Hospital, Sydney, NSW, Australia
- The Kinghorn Cancer Centre, St Vincent's Hospital, Sydney, NSW, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Venessa Chin
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
- The Kinghorn Cancer Centre, St Vincent's Hospital, Sydney, NSW, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Kirsten Fairfax
- School of Medicine, University of Tasmania, Hobart, Australia
| | - Catia Moutinho
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Dan Suan
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Westmead Clinical School, University of Sydney, Sydney, NSW, Australia
| | - Hanlee Ji
- School of Medicine, Stanford University, Palo Alto, CA, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Joseph E Powell
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, Australia.
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8
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Kucuk E, van der Sanden BPGH, O'Gorman L, Kwint M, Derks R, Wenger AM, Lambert C, Chakraborty S, Baybayan P, Rowell WJ, Brunner HG, Vissers LELM, Hoischen A, Gilissen C. Comprehensive de novo mutation discovery with HiFi long-read sequencing. Genome Med 2023; 15:34. [PMID: 37158973 PMCID: PMC10169305 DOI: 10.1186/s13073-023-01183-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Long-read sequencing (LRS) techniques have been very successful in identifying structural variants (SVs). However, the high error rate of LRS made the detection of small variants (substitutions and short indels < 20 bp) more challenging. The introduction of PacBio HiFi sequencing makes LRS also suited for detecting small variation. Here we evaluate the ability of HiFi reads to detect de novo mutations (DNMs) of all types, which are technically challenging variant types and a major cause of sporadic, severe, early-onset disease. METHODS We sequenced the genomes of eight parent-child trios using high coverage PacBio HiFi LRS (~ 30-fold coverage) and Illumina short-read sequencing (SRS) (~ 50-fold coverage). De novo substitutions, small indels, short tandem repeats (STRs) and SVs were called in both datasets and compared to each other to assess the accuracy of HiFi LRS. In addition, we determined the parent-of-origin of the small DNMs using phasing. RESULTS We identified a total of 672 and 859 de novo substitutions/indels, 28 and 126 de novo STRs, and 24 and 1 de novo SVs in LRS and SRS respectively. For the small variants, there was a 92 and 85% concordance between the platforms. For the STRs and SVs, the concordance was 3.6 and 0.8%, and 4 and 100% respectively. We successfully validated 27/54 LRS-unique small variants, of which 11 (41%) were confirmed as true de novo events. For the SRS-unique small variants, we validated 42/133 DNMs and 8 (19%) were confirmed as true de novo event. Validation of 18 LRS-unique de novo STR calls confirmed none of the repeat expansions as true DNM. Confirmation of the 23 LRS-unique SVs was possible for 19 candidate SVs of which 10 (52.6%) were true de novo events. Furthermore, we were able to assign 96% of DNMs to their parental allele with LRS data, as opposed to just 20% with SRS data. CONCLUSIONS HiFi LRS can now produce the most comprehensive variant dataset obtainable by a single technology in a single laboratory, allowing accurate calling of substitutions, indels, STRs and SVs. The accuracy even allows sensitive calling of DNMs on all variant levels, and also allows for phasing, which helps to distinguish true positive from false positive DNMs.
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Affiliation(s)
- Erdi Kucuk
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bart P G H van der Sanden
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Luke O'Gorman
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Michael Kwint
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | | | | | | | | | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
- Department of Internal Medicine, Radboud University Medical Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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Chesneau B, Ivashchenko V, Habib C, Gaston V, Escudié F, Morel G, Capri Y, Vincent-Delorme C, Calvas P, Chassaing N, Plaisancié J. Evaluation of somatic and/or germline mosaicism in congenital malformation of the eye. Eur J Hum Genet 2023; 31:526-530. [PMID: 36404347 PMCID: PMC10172375 DOI: 10.1038/s41431-022-01234-3] [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: 08/24/2022] [Revised: 10/17/2022] [Accepted: 11/01/2022] [Indexed: 11/22/2022] Open
Abstract
Microphthalmia, Anophthalmia and Coloboma (MAC) form a spectrum of congenital eye malformations responsible for severe visual impairment. Despite the exploration of hundreds of genes by High-Throughput Sequencing (HTS), most of the patients remain without genetic diagnosis. One explanation could be the not yet demonstrated involvement of somatic mosaicism (undetected by conventional analysis pipelines) in those patients. Furthermore, the proportion of parental germline mosaicism in presumed de novo variations is still unknown in ocular malformations. Thus, using dedicated bioinformatics pipeline designed to detect mosaic variants, we reanalysed the sequencing data obtained from a 119 ocular development genes panel performed on blood samples of 78 probands with sporadic MAC without genetic diagnosis. Using the same HTS strategy, we sequenced 80 asymptomatic parents of 41 probands carrying a disease-causing variant in an ocular development gene considered de novo after Sanger sequencing of both parents. Reanalysis of the previously sequencing data did not find any mosaic variant in probands without genetic diagnosis. However, HTS of parents revealed undetected SOX2 and PAX6 mosaic variants in two parents. Finally, this work, performed on two large cohorts of patients with MAC spectrum, provides for the first time an overview of the interest of looking for mosaicism in ocular development disorders. Somatic mosaicism does not appear to be frequent in MAC spectrum and might explain only few diagnoses. Thus, other approaches such as whole genome sequencing should be considered in those patients. Parental mosaicism is however not that rare (around 5%) and challenging for genetic counselling.
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Affiliation(s)
- Bertrand Chesneau
- Service de Génétique Médicale, Hôpital Purpan, CHU de Toulouse, Toulouse, France
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU de Toulouse, Toulouse, France
| | | | - Christophe Habib
- Service de Génétique Médicale, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Véronique Gaston
- Service de Génétique Médicale, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Fréderic Escudié
- Département d'anatomopathologie, IUCT Oncopole, Toulouse, France
| | - Godelieve Morel
- Service de Génétique Médicale, CHU de Rennes, Rennes, France
| | - Yline Capri
- Service de Génétique Médicale, Hôpital Robert Debré, APHP, Paris, France
| | | | - Patrick Calvas
- Service de Génétique Médicale, Hôpital Purpan, CHU de Toulouse, Toulouse, France
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU de Toulouse, Toulouse, France
| | - Nicolas Chassaing
- Service de Génétique Médicale, Hôpital Purpan, CHU de Toulouse, Toulouse, France
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU de Toulouse, Toulouse, France
| | - Julie Plaisancié
- Service de Génétique Médicale, Hôpital Purpan, CHU de Toulouse, Toulouse, France.
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU de Toulouse, Toulouse, France.
- INSERM U1214, ToNIC, Université Toulouse III, Toulouse, France.
