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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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2
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Cobanogullari H, Akcan N, Ergoren M. Non-Invasive Screening Test Paradox in a Case Born with Mixed Gonadal Dysgenesis (45,X/46,Xy). Balkan J Med Genet 2023; 26:57-62. [PMID: 37576786 PMCID: PMC10413989 DOI: 10.2478/bjmg-2023-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
Noninvasive prenatal testing (NIPT) is commonly used to screen for fetal trisomy 13, 18, and 21 and often for sex chromosomal aneuploidies (SCAs). Although the testing is also used for sex chromosomal aneuploidies, it is not as efficient as it is for common trisomies. In this particular study, we present a case for whom the NIPT diagnosis was originally 45,X and who was diagnosed with mixed gonadal dysgenesis 45,X/46,XY after birth. A 38-year-old [G3P3] pregnant woman underwent NIPT at 15 weeks' gestation and was found to be at probable risk for 45,X. Because cordocentesis is an invasive procedure, the pregnant woman did not want to undergo cordocentesis. Consequently, postnatal cytogenetic analysis was performed and the baby's karyotype was shown to be 45,X/46,X,+mar?. No numerical and/or structural anomalies were observed in the karyotypes of parents and siblings. Based on the microarray analysis of the analyzed sample, one copy of the X chromosome was detected in all cells and the presence of one copy of the Y chromosome was detected in a ~40% mosaic state: arr(X) x1,(Y)x1[0.4]. SRY gene duplication on Y chromosome was confirmed by fluorescence in situ hybridization (FISH) and microarray analysis. The patient's clinical examination showed ambiguous genitalia (clitoromegaly) and dysmorphic facial features. The baby underwent surgery for aortic coarctation. The results were consistent with a genetic diagnosis of 45,X/46,XY mixed gonadal dysgenesis. Genetic counselling was offered to the family. In conclusion, NIPT still has potential limitations in correctly identifying sex chromosomes and mosaicism that may mislead clinicians and families.
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Affiliation(s)
- H. Cobanogullari
- Near East University, Institute of Graduate Studies, Department of Molecular Medicine, Nicosia, 99138, Cyprus
| | - N. Akcan
- Near East University, Faculty of Medicine, Department of Pediatrics, Nicosia, 99138, Cyprus
| | - M.C. Ergoren
- Near East University, Institute of Graduate Studies, Department of Molecular Medicine, Nicosia, 99138, Cyprus
- Near East University Hospital, Laboratory of Medical Genetics Diagnosis, Nicosia, 99138, Cyprus
- Near East University, Faculty of Medicine, Department of Medical Genetics, Nicosia, 99138, Cyprus
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3
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Sagath L, Lehtokari VL, Wallgren-Pettersson C, Pelin K, Kiiski K. A custom ddPCR method for the detection of copy number variations in the nebulin triplicate region. PLoS One 2022; 17:e0267793. [PMID: 35576196 PMCID: PMC9109913 DOI: 10.1371/journal.pone.0267793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
The human genome contains repetitive regions, such as segmental duplications, known to be prone to copy number variation. Segmental duplications are highly identical and homologous sequences, posing a specific challenge for most mutation detection methods. The giant nebulin gene is expressed in skeletal muscle. It harbors a large segmental duplication region composed of eight exons repeated three times, the so-called triplicate region. Mutations in nebulin are known to cause nemaline myopathy and other congenital myopathies. Using our custom targeted Comparative Genomic Hybridization arrays, we have previously shown that copy number variations in the nebulin triplicate region are pathogenic when the copy number of the segmental duplication block deviates two or more copies from the normal number, which is three per allele. To complement our Comparative Genomic Hybridization arrays, we have established a custom Droplet Digital PCR method for the detection of copy number variations within the nebulin triplicate region. The custom Droplet Digital PCR assays allow sensitive, rapid, high-throughput, and cost-effective detection of copy number variations within this region and is ready for implementation a screening method for disease-causing copy number variations of the nebulin triplicate region. We suggest that Droplet Digital PCR may also be used in the study and diagnostics of other segmental duplication regions of the genome.
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Affiliation(s)
- Lydia Sagath
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- * E-mail: , (LS); (KK)
| | - Vilma-Lotta Lehtokari
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Carina Wallgren-Pettersson
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Katarina Pelin
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Kirsi Kiiski
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- * E-mail: , (LS); (KK)
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4
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Clinical and molecular cytogenetic description of a female patient with de novo 18q inversion duplication/deletion. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Transient myeloproliferative disorder as the presenting feature for mosaic trisomy 21. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006126. [PMID: 34789514 PMCID: PMC8751406 DOI: 10.1101/mcs.a006126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/16/2021] [Indexed: 11/25/2022] Open
Abstract
Trisomy 21 is a common congenital disorder with well-documented clinical manifestations, including an increased risk for the transient myeloproliferative disorder as a neonate and leukemia in childhood and adolescence. Transient myeloproliferative disorder is only known to occur in hematopoietic cells with trisomy 21. Children with mosaic trisomy 21 also have a risk for hematological malignancies. We present a nondysmorphic neonate, with a negative noninvasive prenatal screening of maternal blood for trisomy 21, who came to medical attention because of ruddy skin. He was found to have mild polycythemia, thrombocytopenia, and developed peripheral blasts. His clinical presentation was consistent with transient myeloproliferative disorder, which is only seen with trisomy 21. Cytogenetic studies of peripheral blood are positive for mosaic trisomy 21.
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6
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Tulay P, Ergoren MC, Alkaya A, Yayci E, Sag SO, Temel SG. Inconsistency of Karyotyping and Array Comparative Genomic Hybridization (aCGH) in a Mosaic Turner Syndrome Case. Glob Med Genet 2021; 7:128-132. [PMID: 33693446 PMCID: PMC7938938 DOI: 10.1055/s-0041-1722974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Purpose
Turner syndrome is a sex chromosomal aberration where majority of the patients have 45,X karyotype, while several patients are mosaic involving 45,X/46,XX; 46,X,i(Xq); and other variants. Cytogenetic analysis, karyotyping, is considered to be the “gold standard” to detect numerical and structural chromosomal abnormalities. In the recent years, alternative approaches, such as array comparative genomic hybridization (aCGH), have been widely used in genetic analysis to detect numerical abnormalities as well as unbalanced structural rearrangements. In this study, we report the use of karyotyping as well as aCGH in detecting a possible Turner syndrome variant.
Methods
An apparent 16-year-old female was clinically diagnosed as Turner syndrome with premature ovarian failure and short stature. The genetic diagnosis was performed for the patient and the parents by karyotyping analysis. aCGH was also performed for the patient.
Main Findings
Cytogenetic analysis of the patient was performed showing variant Turner syndrome (46,X,i(X)(q10)[26]/46,X,del(X)(q11.2)[11]/45,X[8]/46,XX[5]). The patient's aCGH result revealed that she has a deletion of 57,252kb of Xp22.33-p11.21 region; arr[GRCh37] Xp22.33-p11.21 (310,932–57,563–078)X1. Both aCGH and fluorescence in situ hybridization (FISH) results suggested that
short stature Homeobox-containing
(
SHOX
) gene, which is located on Xp22.33, was deleted, though FISH result indicated that this was in a mosaic pattern.
Conclusion
In the recent years, aCGH has become the preferred method in detecting numerical abnormalities and unbalanced chromosomal rearrangements. However, its use is hindered by its failure of detecting mosaicism, especially low-level partial mosaicism. Therefore, although the resolution of the aCGH is higher, the cytogenetic investigation is still the first in line to detect mosaicism.
