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  1. Article: A Highly Sensitive Flow Cytometric Approach to Detect Rare Antigen-Specific T Cells: Development and Comparison to Standard Monitoring Tools.

    Dror Levinsky, Meytal / Brenner, Baruch / Yalon, Michal / Levi, Zohar / Livneh, Zvi / Cohen, Zoya / Paz-Elizur, Tamar / Grossman, Rachel / Ram, Zvi / Volovitz, Ilan

    Cancers

    2023  Volume 15, Issue 3

    Abstract: Personalized vaccines against patient-unique tumor-associated antigens represent a promising new approach for cancer immunotherapy. Vaccine efficacy is assessed by quantification of changes in the frequency and/or the activity of antigen-specific T cells. ...

    Abstract Personalized vaccines against patient-unique tumor-associated antigens represent a promising new approach for cancer immunotherapy. Vaccine efficacy is assessed by quantification of changes in the frequency and/or the activity of antigen-specific T cells. Enzyme-linked immunosorbent spot (ELISpot) and flow cytometry (FCM) are methodologies frequently used for assessing vaccine efficacy. We tested these methodologies and found that both ELISpot and standard FCM [monitoring CD3/CD4/CD8/IFNγ/Viability+CD14+CD19 (dump)] demonstrate background IFNγ secretion, which, in many cases, was higher than the antigen-specific signal measured by the respective methodology (frequently ranging around 0.05-0.2%). To detect such weak T-cell responses, we developed an FCM panel that included two early activation markers, 4-1BB (CD137) and CD40L (CD154), in addition to the above-cited markers. These two activation markers have a close to zero background expression and are rapidly upregulated following antigen-specific activation. They enabled the quantification of rare T cells responding to antigens within the assay well. Background IFNγ-positive CD4 T cell frequencies decreased to 0.019% ± 0.028% and CD8 T cells to 0.009% ± 0.013%, which are 19 and 13 times lower, respectively, than without the use of these markers. The presented methodology enables highly sensitive monitoring of T-cell responses to tumor-associated antigens in the very low, but clinically relevant, frequencies.
    Language English
    Publishing date 2023-01-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers15030574
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: TENT4A Non-Canonical Poly(A) Polymerase Regulates DNA-Damage Tolerance via Multiple Pathways That Are Mutated in Endometrial Cancer.

    Swain, Umakanta / Friedlander, Gilgi / Sehrawat, Urmila / Sarusi-Portuguez, Avital / Rotkopf, Ron / Ebert, Charlotte / Paz-Elizur, Tamar / Dikstein, Rivka / Carell, Thomas / Geacintov, Nicholas E / Livneh, Zvi

    International journal of molecular sciences

    2021  Volume 22, Issue 13

    Abstract: TENT4A (PAPD7) is a non-canonical poly(A) polymerase, of which little is known. Here, we show that TENT4A regulates multiple biological pathways and focuses on its multilayer regulation of translesion DNA synthesis (TLS), in which error-prone DNA ... ...

    Abstract TENT4A (PAPD7) is a non-canonical poly(A) polymerase, of which little is known. Here, we show that TENT4A regulates multiple biological pathways and focuses on its multilayer regulation of translesion DNA synthesis (TLS), in which error-prone DNA polymerases bypass unrepaired DNA lesions. We show that TENT4A regulates mRNA stability and/or translation of DNA polymerase η and RAD18 E3 ligase, which guides the polymerase to replication stalling sites and monoubiquitinates PCNA, thereby enabling recruitment of error-prone DNA polymerases to damaged DNA sites. Remarkably, in addition to the effect on RAD18 mRNA stability via controlling its poly(A) tail, TENT4A indirectly regulates RAD18 via the tumor suppressor CYLD and via the long non-coding antisense RNA
    MeSH term(s) Blotting, Western ; Cell Line, Tumor ; Chromosomal Proteins, Non-Histone/genetics ; Chromosomal Proteins, Non-Histone/metabolism ; Computational Biology ; DNA Damage/genetics ; DNA Damage/physiology ; DNA Repair/genetics ; DNA Repair/physiology ; DNA Replication/genetics ; DNA Replication/physiology ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Endometrial Neoplasms/genetics ; Endometrial Neoplasms/metabolism ; Female ; HEK293 Cells ; Humans ; Immunoprecipitation ; MCF-7 Cells ; Mutation/genetics ; Polymerase Chain Reaction ; Polynucleotide Adenylyltransferase/genetics ; Polynucleotide Adenylyltransferase/metabolism ; RNA Stability/genetics ; RNA Stability/physiology ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination/genetics ; Ubiquitination/physiology
    Chemical Substances Chromosomal Proteins, Non-Histone ; DNA-Binding Proteins ; PAXIP1 protein, human ; RAD18 protein, human ; RNA, Messenger ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Polynucleotide Adenylyltransferase (EC 2.7.7.19) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; TENT4A protein, human (EC 2.7.7.7)
    Language English
    Publishing date 2021-06-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms22136957
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: TENT4A Non-Canonical Poly(A) Polymerase Regulates DNA-Damage Tolerance via Multiple Pathways That Are Mutated in Endometrial Cancer