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10
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Francis DI, Stark Z, Scheffer IE, Tan TY, Murali K, Gallacher L, Amor DJ, Goel H, Downie L, Stutterd CA, Krzesinski EI, Vasudevan A, Oertel R, Petrovic V, Boys A, Wei V, Burgess T, Dun K, Oliver KL, Baxter A, Hackett A, Ayres S, Lunke S, Kalitsis P, Wall M. Comparing saliva and blood for the detection of mosaic genomic abnormalities that cause syndromic intellectual disability. Eur J Hum Genet 2022; 31:521-525. [PMID: 36446895 PMCID: PMC10172398 DOI: 10.1038/s41431-022-01232-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/23/2022] [Accepted: 10/31/2022] [Indexed: 11/30/2022] Open
Abstract
AbstractWe aimed to determine whether SNP-microarray genomic testing of saliva had a greater diagnostic yield than blood for pathogenic copy number variants (CNVs). We selected patients who underwent CMA testing of both blood and saliva from 23,289 blood and 21,857 saliva samples. Our cohort comprised 370 individuals who had testing of both, 224 with syndromic intellectual disability (ID) and 146 with isolated ID. Mosaic pathogenic CNVs or aneuploidy were detected in saliva but not in blood in 20/370 (4.4%). All 20 individuals had syndromic ID, accounting for 9.1% of the syndromic ID sub-cohort. Pathogenic CNVs were large in size (median of 46 Mb), and terminal in nature, with median mosaicism of 27.5% (not exceeding 40%). By contrast, non-mosaic pathogenic CNVs were 100% concordant between blood and saliva, considerably smaller in size (median of 0.65 Mb), and predominantly interstitial in location. Given that salivary microarray testing has increased diagnostic utility over blood in individuals with syndromic ID, we recommend it as a first-tier testing in this group.
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11
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Ip A, Della Pia A, Kim GY(G, Lofters J, Behrmann J, Patel D, Kats S, Estella JJ, De Dios I, Ma W, Pecora AL, Goy AH, Koprivnikar J, McCloskey JK, Albitar M. Reliability of Cell-Free DNA and Targeted NGS in Predicting Chromosomal Abnormalities of Patients With Myeloid Neoplasms. Front Oncol 2022; 12:923809. [PMID: 35774119 PMCID: PMC9238409 DOI: 10.3389/fonc.2022.923809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/11/2022] [Indexed: 11/17/2022] Open
Abstract
Introduction Cytogenetic analysis is important for stratifying patients with various neoplasms. We explored the use of targeted next generation sequencing (NGS) in detecting chromosomal structural abnormalities or copy number variations (CNVs) in patients with myeloid neoplasms. Methods Plasma cell-free DNA (cfDNA) from 2821 myeloid or lymphoid neoplasm patients were collected. cfDNA was sequenced using a 275 gene panel. CNVkit software was used for analyzing and visualizing CNVs. Cytogenetic data from corresponding bone marrow (BM) samples was available on 89 myeloid samples. Results Of the 2821 samples, 1539 (54.5%) showed evidence of mutations consistent with the presence of neoplastic clones in circulation. Of these 1539 samples, 906 (59%) showed abnormalities associated with myeloid neoplasms and 633 (41%) with lymphoid neoplasms. Chromosomal structural abnormalities in cfDNA were detected in 146 (16%) myeloid samples and 76 (12%) lymphoid samples. Upon comparison of the myeloid samples with 89 BM patients, NGS testing was able to reliably detect chromosomal gain or loss, except for fusion abnormalities. When cytogenetic abnormalities were classified according to prognostic classes, there was a complete (100%) concordance between cfDNA NGS data and cytogenetic data. Conclusions This data shows that liquid biopsy using targeted NGS is reliable in detecting chromosomal structural abnormalities in myeloid neoplasms. In specific circumstances, targeted NGS may be reliable and efficient to provide adequate information without the need for BM biopsy considering broad mutation profiling can be obtained through adequate sequencing within the same test. Overall, this study supports the use of liquid biopsy for early diagnosis and monitoring of patients with myeloid neoplasms.
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Affiliation(s)
- Andrew Ip
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Alexandra Della Pia
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- Ernest Mario School of Pharmacy at Rutgers University, Department of Pharmacy Practice and Administration, Piscataway, NJ, United States
| | - Gee Youn (Geeny) Kim
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- Ernest Mario School of Pharmacy at Rutgers University, Department of Pharmacy Practice and Administration, Piscataway, NJ, United States
| | - Jason Lofters
- Englewood Health Internal Medicine Residency Program, Englewood, NJ, United States
| | - James Behrmann
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Dylon Patel
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Simone Kats
- Ernest Mario School of Pharmacy at Rutgers University, Department of Pharmacy Practice and Administration, Piscataway, NJ, United States
| | | | - Ivan De Dios
- Genomic Testing Cooperative, Hematology, Irvine, CA, United States
| | - Wanlong Ma
- Genomic Testing Cooperative, Hematology, Irvine, CA, United States
| | - Andrew L. Pecora
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Andre H. Goy
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Jamie Koprivnikar
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
| | - James K. McCloskey
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
| | - Maher Albitar
- Genomic Testing Cooperative, Hematology, Irvine, CA, United States
- *Correspondence: Maher Albitar,
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12
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Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology. Genes (Basel) 2022; 13:genes13020333. [PMID: 35205378 PMCID: PMC8871714 DOI: 10.3390/genes13020333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
During the last decade, genetic testing has emerged as an important etiological diagnostic tool for Mendelian diseases, including pediatric neurological conditions. A genetic diagnosis has a considerable impact on disease management and treatment; however, many cases remain undiagnosed after applying standard diagnostic sequencing techniques. This review discusses various methods to improve the molecular diagnostic rates in these genomic cold cases. We discuss extended analysis methods to consider, non-Mendelian inheritance models, mosaicism, dual/multiple diagnoses, periodic re-analysis, artificial intelligence tools, and deep phenotyping, in addition to integrating various omics methods to improve variant prioritization. Last, novel genomic technologies, including long-read sequencing, artificial long-read sequencing, and optical genome mapping are discussed. In conclusion, a more comprehensive molecular analysis and a timely re-analysis of unsolved cases are imperative to improve diagnostic rates. In addition, our current understanding of the human genome is still limited due to restrictions in technologies. Novel technologies are now available that improve upon some of these limitations and can capture all human genomic variation more accurately. Last, we recommend a more routine implementation of high molecular weight DNA extraction methods that is coherent with the ability to use and/or optimally benefit from these novel genomic methods.
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13
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Morton SU, Quiat D, Seidman JG, Seidman CE. Genomic frontiers in congenital heart disease. Nat Rev Cardiol 2022; 19:26-42. [PMID: 34272501 PMCID: PMC9236191 DOI: 10.1038/s41569-021-00587-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
The application of next-generation sequencing to study congenital heart disease (CHD) is increasingly providing new insights into the causes and mechanisms of this prevalent birth anomaly. Whole-exome sequencing analysis identifies damaging gene variants altering single or contiguous nucleotides that are assigned pathogenicity based on statistical analyses of families and cohorts with CHD, high expression in the developing heart and depletion of damaging protein-coding variants in the general population. Gene classes fulfilling these criteria are enriched in patients with CHD and extracardiac abnormalities, evidencing shared pathways in organogenesis. Developmental single-cell transcriptomic data demonstrate the expression of CHD-associated genes in particular cell lineages, and emerging insights indicate that genetic variants perturb multicellular interactions that are crucial for cardiogenesis. Whole-genome sequencing analyses extend these observations, identifying non-coding variants that influence the expression of genes associated with CHD and contribute to the estimated ~55% of unexplained cases of CHD. These approaches combined with the assessment of common and mosaic genetic variants have provided a more complete knowledge of the causes and mechanisms of CHD. Such advances provide knowledge to inform the clinical care of patients with CHD or other birth defects and deepen our understanding of the complexity of human development. In this Review, we highlight known and candidate CHD-associated human genes and discuss how the integration of advances in developmental biology research can provide new insights into the genetic contributions to CHD.