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Affiliation(s)
- Pinar Tulay
- Near East University, Faculty of Medicine, Department of Medical Genetics, Nicosia, Cyprus.,Near East University, DESAM Institute, Nicosia, Cyprus
| | - Mahmut Cerkez Ergoren
- Near East University, Faculty of Medicine, Department of Medical Genetics, Nicosia, Cyprus.,Near East University, DESAM Institute, Nicosia, Cyprus
| | - Ahmet Alkaya
- Bilecik Seyh Edebali University, Graduate School of Applied Sciences, Gulumbe Yerleskesi, Bilecik, Turkey
| | - Eyup Yayci
- Near East University, Faculty of Medicine, Department of Gynecology and Obstetrics, Nicosia, Cyprus
| | - Sebnem Ozemri Sag
- Uludag University, Faculty of Medicine, Department of Medical Genetics, Bursa, Turkey
| | - Sehime Gulsum Temel
- Uludag University, Faculty of Medicine, Department of Medical Genetics, Bursa, Turkey.,Uludag University, Faculty of Medicine, Department of Histology and Embryology, Bursa, Turkey
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7
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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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8
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Lalonde E, Rentas S, Lin F, Dulik MC, Skraban CM, Spinner NB. Genomic Diagnosis for Pediatric Disorders: Revolution and Evolution. Front Pediatr 2020; 8:373. [PMID: 32733828 PMCID: PMC7360789 DOI: 10.3389/fped.2020.00373] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
Powerful, recent advances in technologies to analyze the genome have had a profound impact on the practice of medical genetics, both in the laboratory and in the clinic. Increasing utilization of genome-wide testing such as chromosomal microarray analysis and exome sequencing have lead a shift toward a "genotype-first" approach. Numerous techniques are now available to diagnose a particular syndrome or phenotype, and while traditional techniques remain efficient tools in certain situations, higher-throughput technologies have become the de facto laboratory tool for diagnosis of most conditions. However, selecting the right assay or technology is challenging, and the wrong choice may lead to prolonged time to diagnosis, or even a missed diagnosis. In this review, we will discuss current core technologies for the diagnosis of classic genetic disorders to shed light on the benefits and disadvantages of these strategies, including diagnostic efficiency, variant interpretation, and secondary findings. Finally, we review upcoming technologies posed to impart further changes in the field of genetic diagnostics as we move toward "genome-first" practice.
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Affiliation(s)
- Emilie Lalonde
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Stefan Rentas
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Fumin Lin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Matthew C. Dulik
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Cara M. Skraban
- Division of Human Genetics, Department of Pediatrics, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Nancy B. Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
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9
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Muyas F, Zapata L, Guigó R, Ossowski S. The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues. Genome Med 2020; 12:49. [PMID: 32460841 PMCID: PMC7254727 DOI: 10.1186/s13073-020-00746-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/08/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Mosaic mutations acquired during early embryogenesis can lead to severe early-onset genetic disorders and cancer predisposition, but are often undetectable in blood samples. The rate and mutational spectrum of embryonic mosaic mutations (EMMs) have only been studied in few tissues, and their contribution to genetic disorders is unknown. Therefore, we investigated how frequent mosaic mutations occur during embryogenesis across all germ layers and tissues. METHODS Mosaic mutation detection in 49 normal tissues from 570 individuals (Genotype-Tissue Expression (GTEx) cohort) was performed using a newly developed multi-tissue, multi-individual variant calling approach for RNA-seq data. Our method allows for reliable identification of EMMs and the developmental stage during which they appeared. RESULTS The analysis of EMMs in 570 individuals revealed that newborns on average harbor 0.5-1 EMMs in the exome affecting multiple organs (1.3230 × 10-8 per nucleotide per individual), a similar frequency as reported for germline de novo mutations. Our multi-tissue, multi-individual study design allowed us to distinguish mosaic mutations acquired during different stages of embryogenesis and adult life, as well as to provide insights into the rate and spectrum of mosaic mutations. We observed that EMMs are dominated by a mutational signature associated with spontaneous deamination of methylated cytosines and the number of cell divisions. After birth, cells continue to accumulate somatic mutations, which can lead to the development of cancer. Investigation of the mutational spectrum of the gastrointestinal tract revealed a mutational pattern associated with the food-borne carcinogen aflatoxin, a signature that has so far only been reported in liver cancer. CONCLUSIONS In summary, our multi-tissue, multi-individual study reveals a surprisingly high number of embryonic mosaic mutations in coding regions, implying novel hypotheses and diagnostic procedures for investigating genetic causes of disease and cancer predisposition.
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Affiliation(s)
- Francesc Muyas
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Luis Zapata
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Roderic Guigó
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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10
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Cao Y, Tokita MJ, Chen ES, Ghosh R, Chen T, Feng Y, Gorman E, Gibellini F, Ward PA, Braxton A, Wang X, Meng L, Xiao R, Bi W, Xia F, Eng CM, Yang Y, Gambin T, Shaw C, Liu P, Stankiewicz P. A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing. Genome Med 2019; 11:48. [PMID: 31349857 PMCID: PMC6660700 DOI: 10.1186/s13073-019-0658-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 07/11/2019] [Indexed: 12/23/2022] Open
Abstract
Background Although mosaic variation has been known to cause disease for decades, high-throughput sequencing technologies with the analytical sensitivity to consistently detect variants at reduced allelic fractions have only recently emerged as routine clinical diagnostic tests. To date, few systematic analyses of mosaic variants detected by diagnostic exome sequencing for diverse clinical indications have been performed. Methods To investigate the frequency, type, allelic fraction, and phenotypic consequences of clinically relevant somatic mosaic single nucleotide variants (SNVs) and characteristics of the corresponding genes, we retrospectively queried reported mosaic variants from a cohort of ~ 12,000 samples submitted for clinical exome sequencing (ES) at Baylor Genetics. Results We found 120 mosaic variants involving 107 genes, including 80 mosaic SNVs in proband samples and 40 in parental/grandparental samples. Average mosaic alternate allele fraction (AAF) detected in autosomes and in X-linked disease genes in females was 18.2% compared with 34.8% in X-linked disease genes in males. Of these mosaic variants, 74 variants (61.7%) were classified as pathogenic or likely pathogenic and 46 (38.3%) as variants of uncertain significance. Mosaic variants occurred in disease genes associated with autosomal dominant (AD) or AD/autosomal recessive (AR) (67/120, 55.8%), X-linked (33/120, 27.5%), AD/somatic (10/120, 8.3%), and AR (8/120, 6.7%) inheritance. Of note, 1.7% (2/120) of variants were found in genes in which only somatic events have been described. Nine genes had recurrent mosaic events in unrelated individuals which accounted for 18.3% (22/120) of all detected mosaic variants in this study. The proband group was enriched for mosaicism affecting Ras signaling pathway genes. Conclusions In sum, an estimated 1.5% of all molecular diagnoses made in this cohort could be attributed to a mosaic variant detected in the proband, while parental mosaicism was identified in 0.3% of families analyzed. As ES design favors breadth over depth of coverage, this estimate of the prevalence of mosaic variants likely represents an underestimate of the total number of clinically relevant mosaic variants in our cohort. Electronic supplementary material The online version of this article (10.1186/s13073-019-0658-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ye Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA.,Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mari J Tokita
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Edward S Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Rajarshi Ghosh
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | | | | | | | | | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | | | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Statistics, Rice University, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA. .,Baylor Genetics, Houston, TX, USA.
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA. .,Baylor Genetics, Houston, TX, USA.
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11
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De novo unbalanced translocations have a complex history/aetiology. Hum Genet 2018; 137:817-829. [DOI: 10.1007/s00439-018-1941-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022]
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12
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La Cognata V, Morello G, Gentile G, Cavalcanti F, Cittadella R, Conforti FL, De Marco EV, Magariello A, Muglia M, Patitucci A, Spadafora P, D’Agata V, Ruggieri M, Cavallaro S. NeuroArray: A Customized aCGH for the Analysis of Copy Number Variations in Neurological Disorders. Curr Genomics 2018; 19:431-443. [PMID: 30258275 PMCID: PMC6128384 DOI: 10.2174/1389202919666180404105451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/02/2018] [Accepted: 03/13/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Neurological disorders are a highly heterogeneous group of pathological conditions that affect both the peripheral and the central nervous system. These pathologies are characterized by a complex and multifactorial etiology involving numerous environmental agents and genetic susceptibility factors. For this reason, the investigation of their pathogenetic basis by means of traditional methodological approaches is rather arduous. High-throughput genotyping technologies, including the microarray-based comparative genomic hybridization (aCGH), are currently replacing classical detection methods, providing powerful molecular tools to identify genomic unbalanced structural rearrangements and explore their role in the pathogenesis of many complex human diseases. METHODS In this report, we comprehensively describe the design method, the procedures, validation, and implementation of an exon-centric customized aCGH (NeuroArray 1.0), tailored to detect both single and multi-exon deletions or duplications in a large set of multi- and monogenic neurological diseases. This focused platform enables a targeted measurement of structural imbalances across the human genome, targeting the clinically relevant genes at exon-level resolution. CONCLUSION An increasing use of the NeuroArray platform may offer new insights in investigating potential overlapping gene signatures among neurological conditions and defining genotype-phenotype relationships.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sebastiano Cavallaro
- Address correspondence to this author at the Institute of Neurological Sciences, National Research Council, Via Paolo Gaifami 18, 95125, Catania, Italy; Tel: +39-095-7338111; E-mail:
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13
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Waggoner D, Wain KE, Dubuc AM, Conlin L, Hickey SE, Lamb AN, Martin CL, Morton CC, Rasmussen K, Schuette JL, Schwartz S, Miller DT. Yield of additional genetic testing after chromosomal microarray for diagnosis of neurodevelopmental disability and congenital anomalies: a clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2018; 20:1105-1113. [PMID: 29915380 PMCID: PMC6410698 DOI: 10.1038/s41436-018-0040-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 04/04/2018] [Indexed: 11/16/2022] Open
Abstract
Purpose: Chromosomal microarray (CMA) is recommended as the first tier test in evaluation of individuals with neurodevelopmental disability and congenital anomalies. CMA may not detect balanced cytogenomic abnormalities or uniparental disomy (UPD), and deletion/duplications and regions of homozygosity may require additional testing to clarify the mechanism and inform accurate counseling. We conducted an evidence review to synthesize data regarding the benefit of additional testing after CMA to inform a genetic diagnosis. Methods: The review was guided by key questions related to the detection of genomic events that may require additional testing. A PubMed search for original research articles, systematic reviews, and meta-analyses were evaluated from articles published between January 1, 1983 and March 31, 2017. Based on the key questions, articles were retrieved and data extracted in parallel with comparison of results and discussion to resolve discrepancies. Variables assessed included study design and outcomes. Results: A narrative synthesis was created for each question to describe the occurrence of, and clinical significance of, additional diagnostic findings from subsequent testing performed after CMA. Conclusion: These findings may be used to assist the laboratory and clinician when making recommendations about additional testing after CMA, as it impacts clinical care, counseling, and diagnosis.
