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Hua F, Hu Y, He GC, Lai SH, He Y, Zhang S, Deng Y, Han Y, Liu XD, Yang K, Zhong HX, Xiao J, Zheng ZZ, Yi H. Case report: TP53 c.848G>A germline mutation as a possible screening target at initial diagnosis for acute lymphoblastic leukemia. Hematology 2024; 29:2377860. [PMID: 39007733 DOI: 10.1080/16078454.2024.2377860] [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: 09/25/2023] [Accepted: 07/03/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUD Li-Fraumeni syndrome is a hereditary tumor syndrome characterized by an elevated risk of malignancy, particularly acute lymphoblastic leukemia (ALL), which can be caused by the heterozygous germline mutation. TP53 gene germline mutation is considered a potential risk factor and crucial prognostic parameter for acute leukemia development and diagnosis, but rarely occurs in adults, and its specific pathogenic significance in acute leukemia is unclear. CASE PRESENTATION We describes a case of a 45-year-old woman diagnosed with ALL. Whole-exome sequencing approach identified one of the TP53 germline mutations from her bone marrow sample with possible pathogenic significance, c.848G>A (p.Arg283His) heterozygous missense mutation located on exon 8, which was further verified in her hair, oral mucous and nail samples. Family pedigree screening revealed that the same TP53 genetic variant was present in the patient's father and non-donor son, whereas not in the donor. Digital PCR observed that this point mutation frequency dropped post-transplantation but remained low during maintenance therapy when the patient was leukemia-free. CONCLUSION This suspected Li-Fraumeni syndrome case report with a likely pathogenic heterozygous TP53 variant expands the cancer genetic spectrum. Screening her family members for mutations facilitates identifying the optimal relative donor and avoids unnecessary treatment by monitoring TP53 germline mutations for minimal residual disease following hematopoietic stem cell transplantation. Its potential roles in hematological malignant tumor development and clinical pathogenic implications necessitate further probing.
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Affiliation(s)
- Fang Hua
- Department of Hematology, The General Hospital of Western Theater Command, PLA, Chengdu, People's Republic of China
- Department of Hematology, Zigong First People's Hospital, Zigong, People's Republic of China
| | - Yue Hu
- Department of Hematology, The General Hospital of Western Theater Command, PLA, Chengdu, People's Republic of China
- North Sichuan Medical College Graduate School, Nanchong, People's Republic of China
| | - Guang-Cui He
- Department of Hematology, The General Hospital of Western Theater Command, PLA, Chengdu, People's Republic of China
| | - Si-Han Lai
- Department of Hematology, The General Hospital of Western Theater Command, PLA, Chengdu, People's Republic of China
| | - Ying He
- Department of Hematology, The General Hospital of Western Theater Command, PLA, Chengdu, People's Republic of China
| | - Shan Zhang
- Department of Hematology, The General Hospital of Western Theater Command, PLA, Chengdu, People's Republic of China
| | - Yan Deng
- Department of Hematology, The General Hospital of Western Theater Command, PLA, Chengdu, People's Republic of China
| | - Ying Han
- Department of Hematology, The General Hospital of Western Theater Command, PLA, Chengdu, People's Republic of China
| | - Xiao-Dong Liu
- Department of Hematology, Zigong First People's Hospital, Zigong, People's Republic of China
| | - Kun Yang
- Department of Hematology, Zigong First People's Hospital, Zigong, People's Republic of China
| | - Hui-Xiu Zhong
- Department of Laboratory Medicine, Zigong First People's Hospital, Zigong, People's Republic of China
| | - Jian Xiao
- Department of Hematology, Zigong First People's Hospital, Zigong, People's Republic of China
| | - Zhong-Zheng Zheng
- Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, People's Republic of China
| | - Hai Yi
- Department of Hematology, The General Hospital of Western Theater Command, PLA, Chengdu, People's Republic of China
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Dalfovo D, Scandino R, Paoli M, Valentini S, Romanel A. Germline determinants of aberrant signaling pathways in cancer. NPJ Precis Oncol 2024; 8:57. [PMID: 38429380 PMCID: PMC10907629 DOI: 10.1038/s41698-024-00546-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 02/16/2024] [Indexed: 03/03/2024] Open