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Affiliation(s)
- Sarah U. Morton
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,These authors contributed equally: Sarah U. Morton, Daniel Quiat
| | - Daniel Quiat
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Cardiology, Boston Children’s Hospital, Boston, MA, USA.,These authors contributed equally: Sarah U. Morton, Daniel Quiat
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard University, Boston, MA, USA.,
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14
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Domogala DD, Gambin T, Zemet R, Wu CW, Schulze KV, Yang Y, Wilson TA, Machol I, Liu P, Stankiewicz P. Detection of low-level parental somatic mosaicism for clinically relevant SNVs and indels identified in a large exome sequencing dataset. Hum Genomics 2021; 15:72. [PMID: 34930489 PMCID: PMC8686574 DOI: 10.1186/s40246-021-00369-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/27/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Due to the limitations of the current routine diagnostic methods, low-level somatic mosaicism with variant allele fraction (VAF) < 10% is often undetected in clinical settings. To date, only a few studies have attempted to analyze tissue distribution of low-level parental mosaicism in a large clinical exome sequencing (ES) cohort. METHODS Using a customized bioinformatics pipeline, we analyzed apparent de novo single-nucleotide variants or indels identified in the affected probands in ES trio data at Baylor Genetics clinical laboratories. Clinically relevant variants with VAFs between 30 and 70% in probands and lower than 10% in one parent were studied. DNA samples extracted from saliva, buccal cells, redrawn peripheral blood, urine, hair follicles, and nail, representing all three germ layers, were tested using PCR amplicon next-generation sequencing (amplicon NGS) and droplet digital PCR (ddPCR). RESULTS In a cohort of 592 clinical ES trios, we found 61 trios, each with one parent suspected of low-level mosaicism. In 21 parents, the variants were validated using amplicon NGS and seven of them by ddPCR in peripheral blood DNA samples. The parental VAFs in blood samples varied between 0.08 and 9%. The distribution of VAFs in additional tissues ranged from 0.03% in hair follicles to 9% in re-drawn peripheral blood. CONCLUSIONS Our study illustrates the importance of analyzing ES data using sensitive computational and molecular methods for low-level parental somatic mosaicism for clinically relevant variants previously diagnosed in routine clinical diagnostics as apparent de novo.
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Affiliation(s)
- Daniel D Domogala
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas at MD Anderson, Houston, TX, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chung Wah Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Katharina V Schulze
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- AiLife Diagnostics, 1920 Country Place Pkwy Suite 100, Pearland, TX, USA
| | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | | | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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15
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Cook CB, Armstrong L, Boerkoel CF, Clarke LA, du Souich C, Demos MK, Gibson WT, Gill H, Lopez E, Patel MS, Selby K, Abu-Sharar Z, Elliott AM, Friedman JM. Somatic mosaicism detected by genome-wide sequencing in 500 parent-child trios with suspected genetic disease: clinical and genetic counseling implications. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006125. [PMID: 34697084 PMCID: PMC8751411 DOI: 10.1101/mcs.a006125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/13/2021] [Indexed: 01/28/2023] Open
Abstract
Identifying genetic mosaicism is important in establishing a diagnosis, assessing recurrence risk, and providing accurate genetic counseling. Next-generation sequencing has allowed for the identification of mosaicism at levels below those detectable by conventional Sanger sequencing or chromosomal microarray analysis. The CAUSES Clinic was a pediatric translational trio-based genome-wide (exome or genome) sequencing study of 500 families (531 children) with suspected genetic disease at BC Children's and Women's Hospitals. Here we present 12 cases of apparent mosaicism identified in the CAUSES cohort: nine cases of parental mosaicism for a disease-causing variant found in a child and three cases of mosaicism in the proband for a de novo variant. In six of these cases, there was no evidence of mosaicism on Sanger sequencing—the variant was not detected on Sanger sequencing in three cases, and it appeared to be heterozygous in three others. These cases are examples of six clinical manifestations of mosaicism: a proband with classical clinical features of mosaicism (e.g., segmental abnormalities of skin pigmentation or asymmetrical growth of bilateral body parts), a proband with unusually mild manifestations of a disease, a mosaic proband who is clinically indistinguishable from the constitutive phenotype, a mosaic parent with no clinical features of the disease, a mosaic parent with mild manifestations of the disease, and a family in which both parents are unaffected and two siblings have the same disease-causing constitutional mutation. Our data demonstrate the importance of considering the possibility of mosaicism whenever exome or genome sequencing is performed and that its detection via genome-wide sequencing can permit more accurate genetic counseling.
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Affiliation(s)
- Courtney B Cook
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Linlea Armstrong
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Cornelius F Boerkoel
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Lorne A Clarke
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Christèle du Souich
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Michelle K Demos
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | - William T Gibson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Harinder Gill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Elena Lopez
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Millan S Patel
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Kathryn Selby
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | - Ziad Abu-Sharar
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | | | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4.,Women's Health Research Institute, Vancouver, British Columbia, Canada V6H 2N9
| | - Jan M Friedman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
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16
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Hochstenbach R, Liehr T, Hastings RJ. Chromosomes in the genomic age. Preserving cytogenomic competence of diagnostic genome laboratories. Eur J Hum Genet 2021; 29:541-552. [PMID: 33311710 PMCID: PMC8115145 DOI: 10.1038/s41431-020-00780-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 10/26/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
Participation of clinical genetic laboratories in External Quality Assessment schemes (EQAs) is a powerful method to ascertain if any improvement or additional training is required in the diagnostic service. Here, we provide evidence from recent EQAs that the competence in recognizing and interpreting cytogenetic aberrations is variable and could impact patient management. We identify several trends that could affect cytogenomic competence. Firstly, as a result of the age distribution among clinical laboratory geneticists (CLGs) registered at the European Board of Medical Genetics, about 25-30% of those with experience in cytogenetics will retire during the next decade. At the same time, there are about twice as many molecular geneticists to cytogeneticists among the younger CLGs. Secondly, when surveying training programs for CLG, we observed that not all programs guarantee that candidates gather sufficient experience in clinical cytogenomics. Thirdly, we acknowledge that whole genome sequencing (WGS) has a great attraction to biomedical scientists that wish to enter a training program for CLG. This, with a larger number of positions available, makes a choice for specialization in molecular genetics logical. However, current WGS technology cannot provide a diagnosis in all cases. Understanding the etiology of chromosomal rearrangements is essential for appropriate follow-up and for ascertaining recurrence risks. We define the minimal knowledge a CLG should have about cytogenomics in a world dominated by WGS, and discuss how laboratory directors and boards of professional organizations in clinical genetics can uphold cytogenomic competence by providing adequate CLG training programs and attracting sufficient numbers of trainees.
