1
|
Gudmundsson S, Carlston CM, O'Donnell-Luria A. Interpreting variants in genes affected by clonal hematopoiesis in population data. Hum Genet 2024; 143:545-549. [PMID: 36739343 PMCID: PMC10400727 DOI: 10.1007/s00439-023-02526-4] [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: 08/29/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023]
Abstract
Reference population databases like the Genome Aggregation Database (gnomAD) have improved our ability to interpret the human genome. Variant frequencies and frequency-derived tools (such as depletion scores) have become fundamental to variant interpretation and the assessment of variant-gene-disease relationships. Clonal hematopoiesis (CH) obstructs variant interpretation as somatic variants that provide proliferative advantage will affect variant frequencies, depletion scores, and downstream filtering. Further, default filtering of variants or genes associated with CH risks filtering bona fide germline variants as variants associated with CH can also cause Mendelian conditions. Here, we provide our insights on interpreting population variant data in genes affected by clonal hematopoiesis, as well as recommendations for careful review of 36 established CH genes associated with neurodevelopmental conditions.
Collapse
Affiliation(s)
- Sanna Gudmundsson
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Colleen M Carlston
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
| |
Collapse
|
2
|
Pollard RD, Wilkerson MD, Rajagopal PS. Identification of germline population variants misclassified as cancer-associated somatic variants. Front Med (Lausanne) 2024; 11:1361317. [PMID: 38572163 PMCID: PMC10987807 DOI: 10.3389/fmed.2024.1361317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction Databases used for clinical interpretation in oncology rely on genetic data derived primarily from patients of European ancestry, leading to biases in cancer genetics research and clinical practice. One practical issue that arises in this context is the potential misclassification of multi-ancestral population variants as tumor-associated because they are not represented in reference genomes against which tumor sequencing data is aligned. Methods To systematically find misclassified variants, we compared somatic variants in census genes from the Catalogue of Somatic Mutations in Cancer (COSMIC) V99 with multi-ancestral population variants from the Genome Aggregation Databases' Linkage Disequilibrium (GnomAD). By comparing genomic coordinates, reference, and alternate alleles, we could identify misclassified variants in genes associated with cancer. Results We found 192 of 208 genes in COSMIC's cancer-associated census genes (92.31%) to be associated with variant misclassifications. Among the 1,906,732 variants in COSMIC, 6,957 variants (0.36%) aligned with normal population variants in GnomAD, concerning for misclassification. The African / African American ancestral population included the greatest number of misclassified variants and also had the greatest number of unique misclassified variants. Conclusion The direct, systematic comparison of variants from COSMIC for co-occurrence in GnomAD supports a more accurate interpretation of tumor sequencing data and reduces bias related to genomic ancestry.
Collapse
Affiliation(s)
- Rebecca D. Pollard
- Maret School, Washington, DC, United States
- Metis Foundation, San Antonio, TX, United States
| | - Matthew D. Wilkerson
- Center for Military Precision Health, Uniformed Services University, Bethesda, MD, United States
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Padma Sheila Rajagopal
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| |
Collapse
|
3
|
Marechal E, Poliard A, Henry K, Moreno M, Legrix M, Macagno N, Mondielli G, Fauquier T, Barlier A, Etchevers HC. Multiple congenital malformations arise from somatic mosaicism for constitutively active Pik3ca signaling. Front Cell Dev Biol 2022; 10:1013001. [PMID: 36353506 PMCID: PMC9637999 DOI: 10.3389/fcell.2022.1013001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2022] Open
Abstract