    Umakanta Swain / Gilgi Friedlander / Urmila Sehrawat / Avital Sarusi-Portuguez / Ron Rotkopf / Charlotte Ebert / Tamar Paz-Elizur / Rivka Dikstein / Thomas Carell / Nicholas E. Geacintov / Zvi Livneh

    International Journal of Molecular Sciences, Vol 22, Iss 6957, p

    2021  Volume 6957

    Abstract: TENT4A (PAPD7) is a non-canonical poly(A) polymerase, of which little is known. Here, we show that TENT4A regulates multiple biological pathways and focuses on its multilayer regulation of translesion DNA synthesis (TLS), in which error-prone DNA ... ...

    Abstract TENT4A (PAPD7) is a non-canonical poly(A) polymerase, of which little is known. Here, we show that TENT4A regulates multiple biological pathways and focuses on its multilayer regulation of translesion DNA synthesis (TLS), in which error-prone DNA polymerases bypass unrepaired DNA lesions. We show that TENT4A regulates mRNA stability and/or translation of DNA polymerase η and RAD18 E3 ligase, which guides the polymerase to replication stalling sites and monoubiquitinates PCNA, thereby enabling recruitment of error-prone DNA polymerases to damaged DNA sites. Remarkably, in addition to the effect on RAD18 mRNA stability via controlling its poly(A) tail, TENT4A indirectly regulates RAD18 via the tumor suppressor CYLD and via the long non-coding antisense RNA PAXIP1-AS2 , which had no known function. Knocking down the expression of TENT4A or CYLD , or overexpression of PAXIP1-AS2 led each to reduced amounts of the RAD18 protein and DNA polymerase η, leading to reduced TLS, highlighting PAXIP1-AS2 as a new TLS regulator. Bioinformatics analysis revealed that TLS error-prone DNA polymerase genes and their TENT4A -related regulators are frequently mutated in endometrial cancer genomes, suggesting that TLS is dysregulated in this cancer.
    Keywords TLS ; DNA repair ; poly(A) RNA polymerase ; translesion ; lesion bypass ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 612
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: DNA sequence context greatly affects the accuracy of bypass across an ultraviolet light 6-4 photoproduct in mammalian cells.

    Shriber, Pola / Leitner-Dagan, Yael / Geacintov, Nicholas / Paz-Elizur, Tamar / Livneh, Zvi

    Mutation research

    2015  Volume 780, Page(s) 71–76

    Abstract: Translesion DNA synthesis (TLS) is a DNA damage tolerance mechanism carried out by low-fidelity DNA polymerases that bypass DNA lesions, which overcomes replication stalling. Despite the miscoding nature of most common DNA lesions, several of them are ... ...