Abstract
Cancer is a complex disease influenced by a heterogeneous landscape of both germline genetic variants and somatic aberrations. While there is growing evidence suggesting an interplay between germline and somatic variants, and a substantial number of somatic aberrations in specific pathways are now recognized as hallmarks in many well-known forms of cancer, the interaction landscape between germline variants and the aberration of those pathways in cancer remains largely unexplored. Utilizing over 8500 human samples across 33 cancer types characterized by TCGA and considering binary traits defined using a large collection of somatic aberration profiles across ten well-known oncogenic signaling pathways, we conducted a series of GWAS and identified genome-wide and suggestive associations involving 276 SNPs. Among these, 94 SNPs revealed cis-eQTL links with cancer-related genes or with genes functionally correlated with the corresponding traits' oncogenic pathways. GWAS summary statistics for all tested traits were then used to construct a set of polygenic scores employing a customized computational strategy. Polygenic scores for 24 traits demonstrated significant performance and were validated using data from PCAWG and CCLE datasets. These scores showed prognostic value for clinical variables and exhibited significant effectiveness in classifying patients into specific cancer subtypes or stratifying patients with cancer-specific aggressive phenotypes. Overall, we demonstrate that germline genetics can describe patients' genetic liability to develop specific cancer molecular and clinical profiles.
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Affiliation(s)
- Davide Dalfovo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, (TN), Italy
| | - Riccardo Scandino
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, (TN), Italy
| | - Marta Paoli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, (TN), Italy
| | - Samuel Valentini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, (TN), Italy
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, (TN), Italy.
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Benafif S, Ni Raghallaigh H, McHugh J, Eeles R. Genetics of prostate cancer and its utility in treatment and screening. ADVANCES IN GENETICS 2021; 108:147-199. [PMID: 34844712 DOI: 10.1016/bs.adgen.2021.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Prostate cancer heritability is attributed to a combination of rare, moderate to highly penetrant genetic variants as well as commonly occurring variants conferring modest risks [single nucleotide polymorphisms (SNPs)]. Some of the former type of variants (e.g., BRCA2 mutations) predispose particularly to aggressive prostate cancer and confer poorer prognoses compared to men who do not carry mutations. Molecularly targeted treatments such as PARP inhibitors have improved outcomes in men carrying somatic and/or germline DNA repair gene mutations. Ongoing clinical trials are exploring other molecular targeted approaches based on prostate cancer somatic alterations. Genome wide association studies have identified >250 loci that associate with prostate cancer risk. Multi-ancestry analyses have identified shared as well as population specific risk SNPs. Prostate cancer risk SNPs can be used to estimate a polygenic risk score (PRS) to determine an individual's genetic risk of prostate cancer. The odds ratio of prostate cancer development in men whose PRS lies in the top 1% of the risk profile ranges from 9 to 11. Ongoing studies are investigating the utility of a prostate cancer PRS to target population screening to those at highest risk. With the advent of personalized medicine and development of DNA sequencing technologies, access to clinical genetic testing is increasing, and oncology guidelines from bodies such as NCCN and ESMO have been updated to provide criteria for germline testing of "at risk" healthy men as well as those with prostate cancer. Both germline and somatic prostate cancer research have significantly evolved in the past decade and will lead to further development of precision medicine approaches to prostate cancer treatment as well as potentially developing precision population screening models.
