1
|
Waldvogel SM, Posey JE, Goodell MA. Human embryonic genetic mosaicism and its effects on development and disease. Nat Rev Genet 2024; 25:698-714. [PMID: 38605218 PMCID: PMC11408116 DOI: 10.1038/s41576-024-00715-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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.
Collapse
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.
| |
Collapse
|
2
|
Ward A, Farengo-Clark D, McKenna DB, Safonov A, Good M, Le A, Kessler L, Shah PD, Bradbury AR, Domchek SM, Nathanson KL, Powers J, Maxwell KN. Clinical management of TP53 mosaic variants found on germline genetic testing. Cancer Genet 2024; 284-285:43-47. [PMID: 38677009 PMCID: PMC11168919 DOI: 10.1016/j.cancergen.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 03/23/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Germline heterozygous TP53 pathogenic variants (PVs) cause Li Fraumeni Syndrome (LFS, OMIM#151623). TP53 PVs at lower-than-expected variant allele frequencies (VAF) may reflect postzygotic mosaicism (PZM) or clonal hematopoiesis (CH); however, no guidelines exist for workup and clinical management. PATIENTS AND METHODS Retrospective analysis of probands who presented to an academic cancer genetics program with a TP53 PV result on germline genetic testing. RESULTS Twenty-one of 125 unrelated probands (17 %) were found to harbor a TP53 PV with VAF<30 % or a designation of "mosaic". A diagnosis of PZM was made in nine (43 %) due to a clinical phenotype consistent with LFS with (n = 8) or without (n = 1) positive ancillary tissue testing. Twelve patients (57 %) were diagnosed with presumed CH (pCH) due to a diagnosis of a myeloproliferative neoplasm, negative ancillary tissue testing, clinical phenotype not meeting LFS criteria, no cancer, and/or no first cancer age<50. Of the 19 patients with biological offspring, nine had either partial or complete offspring testing, all negative. CONCLUSIONS Determining the etiology of low VAF TP53 PVs requires ancillary tissue testing and incorporation of clinical phenotype. Discerning PZM versus CH is important to provide optimal care and follow-up.
Collapse
Affiliation(s)
- Abigail Ward
- Master of Science in Genetic Counseling Program, Perelman School of Medicine, University of Pennsylvania, USA
| | - Dana Farengo-Clark
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Danielle B McKenna
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Anton Safonov
- Division of Translational Medicine and Human Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Madeline Good
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Anh Le
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Lisa Kessler
- Master of Science in Genetic Counseling Program, Perelman School of Medicine, University of Pennsylvania, USA
| | - Payal D Shah
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Angela R Bradbury
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Susan M Domchek
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA; Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Katherine L Nathanson
- Division of Translational Medicine and Human Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jacquelyn Powers
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA
| | - Kara N Maxwell
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, USA; Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Corporal Michael Crescenz Veterans Affairs Medical Center, Philadelphia, PA, USA.
| |
Collapse
|
3
|
Wenger D, Kurumety S, Aydi ZB. A case report: invasive ductal carcinoma in mosaic Li-Fraumeni syndrome. J Surg Case Rep 2022; 2022:rjac408. [PMID: 36168441 PMCID: PMC9509207 DOI: 10.1093/jscr/rjac408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/23/2022] [Indexed: 11/22/2022] Open
Abstract
Li-Fraumeni syndrome (LFS) is a rare autosomal dominant condition caused by pathogenic variants in the TP53 tumor suppressor gene and characterized by a high lifetime risk of various cancers with a very early age of onset. We are presenting a 41-year-old woman with right invasive ductal cancer and no family history of cancers, diagnosed with mosaic LFS confirmed with blood and skin punch biopsy samples. She was treated with neoadjuvant chemotherapy, mastectomy and sentinel node biopsy with completion axillary dissection. Adjuvant radiation was not recommended due to increased risk of secondary cancers. She also elected to undergo risk reducing contralateral mastectomy. Further research is warranted to determine the appropriate clinical management and surveillance strategies in patients with mosaic LFS as whether individuals with mosaic LFS have differing cancer risks in comparison to classic germline LFS is unknown.
Collapse
Affiliation(s)
- Danielle Wenger
- University of Arizona College of Medicine – Phoenix , Phoenix, AZ 85006 , USA
| | - Sasha Kurumety
- Department of Radiology, Houston Methodist Hospital , Houston, TX 77030 , USA
| | - Zeynep B Aydi
- Department of Surgery, University of Arizona College of Medicine – Phoenix , Phoenix, AZ 85006 , USA
- Department of Surgical Oncology, Banner MD Anderson Cancer Center , Phoenix, AZ 85006 , USA
| |
Collapse
|
4
|
Chen JL, Miller DT, Schmidt LS, Malkin D, Korf BR, Eng C, Kwiatkowski DJ, Giannikou K. Mosaicism in Tumor Suppressor Gene Syndromes: Prevalence, Diagnostic Strategies, and Transmission Risk. Annu Rev Genomics Hum Genet 2022; 23:331-361. [PMID: 36044908 DOI: 10.1146/annurev-genom-120121-105450] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A mosaic state arises when pathogenic variants are acquired in certain cell lineages during postzygotic development, and mosaic individuals may present with a generalized or localized phenotype. Here, we review the current state of knowledge regarding mosaicism for eight common tumor suppressor genes-NF1, NF2, TSC1, TSC2, PTEN, VHL, RB1, and TP53-and their related genetic syndromes/entities. We compare and discuss approaches for comprehensive diagnostic genetic testing, the spectrum of variant allele frequency, and disease severity. We also review affected individuals who have no mutation identified after conventional genetic analysis, as well as genotype-phenotype correlations and transmission risk for each tumor suppressor gene in full heterozygous and mosaic patients. This review provides new insight into similarities as well as marked differences regarding the appreciation of mosaicism in these tumor suppressor syndromes.