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Affiliation(s)
- Darrel Waggoner
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
| | - Karen E Wain
- Autism & Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Adrian M Dubuc
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Laura Conlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Scott E Hickey
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Allen N Lamb
- Department of Pathology, ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Christa Lese Martin
- Autism & Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Cynthia C Morton
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Obstetrics and Gynecology and Reproductive Biology, Brigham and Women's Hospital, Broad Institute of MIT and Harvard, Harvard Medical School, Boston, Massachusetts, USA.,Division of Evolution and Genomics Science, School of Biological Sciences, Manchester Academic Health Science Center, Manchester, UK
| | - Kristen Rasmussen
- Department of Medical Genetics, Marshfield Clinic, Marshfield, Wisconsin, USA
| | - Jane L Schuette
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Stuart Schwartz
- Laboratory Corporation of America® Holdings, Burlington, North Carolina, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
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14
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Armstrong ME, Weaver DD, Lah MD, Vance GH, Landis BJ, Ware SM, Helm BM. Novel phenotype of 5p13.3-q11.2 duplication resulting from supernumerary marker chromosome 5: implications for management and genetic counseling. Mol Cytogenet 2018; 11:23. [PMID: 29599822 PMCID: PMC5870180 DOI: 10.1186/s13039-018-0372-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/22/2018] [Indexed: 01/04/2023] Open
Abstract
Background Supernumerary marker chromosomes derived from chromosome 5 (SMC5) and 5p13 duplication syndrome are rare disorders, and phenotypic descriptions of patients are necessary to better define genotype-phenotype correlations for accurate, comprehensive genetic counseling. The purpose of this study is to highlight the unique findings of a patient with a 5p13.3-q11.2 duplication arising from a SMC5 and compare and contrast the phenotype with cases in the literature. Case presentation We report on an adult male with a 22 Mb duplication of chromosome 5p13.3-q11.2 resulting from a small SMC5. The patient has a history of prenatal polyhydramnios, dysmorphic features, respiratory issues, talipes equinovarus, hypotonia, developmental delay, and autistic features. The patient also has novel features of aortic dilation, pectus excavatum, kyphoscoliosis, and skin striae, suggestive of a connective tissue disorder. Despite these features he did not meet clinical diagnostic criteria for a well-characterized connective tissue disorder. Additional molecular genetic testing for syndromic and non-syndromic aortic aneurysms was negative. Conclusions Many of the patient’s features are consistent with individuals reported with 5p13 duplication syndrome and similar cases of SMC5, including polyhydramnios, macrocephaly, dolichocephaly, pre-auricular pits, arachnodactyly, respiratory problems, and developmental delays. It is unclear if the patient’s unique features of aortic dilation, pectus excavatum, kyphoscoliosis, and skin striae could be novel features of the SMC5 given its rarity and the few well-phenotyped adults in the literature. This report reviews the literature and provides additional phenotypic information to define the genotype-phenotype correlation of SMC5 and 5p13 duplication syndrome.
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Affiliation(s)
- Margaret E Armstrong
- 1Department of Medical and Molecular Genetics and Department of Pediatrics, Indiana University School of Medicine, 550 N. University Blvd, AOC 5001, Indianapolis, Indiana 46202 USA.,3Department of Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, Iowa USA
| | - David D Weaver
- 1Department of Medical and Molecular Genetics and Department of Pediatrics, Indiana University School of Medicine, 550 N. University Blvd, AOC 5001, Indianapolis, Indiana 46202 USA
| | - Melissa D Lah
- 1Department of Medical and Molecular Genetics and Department of Pediatrics, Indiana University School of Medicine, 550 N. University Blvd, AOC 5001, Indianapolis, Indiana 46202 USA
| | - Gail H Vance
- 1Department of Medical and Molecular Genetics and Department of Pediatrics, Indiana University School of Medicine, 550 N. University Blvd, AOC 5001, Indianapolis, Indiana 46202 USA.,2Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana USA
| | - Benjamin J Landis
- 1Department of Medical and Molecular Genetics and Department of Pediatrics, Indiana University School of Medicine, 550 N. University Blvd, AOC 5001, Indianapolis, Indiana 46202 USA.,2Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana USA
| | - Stephanie M Ware
- 1Department of Medical and Molecular Genetics and Department of Pediatrics, Indiana University School of Medicine, 550 N. University Blvd, AOC 5001, Indianapolis, Indiana 46202 USA.,2Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana USA
| | - Benjamin M Helm
- 1Department of Medical and Molecular Genetics and Department of Pediatrics, Indiana University School of Medicine, 550 N. University Blvd, AOC 5001, Indianapolis, Indiana 46202 USA
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15
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Nakayama T, Ishii A, Yoshida T, Nasu H, Shimojima K, Yamamoto T, Kure S, Hirose S. Somatic mosaic deletions involving SCN1A
cause Dravet syndrome. Am J Med Genet A 2018; 176:657-662. [DOI: 10.1002/ajmg.a.38596] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 10/09/2017] [Accepted: 12/07/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Tojo Nakayama
- Department of Pediatrics; Tohoku University School of Medicine; Sendai Japan
| | - Atsushi Ishii
- Department of Pediatrics; School of Medicine; Fukuoka University; Fukuoka Japan
- Central Research Institute for the Molecular Pathomechanisms of Epilepsy; Fukuoka University; Fukuoka Japan
| | - Takeshi Yoshida
- Department of Pediatrics; Kyoto University Graduate School of Medicine; Kyoto Japan
| | - Hirosato Nasu
- National Epilepsy Center; Shizuoka Institute of Epilepsy and Neurological Disorders; Shizuoka Japan
| | - Keiko Shimojima
- Tokyo Women's Medical University Institute for Integrated Medical Sciences; Tokyo Japan
| | - Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute for Integrated Medical Sciences; Tokyo Japan
| | - Shigeo Kure
- Department of Pediatrics; Tohoku University School of Medicine; Sendai Japan
| | - Shinichi Hirose
- Department of Pediatrics; School of Medicine; Fukuoka University; Fukuoka Japan
- Central Research Institute for the Molecular Pathomechanisms of Epilepsy; Fukuoka University; Fukuoka Japan
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16
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King DA, Sifrim A, Fitzgerald TW, Rahbari R, Hobson E, Homfray T, Mansour S, Mehta SG, Shehla M, Tomkins SE, Vasudevan PC, Hurles ME. Detection of structural mosaicism from targeted and whole-genome sequencing data. Genome Res 2017; 27:1704-1714. [PMID: 28855261 PMCID: PMC5630034 DOI: 10.1101/gr.212373.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 07/18/2017] [Indexed: 01/11/2023]
Abstract
Structural mosaic abnormalities are large post-zygotic mutations present in a subset of cells and have been implicated in developmental disorders and cancer. Such mutations have been conventionally assessed in clinical diagnostics using cytogenetic or microarray testing. Modern disease studies rely heavily on exome sequencing, yet an adequate method for the detection of structural mosaicism using targeted sequencing data is lacking. Here, we present a method, called MrMosaic, to detect structural mosaic abnormalities using deviations in allele fraction and read coverage from next-generation sequencing data. Whole-exome sequencing (WES) and whole-genome sequencing (WGS) simulations were used to calculate detection performance across a range of mosaic event sizes, types, clonalities, and sequencing depths. The tool was applied to 4911 patients with undiagnosed developmental disorders, and 11 events among nine patients were detected. For eight of these 11 events, mosaicism was observed in saliva but not blood, suggesting that assaying blood alone would miss a large fraction, possibly >50%, of mosaic diagnostic chromosomal rearrangements.