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Affiliation(s)
- S Benafif
- The Institute of Cancer Research, London, United Kingdom.
| | | | - J McHugh
- The Institute of Cancer Research, London, United Kingdom
| | - R Eeles
- The Institute of Cancer Research, London, United Kingdom
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Paul P, Deka H, Malakar AK, Halder B, Chakraborty S. Nasopharyngeal carcinoma: understanding its molecular biology at a fine scale. Eur J Cancer Prev 2018; 27:33-41. [PMID: 27748661 DOI: 10.1097/cej.0000000000000314] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Among all cancers, the incidence of nasopharyngeal carcinoma (NPC) is quite high in the endemic regions. NPC is a head and neck cancer with poor survival rate, and is rare throughout most of the world but common in certain geographic areas, like southern Asia and some regions of North East India (Nagaland, Manipur, and Mizoram). A clear understanding of its etiology is still lacking, but NPC is widely suspected to be the result of both genetic susceptibility and exposure to environmental factors or Epstein-Barr virus infection. Diagnosis in the early stages needs a high index of clinical acumen, and, although most cross-sectional imaging investigations show the tumor with precision, confirmation is dependent on histology. This article reviews all related research reports on NPC histopathological classifications worldwide that have been published within the past 20 years. Genome-wide association studies suggested that there might be common disease mechanisms between that disease and NPC. Personalized management rules, quality assessment of life in patients, and an understanding of the essential mechanisms of recurrence could be directed toward research into recurrent NPC. Hence, this literature would offer otolaryngologists a deeper insight into the etiological and management aspects of NPC.
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Affiliation(s)
- Prosenjit Paul
- Department of Biotechnology, Assam University, Silchar, Assam, India
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Tolbert VP, Coggins GE, Maris JM. Genetic susceptibility to neuroblastoma. Curr Opin Genet Dev 2017; 42:81-90. [PMID: 28458126 DOI: 10.1016/j.gde.2017.03.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/15/2017] [Accepted: 03/21/2017] [Indexed: 12/11/2022]
Abstract
Until recently, the genetic basis of neuroblastoma, a heterogeneous neoplasm arising from the developing sympathetic nervous system, remained undefined. The discovery of gain-of-function mutations in the ALK receptor tyrosine kinase gene as the major cause of familial neuroblastoma led to the discovery of identical somatic mutations and rapid advancement of ALK as a tractable therapeutic target. Inactivating mutations in a master regulator of neural crest development, PHOX2B, have also been identified in a subset of familial neuroblastomas. Other high penetrance susceptibility alleles likely exist, but together these heritable mutations account for less than 10% of neuroblastoma cases. A genome-wide association study of a large neuroblastoma cohort identified common and rare polymorphisms highly associated with the disease. Ongoing resequencing efforts aim to further define the genetic landscape of neuroblastoma.
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Affiliation(s)
- Vanessa P Tolbert
- University of California San Francisco School of Medicine, United States
| | | | - John M Maris
- University of Pennsylvania, United States; Children's Hospital of Philadelphia, United States.
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Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo GW, Gutkind JS, Ideker T. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discov 2017; 7:410-423. [PMID: 28188128 DOI: 10.1158/2159-8290.cd-16-1045] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 02/06/2017] [Accepted: 02/08/2017] [Indexed: 02/06/2023]
Abstract
Recent studies have characterized the extensive somatic alterations that arise during cancer. However, the somatic evolution of a tumor may be significantly affected by inherited polymorphisms carried in the germline. Here, we analyze genomic data for 5,954 tumors to reveal and systematically validate 412 genetic interactions between germline polymorphisms and major somatic events, including tumor formation in specific tissues and alteration of specific cancer genes. Among germline-somatic interactions, we found germline variants in RBFOX1 that increased incidence of SF3B1 somatic mutation by 8-fold via functional alterations in RNA splicing. Similarly, 19p13.3 variants were associated with a 4-fold increased likelihood of somatic mutations in PTEN. In support of this association, we found that PTEN knockdown sensitizes the MTOR pathway to high expression of the 19p13.3 gene GNA11 Finally, we observed that stratifying patients by germline polymorphisms exposed distinct somatic mutation landscapes, implicating new cancer genes. This study creates a validated resource of inherited variants that govern where and how cancer develops, opening avenues for prevention research.Significance: This study systematically identifies germline variants that directly affect tumor evolution, either by dramatically increasing alteration frequency of specific cancer genes or by influencing the site where a tumor develops. Cancer Discovery; 7(4); 410-23. ©2017 AACR.See related commentary by Geeleher and Huang, p. 354This article is highlighted in the In This Issue feature, p. 339.