Recurrent missense mutations of the PIK3CA oncogene are among the most frequent drivers of human cancers. These often lead to constitutive activation of its product p110α, a phosphatidylinositol 3-kinase (PI3K) catalytic subunit. In addition to causing a broad range of cancers, the H1047R mutation is also found in affected tissues of a distinct set of congenital tumors and malformations. Collectively termed PIK3CA-related disorders (PRDs), these lead to overgrowth of brain, adipose, connective and musculoskeletal tissues and/or blood and lymphatic vessel components. Vascular malformations are frequently observed in PRD, due to cell-autonomous activation of PI3K signaling within endothelial cells. These, like most muscle, connective tissue and bone, are derived from the embryonic mesoderm. However, important organ systems affected in PRDs are neuroectodermal derivatives. To further examine their development, we drove the most common post-zygotic activating mutation of Pik3ca in neural crest and related embryonic lineages. Outcomes included macrocephaly, cleft secondary palate and more subtle skull anomalies. Surprisingly, Pik3ca-mutant subpopulations of neural crest origin were also associated with widespread cephalic vascular anomalies. Mesectodermal neural crest is a major source of non-endothelial connective tissue in the head, but not the body. To examine the response of vascular connective tissues of the body to constitutive Pik3ca activity during development, we expressed the mutation by way of an Egr2 (Krox20) Cre driver. Lineage tracing led us to observe new lineages that had normally once expressed Krox20 and that may be co-opted in pathogenesis, including vascular pericytes and perimysial fibroblasts. Finally, Schwann cell precursors having transcribed either Krox20 or Sox10 and induced to express constitutively active PI3K were associated with vascular and other tumors. These murine phenotypes may aid discovery of new candidate human PRDs affecting craniofacial and vascular smooth muscle development as well as the reciprocal paracrine signaling mechanisms leading to tissue overgrowth.
Collapse
Affiliation(s)
- Elise Marechal
- INSERM, MMG, U1251, MarMaRa Institute, Aix Marseille University, Marseille, France
| | - Anne Poliard
- URP 2496 Orofacial Pathologies, Imagery and Biotherapies, CNRS, GDR 2031 CREST-NET, Université Paris Cité, Montrouge, France
- School of Dentistry, Université Paris Cité, Montrouge, France
| | - Kilian Henry
- School of Dentistry, Université Paris Cité, Montrouge, France
| | - Mathias Moreno
- INSERM, MMG, U1251, MarMaRa Institute, Aix Marseille University, Marseille, France
| | - Mathilde Legrix
- INSERM, MMG, U1251, MarMaRa Institute, Aix Marseille University, Marseille, France
| | - Nicolas Macagno
- INSERM, MMG, U1251, MarMaRa Institute, Aix Marseille University, Marseille, France
| | - Grégoire Mondielli
- INSERM, MMG, U1251, MarMaRa Institute, Aix Marseille University, Marseille, France
| | - Teddy Fauquier
- INSERM, MMG, U1251, MarMaRa Institute, Aix Marseille University, Marseille, France
| | - Anne Barlier
- INSERM, MMG, U1251, MarMaRa Institute, Aix Marseille University, Marseille, France
- AP-HM, MMG, MarMaRa Institute, La Conception Hospital Laboratory of Molecular Biology, Marseille, France
| | - Heather C. Etchevers
- INSERM, MMG, U1251, CNRS, GDR 2031 CREST-NET, MarMaRa Institute, Aix Marseille University, Marseille, France
- *Correspondence: Heather C. Etchevers,
| |
Collapse
|
4
|
Zhu W, Deo RC, MacRae CA. Single Cell Biology: Exploring Somatic Cell Behaviors, Competition and Selection in Chronic Disease. Front Pharmacol 2022; 13:867431. [PMID: 35656307 PMCID: PMC9152313 DOI: 10.3389/fphar.2022.867431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
The full range of cell functions is under-determined in most human diseases. The evidence that somatic cell competition and clonal imbalance play a role in non-neoplastic chronic disease reveal a need for a dedicated effort to explore single cell function if we are to understand the mechanisms by which cell population behaviors influence disease. It will be vital to document not only the prevalent pathologic behaviors but also those beneficial functions eliminated or suppressed by competition. An improved mechanistic understanding of the role of somatic cell biology will help to stratify chronic disease, define more precisely at an individual level the role of environmental factors and establish principles for prevention and potential intervention throughout the life course and across the trajectory from wellness to disease.
Collapse
Affiliation(s)
- Wandi Zhu
- Cardiovascular Medicine Division and Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Rahul C Deo
- Cardiovascular Medicine Division and Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Calum A MacRae
- Cardiovascular Medicine Division and Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| |
Collapse
|