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Affiliation(s)
- Ron Hochstenbach
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Department of Clinical Genetics, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands.
| | - Thomas Liehr
- University Clinic Jena, Institute of Human Genetics, Am Klinikum 1, 07747, Jena, Germany
| | - Rosalind J Hastings
- GenQA, Level 1, The Women's Centre, John Radcliffe Hospital, Oxford University Hospitals Foundation Trust, Headley Way, Headington, Oxford, OX3 9DU, UK
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17
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Shabrish S, Mittra I. Cytokine Storm as a Cellular Response to dsDNA Breaks: A New Proposal. Front Immunol 2021; 12:622738. [PMID: 33597956 PMCID: PMC7882731 DOI: 10.3389/fimmu.2021.622738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/07/2021] [Indexed: 12/20/2022] Open
Abstract
Pathogenesis of cytokine storm is poorly understood. In this article we propose a new mechanism and suggest innovative therapeutic avenues for its prevention. We have reported that particles of cell-free chromatin (cfCh) that are released from the billions of cells that die in the body everyday can illegitimately integrate into genomes of healthy cells to trigger dsDNA breaks. The latter leads to apoptosis and/or intense activation of inflammatory cytokines in the affected cells. We hypothesise that a similar phenomenon of dsDNA breaks and inflammation is involved in cytokine storm. The abundant cfCh particles that are released from dying host cells following viral/microbial invasion initiate a cascading effect of more cell death resulting in a vicious cycle of further DNA damage, apoptosis and hyper-inflammation which culminate in cytokine storm. We propose that this unrelenting vicious cycle of cellular DNA damage and cytokine storm may be the underlying cause of high mortality from severe COVID-19. We discuss results of our preclinical studies wherein we have shown that endotoxin induced cytokine storm in mice can be reversed by three different agents that have the ability to inactivate cfCh. These agents may be worthy of investigation in clinical trials to reduce mortality from COVID-19.
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Affiliation(s)
- Snehal Shabrish
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, and Homi Bhabha National Institute, Mumbai, India
| | - Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, and Homi Bhabha National Institute, Mumbai, India
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18
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Rydzanicz M, Olszewski P, Kedra D, Davies H, Filipowicz N, Bruhn-Olszewska B, Cavalli M, Szczałuba K, Młynek M, Machnicki MM, Stawiński P, Kostrzewa G, Krajewski P, Śladowski D, Chrzanowska K, Dumanski JP, Płoski R. Variable degree of mosaicism for tetrasomy 18p in phenotypically discordant monozygotic twins-Diagnostic implications. Mol Genet Genomic Med 2020; 9:e1526. [PMID: 33319479 PMCID: PMC7963419 DOI: 10.1002/mgg3.1526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 11/23/2022] Open
Abstract
Background Phenotypically discordant monozygotic twins (PDMZTs) offer a unique opportunity to study post‐zygotic genetic variation and provide insights into the linkage between genotype and phenotype. We report a comprehensive analysis of a pair of PDMZTs. Methods Dysmorphic features and delayed neuro‐motor development were observed in the proband, whereas her twin sister was phenotypically normal. Four tissues (blood, skin, hair follicles, and buccal mucosa) from both twins were studied using four complementary methods, including whole‐exome sequencing, karyotyping, array CGH, and SNP array. Results In the proband, tetrasomy 18p affecting all studied tissues except for blood was identified. Karyotyping of fibroblasts revealed isochromosome 18p [i(18p)] in all metaphases. The corresponding analysis of the phenotypically normal sister surprisingly revealed low‐level mosaicism (5.4%) for i(18p) in fibroblasts. Conclusion We emphasize that when mosaicism is suspected, multiple tissues should be studied and we highlight the usefulness of non‐invasive sampling of hair follicles and buccal mucosa as a convenient source of non‐mesoderm‐derived DNA, which complements the analysis of mesoderm using blood. Moreover, low‐level mosaic tetrasomy 18p is well tolerated and such low‐level mosaicism, readily detected by karyotyping, can be missed by other methods. Finally, mosaicism for low‐level tetrasomy 18p might be more common in the general population than it is currently recognized, due to detection limitations.
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Affiliation(s)
| | - Pawel Olszewski
- Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland
| | - Darek Kedra
- Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Natalia Filipowicz
- Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland
| | - Bozena Bruhn-Olszewska
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marco Cavalli
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Marlena Młynek
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Marcin M Machnicki
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Grażyna Kostrzewa
- Department of Forensic Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Paweł Krajewski
- Department of Forensic Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Dariusz Śladowski
- Department of Transplantology and Central Tissue Bank, Centre for Biostructure, Medical University of Warsaw, Warsaw, Poland
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Jan P Dumanski
- Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland.,Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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19
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Groopman EE, Povysil G, Goldstein DB, Gharavi AG. Rare genetic causes of complex kidney and urological diseases. Nat Rev Nephrol 2020; 16:641-656. [PMID: 32807983 PMCID: PMC7772719 DOI: 10.1038/s41581-020-0325-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 02/08/2023]
Abstract
Although often considered a single-entity, chronic kidney disease (CKD) comprises many pathophysiologically distinct disorders that result in persistently abnormal kidney structure and/or function, and encompass both monogenic and polygenic aetiologies. Rare inherited forms of CKD frequently span diverse phenotypes, reflecting genetic phenomena including pleiotropy, incomplete penetrance and variable expressivity. Use of chromosomal microarray and massively parallel sequencing technologies has revealed that genomic disorders and monogenic aetiologies contribute meaningfully to seemingly complex forms of CKD across different clinically defined subgroups and are characterized by high genetic and phenotypic heterogeneity. Investigations of prevalent genomic disorders in CKD have integrated genetic, bioinformatic and functional studies to pinpoint the genetic drivers underlying their renal and extra-renal manifestations, revealing both monogenic and polygenic mechanisms. Similarly, massively parallel sequencing-based analyses have identified gene- and allele-level variation that contribute to the clinically diverse phenotypes observed for many monogenic forms of nephropathy. Genome-wide sequencing studies suggest that dual genetic diagnoses are found in at least 5% of patients in whom a genetic cause of disease is identified, highlighting the fact that complex phenotypes can also arise from multilocus variation. A multifaceted approach that incorporates genetic and phenotypic data from large, diverse cohorts will help to elucidate the complex relationships between genotype and phenotype for different forms of CKD, supporting personalized medicine for individuals with kidney disease.
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Affiliation(s)
- Emily E Groopman
- Division of Nephrology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University College of Physicians and Surgeons, New York, NY, USA.
- Institute for Genomic Medicine, Columbia University, New York, NY, USA.
- Center for Precision Medicine and Genomics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
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20
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Villela D, de Barros JS, da Costa SS, Aguiar TFM, Campagnari F, Vianna-Morgante AM, Krepischi ACV, Rosenberg C. Detection of mosaicism for segmental and whole chromosome imbalances by targeted sequencing. Ann Hum Genet 2020; 85:18-26. [PMID: 32761927 DOI: 10.1111/ahg.12402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 11/29/2022]
Abstract
Mosaic segmental and whole chromosome copy number alterations are postzygotic variations known to be associated with several disorders. We have previously presented an efficient targeted sequencing approach to simultaneously detect point mutations and copy number variations (CNVs). In this study, we evaluated the efficiency of this approach to detect mosaic CNVs, using seven postnatal and 19 tumor samples, previously characterized by chromosomal microarray analyses (CMA). These samples harbored a total of 28 genomic imbalances ranging in size from 0.68 to 171 Mb, and present in 10-80% of the cells. All CNV regions covered by the platform were correctly identified in postnatal samples, and only seven out of 19 CNVs from tumor samples were not identified either because of a lack of target probes in the affected genomic regions or an absence of minimum reads for an alteration call. These results demonstrate that, in a research setting, this is a robust approach for detecting mosaicism in cases of segmental and whole chromosome alterations. Although the current sequencing platform presented a resolution similar to genomic microarrays, it is still necessary to further validate this approach in a clinical setting in order to replace CMA and sequencing analyses by a single test.