Collapse
Affiliation(s)
- Jillian L Chen
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Boston University School of Medicine, Boston, Massachusetts, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.,Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - David Malkin
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - David J Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA;
| | - Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Division of Hematology and Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California, USA;
| |
Collapse
|
5
|
Schwartz AN, Hyman SR, Stokes SM, Castillo D, Tung NM, Weitzel JN, Rana HQ, Garber JE. Evaluation of TP53 Variants Detected on Peripheral Blood or Saliva Testing: Discerning Germline From Somatic TP53 Variants. JCO Precis Oncol 2021; 5:1677-1686. [PMID: 34994652 DOI: 10.1200/po.21.00278] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/15/2021] [Accepted: 09/24/2021] [Indexed: 01/04/2023] Open
Abstract
PURPOSE Multigene panel testing (MGPT) identifies TP53 pathogenic or likely pathogenic (P/LP) variants in patients with diverse phenotypes, of which only one is classic Li-Fraumeni syndrome. Low variant allelic fraction (VAF) in TP53 found on germline testing may suggest aberrant clonal expansion or constitutional mosaicism. We evaluated TP53-positive probands seen in a cancer genetics program to determine germline versus somatic status. METHODS We reviewed TP53-positive probands from 2012 to 2019 identified by MGPT on blood or saliva (N = 84). Available VAFs were collected. Probands with a familial variant, who met Li-Fraumeni syndrome testing criteria or who carried a founder variant, were considered germline. For those with uncertain germline status, TP53 variants were further examined using ancillary data of family members and somatic tissue. RESULTS Of the 84 probands, 54.7% had germline variants with 33.3% meeting criteria for germline status and 21.4% confirmed through ancillary testing. Aberrant clonal expansion comprised 13.1% with clonal hematopoiesis of indeterminate potential and 2.4% with a hematologic malignancy. Constitutional mosaicism was confirmed in 8.3% probands. Definitive status could not be determined in 3.6% despite ancillary assessment, and 17.9% did not have ancillary testing. CONCLUSION A TP53 P/LP variant found on peripheral blood or saliva MGPT does not always originate in the germline. In a clinical cancer genetics cohort, approximately half of the patients had TP53 P/LP germline variants; these patients plus those with constitutional mosaicism require intensified surveillance. A framework of multiple strategies enables discernment of germline from constitutional mosaic and acquired variants, which is essential for appropriate management.
Collapse
Affiliation(s)
- Alison N Schwartz
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sophie R Hyman
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Samantha M Stokes
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Danielle Castillo
- Division of Clinical Cancer Genomics, Beckman Research Institute, City of Hope, Duarte, CA
| | - Nadine M Tung
- Harvard Medical School, Boston, MA
- Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Boston, MA
| | | | - Huma Q Rana
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Judy E Garber
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| |
Collapse
|
6
|
Peacock EG, Grenon LM, Batalini F, Tung N. Challenges in Interpreting TP53 Pathogenic Variants With a Low Minor Allele Frequency in Germline Genetic Testing: A Case Report of a Patient With Mosaic Li-Fraumeni Syndrome. JCO Precis Oncol 2020; 4:91-95. [DOI: 10.1200/po.19.00279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
| | | | | | - Nadine Tung
- Beth Israel Deaconess Medical Center, Boston, MA
| |
Collapse
|
7
|
Pre- and Post-Zygotic TP53 De Novo Mutations in SHH-Medulloblastoma. Cancers (Basel) 2020; 12:cancers12092503. [PMID: 32899294 PMCID: PMC7564492 DOI: 10.3390/cancers12092503] [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: 07/30/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 11/26/2022] Open
Abstract
Simple Summary Medulloblastoma is the most common malignant brain tumor in children. In a subset of cases, a causal factor is a constitutive mutation of the TP53 gene, which may be inherited or arise for the first time in a patient (de novo). Using an immunohistochemistry assay as a screening tool, we selected patients suspected of harboring a TP53 mutation and offered genetic counseling and germline testing. Our study, which was the first to investigate the parental origin of TP53 mutations in medulloblastoma, allowed the identification of two additional cases with de novo mutations. Moreover, we demonstrated that in one patient the mutation originated at a post-zygotic stage, resulting in somatic mosaicism. These findings have important implications for genetic counseling since they highlight the occurrence of both pre- and post-zygotic TP53 de novo mutations in medulloblastoma, pointing out that in a specific subgroup of patients genetic testing should be offered regardless of family history. Abstract Li-Fraumeni syndrome (LFS) is an autosomal dominant disorder caused by mutations in the TP53 gene, predisposing to a wide spectrum of early-onset cancers, including brain tumors. In medulloblastoma patients, the role of TP53 has been extensively investigated, though the prevalence of de novo mutations has not been addressed. We characterized TP53 mutations in a monocentric cohort of consecutive Sonic Hedgehog (SHH)-activated medulloblastoma patients. Germline testing was offered based on tumor p53 immunostaining positivity. Among 24 patients, three (12.5%) showed tumor p53 overexpression, of whom two consented to undergo germline testing and resulted as carriers of TP53 mutations. In the first case, family history was uneventful and the mutation was not found in either of the parents. The second patient, with a family history suggestive of LFS, unexpectedly resulted as a carrier of the mosaic mutation c.742=/C>T p.(Arg248=/Trp). The allele frequency was 26% in normal tissues and 42–77% in tumor specimens. Loss of heterozygosity (LOH) in the tumor was also confirmed. Notably, the mosaic case has been in complete remission for more than one year, while the first patient, as most TP53-mutated medulloblastoma cases from other cohorts, showed a severe and rapidly progressive disease. Our study reported the first TP53 mosaic mutation in medulloblastoma patients and confirmed the importance of germline testing in p53 overexpressed SHH-medulloblastoma, regardless of family history.