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Affiliation(s)
- Daniel A King
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Alejandro Sifrim
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Tomas W Fitzgerald
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Raheleh Rahbari
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Emma Hobson
- Department of Clinical Genetics, Chapel Allerton Hospital, Leeds LS7 4SA, United Kingdom
| | - Tessa Homfray
- Southwest Thames Regional Genetics Centre, St George's Healthcare NHS Trust, London SW17 0RE, United Kingdom
| | - Sahar Mansour
- Southwest Thames Regional Genetics Centre, St George's Healthcare NHS Trust, London SW17 0RE, United Kingdom
| | - Sarju G Mehta
- East Anglian Regional Genetics Service, Addenbrookes Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Mohammed Shehla
- South East Thames Regional Genetics Centre, Guy's Hospital, London SE1 9RT, United Kingdom
| | - Susan E Tomkins
- Department of Clinical Genetics, St Michael's Hospital, Bristol BS2 8EG, United Kingdom
| | | | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
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17
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Reittinger AM, Helm BM, Boles DJ, Gadi IK, Schrier Vergano SA. A prenatal diagnosis of mosaic trisomy 5 reveals a postnatal complete uniparental disomy of chromosome 5 with multiple congenital anomalies. Am J Med Genet A 2017; 173:2528-2533. [PMID: 28653809 DOI: 10.1002/ajmg.a.38344] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/25/2017] [Accepted: 06/06/2017] [Indexed: 11/11/2022]
Abstract
Mosaic trisomy 5 is a very rare condition in liveborns, with few cases reported in the last four decades. There are some reports of prenatally diagnosed mosaic trisomy 5 resulting in phenotypically normal offspring, suggesting a low level of mosaicism, but there are also reports associated with multiple congenital anomalies, cardiovascular malformations, and intrauterine growth restriction. We report an infant male diagnosed with mosaic trisomy 5 (5/15 cells) via amniocentesis. The patient was subsequently found to have uniparental disomy 5 (UPD5) by postnatal chromosome microarray, but high-resolution chromosome analysis on peripheral blood did not identify trisomy 5. Dysmorphic features included a tall forehead with low anterior hairline, hypertelorism, low-set ears, and a prominent nose and midface. Other anomalies included bilateral bifid thumbs, hypospadias, a perineal fistula, unilateral multicystic kidney, and decreased subcutaneous fat with loose skin. He had complex congenital heart disease consisting of ventricular and atrial septal defects and polyvalvular defects. The patient died at age one after a prolonged admission. We add this case to the literature with the added benefit of data from a postnatal microarray, which was not available in other cases, to broaden the phenotype of mosaic trisomy 5 and UPD5.With the current available technology, we stress the importance of postnatal genetic testing to confirm prenatal cytogenetic findings in order to further define such phenotypes. This will provide the most accurate information and counseling to affected families.
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Affiliation(s)
- Andrew M Reittinger
- Department of Pediatrics, Eastern Virginia Medical School, Norfolk, Virginia
| | - Benjamin M Helm
- Department of Medical & Molecular Genetics, Indiana University School of Medicine and Riley Hospital for Children at IU Health, Indianapolis, Indiana
| | - Debra J Boles
- Quest Diagnostics, Nichols Institute, Chantilly, Virginia
| | - Inder K Gadi
- Laboratory Corporation of America, Research Triangle Park, North Carolina
| | - Samantha A Schrier Vergano
- Department of Pediatrics, Eastern Virginia Medical School, Norfolk, Virginia.,Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, Virginia
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18
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Oneda B, Asadollahi R, Azzarello-Burri S, Niedrist D, Baldinger R, Masood R, Schinzel A, Latal B, Jenni OG, Rauch A. Low-Level Chromosomal Mosaicism in Neurodevelopmental Disorders. Mol Syndromol 2017; 8:266-271. [PMID: 28878611 DOI: 10.1159/000477189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2017] [Indexed: 11/19/2022] Open
Abstract
Chromosomal mosaicism, which represents a diagnostic challenge for detection and interpretation, has been described in several genetic conditions. It can contribute to a large phenotypic variation in diseases. At analysis of a well-characterized cohort of 714 patients with neurodevelopmental disorders (NDDs) of unknown etiology using a high-resolution chromosomal microarray platform, we found 2 cases (0.28%) of low-level mosaicism and defined a previously detected extra chromosome in a third patient. Two of the cases were mosaics for segmental imbalances (a partial trisomy 3q26.1q27.3 and a partial monosomy 18q21.2qter with 14.6 and 20% mosaic ratios in lymphocytes, respectively), and 1 was a mosaic for an entire chromosome (trisomy 14, mosaic ratio 20%). Our diagnostic yield is in line with the ratios previously published in patients with intellectual disability. Notably, the partial trisomy 3q26.1q27.3 case is an example of a rare and unusual class of a rearranged neocentric ring chromosome, which can neither be categorized in class I, nor in class II of such rearrangements. Our cases further elucidate the phenotypes related to the aberrations of the specific chromosome segments observed and underline the important role of low-level mosaics in the pathogenesis of NDDs of unknown etiology even in the absence of clinical signs of mosaicism.
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Affiliation(s)
- Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Reza Asadollahi
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | | | - Dunja Niedrist
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Rosa Baldinger
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Rahim Masood
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Albert Schinzel
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Bea Latal
- Child Development Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Oskar G Jenni
- Child Development Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
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19
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Maternal mosaicism for IDUA deletion clarifies recurrence risk in MPS I. Hum Genome Var 2016; 3:16031. [PMID: 27766162 PMCID: PMC5052355 DOI: 10.1038/hgv.2016.31] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 11/08/2022] Open
Abstract
Mucopolysaccharidosis I (MPS I) is a rare autosomal recessive multisystem lysosomal storage disorder. It is caused by biallelic loss-of-function variants in IDUA, encoding alpha-l iduronidase. Here, we describe an individual affected by MPS I due to a paternally inherited deletion of IDUA exons 1 and 2, c.(?_-88)_(299+1_300-1)del and a whole-gene deletion of IDUA (?_-88?)_(*136?)del secondary to maternal somatic mosaicism. We define a previously unreported mutational mechanism for this disorder.
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20
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Lupski JR. Clinical genomics: from a truly personal genome viewpoint. Hum Genet 2016; 135:591-601. [PMID: 27221143 DOI: 10.1007/s00439-016-1682-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/11/2016] [Indexed: 12/23/2022]
Abstract
The path to Clinical Genomics is punctuated by our understanding of what types of DNA structural and sequence variation contribute to disease, the many technical challenges to detect such variation genome-wide, and the initial struggles to interpret personal genome variation in the context of disease. This review describes one perspective of the development of clinical genomics; whereas the experimental challenges, and hurdles to overcoming them, might be deemed readily apparent, the non-technical issues for clinical implementation may be less obvious. Some of these latter challenges, including: (1) informed consent, (2) privacy, (3) what constitutes potentially pathogenic variation contributing to disease, (4) disease penetrance in populations, and (5) the genetic architecture of disease, and the struggles sometimes faced for solutions, are highlighted using illustrative examples.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, 604B, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Texas Children's Hospital, Houston, TX, 77030, USA.
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21
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Yuan B, Liu P, Rogers J, Lupski JR. Copy number analysis of the low-copy repeats at the primate NPHP1 locus by array comparative genomic hybridization. GENOMICS DATA 2016; 8:106-9. [PMID: 27222811 PMCID: PMC4872932 DOI: 10.1016/j.gdata.2016.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 11/28/2022]
Abstract
Array comparative genomic hybridization (aCGH) has been widely used to detect copy number variants (CNVs) in both research and clinical settings. A customizable aCGH platform may greatly facilitate copy number analyses in genomic regions with higher-order complexity, such as low-copy repeats (LCRs). Here we present the aCGH analyses focusing on the 45 kb LCRs [1] at the NPHP1 region with diverse copy numbers in humans. Also, the interspecies aCGH analysis comparing human and nonhuman primates revealed dynamic copy number transitions of the human 45 kb LCR orthologues during primate evolution and therefore shed light on the origin of complexity at this locus. The original aCGH data are available at GEO under GSE73962.