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Affiliation(s)
- Darine Villela
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana Sobral de Barros
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Silvia Souza da Costa
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Talita F M Aguiar
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | - Angela M Vianna-Morgante
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana C V Krepischi
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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21
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Bruel A, Vitobello A, Tran Mau‐Them F, Nambot S, Sorlin A, Denommé‐Pichon A, Delanne J, Moutton S, Callier P, Duffourd Y, Philippe C, Faivre L, Thauvin‐Robinet C. Next‐generation
sequencing approaches and challenges in the diagnosis of developmental anomalies and intellectual disability. Clin Genet 2020; 98:433-444. [DOI: 10.1111/cge.13764] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Ange‐Line Bruel
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Déficiences Intellectuelles de causes rares, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Antonio Vitobello
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Frédéric Tran Mau‐Them
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Sophie Nambot
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Arthur Sorlin
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Maladies dermatologiques en mosaïque Service de dermatologie, CHU Dijon Bourgogne Dijon France
| | - Anne‐Sophie Denommé‐Pichon
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Julian Delanne
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Sébastien Moutton
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Patrick Callier
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Yannis Duffourd
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Christophe Philippe
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Laurence Faivre
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Christel Thauvin‐Robinet
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Déficiences Intellectuelles de causes rares, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
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22
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Liu Q, Karolak JA, Grochowski CM, Wilson TA, Rosenfeld JA, Bacino CA, Lalani SR, Patel A, Breman A, Smith JL, Cheung SW, Lupski JR, Bi W, Stankiewicz P. Parental somatic mosaicism for CNV deletions - A need for more sensitive and precise detection methods in clinical diagnostics settings. Genomics 2020; 112:2937-2941. [PMID: 32387503 DOI: 10.1016/j.ygeno.2020.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 10/25/2022]
Abstract
To further assess the scale and level of parental somatic mosaicism, we queried the CMA database at Baylor Genetics. We selected 50 unrelated families where clinically relevant apparent de novo CNV-deletions were found in the affected probands. Parental blood samples screening using deletion junction-specific PCR revealed four parents with somatic mosaicism. Droplet digital PCR (ddPCR), qPCR, and amplicon-based next-generation sequencing (NGS) were applied to validate these findings. Using ddPCR levels of mosaicism ranged from undetectable to 18.5%. Amplicon-based NGS and qPCR for the father with undetectable mosaicism was able to detect mosaicism at 0.39%. In one mother, ddPCR analysis revealed 15.6%, 10.6%, 8.2%, and undetectable levels of mosaicism in her blood, buccal cells, saliva, and urine samples, respectively. Our data suggest that more sensitive and precise methods, e.g. CNV junction-specific LR-PCR, ddPCR, or qPCR may allow for a more refined assessment of the potential disease recurrence risk for an identified variant.
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Affiliation(s)
- Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
| | | | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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23
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Freeman TM, Wang D, Harris J. Genomic loci susceptible to systematic sequencing bias in clinical whole genomes. Genome Res 2020; 30:415-426. [PMID: 32156711 PMCID: PMC7111519 DOI: 10.1101/gr.255349.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/14/2020] [Indexed: 11/26/2022]
Abstract
Accurate massively parallel sequencing (MPS) of genetic variants is key to many areas of science and medicine, such as cataloging population genetic variation and diagnosing genetic diseases. Certain genomic positions can be prone to higher rates of systematic sequencing and alignment bias that limit accuracy, resulting in false positive variant calls. Current standard practices to differentiate between loci that can and cannot be sequenced with high confidence utilize consensus between different sequencing methods as a proxy for sequencing confidence. These practices have significant limitations, and alternative methods are required to overcome them. We have developed a novel statistical method based on summarizing sequenced reads from whole-genome clinical samples and cataloging them in "Incremental Databases" that maintain individual confidentiality. Allele statistics were cataloged for each genomic position that consistently showed systematic biases with the corresponding MPS sequencing pipeline. We found systematic biases present at ∼1%-3% of the human autosomal genome across five patient cohorts. We identified which genomic regions were more or less prone to systematic biases, including large homopolymer flanks (odds ratio = 23.29-33.69) and the NIST high confidence genomic regions (odds ratio = 0.154-0.191). We confirmed our predictions on a gold-standard reference genome and showed that these systematic biases can lead to suspect variant calls within clinical panels. Our results recommend increased caution to address systematic biases in whole-genome sequencing and alignment. This study provides the implementation of a simple statistical approach to enhance quality control of clinically sequenced samples by flagging variants at suspect loci for further analysis or exclusion.
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Affiliation(s)
- Timothy M Freeman
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, United Kingdom
| | - Dennis Wang
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, United Kingdom
- NIHR Sheffield Biomedical Research Centre, Sheffield S10 2JF, United Kingdom
- Department of Computer Science, University of Sheffield, Sheffield S1 4DP, United Kingdom
| | - Jason Harris
- Personalis, Incorporated, Menlo Park, California 94025, USA
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24
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Maria AG, Suzuki M, Berthon A, Kamilaris C, Demidowich A, Lack J, Zilbermint M, Hannah-Shmouni F, Faucz FR, Stratakis CA. Mosaicism for KCNJ5 Causing Early-Onset Primary Aldosteronism due to Bilateral Adrenocortical Hyperplasia. Am J Hypertens 2020; 33:124-130. [PMID: 31637427 DOI: 10.1093/ajh/hpz172] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/19/2019] [Accepted: 10/18/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Somatic variants in KCNJ5 are the most common cause of primary aldosteronism (PA). There are few patients with PA in whom the disease is caused by germline variants in the KCNJ5 potassium channel gene (familial hyperaldosteronism type III-FH-III). METHODS A 5-year-old patient who developed hypertension due to bilateral adrenocortical hyperplasia (BAH) causing PA had negative peripheral DNA testing for any known genetic causes of PA. He was treated medically with adequate control of his PA but by the third decade of his life, due to worsening renal function, he underwent bilateral adrenalectomy. RESULTS Focused exome sequencing in multiple nodules of his BAH uncovered a "hot-spot" pathogenic KCNJ5 variant, while repeated Sanger sequencing showed no detectable DNA defects in peripheral blood and other tissues. However, whole exome, "deep" sequencing revealed that 0.23% of copies of germline DNA did in fact carry the same KCNJ5 variant that was present in the adrenocortical nodules, suggesting low level germline mosaicism for this PA-causing KCNJ5 defect. CONCLUSIONS Thus, this patient represents a unique case of BAH due to a mosaic KCNJ5 defect. Undoubtedly, his milder PA compared with other known cases of FH-III, was due to his mosaicism. This case has a number of implications for the prognosis, treatment, and counseling of the many patients with PA due to BAH that are seen in hypertension clinics.