Collapse
|
8
|
Pazdirek F, Minarik M, Benesova L, Halkova T, Belsanova B, Macek M, Stepanek L, Hoch J. Monitoring of Early Changes of Circulating Tumor DNA in the Plasma of Rectal Cancer Patients Receiving Neoadjuvant Concomitant Chemoradiotherapy: Evaluation for Prognosis and Prediction of Therapeutic Response. Front Oncol 2020; 10:1028. [PMID: 32793464 PMCID: PMC7394215 DOI: 10.3389/fonc.2020.01028] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 05/22/2020] [Indexed: 12/13/2022] Open
Abstract
Introduction: Patients with locally advanced rectal cancer (LARC) are undergoing neoadjuvant chemoradiotherapy (NCRT) prior to surgery. Although in some patients the NCRT is known to prevent local recurrence, it is also accompanied by side effects. Accordingly, there is an unmet need to identify predictive markers allowing to identify non-responders to avoid its adverse effects. We monitored circulating tumor DNA (ctDNA) as a potential liquid biopsy-based biomarker. We have investigated ctDNA changes plasma during the early days of NCRT and its relationship to the overall therapy outcome. Methods and Patients: The studied cohort included 36 LARC patients (stage II or III) undergoing NCRT with subsequent surgical treatment. We have detected somatic mutations in tissue biopsies taken during endoscopic examination prior to the therapy. CtDNA was extracted from patient plasma samples prior to therapy and at the end of the first week. In order to optimize the analytical costs of liquid-biopsy testing, we have utilized a two-level approach in which first a low-cost detection method of denaturing capillary electrophoresis was used followed by examination of initially negative samples by a high-sensitivity BEAMING assay. The ctDNA was related to clinical parameters including tumor regression grade (TRG) and TNM tumor staging. Results: We have detected a somatic mutation in 33 out of 36 patients (91.7%). Seven patients (7/33, 21.2%) had ctDNA present prior to therapy. The ctDNA positivity before treatment reduced post-operative disease-free survival and overall survival by an average of 1.47 and 1.41 years, respectively (p = 0.015, and p = 0.010). In all patients, ctDNA was strongly reduced or completely eliminated from plasma by the end of the first week of NCRT, with no correlation to any of the parameters analyzed. Conclusions: The baseline ctDNA presence represented a statistically significant negative prognostic biomarker for the overall patient survival. As ctDNA was reduced indiscriminately from circulation of all patients, dynamics during the first week of NCRT is not suited for predicting the outcome of LARC. However, the general effect of rapid ctDNA disappearance apparently occurring during the initial days of NCRT is noteworthy and should further be studied.
Collapse
Affiliation(s)
- Filip Pazdirek
- Department of Surgery, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Marek Minarik
- Department of Surgery, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia.,Elphogene, Prague, Czechia
| | - Lucie Benesova
- Center for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Prague, Czechia
| | - Tereza Halkova
- Center for Applied Genomics of Solid Tumors (CEGES), Genomac Research Institute, Prague, Czechia
| | | | - Milan Macek
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Lubomír Stepanek
- Institute of Biophysics and Informatics, 1st Faculty of Medicine, Charles University, Prague, Czechia
| | - Jiri Hoch
- Department of Surgery, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| |
Collapse
|
9
|
Donovan LN, Kohlmann W, Snow AK, Neklason DW, Schiffman JD, Maese L. Germ Cell Mosaicism: A Rare Cause of Li-Fraumeni Recurrence Among Siblings. JCO Precis Oncol 2020; 4:PO.20.00064. [PMID: 32923893 PMCID: PMC7446446 DOI: 10.1200/po.20.00064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Wendy Kohlmann
- University of Utah Huntsman Cancer Institute, Salt Lake City, UT
| | - Angela K. Snow
- University of Utah Huntsman Cancer Institute, Salt Lake City, UT
| | - Deborah W. Neklason
- University of Utah Huntsman Cancer Institute, Salt Lake City, UT
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT
| | - Joshua D. Schiffman
- University of Utah Huntsman Cancer Institute, Salt Lake City, UT
- University of Utah Department of Pediatrics, Salt Lake City, UT
| | - Luke Maese
- University of Utah Huntsman Cancer Institute, Salt Lake City, UT
- University of Utah Department of Pediatrics, Salt Lake City, UT
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Mester JL, Jackson SA, Postula K, Stettner A, Solomon S, Bissonnette J, Murphy PD, Klein RT, Hruska KS. Apparently Heterozygous TP53 Pathogenic Variants May Be Blood Limited in Patients Undergoing Hereditary Cancer Panel Testing. J Mol Diagn 2020; 22:396-404. [DOI: 10.1016/j.jmoldx.2019.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/26/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
|
12
|
Ma X, Shao Y, Tian L, Flasch DA, Mulder HL, Edmonson MN, Liu Y, Chen X, Newman S, Nakitandwe J, Li Y, Li B, Shen S, Wang Z, Shurtleff S, Robison LL, Levy S, Easton J, Zhang J. Analysis of error profiles in deep next-generation sequencing data. Genome Biol 2019; 20:50. [PMID: 30867008 PMCID: PMC6417284 DOI: 10.1186/s13059-019-1659-6] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/19/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Sequencing errors are key confounding factors for detecting low-frequency genetic variants that are important for cancer molecular diagnosis, treatment, and surveillance using deep next-generation sequencing (NGS). However, there is a lack of comprehensive understanding of errors introduced at various steps of a conventional NGS workflow, such as sample handling, library preparation, PCR enrichment, and sequencing. In this study, we use current NGS technology to systematically investigate these questions. RESULTS By evaluating read-specific error distributions, we discover that the substitution error rate can be computationally suppressed to 10-5 to 10-4, which is 10- to 100-fold lower than generally considered achievable (10-3) in the current literature. We then quantify substitution errors attributable to sample handling, library preparation, enrichment PCR, and sequencing by using multiple deep sequencing datasets. We find that error rates differ by nucleotide substitution types, ranging from 10-5 for A>C/T>G, C>A/G>T, and C>G/G>C changes to 10-4 for A>G/T>C changes. Furthermore, C>T/G>A errors exhibit strong sequence context dependency, sample-specific effects dominate elevated C>A/G>T errors, and target-enrichment PCR led to ~ 6-fold increase of overall error rate. We also find that more than 70% of hotspot variants can be detected at 0.1 ~ 0.01% frequency with the current NGS technology by applying in silico error suppression. CONCLUSIONS We present the first comprehensive analysis of sequencing error sources in conventional NGS workflows. The error profiles revealed by our study highlight new directions for further improving NGS analysis accuracy both experimentally and computationally, ultimately enhancing the precision of deep sequencing.