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Affiliation(s)
- Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, La Jolla, California. .,Moores Cancer Center, University of California, San Diego, La Jolla, California.,Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, California
| | - Rachel Marty
- Bioinformatics Program, University of California, San Diego, La Jolla, California
| | - Matan Hofree
- Department of Computer Science, University of California, San Diego, La Jolla, California
| | - Andrew M Gross
- Bioinformatics Program, University of California, San Diego, La Jolla, California
| | - James Jensen
- Bioinformatics Program, University of California, San Diego, La Jolla, California
| | - Kathleen M Fisch
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, La Jolla, California.,Moores Cancer Center, University of California, San Diego, La Jolla, California.,Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California.,Department of Medicine, Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, California
| | - Xingyu Wu
- Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Christopher DeBoever
- Bioinformatics Program, University of California, San Diego, La Jolla, California
| | - Eric L Van Nostrand
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
| | - Yan Song
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
| | - Emily Wheeler
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
| | - Jason F Kreisberg
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, La Jolla, California.,Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California
| | - Scott M Lippman
- Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Gene W Yeo
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
| | - J Silvio Gutkind
- Moores Cancer Center, University of California, San Diego, La Jolla, California.,Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California
| | - Trey Ideker
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, La Jolla, California.,Moores Cancer Center, University of California, San Diego, La Jolla, California.,Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, California.,Bioinformatics Program, University of California, San Diego, La Jolla, California.,Department of Computer Science, University of California, San Diego, La Jolla, California
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7
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Benafif S, Eeles R. Genetic predisposition to prostate cancer. Br Med Bull 2016; 120:75-89. [PMID: 27941040 DOI: 10.1093/bmb/ldw039] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 08/31/2016] [Accepted: 09/04/2016] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Prostate cancer (PrCa) is the commonest non-cutaneous cancer in men in the UK. Epidemiological evidence as well as twin studies points towards a genetic component contributing to aetiology. SOURCES OF DATA Key recently published literature. AREAS OF AGREEMENT A family history of PrCa doubles the risk of disease development in first-degree relatives. Linkage and genetic sequencing studies identified rare moderate-high-risk gene loci, which predispose to PrCa development when altered by mutation. Genome-wide association studies have identified common single-nucleotide polypmorphisms (SNPs), which confer a cumulative risk of PrCa development with increasing number of risk alleles. There are emerging data that castrate-resistant disease is associated with mutations in DNA repair genes. AREAS OF CONTROVERSY Linkage studies investigating possible high-risk loci leading to PrCa development identified possible loci on several chromosomes, but most have not been consistently replicated by subsequent studies. Germline SNPs related to prostate specific antigen (PSA) levels and to normal tissue radiosensitivity have also been identified though not all have been validated in subsequent studies. GROWING POINTS Utilizing germline SNP profiles as well as identifying high-risk genetic variants could target screening to high-risk groups, avoiding the drawbacks of PSA screening. AREAS TIMELY FOR DEVELOPING RESEARCH Incorporating genetics into PrCa screening is being investigated currently using both common SNP profiles and higher risk rare variants. Knowledge of germline genetic defects will allow the development of targeted screening programs, preventive strategies and the personalized treatment of PrCa.