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Affiliation(s)
- Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA
| | - Jeffrey Rogers
- 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; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
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22
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Daly AF, Yuan B, Fina F, Caberg JH, Trivellin G, Rostomyan L, de Herder WW, Naves LA, Metzger D, Cuny T, Rabl W, Shah N, Jaffrain-Rea ML, Zatelli MC, Faucz FR, Castermans E, Nanni-Metellus I, Lodish M, Muhammad A, Palmeira L, Potorac I, Mantovani G, Neggers SJ, Klein M, Barlier A, Liu P, Ouafik L, Bours V, Lupski JR, Stratakis CA, Beckers A. Somatic mosaicism underlies X-linked acrogigantism syndrome in sporadic male subjects. Endocr Relat Cancer 2016; 23:221-33. [PMID: 26935837 PMCID: PMC4877443 DOI: 10.1530/erc-16-0082] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/01/2016] [Indexed: 12/15/2022]
Abstract
Somatic mosaicism has been implicated as a causative mechanism in a number of genetic and genomic disorders. X-linked acrogigantism (XLAG) syndrome is a recently characterized genomic form of pediatric gigantism due to aggressive pituitary tumors that is caused by submicroscopic chromosome Xq26.3 duplications that include GPR101 We studied XLAG syndrome patients (n= 18) to determine if somatic mosaicism contributed to the genomic pathophysiology. Eighteen subjects with XLAG syndrome caused by Xq26.3 duplications were identified using high-definition array comparative genomic hybridization (HD-aCGH). We noted that males with XLAG had a decreased log2ratio (LR) compared with expected values, suggesting potential mosaicism, whereas females showed no such decrease. Compared with familial male XLAG cases, sporadic males had more marked evidence for mosaicism, with levels of Xq26.3 duplication between 16.1 and 53.8%. These characteristics were replicated using a novel, personalized breakpoint junction-specific quantification droplet digital polymerase chain reaction (ddPCR) technique. Using a separate ddPCR technique, we studied the feasibility of identifying XLAG syndrome cases in a distinct patient population of 64 unrelated subjects with acromegaly/gigantism, and identified one female gigantism patient who had had increased copy number variation (CNV) threshold for GPR101 that was subsequently diagnosed as having XLAG syndrome on HD-aCGH. Employing a combination of HD-aCGH and novel ddPCR approaches, we have demonstrated, for the first time, that XLAG syndrome can be caused by variable degrees of somatic mosaicism for duplications at chromosome Xq26.3. Somatic mosaicism was shown to occur in sporadic males but not in females with XLAG syndrome, although the clinical characteristics of the disease were similarly severe in both sexes.
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Affiliation(s)
- Adrian F Daly
- Department of Endocrinology, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TexasUSA
| | - Frederic Fina
- Assistance Publique Hôpitaux de Marseille (AP-HM), Hôpital Nord, Service de Transfert d'Oncologie Biologique, Marseille, France Laboratoire de Biologie Médicale, and Aix-Marseille UniversitéInserm, CRO2 UMR_S 911, Marseille, France
| | - Jean-Hubert Caberg
- Department of Human Genetics, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - Giampaolo Trivellin
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Liliya Rostomyan
- Department of Endocrinology, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - Wouter W de Herder
- Section of Endocrinology, Department of Medicine, Erasmus University Medical Center Rotterdam and Pituitary Center Rotterdam, Rotterdam, The Netherlands
| | - Luciana A Naves
- Department of Endocrinology, University of Brasilia, Brasilia, Brazil
| | - Daniel Metzger
- Endocrinology and Diabetes Unit, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Thomas Cuny
- Department of Endocrinology, University Hospital, Nancy, France
| | - Wolfgang Rabl
- Kinderklinik, Technische Universität München, Munich, Germany
| | - Nalini Shah
- Department of Endocrinology, KEM Hospital, Mumbai, India
| | - Marie-Lise Jaffrain-Rea
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila and Neuromed Institute, IRCCS, Pozzilli, Italy
| | - Maria Chiara Zatelli
- Section of Endocrinology, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fabio R Faucz
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Emilie Castermans
- Department of Human Genetics, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - Isabelle Nanni-Metellus
- Assistance Publique Hôpitaux de Marseille (AP-HM), Hôpital Nord, Service de Transfert d'Oncologie Biologique, Marseille, France
| | - Maya Lodish
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Ammar Muhammad
- Section of Endocrinology, Department of Medicine, Erasmus University Medical Center Rotterdam and Pituitary Center Rotterdam, Rotterdam, The Netherlands
| | - Leonor Palmeira
- Department of Endocrinology, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - Iulia Potorac
- Department of Endocrinology, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium Department of Human GeneticsCentre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - Giovanna Mantovani
- Endocrinology and Diabetology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Sebastian J Neggers
- Section of Endocrinology, Department of Medicine, Erasmus University Medical Center Rotterdam and Pituitary Center Rotterdam, Rotterdam, The Netherlands
| | - Marc Klein
- Department of Endocrinology, University Hospital, Nancy, France
| | - Anne Barlier
- Laboratory of Molecular Biology, APHM, Hopital la Conception, Aix Marseille Universite, Marseilles, France CRNSCRN2M-UMR 7286, Marseille, France
| | - Pengfei Liu
- Assistance Publique Hôpitaux de Marseille (AP-HM), Hôpital Nord, Service de Transfert d'Oncologie Biologique, Marseille, France
| | - L'Houcine Ouafik
- Laboratoire de Biologie Médicale, and Aix-Marseille Université, Inserm, CRO2 UMR_S 911, Marseille, France
| | - Vincent Bours
- Department of Human Genetics, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
| | - James R Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Albert Beckers
- Department of Endocrinology, Centre Hospitalier Universitaire de Liege, University of Liege, Liege, Belgium
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23
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Fujita A, Waga C, Hachiya Y, Kurihara E, Kumada S, Takeshita E, Nakagawa E, Inoue K, Miyatake S, Tsurusaki Y, Nakashima M, Saitsu H, Goto YI, Miyake N, Matsumoto N. Different X-linked KDM5C mutations in affected male siblings: is maternal reversion error involved? Clin Genet 2016; 90:276-81. [PMID: 26919706 DOI: 10.1111/cge.12767] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/12/2016] [Accepted: 02/23/2016] [Indexed: 02/02/2023]
Abstract
Genetic reversion is the phenomenon of spontaneous gene correction by which gene function is partially or completely rescued. However, it is unknown whether this mechanism always correctly repairs mutations, or is prone to error. We investigated a family of three boys with intellectual disability, and among them we identified two different mutations in KDM5C, located at Xp11.22, using whole-exome sequencing. Two affected boys have c.633delG and the other has c.631delC. We also confirmed de novo germline (c.631delC) and low-prevalence somatic (c.633delG) mutations in their mother. The two mutations are present on the same maternal haplotype, suggesting that a postzygotic somatic mutation or a reversion error occurred at an early embryonic stage in the mother, leading to switched KDM5C mutations in the affected siblings. This event is extremely unlikely to arise spontaneously (with an estimated probability of 0.39-7.5 × 10(-28) ), thus a possible reversion error is proposed here to explain this event. This study provides evidence for reversion error as a novel mechanism for the generation of somatic mutations in human diseases.