    Abstract Translesion DNA synthesis (TLS) is a DNA damage tolerance mechanism carried out by low-fidelity DNA polymerases that bypass DNA lesions, which overcomes replication stalling. Despite the miscoding nature of most common DNA lesions, several of them are bypassed in mammalian cells in a relatively accurate manner, which plays a key role maintaining a low mutation load. Whereas it is generally agreed that TLS across the major UV and sunlight induced DNA lesion, the cyclobutane pyrimidine dimer (CPD), is accurate, there were conflicting reports on whether the same is true for the thymine-thymine pyrimidine-pyrimidone(6-4) ultraviolet light photoproduct (TT6-4PP), which represents the second most common class of UV lesions. Using a TLS assay system based on gapped plasmids carrying site-specific TT6-4PP lesions in defined sequence contexts we show that the DNA sequence context markedly affected both the extent and accuracy of TLS. The sequence exhibiting higher TLS exhibited also higher error-frequency, caused primarily by semi-targeted mutations, at the nearest nucleotides flanking the lesion. Our results resolve the discrepancy reported on TLS across TT6-4PP, and suggest that TLS is more accurate in human cells than in mouse cells.
    MeSH term(s) Animals ; Cell Line, Transformed ; DNA Damage ; Humans ; Mice ; Mutation ; Pyrimidine Dimers/genetics ; Pyrimidine Dimers/metabolism ; Species Specificity ; Ultraviolet Rays/adverse effects
    Chemical Substances Pyrimidine Dimers
    Language English
    Publishing date 2015-10
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 206607-5
    ISSN 1873-135X ; 1383-5718 ; 0027-5107 ; 0165-1110 ; 0165-1161 ; 0165-7992 ; 0921-8777 ; 0165-1218 ; 1383-5726 ; 0167-8817 ; 0921-8734 ; 1383-5742
    ISSN (online) 1873-135X
    ISSN 1383-5718 ; 0027-5107 ; 0165-1110 ; 0165-1161 ; 0165-7992 ; 0921-8777 ; 0165-1218 ; 1383-5726 ; 0167-8817 ; 0921-8734 ; 1383-5742
    DOI 10.1016/j.mrfmmm.2015.08.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: DNA Repair Biomarker for Lung Cancer Risk and its Correlation With Airway Cells Gene Expression.

    Paz-Elizur, Tamar / Leitner-Dagan, Yael / Meyer, Kerstin B / Markus, Barak / Giorgi, Federico M / O'Reilly, Martin / Kim, Hyunjin / Evgy, Yentl / Fluss, Ronen / Freedman, Laurence S / Rintoul, Robert C / Ponder, Bruce / Livneh, Zvi

    JNCI cancer spectrum

    2019  Volume 4, Issue 1, Page(s) pkz067

    Abstract: Background: Improving lung cancer risk assessment is required because current early-detection screening criteria miss most cases. We therefore examined the utility for lung cancer risk assessment of a DNA Repair score obtained from OGG1, MPG, and APE1 ... ...

    Abstract Background: Improving lung cancer risk assessment is required because current early-detection screening criteria miss most cases. We therefore examined the utility for lung cancer risk assessment of a DNA Repair score obtained from OGG1, MPG, and APE1 blood tests. In addition, we examined the relationship between the level of DNA repair and global gene expression.
    Methods: We conducted a blinded case-control study with 150 non-small cell lung cancer case patients and 143 control individuals. DNA Repair activity was measured in peripheral blood mononuclear cells, and the transcriptome of nasal and bronchial cells was determined by RNA sequencing. A combined DNA Repair score was formed using logistic regression, and its correlation with disease was assessed using cross-validation; correlation of expression to DNA Repair was analyzed using Gene Ontology enrichment.
    Results: DNA Repair score was lower in case patients than in control individuals, regardless of the case's disease stage. Individuals at the lowest tertile of DNA Repair score had an increased risk of lung cancer compared to individuals at the highest tertile, with an odds ratio (OR) of 7.2 (95% confidence interval [CI] = 3.0 to 17.5;
    Conclusions: The DNA Repair score, previously shown to be a lung cancer risk factor in the Israeli population, was validated in this independent study as a mechanism-based cancer risk biomarker and can substantially improve current lung cancer risk prediction, assisting prevention and early detection by computed tomography scanning.
    Language English
    Publishing date 2019-09-12
    Publishing country England
    Document type Journal Article
    ISSN 2515-5091
    ISSN (online) 2515-5091
    DOI 10.1093/jncics/pkz067
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: High-resolution genomic assays provide insight into the division of labor between TLS and HDR in mammalian replication of damaged DNA.

    Livneh, Zvi / Cohen, Isadora S / Paz-Elizur, Tamar / Davidovsky, Dana / Carmi, Dalit / Swain, Umakanta / Mirlas-Neisberg, Nataly

    DNA repair

    2016  Volume 44, Page(s) 59–67

    Abstract: The multitude of DNA lesions that continuously form in DNA cannot all be detected and removed prior to replication. Thus, encounters of the replication fork with DNA damage become inevitable. Such encounters inhibit fork progression, leading to ... ...