Collapse
Affiliation(s)
- Xiaotu Ma
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Ying Shao
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Diane A. Flasch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Heather L. Mulder
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Michael N. Edmonson
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Yu Liu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Joy Nakitandwe
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Benshang Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127 China
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127 China
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Sheila Shurtleff
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Leslie L. Robison
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - John Easton
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| |
Collapse
|
13
|
Bowles KR, Mancini-DiNardo D, Coffee B, Cox HC, Qian Y, Elias M, Singh N, Judkins T, Leclair B, Roa BB. Hereditary cancer testing challenges: assembling the analytical pieces to solve the patient clinical puzzle. Future Oncol 2018; 15:65-79. [PMID: 30113232 DOI: 10.2217/fon-2018-0476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Expanded genetic test utilization to guide cancer management has driven the development of larger gene panels and greater diversity in the patient population pursuing testing, resulting in increased identification of atypical or technically challenging genetic findings. To ensure appropriate patient care, it is critical that genetic tests adequately identify and characterize these findings. We describe genetic testing challenges frequently encountered by our laboratory and the methodologies we employ to improve test accuracy for the identification and characterization of atypical genetic findings. While these findings may be individually rare, 15,745 (9%) individuals tested by our laboratory for hereditary cancer risk had an atypical genetic finding, highlighting the importance of employing highly accurate and comprehensive methods in clinical genetic testing.
Collapse
Affiliation(s)
- Karla R Bowles
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | | | - Bradford Coffee
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Hannah C Cox
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Yaping Qian
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Maria Elias
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Nanda Singh
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Thaddeus Judkins
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Benoît Leclair
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Benjamin B Roa
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| |
Collapse
|
14
|
Penkert J, Schmidt G, Hofmann W, Schubert S, Schieck M, Auber B, Ripperger T, Hackmann K, Sturm M, Prokisch H, Hille-Betz U, Mark D, Illig T, Schlegelberger B, Steinemann D. Breast cancer patients suggestive of Li-Fraumeni syndrome: mutational spectrum, candidate genes, and unexplained heredity. Breast Cancer Res 2018; 20:87. [PMID: 30086788 PMCID: PMC6081832 DOI: 10.1186/s13058-018-1011-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/27/2018] [Indexed: 01/07/2023] Open
Abstract
Background Breast cancer is the most prevalent tumor entity in Li-Fraumeni syndrome. Up to 80% of individuals with a Li-Fraumeni-like phenotype do not harbor detectable causative germline TP53 variants. Yet, no systematic panel analyses for a wide range of cancer predisposition genes have been conducted on cohorts of women with breast cancer fulfilling Li-Fraumeni(-like) clinical diagnostic criteria. Methods To specifically help explain the diagnostic gap of TP53 wild-type Li-Fraumeni(-like) breast cancer cases, we performed array-based CGH (comparative genomic hybridization) and panel-based sequencing of 94 cancer predisposition genes on 83 breast cancer patients suggestive of Li-Fraumeni syndrome who had previously had negative test results for causative BRCA1, BRCA2, and TP53 germline variants. Results We identified 13 pathogenic or likely pathogenic germline variants in ten patients and in nine genes, including four copy number aberrations and nine single-nucleotide variants or small indels. Three patients presented as double-mutation carriers involving two different genes each. In five patients (5 of 83; 6% of cohort), we detected causative pathogenic variants in established hereditary breast cancer susceptibility genes (i.e., PALB2, CHEK2, ATM). Five further patients (5 of 83; 6% of cohort) were found to harbor pathogenic variants in genes lacking a firm association with breast cancer susceptibility to date (i.e., Fanconi pathway genes, RECQ family genes, CDKN2A/p14ARF, and RUNX1). Conclusions Our study details the mutational spectrum in breast cancer patients suggestive of Li-Fraumeni syndrome and indicates the need for intensified research on monoallelic variants in Fanconi pathway and RECQ family genes. Notably, this study further reveals a large portion of still unexplained Li-Fraumeni(-like) cases, warranting comprehensive investigation of recently described candidate genes as well as noncoding regions of the TP53 gene in patients with Li-Fraumeni(-like) syndrome lacking TP53 variants in coding regions. Electronic supplementary material The online version of this article (10.1186/s13058-018-1011-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Judith Penkert
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany.