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Affiliation(s)
- Andrea G Maria
- Section on Genetics & Endocrinology, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Mari Suzuki
- Section on Genetics & Endocrinology, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
- National Institute of Diabetes and Digestive and Kidney Disorders, Bethesda, Maryland, USA
| | - Annabel Berthon
- Section on Genetics & Endocrinology, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Crystal Kamilaris
- Section on Genetics & Endocrinology, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Andrew Demidowich
- Section on Genetics & Endocrinology, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Disease, Frederick, Maryland, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Mihail Zilbermint
- Section on Genetics & Endocrinology, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
- Division of Endocrinology, Diabetes, and Metabolism, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Johns Hopkins Community Physicians at Suburban Hospital, Bethesda, Maryland, USA
| | - Fady Hannah-Shmouni
- Section on Genetics & Endocrinology, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Fabio R Faucz
- Section on Genetics & Endocrinology, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Constantine A Stratakis
- Section on Genetics & Endocrinology, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
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25
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SATB2-associated syndrome: first report of a gonadal and somatic mosaicism for an intragenic copy number variation. Clin Dysmorphol 2020; 28:205-210. [PMID: 31425298 DOI: 10.1097/mcd.0000000000000293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gonadal mosaicism has been reported in a variety of dominant or X-linked conditions and should be considered in all cases of apparent de-novo variation. Recently, some cases of supposed parental germline mosaicism have been shown to result from low-level somatic mosaicism. In most of the cases, mosaicism has been reported for pathogenic single nucleotide variants with only a few cases of copy number variation mosaicism described so far. Herein, we present the first case of parental somatic and gonadal copy number variation mosaicism in the SATB2 gene. We report three brothers presenting with the SATB2-associated syndrome. They all carry the same 121-kb heterozygous intragenic deletion of SATB2. Parental somatic mosaicism was detected by array-comparative genomic hybridization on a maternal blood sample and confirmed by Fluorescence in situ hybridization analysis on blood and buccal cells. This clinical report highlights the importance of investigating for parental somatic mosaicism to estimate the proper recurrence risk for subsequent pregnancy.
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26
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Gardner EJ, Prigmore E, Gallone G, Danecek P, Samocha KE, Handsaker J, Gerety SS, Ironfield H, Short PJ, Sifrim A, Singh T, Chandler KE, Clement E, Lachlan KL, Prescott K, Rosser E, FitzPatrick DR, Firth HV, Hurles ME. Contribution of retrotransposition to developmental disorders. Nat Commun 2019; 10:4630. [PMID: 31604926 PMCID: PMC6789007 DOI: 10.1038/s41467-019-12520-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 09/11/2019] [Indexed: 02/08/2023] Open
Abstract
Mobile genetic Elements (MEs) are segments of DNA which can copy themselves and other transcribed sequences through the process of retrotransposition (RT). In humans several disorders have been attributed to RT, but the role of RT in severe developmental disorders (DD) has not yet been explored. Here we identify RT-derived events in 9738 exome sequenced trios with DD-affected probands. We ascertain 9 de novo MEs, 4 of which are likely causative of the patient's symptoms (0.04%), as well as 2 de novo gene retroduplications. Beyond identifying likely diagnostic RT events, we estimate genome-wide germline ME mutation rate and selective constraint and demonstrate that coding RT events have signatures of purifying selection equivalent to those of truncating mutations. Overall, our analysis represents a comprehensive interrogation of the impact of retrotransposition on protein coding genes and a framework for future evolutionary and disease studies.
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Affiliation(s)
- Eugene J Gardner
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SA, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SA, UK
| | - Giuseppe Gallone
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SA, UK
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SA, UK
| | - Kaitlin E Samocha
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SA, UK
| | - Juliet Handsaker
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SA, UK
| | - Sebastian S Gerety
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SA, UK
| | - Holly Ironfield
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SA, UK
| | - Patrick J Short
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SA, UK
| | - Alejandro Sifrim
- Department of Human Genetics, KU Leuven, Herestraat 49, Box 602, Leuven, B-3000, Belgium
| | - Tarjinder Singh
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SA, UK
| | - Kate E Chandler
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, Greater, Manchester, M13 9WL, UK
| | - Emma Clement
- Department of Clinical Genetics, North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Trust, Holborn, London, WC1N 3JH, UK
| | - Katherine L Lachlan
- Wessex Clinical Genetics Service, Southampton University Hospitals NHS Foundation Trust, Princess Anne Hospital, Southampton, SO16 5YA, UK.,Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, SO17 1BJ, UK
| | - Katrina Prescott
- Clinical Genetics Department, Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Chapel Allerton Hospital, Leeds, LS7 4SA, UK
| | - Elisabeth Rosser
- Department of Clinical Genetics, North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Trust, Holborn, London, WC1N 3JH, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, WGH, Edinburgh, EH4 2SP, UK
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SA, UK.,East Anglian Medical Genetics Service, Box 134, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, CB10 1SA, UK.
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27
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Clinically-relevant postzygotic mosaicism in parents and children with developmental disorders in trio exome sequencing data. Nat Commun 2019; 10:2985. [PMID: 31278258 PMCID: PMC6611863 DOI: 10.1038/s41467-019-11059-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/12/2019] [Indexed: 12/22/2022] Open
Abstract
Mosaic genetic variants can have major clinical impact. We systematically analyse trio exome sequence data from 4,293 probands from the DDD Study with severe developmental disorders for pathogenic postzygotic mosaicism (PZM) in the child or a clinically-unaffected parent, and use ultrahigh-depth sequencing to validate candidate mosaic variants. We observe that levels of mosaicism for small genetic variants are usually equivalent in both saliva and blood and ~3% of causative de novo mutations exhibit PZM; this is an important observation, as the sibling recurrence risk is extremely low. We identify parental PZM in 21 trios (0.5% of trios), resulting in a substantially increased sibling recurrence risk in future pregnancies. Together, these forms of mosaicism account for 40 (1%) diagnoses in our cohort. Likely child-PZM mutations occur equally on both parental haplotypes, and the penetrance of detectable mosaic pathogenic variants overall is likely to be less than half that of constitutive variants.
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28
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Raghuram GV, Chaudhary S, Johari S, Mittra I. Illegitimate and Repeated Genomic Integration of Cell-Free Chromatin in the Aetiology of Somatic Mosaicism, Ageing, Chronic Diseases and Cancer. Genes (Basel) 2019; 10:genes10060407. [PMID: 31142004 PMCID: PMC6628102 DOI: 10.3390/genes10060407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 12/19/2022] Open
Abstract
Emerging evidence suggests that an individual is a complex mosaic of genetically divergent cells. Post-zygotic genomes of the same individual can differ from one another in the form of single nucleotide variations, copy number variations, insertions, deletions, inversions, translocations, other structural and chromosomal variations and footprints of transposable elements. High-throughput sequencing has led to increasing detection of mosaicism in healthy individuals which is related to ageing, neuro-degenerative disorders, diabetes mellitus, cardiovascular diseases and cancer. These age-related disorders are also known to be associated with significant increase in DNA damage and inflammation. Herein, we discuss a newly described phenomenon wherein the genome is under constant assault by illegitimate integration of cell-free chromatin (cfCh) particles that are released from the billions of cells that die in the body every day. We propose that such repeated genomic integration of cfCh followed by dsDNA breaks and repair by non-homologous-end-joining as well as physical damage to chromosomes occurring throughout life may lead to somatic/chromosomal mosaicism which would increase with age. We also discuss the recent finding that genomic integration of cfCh and the accompanying DNA damage is associated with marked activation of inflammatory cytokines. Thus, the triple pathologies of somatic mosaicism, DNA/chromosomal damage and inflammation brought about by a common mechanism of genomic integration of cfCh may help to provide an unifying model for the understanding of aetiologies of the inter-related conditions of ageing, degenerative disorders and cancer.