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Affiliation(s)
- A Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - C Waga
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Y Hachiya
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - E Kurihara
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - S Kumada
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - E Takeshita
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - E Nakagawa
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - K Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - S Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Y Tsurusaki
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - M Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - H Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Y-I Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - N Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - N Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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24
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Qin L, Wang J, Tian X, Yu H, Truong C, Mitchell JJ, Wierenga KJ, Craigen WJ, Zhang VW, Wong LJC. Detection and Quantification of Mosaic Mutations in Disease Genes by Next-Generation Sequencing. J Mol Diagn 2016; 18:446-453. [PMID: 26944031 DOI: 10.1016/j.jmoldx.2016.01.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 01/08/2016] [Accepted: 01/14/2016] [Indexed: 12/19/2022] Open
Abstract
The identification of mosaicism is important in establishing a disease diagnosis, assessing recurrence risk, and genetic counseling. Next-generation sequencing (NGS) with deep sequence coverage enhances sensitivity and allows for accurate quantification of the level of mosaicism. NGS identifies low-level mosaicism that would be undetectable by conventional Sanger sequencing. A customized DNA probe library was used for capturing targeted genes, followed by deep NGS analysis. The mean coverage depth per base was approximately 800×. The NGS sequence data were analyzed for single-nucleotide variants and copy number variations. Mosaic mutations in 10 cases/families were detected and confirmed by NGS analysis. Mosaicism was identified for autosomal dominant (JAG1, COL3A1), autosomal recessive (PYGM), and X-linked (PHKA2, PDHA1, OTC, and SLC6A8) disorders. The mosaicism was identified either in one or more tissues from the probands or in a parent of an affected child. When analyzing data from patients with unusual testing results or inheritance patterns, it is important to further evaluate the possibility of mosaicism. Deep NGS analysis not only provides insights into the spectrum of mosaic mutations but also underlines the importance of the detection of mosaicism as an integral part of clinical molecular diagnosis and genetic counseling.
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Affiliation(s)
- Lan Qin
- Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Jing Wang
- Baylor Miraca Genetics Laboratories, Houston, Texas; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Xia Tian
- Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Hui Yu
- Baylor Miraca Genetics Laboratories, Houston, Texas
| | | | - John J Mitchell
- Division of Pediatric Endocrinology, Montreal Children's Hospital, Montreal, Quebec, Canada
| | - Klaas J Wierenga
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Victor Wei Zhang
- Baylor Miraca Genetics Laboratories, Houston, Texas; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Lee-Jun C Wong
- Baylor Miraca Genetics Laboratories, Houston, Texas; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.
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25
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Ghosh S, Das PJ, McQueen CM, Gerber V, Swiderski CE, Lavoie JP, Chowdhary BP, Raudsepp T. Analysis of genomic copy number variation in equine recurrent airway obstruction (heaves). Anim Genet 2016; 47:334-44. [PMID: 26932307 DOI: 10.1111/age.12426] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2016] [Indexed: 12/18/2022]
Abstract
We explored the involvement of genomic copy number variants (CNVs) in susceptibility to recurrent airway obstruction (RAO), or heaves-an asthmalike inflammatory disease in horses. Analysis of 16 RAO-susceptible (cases) and six RAO-resistant (control) horses on a custom-made whole-genome 400K equine tiling array identified 245 CNV regions (CNVRs), 197 previously known and 48 new, distributed on all horse autosomes and the X chromosome. Among the new CNVRs, 30 were exclusively found in RAO cases and were further analyzed by quantitative PCR, including additional cases and controls. Suggestive association (P = 0.03; corrected P = 0.06) was found between RAO and a loss on chromosome 5 involving NME7, a gene necessary for ciliary functions in lungs and involved in primary ciliary dyskinesia in humans. The CNVR could be a potential marker for RAO susceptibility but needs further study in additional RAO cohorts. Other CNVRs were not associated with RAO, although several involved genes of interest, such as SPI2/SERPINA1 from the serpin gene family, which are associated with chronic obstructive pulmonary disease and asthma in humans. The SPI2/SERPINA1 CNVR showed striking variation among horses, but it was not significantly different between RAO cases and controls. The findings provide baseline information on the relationship between CNVs and RAO susceptibility. Discovery of new CNVs and the use of a larger population of RAO-affected and control horses are needed to shed more light on their significance in modulating this complex and heterogeneous disease.
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Affiliation(s)
- S Ghosh
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - P J Das
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA.,National Research Centre on Yak (ICAR), Dirang, Arunachal Pradesh, 790101, India
| | - C M McQueen
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - V Gerber
- Department of Veterinary Medicine, University of Bern, Bern, Switzerland
| | - C E Swiderski
- Department of Clinical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - J-P Lavoie
- Department of Clinical Sciences, University of Montreal, Montreal, QC, J2S 7C6, Canada
| | - B P Chowdhary
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA.,New Research Complex, Qatar University, Doha, 2713, Qatar
| | - T Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
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26
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Abstract
PURPOSE OF REVIEW Disorders of sexual development (DSD) are a genetic and phenotypic heterogeneous group of congenital disorders. This review focuses on the genetics of DSD and aims to recognize and contextualize, in a systematic way, based on the classification and the genetic mechanisms, the latest developments in the field of DSD diagnostics. RECENT FINDINGS Due to the current diagnostic armamentarium, during the past decade, the field of DSD diagnostics has changed dramatically from the recognition of few genes and cytogenetic abnormalities, to the identification of multiple genes and a wide arrange of genetic mechanisms involved in the genesis of DSD. In addition, the phenotypes associated with the genetic mechanism have expanded tremendously. SUMMARY Despite the current diagnostic limitations, the landscape for genetics of DSD is encouraging due to discovery of new genes, their interactions, and the recognition of the variety of mechanisms involved.
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27
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Darcy D, Atwal PS, Angell C, Gadi I, Wallerstein R. Mosaic paternal genome-wide uniparental isodisomy with down syndrome. Am J Med Genet A 2015. [PMID: 26219535 DOI: 10.1002/ajmg.a.37187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We report on a 6-month-old girl with two apparent cell lines; one with trisomy 21, and the other with paternal genome-wide uniparental isodisomy (GWUPiD), identified using single nucleotide polymorphism (SNP) based microarray and microsatellite analysis of polymorphic loci. The patient has Beckwith-Wiedemann syndrome (BWS) due to paternal uniparental disomy (UPD) at chromosome location 11p15 (UPD 11p15), which was confirmed through methylation analysis. Hyperinsulinemic hypoglycemia is present, which is associated with paternal UPD 11p15.5; and she likely has medullary nephrocalcinosis, which is associated with paternal UPD 20, although this was not biochemically confirmed. Angelman syndrome (AS) analysis was negative but this testing is not completely informative; she has no specific features of AS. Clinical features of this patient include: dysmorphic features consistent with trisomy 21, tetralogy of Fallot, hemihypertrophy, swirled skin hyperpigmentation, hepatoblastoma, and Wilms tumor. Her karyotype is 47,XX,+21[19]/46,XX[4], and microarray results suggest that the cell line with trisomy 21 is biparentally inherited and represents 40-50% of the genomic material in the tested specimen. The difference in the level of cytogenetically detected mosaicism versus the level of mosaicism observed via microarray analysis is likely caused by differences in the test methodologies. While a handful of cases of mosaic paternal GWUPiD have been reported, this patient is the only reported case that also involves trisomy 21. Other GWUPiD patients have presented with features associated with multiple imprinted regions, as does our patient.
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Affiliation(s)
- Diana Darcy
- Silicon Valley Genetics Center, Santa Clara Valley Medical Center, San Jose, California
| | | | - Cathy Angell
- Neonatology, O'Connor Hospital, San Jose, California
| | - Inder Gadi
- Laboratory Corporation of America, Research Triangle Park, North Carolina
| | - Robert Wallerstein
- Silicon Valley Genetics Center, Santa Clara Valley Medical Center, San Jose, California
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28
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Birth of a child with trisomy 9 mosaicism syndrome associated with paternal isodisomy 9: case of a positive noninvasive prenatal test result unconfirmed by invasive prenatal diagnosis. Mol Cytogenet 2015; 8:44. [PMID: 26120364 PMCID: PMC4482096 DOI: 10.1186/s13039-015-0145-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/25/2015] [Indexed: 12/31/2022] Open
Abstract
Background Non-invasive prenatal testing (NIPT) is currently used as a frontline screening test to identify fetuses with common aneuploidies. Occasionally, incidental NIPT results are conveyed to the clinician suggestive of fetuses with rare chromosome disease syndromes. We describe a child with trisomy 9 (T9) mosaicism where the prenatal history reported a positive NIPT result for T9 that was unconfirmed by conventional prenatal diagnosis. Methods NIPT was performed by low coverage whole genome plasma DNA sequencing. Karyotyping and fluorescent in situ hybridization (FISH) analysis with chromosome 9p-ter and 9q-ter probes was used to determine the somatic cell level of T9 mosaicism in the fetus and child. Quantitative fluorescent PCR (Q-PCR) of highly polymorphic short tandem repeat (STR) chromosome 9 markers was also performed to investigate the nature of the T9 mosaicism and the parental origin. Results A 22 month old girl presented with severe developmental delay, congenital cerebral dysplasia and congenital heart disease consistent with phenotypes associated with T9 mosaicism syndrome. Review of the prenatal testing history revealed a positive NIPT result for chromosome T9. However, follow up confirmatory karyotyping and FISH analysis of fetal cells returned a normal karyotype. Post-natal studies of somatic cell T9 mosaicism by FISH detected levels of approximately 20 % in blood and buccal cells. Q-PCR STR analysis of family DNA samples suggested that the T9 mosaicism originated by post-zygotic trisomic rescue of a paternal meiotic II chromosome 9 non-disjunction error resulting in the formation of two distinct somatic cell lines in the proband, one with paternal isodisomy 9 and one with T9. Conclusion This study shows that NIPT may also be a useful screening technology to increase prenatal detection rates of rare fetal chromosome disease syndromes.