| | - Gunnar Schmidt
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Stephanie Schubert
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Maximilian Schieck
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Partner Site Dresden, Dresden, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ursula Hille-Betz
- Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Dorothea Mark
- Department of Internal Medicine, Hematology/Oncology, University Hospital Frankfurt, Frankfurt, Germany
| | - Thomas Illig
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Brigitte Schlegelberger
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| |
Collapse
|
15
|
Okur V, Chung WK. The impact of hereditary cancer gene panels on clinical care and lessons learned. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a002154. [PMID: 29162654 PMCID: PMC5701305 DOI: 10.1101/mcs.a002154] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mutations in hereditary cancer syndromes account for a modest fraction of all cancers; however, identifying patients with these germline mutations offers tremendous health benefits to both patients and their family members. There are about 60 genes that confer a high lifetime risk of specific cancers, and this information can be used to tailor prevention, surveillance, and treatment. With advances in next-generation sequencing technologies and the elimination of gene patents for evaluating genetic information, we are now able to analyze multiple genes simultaneously, leading to the widespread clinical use of gene panels for germline cancer testing. Over the last 4 years since these panels were introduced, we have learned about the diagnostic yield of testing, the expanded phenotypes of the patients with mutations, and the clinical utility of genetic testing in patients with cancer and/or without cancer but with a family history of cancer. We have also experienced challenges including the large number of variants of unknown significance (VUSs), identification of somatic mutations and need to differentiate these from germline mutations, technical issues with particular genes and mutations, insurance coverage and reimbursement issues, lack of access to data, and lack of clinical management guidelines for newer and, especially, moderate and low-penetrance genes. The lessons learned from cancer genetic testing panels are applicable to other clinical areas as well and highlight the problems to be solved as we advance genomic medicine.
Collapse
Affiliation(s)
- Volkan Okur
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
| | - Wendy K Chung
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA; .,Department of Medicine, Columbia University Medical Center, New York, New York 10032, USA
| |
Collapse
|
16
|
Renaux-Petel M, Charbonnier F, Théry JC, Fermey P, Lienard G, Bou J, Coutant S, Vezain M, Kasper E, Fourneaux S, Manase S, Blanluet M, Leheup B, Mansuy L, Champigneulle J, Chappé C, Longy M, Sévenet N, Paillerets BBD, Guerrini-Rousseau L, Brugières L, Caron O, Sabourin JC, Tournier I, Baert-Desurmont S, Frébourg T, Bougeard G. Contribution of de novo and mosaic TP53 mutations to Li-Fraumeni syndrome. J Med Genet 2017; 55:173-180. [DOI: 10.1136/jmedgenet-2017-104976] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/28/2017] [Accepted: 10/09/2017] [Indexed: 01/06/2023]
Abstract
BackgroundDevelopment of tumours such as adrenocortical carcinomas (ACC), choroid plexus tumours (CPT) or female breast cancers before age 31 or multiple primary cancers belonging to the Li-Fraumeni (LFS) spectrum is, independently of the familial history, highly suggestive of a germline TP53 mutation. The aim of this study was to determine the contribution of de novo and mosaic mutations to LFS.Methods and resultsAmong 328 unrelated patients harbouring a germline TP53 mutation identified by Sanger sequencing and/or QMPSF, we could show that the mutations had occurred de novo in 40 cases, without detectable parental age effect. Sanger sequencing revealed two mosaic mutations in a child with ACC and in an unaffected father of a child with medulloblastoma. Re-analysis of blood DNA by next-generation sequencing, performed at a depth above 500X, from 108 patients suggestive of LFS without detectable TP53 mutations, allowed us to identify 6 additional cases of mosaic TP53 mutations, in 2/49 children with ACC, 2/21 children with CPT, in 1/31 women with breast cancer before age 31 and in a patient who developed an osteosarcoma at age 12, a breast carcinoma and a breast sarcoma at age 35.ConclusionsThis study performed on a large series of TP53 mutation carriers allows estimating the contribution to LFS of de novo mutations to at least 14% (48/336) and suggests that approximately one-fifth of these de novo mutations occur during embryonic development. Considering the medical impact of TP53 mutation identification, medical laboratories in charge of TP53 testing should ensure the detection of mosaic mutations.
Collapse
|
17
|
Andrade RC, Dos Santos ACE, de Aguirre Neto JC, Nevado J, Lapunzina P, Vargas FR. TP53 and CDKN1A mutation analysis in families with Li-Fraumeni and Li-Fraumeni like syndromes. Fam Cancer 2017; 16:243-248. [PMID: 27714481 DOI: 10.1007/s10689-016-9935-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Li-Fraumeni and Li-Fraumeni like syndromes (LFS/LFL) represent rare cancer-prone conditions associated mostly with sarcomas, breast cancer, brain tumors, and adrenocortical carcinomas. TP53 germline mutations are present in up to 80 % of families with classic Li-Fraumeni syndrome, and in 20-60 % of families with Li-Fraumeni like phenotypes. The frequency of LFS/LFL families with no TP53 mutations detected suggests the involvement of other genes in the syndrome. In this study, we searched for mutations in TP53 in 39 probands from families with criteria for LFS/LFL. We also searched for mutations in the gene encoding the main mediator of p53 in cell cycle arrest, CDKN1A/p21, in all patients with no mutations in TP53. Eight probands carried germline disease-causing mutations in TP53: six missense mutations and two partial gene deletions. No mutations in CDKN1A coding region were detected. TP53 partial deletions in our cohort represented 25 % (2/8) of the mutations found, a much higher frequency than usually reported, emphasizing the need to search for TP53 rearrangements in patients with LFS/LFL phenotypes. Two benign tumors were detected in two TP53 mutation carriers: an adrenocortical adenoma and a neurofibroma, which raises a question about the possible implication of TP53 mutations on the development of such lesions.