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Affiliation(s)
- Gorantla V Raghuram
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
| | - Shahid Chaudhary
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
| | - Shweta Johari
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
| | - Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
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29
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Abstract
Single-cell omics studies provide unique information regarding cellular heterogeneity at various levels of the molecular biology central dogma. This knowledge facilitates a deeper understanding of how underlying molecular and architectural changes alter cell behavior, development, and disease processes. The emerging microchip-based tools for single-cell omics analysis are enabling the evaluation of cellular omics with high throughput, improved sensitivity, and reduced cost. We review state-of-the-art microchip platforms for profiling genomics, epigenomics, transcriptomics, proteomics, metabolomics, and multi-omics at single-cell resolution. We also discuss the background of and challenges in the analysis of each molecular layer and integration of multiple levels of omics data, as well as how microchip-based methodologies benefit these fields. Additionally, we examine the advantages and limitations of these approaches. Looking forward, we describe additional challenges and future opportunities that will facilitate the improvement and broad adoption of single-cell omics in life science and medicine.
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Affiliation(s)
- Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
| | - Amanda Finck
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
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30
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Ouwens KG, Jansen R, Tolhuis B, Slagboom PE, Penninx BW, Boomsma DI. A characterization of postzygotic mutations identified in monozygotic twins. Hum Mutat 2018; 39:1393-1401. [PMID: 29980163 PMCID: PMC6175188 DOI: 10.1002/humu.23586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 06/15/2018] [Accepted: 07/03/2018] [Indexed: 01/09/2023]
Abstract
Postzygotic mutations are DNA changes acquired from the zygote stage onwards throughout the lifespan. These changes lead to differences in DNA sequence among cells of an individual, potentially contributing to the etiology of complex disorders. Here we compared whole genome DNA sequence data of two monozygotic twin pairs, 40 and 100 years old, to detect somatic mosaicism. DNA samples were sequenced twice on two Illumina platforms (13X and 40X read depth) for increased specificity. Using differences in allelic ratios resulted in sets of 1,720 and 1,739 putative postzygotic mutations in the 40-year-old twin pair and 100-year-old twin pair, respectively, for subsequent enrichment analysis. This set of putative mutations was strongly (p < 4.37e-91) enriched in both twin pairs for regulatory elements. The corresponding genes were significantly enriched for genes that are alternatively spliced, and for genes involved in GTPase activity. This research shows that somatic mosaicism can be detected in monozygotic twin pairs by using allelic ratios calculated from DNA sequence data and that the mutations which are found by this approach are not randomly distributed throughout the genome.
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Affiliation(s)
- Klaasjan G. Ouwens
- Department of Biological PsychologyVU University AmsterdamAmsterdamThe Netherlands
- Genalice Core BVNijkerkThe Netherlands
| | - Rick Jansen
- Department of PsychiatryVU University Medical CenterAmsterdamThe Netherlands
| | | | - P. Eline Slagboom
- Department of Molecular EpidemiologyLeids Universitair Medisch CentrumLeidenThe Netherlands
| | | | - Dorret I. Boomsma
- Department of Biological PsychologyVU University AmsterdamAmsterdamThe Netherlands
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31
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A survey of undetected, clinically relevant chromosome abnormalities when replacing postnatal karyotyping by Whole Genome Sequencing. Eur J Med Genet 2018; 62:103543. [PMID: 30248410 DOI: 10.1016/j.ejmg.2018.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 07/30/2018] [Accepted: 09/18/2018] [Indexed: 11/21/2022]
Abstract
Whole genome sequencing (WGS) holds the potential to identify pathogenic gene mutations, copy number variation, uniparental disomy and structural rearrangements in a single genetic test. With its high diagnostic yield and decreasing costs, the question arises whether WGS can serve as a single test for all referrals to diagnostic genome laboratories ("one test fits all"). Here, we provide an estimate for the proportion of clinically relevant aberrations identified by light microscopy in postnatal referrals that would go undetected by WGS. To this end, we compiled the clinically relevant abnormal findings for each of the different referral categories in our laboratory during the period 2006-2015. We assumed that WGS would be performed on 300-500 bp DNA fragments with 150-bp paired sequence reads, and that the mean genome coverage is 30x, corresponding to current practice. For the detection of chromosomal mosaicism we set minimum thresholds of 10% for monosomy and 20% for trisomy. Based on the literature we assumed that balanced Robertsonian translocations and ∼9% of other, balanced chromosome rearrangements would not be detectable because of breakpoints in sequences of repetitive DNA. Based on our analysis of all 14,957 referrals, including 1455 abnormal cases, we show that at least 8.1% of these abnormalities would escape detection (corresponding to 0.79% of all referrals). The highest rate occurs in referrals of premature ovarian failure, as 73.3% of abnormalities would not be identified because of the frequent occurrence of low-level sex chromosome mosaicism. Among referrals of recurrent miscarriage, 25.6% of abnormalities would go undetected, mainly because of a high proportion of balanced Robertsonian translocations. In referrals of mental retardation (with or without multiple congenital anomalies) the abnormality would be missed in only 0.35% of referrals. These include cases without imbalances of unique DNA sequences but of clinical relevance, as for example, r(20) epilepsy syndrome. The expected shift to large-scale implementation of WGS ("one test fits most") as initial genetic test will be beneficial to patients and their families, since a cause for the clinical phenotype can be identified in more cases by a single genetic test at an early phase in the diagnostic process. However, a niche for genome analysis by light microscopy will remain. For example, in referrals of newborns with a suspicion of Down syndrome, karyotyping is not only a cost-effective method for providing a quick diagnosis, but also discriminates between trisomy 21 and a Robertsonian translocation involving chromosome 21. Thus, when replacing karyotyping by WGS, one must be aware of the rates and spectra of undetected abnormalities. In addition, it is equally important that requirements for cytogenetic follow-up studies are recognized.