    Abstract The multitude of DNA lesions that continuously form in DNA cannot all be detected and removed prior to replication. Thus, encounters of the replication fork with DNA damage become inevitable. Such encounters inhibit fork progression, leading to replication fork arrest or to replication re-priming downstream of the damage site. Either of these events will result in the formation of gap-lesion structures, in which a damaged base is located in a single stranded stretch of DNA, that is vulnerable to subsequent nicking. The double strand break that would ensue if ssDNA becomes nicked constitutes escalation of the damage from nucleotide(s)-specific to chromosomal scale. Cells employ two universal DNA damage tolerance (DDT) strategies to resolve these situations, by converting the gap-lesion structures into dsDNA without repairing the damage. The first is translesion DNA synthesis (TLS), in which a specialized low-fidelity DNA polymerase inserts a nucleotide opposite the damaged one. TLS is inherently mutagenic, due to the miscoding nature of most damaged nucleotides. The second strategy is homology-dependent repair (HDR), which relies on the presence of an identical intact sister chromatid. The molecular mechanisms that regulate the division of labor between these pathways are poorly understood. This review focuses on the balance between TLS and HDR in mammalian cells, discussing recent findings that were made possible thanks to newly developed high resolution genomic assays, and highlighting the role of the DNA lesion's properties in DDT pathway choice.
    MeSH term(s) Animals ; Base Pair Mismatch ; Biological Assay ; Catalytic Domain ; DNA/genetics ; DNA/metabolism ; DNA Breaks, Double-Stranded/radiation effects ; DNA End-Joining Repair ; DNA Mismatch Repair ; DNA Replication ; DNA, Single-Stranded/genetics ; DNA, Single-Stranded/metabolism ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Humans ; Models, Genetic ; Recombinational DNA Repair ; Ultraviolet Rays
    Chemical Substances DNA, Single-Stranded ; DNA (9007-49-2) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
    Language English
    Publishing date 2016-08
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2071608-4
    ISSN 1568-7856 ; 1568-7864
    ISSN (online) 1568-7856
    ISSN 1568-7864
    DOI 10.1016/j.dnarep.2016.05.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: DNA lesion identity drives choice of damage tolerance pathway in murine cell chromosomes.

    Cohen, Isadora S / Bar, Carmit / Paz-Elizur, Tamar / Ainbinder, Elena / Leopold, Karoline / de Wind, Niels / Geacintov, Nicholas / Livneh, Zvi

    Nucleic acids research

    2015  Volume 43, Issue 3, Page(s) 1637–1645

    Abstract: DNA-damage tolerance (DDT) via translesion DNA synthesis (TLS) or homology-dependent repair (HDR) functions to bypass DNA lesions encountered during replication, and is critical for maintaining genome stability. Here, we present piggyBlock, a new ... ...

    Abstract DNA-damage tolerance (DDT) via translesion DNA synthesis (TLS) or homology-dependent repair (HDR) functions to bypass DNA lesions encountered during replication, and is critical for maintaining genome stability. Here, we present piggyBlock, a new chromosomal assay that, using piggyBac transposition of DNA containing a known lesion, measures the division of labor between the two DDT pathways. We show that in the absence of DNA damage response, tolerance of the most common sunlight-induced DNA lesion, TT-CPD, is achieved by TLS in mouse embryo fibroblasts. Meanwhile, BP-G, a major smoke-induced DNA lesion, is bypassed primarily by HDR, providing the first evidence for this mechanism being the main tolerance pathway for a biologically important lesion in a mammalian genome. We also show that, far from being a last-resort strategy as it is sometimes portrayed, TLS operates alongside nucleotide excision repair, handling 40% of TT-CPDs in repair-proficient cells. Finally, DDT acts in mouse embryonic stem cells, exhibiting the same pattern—mutagenic TLS included—despite the risk of propagating mutations along all cell lineages. The new method highlights the importance of HDR, and provides an effective tool for studying DDT in mammalian cells.
    MeSH term(s) Animals ; Base Sequence ; Cells, Cultured ; Chromosomes ; DNA Damage ; Mice ; Oligonucleotide Probes
    Chemical Substances Oligonucleotide Probes
    Language English
    Publishing date 2015-02-15
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gku1398
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Interrogating DNA repair in cancer risk assessment.

    Paz-Elizur, Tamar / Brenner, Dean E / Livneh, Zvi

    Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

    2005  Volume 14, Issue 7, Page(s) 1585–1587

    MeSH term(s) DNA Repair/genetics ; DNA Repair/physiology ; Genotype ; Humans ; Neoplasms/etiology ; Neoplasms/genetics ; Neoplasms/prevention & control ; Risk Factors
    Language English
    Publishing date 2005-07
    Publishing country United States
    Document type Editorial ; Research Support, Non-U.S. Gov't
    ZDB-ID 1153420-5
    ISSN 1055-9965
    ISSN 1055-9965
    DOI 10.1158/1055-9965.EPI-14-7-ED
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Development of APE1 enzymatic DNA repair assays: low APE1 activity is associated with increase lung cancer risk.