Collapse
Affiliation(s)
| | | | | | - Julián Nevado
- INGEMM, Instituto de Genética Médica y Molecular, IdiPAZ-CIBERER, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Lapunzina
- INGEMM, Instituto de Genética Médica y Molecular, IdiPAZ-CIBERER, Universidad Autónoma de Madrid, Madrid, Spain
| | - Fernando Regla Vargas
- Genetics Division, Instituto Nacional de Câncer, Rio de Janeiro, Brazil. .,Genetics and Molecular Biology Department, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil. .,Birth Defects Epidemiology Laboratory, Fundação Oswaldo Cruz, Av. Brasil 4365 - Pavilhão Leônidas Deane Sala 617, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil.
| |
Collapse
|
18
|
Trubicka J, Filipek I, Iwanowski P, Rydzanicz M, Grajkowska W, Piekutowska-Abramczuk D, Chrzanowska K, Karkucińska-Więckowska A, Iwanicka-Pronicka K, Pronicki M, Łastowska M, Płoski R, Dembowska-Bagińska B. Constitutional mosaicism of a de novo TP53 mutation in a patient with bilateral choroid plexus carcinoma. Cancer Genet 2017; 216-217:79-85. [PMID: 29025599 DOI: 10.1016/j.cancergen.2017.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 07/14/2017] [Accepted: 07/16/2017] [Indexed: 10/19/2022]
Abstract
Choroid plexus tumors (CPT) constitute 2%-5% of all pediatric brain tumors and include high grade choroid plexus carcinoma (CPC). About 40% of CPC patients harbor germline TP53 mutations, associated with diminished survival rates. However, the number of TP53 carriers might be underestimated due to suboptimal ability of Sanger sequencing to identify mosaicism. We describe an 18-month-old boy with ultra-rare, bilateral disseminated CPC and negative family history of cancer. Next generation sequencing (NGS) revealed constitutional mosaicism of de novo TP53 mutation, which was barely detectable by Sanger sequencing. This is the first description of a de novo TP53 mutation mosaicism in a patient with CPC. Up to now four cases of de novo TP53 mutations in CPC patients have been described but none of them were mosaic. Since TP53 mutation mosaicism may have an impact on management of patients and predisposition to other cancers, a reliable method of identification is important. Our results highlight the utility of high-throughput technologies in detection of potentially important genetic markers.
Collapse
Affiliation(s)
- Joanna Trubicka
- Department of Pathology, The Children's Memorial Health Institute, 04-730 Warsaw, Poland.
| | - Iwona Filipek
- Department of Oncology, The Children's Memorial Health Institute, 04-730 Warsaw, Poland
| | - Piotr Iwanowski
- Department of Medical Genetics, The Children's Memorial Health Institute, 04-730 Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Warsaw Medical University, 02-103 Warsaw, Poland
| | - Wiesława Grajkowska
- Department of Pathology, The Children's Memorial Health Institute, 04-730 Warsaw, Poland; Department of Experimental and Clinical Pathology, Mossakowski Medical Research Centre Polish Academy of Sciences, 02-106 Warsaw, Poland
| | | | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, 04-730 Warsaw, Poland
| | | | | | - Maciej Pronicki
- Department of Pathology, The Children's Memorial Health Institute, 04-730 Warsaw, Poland
| | - Maria Łastowska
- Department of Pathology, The Children's Memorial Health Institute, 04-730 Warsaw, Poland; Department of Experimental and Clinical Pathology, Mossakowski Medical Research Centre Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, 02-103 Warsaw, Poland.
| | | |
Collapse
|
19
|
Le M, Mothersill CE, Seymour CB, Rainbow AJ, McNeill FE. An Observed Effect of p53 Status on the Bystander Response to Radiation-Induced Cellular Photon Emission. Radiat Res 2017; 187:169-185. [PMID: 28118118 DOI: 10.1667/rr14342.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In this study, we investigated the potential influence of p53 on ultraviolet (UV) signal generation and response of bystander cells to the UV signals generated by beta-irradiated cells. Five cell lines of various p53 status (HaCaT, mutated; SW48, wild-type; HT29, mutated; HCT116+/+, wild-type; HCT116-/-, null) were irradiated with beta particles from tritium. Signal generation (photon emission at 340 ± 5 nm) was quantified from irradiated cells using a photomultiplier tube. Bystander response (clonogenic survival) was assessed by placing reporter cell flasks directly superior to irradiated signal-emitting cells. All cell lines emitted significant quantities of UV after tritium exposure. The magnitudes of HaCaT and HT29 photon emission at 340 nm were similar to each other while they were significantly different from the stronger signals emitted from SW48, HCT116+/+ and HCT116-/- cells. In regard to the bystander responses, HaCaT, HCT116+/+ and SW48 cells demonstrated significant reductions in survival as a result of exposure to emission signals. HCT116-/- and HT29 cells did not exhibit any changes in survival and thus were considered to be lacking the mechanisms or functions required to elicit a response. The survival response was found not to correlate with the observed signal strength for all experimental permutations; this may be attributed to varying emission spectra from cell line to cell line or differences in response sensitivity. Overall, these results suggest that the UV-mediated bystander response is influenced by the p53 status of the cell line. Wild-type p53 cells (HCT116+/+ and SW48) demonstrated significant responses to UV signals whereas the p53-null cell line (HCT116-/-) lacked any response. The two mutated p53 cell lines exhibited contrasting responses, which may be explained by unique modulation of functions by different point mutations. The reduced response (cell death) exhibited by p53-mutated cells compared to p53 wild-type cells suggests a possible role of the assessed p53 mutations in radiation-induced cancer susceptibility and reduced efficacy of radiation-directed therapy.