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Affiliation(s)
- S Benafif
- Institute of Cancer Research, Oncogenetics, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - R Eeles
- Institute of Cancer Research, Oncogenetics, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
- Royal Marsden NHS Foundation Trust, London, UK
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Raman R, Kotapalli V, Vamsy M, Patnaik SC, Srinivasulu M, Bashyam MD. A positive family history of cancer or lifestyle factors may not explain the high incidence of early-onset colorectal cancer in India. COLORECTAL CANCER 2014. [DOI: 10.2217/crc.14.31] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
SUMMARY Aim: Colorectal cancer (CRC) patients from developing countries such as India exhibit distinct clinico-pathological characteristics including an early age of onset and predominant tumor localization in the rectum. However, the reason(s) for increased occurrence among the young is not clear. Materials & methods: In the current study, we performed a comparative analysis of several epidemiological features in early and late-onset CRC patients from India including association with familial syndromes, diet and lifestyle habits. Results: Surprisingly, there was no significant association of any epidemiological variable with early-onset CRC. Conclusion: Perhaps low penetrance syndromes and/or other genetic causes may be responsible for an early age of onset among Indian CRC patients.
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Affiliation(s)
- Ratheesh Raman
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Viswakalyan Kotapalli
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Mohana Vamsy
- Surgical Oncology, Omega Hospital, Hyderabad, India
| | | | - Mukta Srinivasulu
- Surgical Oncology, MNJ Institute of Oncology & Regional Cancer Centre, Hyderabad, India
| | - Murali D Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
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9
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Alvarez CE. Naturally Occurring Cancers in Dogs: Insights for Translational Genetics and Medicine. ILAR J 2014; 55:16-45. [DOI: 10.1093/ilar/ilu010] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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10
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Hu Y, Zhou M, Li K, Zhang K, Kong X, Zheng Y, Li J, Liu L. Two DNA repair gene polymorphisms on the risk of gastrointestinal cancers: a meta-analysis. Tumour Biol 2013; 35:1715-25. [PMID: 24203816 DOI: 10.1007/s13277-013-1320-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 10/14/2013] [Indexed: 12/13/2022] Open
Abstract
PARP-1 and MGMT play an important role in the DNA repair system and therefore have been implicated in human carcinogenesis. However, the association between the most studied PARP-1 rs1136410: T > C and MGMT rs12917: C > T polymorphism and risk of gastrointestinal (GI) cancers was reported with inconclusive results. Accordingly, a meta-analysis of 23 published case-control studies was conducted to assess the strength of association using crude odds ratios (ORs) with 95% confidence intervals (CIs). Overall, the C allele of PARP-1 rs1136410: T > C polymorphism was significantly associated with increased susceptibility of GI cancers (homozygote comparison: OR = 1.43, 95% CI 1.14-1.81; heterozygote comparison: OR = 1.18, 95% CI 1.07-1.29; dominant model: OR = 1.23, 95% CI 1.12-1.35; recessive model: OR = 1.30, 95% CI 1.04-1.62; allelic comparison: OR = 1.19, 95% CI 1.07-1.32). In the subgroup analysis, still obvious associations were found in the Asian population, gastric cancer, and high-quality studies. For MGMT rs12917: C > T polymorphism, no obvious associations were found for all genetic models overall. However, in the subgroup analysis, we found that the T allele was significantly associated with reduced colorectal cancer risk for heterozygote (OR = 0.83, 95% CI 0.70-0.97) and dominant model (OR = 0.84, 95% CI 0.72-0.98). In conclusion, this meta-analysis suggests that the PARP-1 rs1136410: T > C polymorphism is a susceptibility factor for GI cancers, but the variant allele of MGMT rs12917: C > T polymorphism appears to be a protective factor for colorectal cancer. Large-scale and well-designed case-control studies are necessary to validate the risk identified in the present meta-analysis.
