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Lu D, Wu X, Wu W, Wu S, Li H, Zhang Y, Yan X, Zhai J, Dong X, Feng S, Zhang X, Sun F, Wang S, Cai K. Plasma cell-free DNA 5-hydroxymethylcytosine and whole-genome sequencing signatures for early detection of esophageal cancer. Cell Death Dis 2023; 14:843. [PMID: 38114477 PMCID: PMC10730877 DOI: 10.1038/s41419-023-06329-3] [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: 04/24/2023] [Revised: 11/05/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023]
Abstract
Esophageal cancer is a highly incidence and deadly disease with a poor prognosis, especially in developing countries. Owing to the lack of specific symptoms and early diagnostic biomarkers, most patients are diagnosed with advanced disease, leading to a 5-year survival rate of less than 15%. Early (n = 50) and middle-advanced (n = 50) esophageal squamous cell carcinoma (ESCC) patients, as well as 71 healthy individuals, underwent 5-hydroxymethylcytosine (5hmC) sequencing on their plasma cell-free DNA (cfDNA). A Northern Chinese cohort of cfDNA 5hmC dataset of 150 ESCC patients and 183 healthy individuals were downloaded for validation. A diagnostic model was developed using cfDNA 5hmC signatures and then improved by low-pass whole genome sequencing (WGS) features of cfDNA. Conserved cfDNA 5hmC modification motifs were observed in the two independent ESCC cohorts. The diagnostic model with 5hmC features achieved an AUC of 0.810 and 0.862 in the Southern and Northern cohorts, respectively, with sensitivities of 69.3-74.3% and specificities of 82.4-90.7%. The performance was well maintained in Stage I to Stage IV, with accuracy of 70-100%, but low in Stage 0, 33.3%. Low-pass WGS of cfDNA improved the AUC to 0.934 with a sensitivity of 82.4%, a specificity of 88.2%, and an accuracy of 84.3%, particularly significantly in Stage 0, with an accuracy up to 80%. 5hmC and WGS could efficiently differentiate very early ESCC from healthy individuals. These findings imply a non-invasive and convenient method for ESCC detection when clinical treatments are available and may eventually prolong survival.
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Affiliation(s)
- Di Lu
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xuanzhen Wu
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wendy Wu
- Berry Oncology Corporation, Beijing, 100102, China
| | - Shuangxiu Wu
- Berry Oncology Corporation, Beijing, 100102, China
| | - Hui Li
- Berry Oncology Corporation, Beijing, 100102, China
| | - Yuhong Zhang
- Berry Oncology Corporation, Beijing, 100102, China
| | - Xuebin Yan
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Jianxue Zhai
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoying Dong
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Siyang Feng
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | | | - Fuming Sun
- Berry Oncology Corporation, Beijing, 100102, China
| | - Shaobo Wang
- Berry Oncology Corporation, Beijing, 100102, China
| | - Kaican Cai
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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Wang Y, Ding Q, Prokopec S, Farncombe KM, Bruce J, Casalino S, McCuaig J, Szybowska M, van Engelen K, Lerner-Ellis J, Pugh TJ, Kim RH. Germline whole genome sequencing in adults with multiple primary tumors. Fam Cancer 2023; 22:513-520. [PMID: 37481477 DOI: 10.1007/s10689-023-00343-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/27/2023] [Indexed: 07/24/2023]
Abstract
Multiple primary tumors (MPTs) are a harbinger of hereditary cancer syndromes. Affected individuals often fit genetic testing criteria for a number of hereditary cancer genes and undergo multigene panel testing. Other genomic testing options, such as whole exome (WES) and whole genome sequencing (WGS) are available, but the utility of these genomic approaches as a second-tier test for those with uninformative multigene panel testing has not been explored. Here, we report our germline sequencing results from WGS in 9 patients with MPTs who had non-informative multigene panel testing. Following germline WGS, sequence (agnostic or 735 selected genes) and copy number variant (CNV) analysis was performed according to the American College of Medical Genetics (ACMG) standards and guidelines for interpreting sequence variants and reporting CNVs. In this cohort, WGS, as a second-tier test, did not identify additional pathogenic or likely pathogenic variants in cancer predisposition genes. Although we identified a CHEK2 likely pathogenic variant and a MUTYH pathogenic variant, both were previously identified in the multigene panels and were not explanatory for the presented type of tumors. CNV analysis also failed to identify any pathogenic or likely pathogenic variants in cancer predisposition genes. In summary, after multigene panel testing, WGS did not reveal any additional pathogenic variants in patients with MPTs. Our study, based on a small cohort of patients with MPT, suggests that germline gene panel testing may be sufficient to investigate these cases. Future studies with larger sample sizes may further elucidate the additional utility of WGS in MPTs.
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Affiliation(s)
- Yiming Wang
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Qiliang Ding
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephenie Prokopec
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kirsten M Farncombe
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jeffrey Bruce
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Selina Casalino
- Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Jeanna McCuaig
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Marta Szybowska
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Kalene van Engelen
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- London Health Science Centre, London, Canada
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
- Department of Pediatrics, Western University, London, ON, Canada
| | - Jordan Lerner-Ellis
- Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Trevor J Pugh
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Raymond H Kim
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Ontario Institute for Cancer Research, Toronto, ON, Canada.
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.
- Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada.
- Department of Medicine, University of Toronto, Toronto, ON, Canada.
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Fatemi N, Tu SJ, Chung CC, Moghadam PK, Mojarad EN, Sadeghi A, Totonchi M, Aghdaei HA, Chang JG. Whole exome sequencing identifies MAP3K1, MSH2, and MLH1 as potential cancer-predisposing genes in familial early-onset colorectal cancer. Kaohsiung J Med Sci 2023; 39:896-903. [PMID: 37314251 DOI: 10.1002/kjm2.12715] [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: 01/20/2023] [Revised: 05/01/2023] [Accepted: 05/21/2023] [Indexed: 06/15/2023] Open
Abstract
The incidence of early-onset colorectal cancer (CRC), which affects people under 50, is increasing for unknown reasons. Additionally, no underlying genetic cause is found in 20%-30% of patients suspected of having familial CRC syndrome. Whole exome sequencing (WES) has generated evidence for new genes associated with CRC susceptibility, but many patients remain undiagnosed. This study applied WES in five early-onset CRC patients from three unrelated families to identify novel genetic variants that could be linked to rapid disease development. Furthermore, the candidate variants were validated using Sanger sequencing. Two heterozygote variations, c.1077-2A>G and c.199G>A, were found in the MSH2 and the MLH1 genes, respectively. Sanger sequencing analysis confirmed that these (likely) pathogenic mutations segregated in all the affected families' members. In addition, we identified a rare heterozygote variant (c.175C>T) with suspected pathogenic potential in the MAP3K1 gene; formally the variant is of uncertain significance (VUS). Our findings support the hypothesis that CRC onset may be oligogenic and molecularly heterogeneous. Larger and more robust studies are needed to understand the genetic basis of early-onset CRC development, combined with novel functional analyses and omics approaches.
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Affiliation(s)
- Nayeralsadat Fatemi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Siang-Jyun Tu
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chin-Chun Chung
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Pardis Ketabi Moghadam
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Totonchi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jan-Gowth Chang
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
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