Collapse
Affiliation(s)
- M Le
- a Radiation Sciences Graduate Program and Departments of
| | | | | | | | - F E McNeill
- c Physics and Astronomy, McMaster University, Hamilton Ontario, L8S 4L8, Canada
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Creation of Mice Bearing a Partial Duplication of HPRT Gene Marked with a GFP Gene and Detection of Revertant Cells In Situ as GFP-Positive Somatic Cells. PLoS One 2015; 10:e0136041. [PMID: 26295470 PMCID: PMC4546575 DOI: 10.1371/journal.pone.0136041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 07/29/2015] [Indexed: 12/27/2022] Open
Abstract
It is becoming clear that apparently normal somatic cells accumulate mutations. Such accumulations or propagations of mutant cells are thought to be related to certain diseases such as cancer. To better understand the nature of somatic mutations, we developed a mouse model that enables in vivo detection of rare genetically altered cells via GFP positive cells. The mouse model carries a partial duplication of 3’ portion of X-chromosomal HPRT gene and a GFP gene at the end of the last exon. In addition, although HPRT gene expression was thought ubiquitous, the expression level was found insufficient in vivo to make the revertant cells detectable by GFP positivity. To overcome the problem, we replaced the natural HPRT-gene promoter with a CAG promoter. In such animals, termed HPRT-dup-GFP mouse, losing one duplicated segment by crossover between the two sister chromatids or within a single molecule of DNA reactivates gene function, producing hybrid HPRT-GFP proteins which, in turn, cause the revertant cells to be detected as GFP-positive cells in various tissues. Frequencies of green mutant cells were measured using fixed and frozen sections (liver and pancreas), fixed whole mount (small intestine), or by means of flow cytometry (unfixed splenocytes). The results showed that the frequencies varied extensively among individuals as well as among tissues. X-ray exposure (3 Gy) increased the frequency moderately (~2 times) in the liver and small intestine. Further, in two animals out of 278 examined, some solid tissues showed too many GFP-positive cells to score (termed extreme jackpot mutation). Present results illustrated a complex nature of somatic mutations occurring in vivo. While the HPRT-dup-GFP mouse may have a potential for detecting tissue-specific environmental mutagens, large inter-individual variations of mutant cell frequency cause the results unstable and hence have to be reduced. This future challenge will likely involve lowering the background mutation frequency, thus reducing inter-individual variation.
Collapse
|
22
|
Salo-Mullen EE, Shia J, Brownell I, Allen P, Girotra M, Robson ME, Offit K, Guillem JG, Markowitz AJ, Stadler ZK. Mosaic partial deletion of the PTEN gene in a patient with Cowden syndrome. Fam Cancer 2015; 13:459-67. [PMID: 24609522 DOI: 10.1007/s10689-014-9709-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cowden syndrome is an autosomal dominant condition caused by pathogenic mutations in the phosphatase and tensin homolog (PTEN) gene. Only a small proportion of identified pathogenic mutations have been reported to be large deletions and rearrangements. We report on a female patient with a previous history of breast ductal carcinoma in situ who presented to our institution for management of gastrointestinal hamartomatous polyposis. Although several neoplastic predisposition syndromes were considered, genetic evaluation determined that the patient met clinical diagnostic criteria for Cowden syndrome. Array-based comparative genomic hybridization was performed and revealed a mosaic partial deletion of the PTEN gene. Follow-up clinical history including bilateral thyroid nodules, dermatological findings, and a new primary "triple-negative" adenocarcinoma of the contralateral breast are discussed. We highlight the need for recognition and awareness of mosaicism as it may provide an explanation for variable phenotypic presentations and may alter the genetic counseling risk assessment of affected individuals and family members.
Collapse
Affiliation(s)
- Erin E Salo-Mullen
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 295, New York, NY, 10065, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Behjati S, Maschietto M, Williams RD, Side L, Hubank M, West R, Pearson K, Sebire N, Tarpey P, Futreal A, Brooks T, Stratton MR, Anderson J. A pathogenic mosaic TP53 mutation in two germ layers detected by next generation sequencing. PLoS One 2014; 9:e96531. [PMID: 24810334 PMCID: PMC4014518 DOI: 10.1371/journal.pone.0096531] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/09/2014] [Indexed: 12/30/2022] Open
Abstract
Background Li-Fraumeni syndrome is caused by germline TP53 mutations and is clinically characterized by a predisposition to a range of cancers, most commonly sarcoma, brain tumours and leukemia. Pathogenic mosaic TP53 mutations have only rarely been described. Methods and Findings We describe a 2 years old child presenting with three separate cancers over a 6 month period; two soft tissue mesenchymal tumors and an aggressive metastatic neuroblastoma. As conventional testing of blood DNA by Sanger sequencing for mutations in TP53, ALK, and SDH was negative, whole exome sequencing of the blood DNA of the patient and both parents was performed to screen more widely for cancer predisposing mutations. In the patient's but not the parents' DNA we found a c.743 G>A, p.Arg248Gln (CCDS11118.1) TP53 mutation in 3–20% of sequencing reads, a level that would not generally be detectable by Sanger sequencing. Homozygosity for this mutation was detected in all tumor samples analyzed, and germline mosaicism was demonstrated by analysis of the child's newborn blood spot DNA. The occurrence of separate tumors derived from different germ layers suggests that this de novo mutation occurred early in embryogenesis, prior to gastrulation. Conclusion The case demonstrates pathogenic mosaicim, detected by next generation deep sequencing, that arose in the early stages of embryogenesis.