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Affiliation(s)
- Yue Hu
- Tumor Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
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Rossi D. Inherited susceptibility to chronic lymphocytic leukemia: the good candidates. Leuk Lymphoma 2013; 55:9-10. [PMID: 23734657 DOI: 10.3109/10428194.2013.810741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Davide Rossi
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont , Novara , Italy
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12
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Rowlan JS, Zhang Z, Wang Q, Fang Y, Shi W. New quantitative trait loci for carotid atherosclerosis identified in an intercross derived from apolipoprotein E-deficient mouse strains. Physiol Genomics 2013; 45:332-42. [PMID: 23463770 PMCID: PMC3633429 DOI: 10.1152/physiolgenomics.00099.2012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Carotid atherosclerosis is the primary cause of ischemic stroke. To identify genetic factors contributing to carotid atherosclerosis, we performed quantitative trait locus (QTL) analysis using female mice derived from an intercross between C57BL/6J (B6) and BALB/cJ (BALB) apolipoprotein E (Apoe−/−) mice. We started 266 F2 mice on a Western diet at 6 wk of age and fed them the diet for 12 wk. Atherosclerotic lesions in the left carotid bifurcation and plasma lipid levels were measured. We genotyped 130 microsatellite markers across the entire genome. Three significant QTLs, Cath1 on chromosome (Chr) 12, Cath2 on Chr5, and Cath3 on Chr13, and four suggestive QTLs on Chr6, Chr9, Chr17, and Chr18 were identified for carotid lesions. The Chr6 locus replicated a suggestive QTL and was named Cath4. Six QTLs for HDL, three QTLs for non-HDL cholesterol, and three QTLs for triglyceride were found. Of these, a significant QTL for non-HDL on Chr1 at 60.3 cM, named Nhdl13, and a suggestive QTL for HDL on ChrX were new. A significant locus for HDL (Hdlq5) was overlapping with a suggestive locus for carotid lesions on Chr9. A significant correlation between carotid lesion sizes and HDL cholesterol levels was observed in the F2 population (R = −0.153, P = 0.0133). Thus, we have identified several new QTLs for carotid atherosclerosis and the locus on Chr9 may exert effect through interactions with HDL.
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Affiliation(s)
- Jessica S Rowlan
- Departments of Radiology & Medical Imaging and Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
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Campo E. Whole genome profiling and other high throughput technologies in lymphoid neoplasms--current contributions and future hopes. Mod Pathol 2013; 26 Suppl 1:S97-S110. [PMID: 23281439 DOI: 10.1038/modpathol.2012.179] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The development of high throughput technologies based on the knowledge of the human genome has opened the possibility to search for global genomic alterations in tumors responsible for their development and progression that may have important clinical implications. One of the major applications of this genomic knowledge has been the design of different types of microarray platforms for the analysis of DNA alterations and gene expression profiling (GEP). The main contributions of the DNA studies in lymphoid neoplasms include the definition of relatively characteristic genomic profiles for specific disease entities, the demonstration of common chromosomal alterations across entities, the identification of genes and pathways targeted by the altered chromosomal regions, and the identification of chromosomal alterations with prognostic implications. RNA GEP studies in these tumors have enhanced the molecular characterization of known entities and facilitated the recognition of new subtypes and categories of lymphoid neoplasms, the identification of new biomarkers and prognostic models, and the detection of oncogenic pathways with potential implications for targeted therapies. The recent development of the next generation sequencing (NGS) technologies and its application in lymphoid neoplasms already have provided an initial view of the complex landscape of somatic mutations in these tumors and some findings with important functional and clinical implications. This review addresses the major contributions and limitations of the microarray technologies in the understanding of lymphoid neoplasms and discusses how this knowledge may be transferred into the clinics. The initial results of the NGS studies are also presented.
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Affiliation(s)
- Elías Campo
- Haematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain.