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29
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30
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Lupski JR. Structural variation mutagenesis of the human genome: Impact on disease and evolution. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:419-36. [PMID: 25892534 PMCID: PMC4609214 DOI: 10.1002/em.21943] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/01/2015] [Indexed: 05/19/2023]
Abstract
Watson-Crick base-pair changes, or single-nucleotide variants (SNV), have long been known as a source of mutations. However, the extent to which DNA structural variation, including duplication and deletion copy number variants (CNV) and copy number neutral inversions and translocations, contribute to human genome variation and disease has been appreciated only recently. Moreover, the potential complexity of structural variants (SV) was not envisioned; thus, the frequency of complex genomic rearrangements and how such events form remained a mystery. The concept of genomic disorders, diseases due to genomic rearrangements and not sequence-based changes for which genomic architecture incite genomic instability, delineated a new category of conditions distinct from chromosomal syndromes and single-gene Mendelian diseases. Nevertheless, it is the mechanistic understanding of CNV/SV formation that has promoted further understanding of human biology and disease and provided insights into human genome and gene evolution. Environ. Mol. Mutagen. 56:419-436, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza Room 604B, Houston, Texas
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31
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Vander Pluym JH, O'Sullivan J, Andrew G, Bolduc FV. Genomic characterization of chromosome 8 pericentric trisomy. Clin Case Rep 2015; 3:570-7. [PMID: 26273445 PMCID: PMC4527799 DOI: 10.1002/ccr3.234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/29/2015] [Indexed: 11/10/2022] Open
Abstract
We present a patient with trisomy 8p11.21q11.21 associated with language, gross motor, fine motor, and cognitive delay. Furthermore, using array-based comparative genomic hybridization, we identify the specific genes duplicated in our patient.
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Affiliation(s)
- Juliana H Vander Pluym
- Division of Pediatric Neuroscience, Stollery Children Hospital, University of Alberta Edmonton, Alberta, Canada
| | - Julia O'Sullivan
- Division of Pediatric Neuroscience, Stollery Children Hospital, University of Alberta Edmonton, Alberta, Canada
| | - Gail Andrew
- Division of Neurodevelopmental and Neuromotor Pediatrics, University of Alberta Edmonton, Alberta, Canada
| | - Francois V Bolduc
- Division of Pediatric Neuroscience, Stollery Children Hospital, University of Alberta Edmonton, Alberta, Canada ; Neuroscience and Mental Health Institute, University of Alberta Edmonton, Alberta, Canada
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32
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Somatic mosaicism: implications for disease and transmission genetics. Trends Genet 2015; 31:382-92. [PMID: 25910407 DOI: 10.1016/j.tig.2015.03.013] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 11/21/2022]
Abstract
Nearly all of the genetic material among cells within an organism is identical. However, single-nucleotide variants (SNVs), small insertions/deletions (indels), copy-number variants (CNVs), and other structural variants (SVs) continually accumulate as cells divide during development. This process results in an organism composed of countless cells, each with its own unique personal genome. Thus, every human is undoubtedly mosaic. Mosaic mutations can go unnoticed, underlie genetic disease or normal human variation, and may be transmitted to the next generation as constitutional variants. We review the influence of the developmental timing of mutations, the mechanisms by which they arise, methods for detecting mosaic variants, and the risk of passing these mutations on to the next generation.
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33
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Winberg J, Berggren H, Malm T, Johansson S, Johansson Ramgren J, Nilsson B, Liedén A, Nordenskjöld A, Gustavsson P, Nordgren A. No evidence for mosaic pathogenic copy number variations in cardiac tissue from patients with congenital heart malformations. Eur J Med Genet 2015; 58:129-33. [PMID: 25652018 DOI: 10.1016/j.ejmg.2015.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 01/10/2015] [Indexed: 11/28/2022]
Abstract
The aim of this study was to investigate if pathogenic copy number variations (CNVs) are present in mosaic form in patients with congenital heart malformations. We have collected cardiac tissue and blood samples from 23 patients with congenital heart malformations that underwent cardiac surgery and screened for mosaic gene dose alterations restricted to cardiac tissue using array comparative genomic hybridization (array CGH). We did not find evidence of CNVs in mosaic form after array CGH analysis. Pathogenic CNVs that were present in both cardiac tissue and blood were detected in 2/23 patients (9%), and in addition we found several constitutional CNVs of unclear clinical significance. This is the first study investigating mosaicism for CNVs in heart tissue compared to peripheral blood and the results do not indicate that pathogenic mosaic copy number changes are common in patients with heart malformations. Importantly, in line with previous studies, our results show that constitutional pathogenic CNVs are important factors contributing to congenital heart malformations.
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Affiliation(s)
- Johanna Winberg
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Håkan Berggren
- Pediatric Cardiac Surgery Unit, Queen Silvia Children's Hospital, Gothenburg, Sweden
| | - Torsten Malm
- Pediatric Cardiac Surgery Unit, Children's Hospital, University Hospital, Lund, Sweden
| | - Sune Johansson
- Pediatric Cardiac Surgery Unit, Children's Hospital, University Hospital, Lund, Sweden
| | | | - Boris Nilsson
- Pediatric Cardiac Surgery Unit, Queen Silvia Children's Hospital, Gothenburg, Sweden
| | - Agne Liedén
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Agneta Nordenskjöld
- Department of Woman and Child Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Pediatric Surgery, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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34
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King DA, Jones WD, Crow YJ, Dominiczak AF, Foster NA, Gaunt TR, Harris J, Hellens SW, Homfray T, Innes J, Jones EA, Joss S, Kulkarni A, Mansour S, Morris AD, Parker MJ, Porteous DJ, Shihab HA, Smith BH, Tatton-Brown K, Tolmie JL, Trzaskowski M, Vasudevan PC, Wakeling E, Wright M, Plomin R, Timpson NJ, Hurles ME. Mosaic structural variation in children with developmental disorders. Hum Mol Genet 2015; 24:2733-45. [PMID: 25634561 PMCID: PMC4406290 DOI: 10.1093/hmg/ddv033] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/27/2015] [Indexed: 01/01/2023] Open
Abstract
Delineating the genetic causes of developmental disorders is an area of active investigation. Mosaic structural abnormalities, defined as copy number or loss of heterozygosity events that are large and present in only a subset of cells, have been detected in 0.2–1.0% of children ascertained for clinical genetic testing. However, the frequency among healthy children in the community is not well characterized, which, if known, could inform better interpretation of the pathogenic burden of this mutational category in children with developmental disorders. In a case–control analysis, we compared the rate of large-scale mosaicism between 1303 children with developmental disorders and 5094 children lacking developmental disorders, using an analytical pipeline we developed, and identified a substantial enrichment in cases (odds ratio = 39.4, P-value 1.073e − 6). A meta-analysis that included frequency estimates among an additional 7000 children with congenital diseases yielded an even stronger statistical enrichment (P-value 1.784e − 11). In addition, to maximize the detection of low-clonality events in probands, we applied a trio-based mosaic detection algorithm, which detected two additional events in probands, including an individual with genome-wide suspected chimerism. In total, we detected 12 structural mosaic abnormalities among 1303 children (0.9%). Given the burden of mosaicism detected in cases, we suspected that many of the events detected in probands were pathogenic. Scrutiny of the genotypic–phenotypic relationship of each detected variant assessed that the majority of events are very likely pathogenic. This work quantifies the burden of structural mosaicism as a cause of developmental disorders.