Collapse
Affiliation(s)
- Sam Behjati
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Mariana Maschietto
- Unit of Molecular Haematology and Cancer Biology, UCL Institute of Child Health, London, United Kingdom
| | - Richard D. Williams
- Unit of Molecular Haematology and Cancer Biology, UCL Institute of Child Health, London, United Kingdom
| | - Lucy Side
- Departments of Clinical Genetics, Great Ormond Street Hospital, London, United Kingdom
| | - Mike Hubank
- Unit of Molecular Haematology and Cancer Biology, UCL Institute of Child Health, London, United Kingdom
| | - Rebecca West
- Unit of Molecular Haematology and Cancer Biology, UCL Institute of Child Health, London, United Kingdom
| | - Katie Pearson
- Unit of Molecular Haematology and Cancer Biology, UCL Institute of Child Health, London, United Kingdom
| | - Neil Sebire
- Departments of Histopathology, Great Ormond Street Hospital, London, United Kingdom
| | - Patrick Tarpey
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Andrew Futreal
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Tony Brooks
- Unit of Molecular Haematology and Cancer Biology, UCL Institute of Child Health, London, United Kingdom
| | - Michael R. Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - John Anderson
- Unit of Molecular Haematology and Cancer Biology, UCL Institute of Child Health, London, United Kingdom
- * E-mail:
| |
Collapse
|
24
|
Mitchell G, Ballinger ML, Wong S, Hewitt C, James P, Young MA, Cipponi A, Pang T, Goode DL, Dobrovic A, Thomas DM. High frequency of germline TP53 mutations in a prospective adult-onset sarcoma cohort. PLoS One 2013; 8:e69026. [PMID: 23894400 PMCID: PMC3718831 DOI: 10.1371/journal.pone.0069026] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/05/2013] [Indexed: 11/25/2022] Open
Abstract
Sarcomas are a key feature of Li-Fraumeni and related syndromes (LFS/LFL), associated with germline TP53 mutations. Current penetrance estimates for TP53 mutations are subject to significant ascertainment bias. The International Sarcoma Kindred Study is a clinic-based, prospective cohort of adult-onset sarcoma cases, without regard to family history. The entire cohort was screened for mutations in TP53 using high-resolution melting analysis and Sanger sequencing, and multiplex-ligation-dependent probe amplification and targeted massively parallel sequencing for copy number changes. Pathogenic TP53 mutations were detected in blood DNA of 20/559 sarcoma probands (3.6%); 17 were germline and 3 appeared to be somatically acquired. Of the germline carriers, one appeared to be mosaic, detectable in the tumor and blood, but not epithelial tissues. Germline mutation carriers were more likely to have multiple cancers (47% vs 15% for non-carriers, P = 3.0×10−3), and earlier cancer onset (33 vs 48 years, P = 1.19×10−3). The median survival of mutation carriers following first cancer diagnosis was not significantly different from non-carriers. Only 10/17 (59%) pedigrees met classical or Chompret criteria for LFS. In summary, germline TP53 mutations are not rare in adult patients with sarcoma, with implications for screening, surveillance, treatment and genetic counselling of carriers and family members.
Collapse
Affiliation(s)
- Gillian Mitchell
- Department of Cancer Medicine, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Mandy L. Ballinger
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen Wong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Chelsee Hewitt
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Paul James
- Department of Cancer Medicine, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Mary-Anne Young
- Department of Cancer Medicine, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Arcadi Cipponi
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Tiffany Pang
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - David L. Goode
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Alex Dobrovic
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - David M. Thomas
- Department of Cancer Medicine, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail:
| | | |
Collapse
|
25
|
Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing. Proc Natl Acad Sci U S A 2011; 108:18032-7. [PMID: 22006311 DOI: 10.1073/pnas.1115052108] [Citation(s) in RCA: 710] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Inherited loss-of-function mutations in BRCA1 and BRCA2 and other tumor suppressor genes predispose to ovarian carcinomas, but the overall burden of disease due to inherited mutations is not known. Using targeted capture and massively parallel genomic sequencing, we screened for germ-line mutations in 21 tumor suppressor genes in genomic DNA from women with primary ovarian, peritoneal, or fallopian tube carcinoma. Subjects were consecutively enrolled at diagnosis and not selected for age or family history. All classes of mutations, including point mutations and large genomic deletions and insertions, were detected. Of 360 subjects, 24% carried germ-line loss-of-function mutations: 18% in BRCA1 or BRCA2 and 6% in BARD1, BRIP1, CHEK2, MRE11A, MSH6, NBN, PALB2, RAD50, RAD51C, or TP53. Six of these genes were not previously implicated in inherited ovarian carcinoma. Primary carcinomas were generally characterized by genomic loss of normal alleles of the mutant genes. Of women with inherited mutations, >30% had no family history of breast or ovarian carcinoma, and >35% were 60 y or older at diagnosis. More patients with ovarian carcinoma carry cancer-predisposing mutations and in more genes than previously appreciated. Comprehensive genetic testing for inherited carcinoma is warranted for all women with ovarian, peritoneal, or fallopian tube carcinoma, regardless of age or family history. Clinical genetic testing is currently done gene by gene, with each test costing thousands of dollars. In contrast, massively parallel sequencing allows such testing for many genes simultaneously at low cost.
Collapse
|
26
|
A de novo 22q11.22q11.23 interchromosomal tandem duplication in a boy with developmental delay, hyperactivity, and epilepsy. Am J Med Genet A 2010; 152A:2820-6. [DOI: 10.1002/ajmg.a.33658] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
27
|
Current World Literature. Curr Opin Oncol 2010; 22:70-5. [DOI: 10.1097/cco.0b013e328334b4d9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
28
|
|