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32
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Rohani L, Johnson AA, Naghsh P, Rancourt DE, Ulrich H, Holland H. Concise Review: Molecular Cytogenetics and Quality Control: Clinical Guardians for Pluripotent Stem Cells. Stem Cells Transl Med 2018; 7:867-875. [PMID: 30218497 PMCID: PMC6265634 DOI: 10.1002/sctm.18-0087] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/07/2018] [Indexed: 12/13/2022] Open
Abstract
Now that induced pluripotent stem cell (iPSC)‐based transplants have been performed in humans and organizations have begun producing clinical‐grade iPSCs, it is imperative that strict quality control standards are agreed upon. This is essential as both ESCs and iPSCs have been shown to accumulate genomic aberrations during long‐term culturing. These aberrations can include copy number variations, trisomy, amplifications of chromosomal regions, deletions of chromosomal regions, loss of heterozygosity, and epigenetic abnormalities. Moreover, although the differences between iPSCs and ESCs appear largely negligible when a high enough n number is used for comparison, the reprogramming process can generate further aberrations in iPSCs, including copy number variations and deletions in tumor‐suppressor genes. If mutations or epigenetic signatures are present in parental cells, these can also be carried over into iPSCs. To maximize patient safety, we recommend a set of standards to be utilized when preparing iPSCs for clinical use. Reprogramming methods that do not involve genomic integration should be used. Cultured cells should be grown using feeder‐free and serum‐free systems to avoid animal contamination. Karyotyping, whole‐genome sequencing, gene expression analyses, and standard sterility tests should all become routine quality control tests. Analysis of mitochondrial DNA integrity, whole‐epigenome analyses, as well as single‐cell genome sequencing of large cell populations may also prove beneficial. Furthermore, clinical‐grade stem cells need to be produced under accepted regulatory good manufacturing process standards. The creation of haplobanks that provide major histocompatibility complex matching is also recommended to improve allogeneic stem cell engraftment. Stem Cells Translational Medicine2018;7:867–875
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Affiliation(s)
- Leili Rohani
- Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany.,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Adiv A Johnson
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Pooyan Naghsh
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Derrick E Rancourt
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Heidrun Holland
- Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany
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33
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Dou Y, Gold HD, Luquette LJ, Park PJ. Detecting Somatic Mutations in Normal Cells. Trends Genet 2018; 34:545-557. [PMID: 29731376 PMCID: PMC6029698 DOI: 10.1016/j.tig.2018.04.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 01/12/2023]
Abstract
Somatic mutations have been studied extensively in the context of cancer. Recent studies have demonstrated that high-throughput sequencing data can be used to detect somatic mutations in non-tumor cells. Analysis of such mutations allows us to better understand the mutational processes in normal cells, explore cell lineages in development, and examine potential associations with age-related disease. We describe here approaches for characterizing somatic mutations in normal and non-tumor disease tissues. We discuss several experimental designs and common pitfalls in somatic mutation detection, as well as more recent developments such as phasing and linked-read technology. With the dramatically increasing numbers of samples undergoing genome sequencing, bioinformatic analysis will enable the characterization of somatic mutations and their impact on non-cancer tissues.
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Affiliation(s)
- Yanmei Dou
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Equal contributions
| | - Heather D Gold
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA; Equal contributions
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA; Equal contributions
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
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34
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Dunn P, Albury CL, Maksemous N, Benton MC, Sutherland HG, Smith RA, Haupt LM, Griffiths LR. Next Generation Sequencing Methods for Diagnosis of Epilepsy Syndromes. Front Genet 2018; 9:20. [PMID: 29467791 PMCID: PMC5808353 DOI: 10.3389/fgene.2018.00020] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/16/2018] [Indexed: 12/28/2022] Open
Abstract
Epilepsy is a neurological disorder characterized by an increased predisposition for seizures. Although this definition suggests that it is a single disorder, epilepsy encompasses a group of disorders with diverse aetiologies and outcomes. A genetic basis for epilepsy syndromes has been postulated for several decades, with several mutations in specific genes identified that have increased our understanding of the genetic influence on epilepsies. With 70-80% of epilepsy cases identified to have a genetic cause, there are now hundreds of genes identified to be associated with epilepsy syndromes which can be analyzed using next generation sequencing (NGS) techniques such as targeted gene panels, whole exome sequencing (WES) and whole genome sequencing (WGS). For effective use of these methodologies, diagnostic laboratories and clinicians require information on the relevant workflows including analysis and sequencing depth to understand the specific clinical application and diagnostic capabilities of these gene sequencing techniques. As epilepsy is a complex disorder, the differences associated with each technique influence the ability to form a diagnosis along with an accurate detection of the genetic etiology of the disorder. In addition, for diagnostic testing, an important parameter is the cost-effectiveness and the specific diagnostic outcome of each technique. Here, we review these commonly used NGS techniques to determine their suitability for application to epilepsy genetic diagnostic testing.
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Affiliation(s)
- Paul Dunn
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Cassie L Albury
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Neven Maksemous
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Miles C Benton
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Heidi G Sutherland
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Robert A Smith
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Larisa M Haupt
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
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35
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Copy Number Variation Analysis of 100 Twin Pairs Enriched for Neurodevelopmental Disorders. Twin Res Hum Genet 2018; 21:1-11. [DOI: 10.1017/thg.2017.69] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hundreds of penetrant risk loci have been identified across different neurodevelopmental disorders (NDDs), and these often involve rare (<1% frequency) copy number variations (CNVs), which can involve one or more genes. Monozygotic (MZ) twin pairs are long thought to share 100% of their genomic information. However, genetic differences in the form of postzygotic somatic variants have been reported recently both in typically developing (TD) and in clinically discordant MZ pairs. We sought to investigate the contribution of rare CNVs in 100 twin pairs enriched for NDD phenotypes with a particular focus on postzygotic CNVs in MZ pairs discordant for autism spectrum disorder (ASD) using the Illumina Infinium PsychArray. In our sample, no postzygotic de novo CNVs were found in 55 MZ twin pairs, including the 13 pairs discordant for ASD. We did detect a higher rate of CNVs overlapping genes involved in disorders of the nervous system, such as a rare deletion affecting HNRNPU, in MZ pairs discordant and concordant for ASD in comparison with TD pairs (p = .02). Our results are in concordance with earlier findings that postzygotic de novo CNV events are typically rare in genomic DNA derived from saliva or blood, and suggests that the discordance of NDDs in our sample of twins is not explained by discordant CNVs. Still, studies investigating postzygotic variation in MZ discordant twins using DNA from different tissues and single cells and higher resolution genomics are needed in the future.
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36
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Wilfert AB, Sulovari A, Turner TN, Coe BP, Eichler EE. Recurrent de novo mutations in neurodevelopmental disorders: properties and clinical implications. Genome Med 2017; 9:101. [PMID: 29179772 PMCID: PMC5704398 DOI: 10.1186/s13073-017-0498-x] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Next-generation sequencing (NGS) is now more accessible to clinicians and researchers. As a result, our understanding of the genetics of neurodevelopmental disorders (NDDs) has rapidly advanced over the past few years. NGS has led to the discovery of new NDD genes with an excess of recurrent de novo mutations (DNMs) when compared to controls. Development of large-scale databases of normal and disease variation has given rise to metrics exploring the relative tolerance of individual genes to human mutation. Genetic etiology and diagnosis rates have improved, which have led to the discovery of new pathways and tissue types relevant to NDDs. In this review, we highlight several key findings based on the discovery of recurrent DNMs ranging from copy number variants to point mutations. We explore biases and patterns of DNM enrichment and the role of mosaicism and secondary mutations in variable expressivity. We discuss the benefit of whole-genome sequencing (WGS) over whole-exome sequencing (WES) to understand more complex, multifactorial cases of NDD and explain how this improved understanding aids diagnosis and management of these disorders. Comprehensive assessment of the DNM landscape across the genome using WGS and other technologies will lead to the development of novel functional and bioinformatics approaches to interpret DNMs and drive new insights into NDD biology.
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Affiliation(s)
- Amy B Wilfert
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Tychele N Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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