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Affiliation(s)
- Daniel A King
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Wendy D Jones
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Yanick J Crow
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals, NHS Foundation Trust, Manchester Academic Health Science Centre (MAHSC), Manchester M13 9WL, UK
| | - Anna F Dominiczak
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Nicola A Foster
- University Hospitals of Leicester, NHS Trust, Leicester Royal Infirmary, Leicester LE1 5WW, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Jade Harris
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals, NHS Foundation Trust, Manchester Academic Health Science Centre (MAHSC), Manchester M13 9WL, UK
| | - Stephen W Hellens
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE1 3BZ, UK
| | - Tessa Homfray
- Southwest Thames Regional Genetics Centre, St George's Healthcare NHS Trust, London SW17 0RE, UK
| | - Josie Innes
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals, NHS Foundation Trust, Manchester Academic Health Science Centre (MAHSC), Manchester M13 9WL, UK
| | - Elizabeth A Jones
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals, NHS Foundation Trust, Manchester Academic Health Science Centre (MAHSC), Manchester M13 9WL, UK, Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, MAHSC, Manchester M13 9WL, UK
| | - Shelagh Joss
- West of Scotland Clinical Genetics Service, Southern General Hospital, Glasgow DD1 9SY, UK
| | - Abhijit Kulkarni
- Southwest Thames Regional Genetics Centre, St George's Healthcare NHS Trust, London SW17 0RE, UK
| | - Sahar Mansour
- Southwest Thames Regional Genetics Centre, St George's Healthcare NHS Trust, London SW17 0RE, UK
| | - Andrew D Morris
- School of Molecular, Genetic and Population Health Sciences, University of Edinburgh Medical School, Teviot Place, Edinburgh EH8 9AG, UK
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield, UK
| | - David J Porteous
- Medical Genetics Section, Molecular Medicine Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Hashem A Shihab
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Blair H Smith
- School of Medicine, Dundee University, Mackenzie Building, Kirsty Semple Way, Ninewells Hospital and Medical School, Dundee DD2 4RB, UK
| | - Katrina Tatton-Brown
- Southwest Thames Regional Genetics Centre, St George's Healthcare NHS Trust, London SW17 0RE, UK
| | - John L Tolmie
- West of Scotland Clinical Genetics Service, Southern General Hospital, Glasgow DD1 9SY, UK
| | - Maciej Trzaskowski
- King's College London, MRC Social, Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London SE5 8AF, UK and
| | - Pradeep C Vasudevan
- University Hospitals of Leicester, NHS Trust, Leicester Royal Infirmary, Leicester LE1 5WW, UK
| | - Emma Wakeling
- North West Thames Regional Genetics Service, North West London Hospitals NHS Trust, Watford Rd, Harrow HA1 3UJ, UK
| | - Michael Wright
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE1 3BZ, UK
| | - Robert Plomin
- King's College London, MRC Social, Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London SE5 8AF, UK and
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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Yauk CL, Aardema MJ, Benthem JV, Bishop JB, Dearfield KL, DeMarini DM, Dubrova YE, Honma M, Lupski JR, Marchetti F, Meistrich ML, Pacchierotti F, Stewart J, Waters MD, Douglas GR. Approaches for identifying germ cell mutagens: Report of the 2013 IWGT workshop on germ cell assays(☆). MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 783:36-54. [PMID: 25953399 DOI: 10.1016/j.mrgentox.2015.01.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 01/23/2015] [Indexed: 01/06/2023]
Abstract
This workshop reviewed the current science to inform and recommend the best evidence-based approaches on the use of germ cell genotoxicity tests. The workshop questions and key outcomes were as follows. (1) Do genotoxicity and mutagenicity assays in somatic cells predict germ cell effects? Limited data suggest that somatic cell tests detect most germ cell mutagens, but there are strong concerns that dictate caution in drawing conclusions. (2) Should germ cell tests be done, and when? If there is evidence that a chemical or its metabolite(s) will not reach target germ cells or gonadal tissue, it is not necessary to conduct germ cell tests, notwithstanding somatic outcomes. However, it was recommended that negative somatic cell mutagens with clear evidence for gonadal exposure and evidence of toxicity in germ cells could be considered for germ cell mutagenicity testing. For somatic mutagens that are known to reach the gonadal compartments and expose germ cells, the chemical could be assumed to be a germ cell mutagen without further testing. Nevertheless, germ cell mutagenicity testing would be needed for quantitative risk assessment. (3) What new assays should be implemented and how? There is an immediate need for research on the application of whole genome sequencing in heritable mutation analysis in humans and animals, and integration of germ cell assays with somatic cell genotoxicity tests. Focus should be on environmental exposures that can cause de novo mutations, particularly newly recognized types of genomic changes. Mutational events, which may occur by exposure of germ cells during embryonic development, should also be investigated. Finally, where there are indications of germ cell toxicity in repeat dose or reproductive toxicology tests, consideration should be given to leveraging those studies to inform of possible germ cell genotoxicity.
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Affiliation(s)
- Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
| | | | - Jan van Benthem
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Jack B Bishop
- National Institute of Environmental Health Sciences, NC, USA
| | | | | | | | | | - James R Lupski
- Department of Molecular and Human Genetics, and Department of Pediatrics, Baylor College of Medicine, USA
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | | | - Francesca Pacchierotti
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Italy
| | | | | | - George R Douglas
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
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Parental somatic mosaicism is underrecognized and influences recurrence risk of genomic disorders. Am J Hum Genet 2014; 95:173-82. [PMID: 25087610 DOI: 10.1016/j.ajhg.2014.07.003] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/08/2014] [Indexed: 11/20/2022] Open
Abstract
New human mutations are thought to originate in germ cells, thus making a recurrence of the same mutation in a sibling exceedingly rare. However, increasing sensitivity of genomic technologies has anecdotally revealed mosaicism for mutations in somatic tissues of apparently healthy parents. Such somatically mosaic parents might also have germline mosaicism that can potentially cause unexpected intergenerational recurrences. Here, we show that somatic mosaicism for transmitted mutations among parents of children with simplex genetic disease is more common than currently appreciated. Using the sensitivity of individual-specific breakpoint PCR, we prospectively screened 100 families with children affected by genomic disorders due to rare deletion copy-number variants (CNVs) determined to be de novo by clinical analysis of parental DNA. Surprisingly, we identified four cases of low-level somatic mosaicism for the transmitted CNV in DNA isolated from parental blood. Integrated probabilistic modeling of gametogenesis developed in response to our observations predicts that mutations in parental blood increase recurrence risk substantially more than parental mutations confined to the germline. Moreover, despite the fact that maternally transmitted mutations are the minority of alleles, our model suggests that sexual dimorphisms in gametogenesis result in a greater proportion of somatically mosaic transmitting mothers who are thus at increased risk of recurrence. Therefore, somatic mosaicism together with sexual differences in gametogenesis might explain a considerable fraction of unexpected recurrences of X-linked recessive disease. Overall, our results underscore an important role for somatic mosaicism and mitotic replicative mutational mechanisms in transmission genetics.
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Erickson RP. Recent advances in the study of somatic mosaicism and diseases other than cancer. Curr Opin Genet Dev 2014; 26:73-8. [DOI: 10.1016/j.gde.2014.06.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/27/2014] [Accepted: 06/02/2014] [Indexed: 02/06/2023]
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Aghili L, Foo J, DeGregori J, De S. Patterns of somatically acquired amplifications and deletions in apparently normal tissues of ovarian cancer patients. Cell Rep 2014; 7:1310-9. [PMID: 24794429 DOI: 10.1016/j.celrep.2014.03.071] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 02/06/2014] [Accepted: 03/28/2014] [Indexed: 12/20/2022] Open
Abstract
Little is understood about the occurrence of somatic genomic alterations in normal tissues and their significance in the context of disease. Here, we identified potential somatic copy number alterations (pSCNAs) in apparently normal ovarian tissue and peripheral blood of 423 ovarian cancer patients. There were, on average, two to four pSCNAs per sample detectable at a tissue-level resolution, although some individuals had orders of magnitude more. Accordingly, we estimated the lower bound of the rate of pSCNAs per cell division. Older individuals and BRCA mutation carriers had more pSCNAs than others. pSCNAs significantly overlapped with Alu and G-quadruplexes, and the affected genes were enriched for signaling and regulation. Some of the amplification/deletion hotspots in pan-cancer genomes were hot spots of pSCNAs in normal tissues as well, suggesting that those regions might be inherently unstable. Prevalence of pSCNA in peripheral blood predicted survival, implying that mutations in normal tissues might have consequences for cancer patients.
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Affiliation(s)
- Leila Aghili
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jasmine Foo
- School of Mathematics, University of Minnesota, Minneapolis, MN 55455, USA
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO 80045, USA
| | - Subhajyoti De
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA; Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO 80045, USA; Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA.
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