    Sevilya, Ziv / Leitner-Dagan, Yael / Pinchev, Mila / Kremer, Ran / Elinger, Dalia / Lejbkowicz, Flavio / Rennert, Hedy S / Freedman, Laurence S / Rennert, Gad / Paz-Elizur, Tamar / Livneh, Zvi

    Carcinogenesis

    2015  Volume 36, Issue 9, Page(s) 982–991

    Abstract: The key role of DNA repair in removing DNA damage and minimizing mutations makes it an attractive target for cancer risk assessment and prevention. Here we describe the development of a robust assay for apurinic/apyrimidinic (AP) endonuclease 1 (APE1; ... ...

    Abstract The key role of DNA repair in removing DNA damage and minimizing mutations makes it an attractive target for cancer risk assessment and prevention. Here we describe the development of a robust assay for apurinic/apyrimidinic (AP) endonuclease 1 (APE1; APEX1), an essential enzyme involved in the repair of oxidative DNA damage. APE1 DNA repair enzymatic activity was measured in peripheral blood mononuclear cell protein extracts using a radioactivity-based assay, and its association with lung cancer was determined using conditional logistic regression with specimens from a population-based case-control study with 96 lung cancer cases and 96 matched control subjects. The mean APE1 enzyme activity in case patients was 691 [95% confidence interval (CI) = 655-727] units/ng protein, significantly lower than in control subjects (mean = 793, 95% CI = 751-834 units/ng protein, P = 0.0006). The adjusted odds ratio for lung cancer associated with 1 SD (211 units) decrease in APE1 activity was 2.0 (95% CI = 1.3-3.1; P = 0.002). Comparison of radioactivity- and fluorescence-based assays showed that the two are equivalent, indicating no interference by the fluorescent tag. The APE1Asp148Glu SNP was associated neither with APE1 enzyme activity nor with lung cancer risk. Taken together, our results indicate that low APE1 activity is associated with lung cancer risk, consistent with the hypothesis that 'bad DNA repair', rather than 'bad luck', is involved in cancer etiology. Such assays may be useful, along with additional DNA repair biomarkers, for risk assessment of lung cancer and perhaps other cancers, and for selecting individuals to undergo early detection techniques such as low-dose CT.
    MeSH term(s) Case-Control Studies ; DNA Damage/genetics ; DNA Repair/genetics ; DNA-(Apurinic or Apyrimidinic Site) Lyase/analysis ; DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics ; DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism ; Female ; Fluorescence ; Genetic Predisposition to Disease ; Humans ; Leukocytes, Mononuclear/cytology ; Lung/enzymology ; Lung/pathology ; Lung Neoplasms/enzymology ; Lung Neoplasms/epidemiology ; Lung Neoplasms/genetics ; Male ; Polymorphism, Single Nucleotide ; Risk
    Chemical Substances APEX1 protein, human (EC 4.2.99.18) ; DNA-(Apurinic or Apyrimidinic Site) Lyase (EC 4.2.99.18)
    Language English
    Publishing date 2015-09
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 603134-1
    ISSN 1460-2180 ; 0143-3334
    ISSN (online) 1460-2180
    ISSN 0143-3334
    DOI 10.1093/carcin/bgv082
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Novel molecular targets for risk identification: DNA repair enzyme activities.

    Paz-Elizur, Tamar / Elinger, Dalia / Blumenstein, Sara / Krupsky, Meir / Schechtman, Edna / Livneh, Zvi

    Cancer biomarkers : section A of Disease markers

    2007  Volume 3, Issue 3, Page(s) 129–133

    MeSH term(s) Animals ; DNA Repair ; Genetic Predisposition to Disease ; Humans ; Neoplasms/genetics ; Risk Factors
    Language English
    Publishing date 2007-07-03
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2203517-5
    ISSN 1574-0153 ; 1574-0153 ; 1875-8592
    ISSN (online) 1574-0153
    ISSN 1574-0153 ; 1875-8592
    DOI 10.3233/cbm-2007-3303
    Database MEDical Literature Analysis and Retrieval System OnLINE

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