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Association between TERT-CLPTM1L rs401681[C] allele and NMSC cancer risk: a meta-analysis including 45,184 subjects. Arch Dermatol Res 2012; 305:49-52. [PMID: 22893025 DOI: 10.1007/s00403-012-1275-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 07/01/2012] [Accepted: 07/20/2012] [Indexed: 10/28/2022]
Abstract
Single-nucleotide polymorphism of CLPTM1L-rs401681(C > T) at the 5p15.33 locus is significantly associated with cancer risk as reported in genome-wide association studies, but the reported studies for non-melanoma skin cancer (NMSC) are inconclusive. To assess the association between rs401681[C] allele and NMSC risk, we performed this meta-analysis with four case-control studies involving 5,469 cases and 39,715 controls. Our meta-analysis showed that rs401681[C] allele was associated with NMSC susceptibility in the overall subjects (C vs. T, OR 1.13, 95 % CI 1.07-1.20). In the stratified analysis, the rs401681[C] allele confers susceptibility in Icelanders (C vs. T, OR 1.15, 95 % CI 1.06-1.26) and non-Icelanders (C vs. T, OR 1.13, 95 % CI 1.03-1.24). In the subtype analysis, we found that rs401681[C] allele was a risk factor for BCC, but not SCC in the overall subjects.
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Li FX, Yang XX, He XQ, Hu NY, Wu YS, Li M. Association of 10q23 with colorectal cancer in a Chinese population. Mol Biol Rep 2012; 39:9557-62. [PMID: 22740136 DOI: 10.1007/s11033-012-1820-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 06/10/2012] [Indexed: 12/17/2022]
Abstract
Recently, a genome-wide association study of gastric cancer (GC) reported the significant association of seven genetic variants (rs4072037 and rs4460629 on 1q22; rs753724, rs11187842, rs3765524, rs2274223, and rs3781264 on 10q23) with GC in a Chinese population. These findings were confirmed in a subsequent independent study. However, it remains unknown whether these loci are associated with an increased risk of colorectal cancer (CRC). This study was to test whether the seven single nucleotide polymorphisms (SNPs) associated with GC were also associated with CRC in a Chinese population. The seven SNPs were genotyped using MassARRAY system. Allelic, genotypic, and haplotypic associations of the SNPs with CRC were investigated using χ(2) tests and logistic regression analysis. The SNPs rs3765524 and rs2274223, located on 10q23, were found to have significant protective effects against CRC, with equal odds ratios per allele. The two SNPs located on 1q22 (rs4072037 and rs4460629) showed a weak association with CRC. No significant association was identified with CRC for the remaining three SNPs located on 10q23 (rs753724, rs11187842, and rs3781264). These results suggest that rs3765524 and rs2274223 on 10q23 are associated with a protective effect against CRC in a Chinese population.
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Affiliation(s)
- Fen-Xia Li
- School of Biotechnology, Southern Medical University, Guangzhou 510515, China
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Kerkhof HJM, Evangelou E, Meulenbelt I, van Meurs JBJ, Zeggini E, Valdes AM. Reply to "Human genetic studies on osteoarthritis from clinicians' viewpoints". Osteoarthritis Cartilage 2012; 20:250-1; author reply 252. [PMID: 22233813 DOI: 10.1016/j.joca.2011.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 09/08/2011] [Accepted: 09/21/2011] [Indexed: 02/02/2023]
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Giráldez MD, López-Dóriga A, Bujanda L, Abulí A, Bessa X, Fernández-Rozadilla C, Muñoz J, Cuatrecasas M, Jover R, Xicola RM, Llor X, Piqué JM, Carracedo A, Ruiz-Ponte C, Cosme A, Enríquez-Navascués JM, Moreno V, Andreu M, Castells A, Balaguer F, Castellví-Bel S. Susceptibility genetic variants associated with early-onset colorectal cancer. Carcinogenesis 2012; 33:613-9. [PMID: 22235025 DOI: 10.1093/carcin/bgs009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is the second most common cancer in Western countries. Hereditary forms only correspond to 5% of CRC burden. Recently, genome-wide association studies have identified common low-penetrant CRC genetic susceptibility loci. Early-onset CRC (CRC<50 years old) is especially suggestive of hereditary predisposition although 85-90% of heritability still remains unidentified. CRC<50 patients (n = 191) were compared with a late-onset CRC group (CRC>65 years old) (n = 1264). CRC susceptibility variants at 8q23.3 (rs16892766), 8q24.21 (rs6983267), 10p14 (rs10795668), 11q23.1 (rs3802842), 15q13.3 (rs4779584), 18q21 (rs4939827), 14q22.2 (rs4444235), 16q22.1 (rs9929218), 19q13.1 (rs10411210) and 20p12.3 (rs961253) were genotyped in all DNA samples. A genotype-phenotype correlation with clinical and pathological characteristics in both groups was performed. Risk allele carriers for rs3802842 [Odds ratio (OR) = 1.5, 95% confidence interval (CI) 1.1-2.05, P = 0.0096, dominant model) and rs4779584 (OR = 1.39, 95% CI 1.02-1.9, P = 0.0396, dominant model) were more frequent in the CRC<50 group, whereas homozygotes for rs10795668 risk allele were also more frequent in the early-onset CRC (P = 0.02, codominant model). Regarding early-onset cases, 14q22 (rs4444235), 11q23 (rs3802842) and 20p12 (rs961253) variants were more associated with family history of CRC or tumors of the Lynch syndrome spectrum excluding CRC. In our entire cohort, sum of risk alleles was significantly higher in patients with a CRC family history (OR = 1.40, 95% CI 1.06-1.85, P = 0.01). In conclusion, variants at 10p14 (rs10795668), 11q23.1 (rs3802842) and 15q13.3 (rs4779584) may have a predominant role in predisposition to early-onset CRC. Association of CRC susceptibility variants with some patient's familiar and personal features could be relevant for screening and surveillance strategies in this high-risk group and it should be explored in further studies.
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Affiliation(s)
- María Dolores Giráldez
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), IDIBAPS, University of Barcelona, Villarroel 170, 08036 Barcelona, Catalonia, Spain
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Tang B, Thornton-Wells T, Askland KD. Comparative linkage meta-analysis reveals regionally-distinct, disparate genetic architectures: application to bipolar disorder and schizophrenia. PLoS One 2011; 6:e19073. [PMID: 21559500 PMCID: PMC3084739 DOI: 10.1371/journal.pone.0019073] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Accepted: 03/25/2011] [Indexed: 11/18/2022] Open
Abstract
New high-throughput, population-based methods and next-generation sequencing capabilities hold great promise in the quest for common and rare variant discovery and in the search for ”missing heritability.” However, the optimal analytic strategies for approaching such data are still actively debated, representing the latest rate-limiting step in genetic progress. Since it is likely a majority of common variants of modest effect have been identified through the application of tagSNP-based microarray platforms (i.e., GWAS), alternative approaches robust to detection of low-frequency (1–5% MAF) and rare (<1%) variants are of great importance. Of direct relevance, we have available an accumulated wealth of linkage data collected through traditional genetic methods over several decades, the full value of which has not been exhausted. To that end, we compare results from two different linkage meta-analysis methods—GSMA and MSP—applied to the same set of 13 bipolar disorder and 16 schizophrenia GWLS datasets. Interestingly, we find that the two methods implicate distinct, largely non-overlapping, genomic regions. Furthermore, based on the statistical methods themselves and our contextualization of these results within the larger genetic literatures, our findings suggest, for each disorder, distinct genetic architectures may reside within disparate genomic regions. Thus, comparative linkage meta-analysis (CLMA) may be used to optimize low-frequency and rare variant discovery in the modern genomic era.
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Affiliation(s)
- Brady Tang
- Biostatistics Graduate Program, Brown University, Providence, Rhode Island, United States of America
| | - Tricia Thornton-Wells
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kathleen D. Askland
- Department of Psychiatry and Human Behavior, Butler Hospital, The Warren Alpert School of Medicine of Brown University, Providence, Rhode Island, United States of America
- * E-mail:
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