Repair Variants Research Articles

Genetic Variants of DNA Repair Genes as Predictors of Radiation-Induced Subcutaneous Fibrosis in Oropharyngeal Carcinoma.

PurposeTo investigate the impact of genetic variants of DNA repair and pro-fibrotic pathway genes on the severity of radiation-induced subcutaneous fibrosis in patients of oropharyngeal carcinoma treated with radical radiotherapy.Materials and MethodsPatients of newly diagnosed squamous cell carcinoma of oropharynx being treated with two-dimensional radical radiotherapy were enrolled in the study. Patients who had undergone surgery or were receiving concurrent chemotherapy were excluded. Patients were followed up at 6 weeks post completion of radiotherapy and every 3 months thereafter for a median of 16 months. Subcutaneous fibrosis was graded according to the Radiation Therapy Oncology Group (RTOG) and the European Organization for Research and Treatment of Cancer (EORTC) grading system and the maximum grade was recorded over the length of the patient’s follow-up. Patients with severe fibrosis (≥G3), were compared to patients with minor (≤G2) fibrotic reactions. Eight single nucleotide polymorphisms of 7 DNA repair genes and 2 polymorphisms of a single pro-fibrotic pathway gene were analyzed by Polymerase Chain Reaction and Restriction Fragment Length Polymorphism and were correlated with the severity of subcutaneous fibrosis.Results179 patients were included in the analysis. Subcutaneous fibrosis was seen in 168 (93.9%) patients. 36 (20.1%) patients had severe (grade 3) fibrosis. On multivariate logistic regression analysis, Homozygous CC genotype of XRCC3 (722C>T, rs861539) (p=0.013*, OR 2.350, 95% CI 1.089-5.382), Homozygous AA genotype of ERCC4 Ex8 (1244G>A, rs1800067) (p=0.001**, OR 11.626, 95% CI 2.490-275.901) and Homozygous TT genotype of XRCC5 (1401G>T, rs828907) (p=0.020*, OR 2.188, 95% CI 1.652-7.334) were found to be predictive of severe subcutaneous fibrosis. On haplotype analysis, the cumulative risk of developing severe fibrosis was observed in patients carrying both haplotypes of variant Homozygous AA genotype of ERCC4 Ex8 (1244G>A, rs1800067) and Homozygous TT genotype of XRCC5 (1401 G>T, rs828907) (p=0.010*, OR 26.340, 95% CI 4.014-76.568).ConclusionWe demonstrated significant associations between single nucleotide polymorphisms of DNA repair genes and radiation-induced subcutaneous fibrosis in patients of oropharyngeal carcinoma treated with radiotherapy. We propose to incorporate these genetic markers into predictive models for identifying patients genetically predisposed to the development of radiation-induced fibrosis, thus guiding personalized treatment protocols.

Role of DNA Repair Variants and Diagnostic Radiology Exams in Differentiated Thyroid Cancer Risk: A Pooled Analysis of Two Case-Control Studies.

Given the increased use and diversity of diagnostic procedures, it is important to understand genetic susceptibility to radiation-induced thyroid cancer. On the basis of self-declared diagnostic radiology examination records in addition to existing literature, we estimated the radiation dose delivered to the thyroid gland from diagnostic procedures during childhood and adulthood in two case-control studies conducted in France. A total of 1,071 differentiated thyroid cancer (DTC) cases and 1,188 controls from the combined studies were genotyped using a custom-made Illumina OncoArray DNA chip. We focused our analysis on variants in genes involved in DNA damage response and repair pathways, representing a total of 5,817 SNPs in 571 genes. We estimated the OR per milli-Gray (OR/mGy) of the radiation dose delivered to the thyroid gland using conditional logistic regression. We then used an unconditional logistic regression model to assess the association between DNA repair gene variants and DTC risk. We performed a meta-analysis of the two studies. The OR/mGy was 1.02 (95% confidence interval, 1.00-1.03). We found significant associations between DTC and rs7164173 in CHD2 (P = 5.79 × 10-5), rs6067822 in NFATc2 (P = 9.26 × 10-5), rs1059394 and rs699517 both in ENOSF1/THYS, rs12702628 in RPA3, and an interaction between rs7068306 in MGMT and thyroid radiation doses (P = 3.40 × 10-4). Our results suggest a role for variants in CDH2, NFATc2, ENOSF1/THYS, RPA3, and MGMT in DTC risk. CDH2, NFATc2, ENOSF1/THYS, and RPA3 have not previously been shown to be associated with DTC risk.

Risk-reducing hysterectomy and bilateral salpingo-oophorectomy in female heterozygotes of pathogenic mismatch repair variants: a Prospective Lynch Syndrome Database report

PurposeTo determine impact of risk-reducing hysterectomy and bilateral salpingo-oophorectomy (BSO) on gynecological cancer incidence and death in heterozygotes of pathogenic MMR (path_MMR) variants.MethodsThe Prospective Lynch Syndrome Database was used to investigate the effects of gynecological risk-reducing surgery (RRS) at different ages.ResultsRisk-reducing hysterectomy at 25 years of age prevents endometrial cancer before 50 years in 15%, 18%, 13%, and 0% of path_MLH1, path_MSH2, path_MSH6, and path_PMS2 heterozygotes and death in 2%, 2%, 1%, and 0%, respectively. Risk-reducing BSO at 25 years of age prevents ovarian cancer before 50 years in 6%, 11%, 2%, and 0% and death in 1%, 2%, 0%, and 0%, respectively. Risk-reducing hysterectomy at 40 years prevents endometrial cancer by 50 years in 13%, 16%, 11%, and 0% and death in 1%, 2%, 1%, and 0%, respectively. BSO at 40 years prevents ovarian cancer before 50 years in 4%, 8%, 0%, and 0%, and death in 1%, 1%, 0%, and 0%, respectively.ConclusionLittle benefit is gained by performing RRS before 40 years of age and premenopausal BSO in path_MSH6 and path_PMS2 heterozygotes has no measurable benefit for mortality. These findings may aid decision making for women with LS who are considering RRS.

Uptake of hysterectomy and bilateral salpingo-oophorectomy in carriers of pathogenic mismatch repair variants: a Prospective Lynch Syndrome Database report

PurposeThis study aimed to report the uptake of hysterectomy and/or bilateral salpingo-oophorectomy (BSO) to prevent gynaecological cancers (risk-reducing surgery [RRS]) in carriers of pathogenic MMR (path_MMR) variants. MethodsThe Prospective Lynch Syndrome Database (PLSD) was used to investigate RRS by a cross-sectional study in 2292 female path_MMR carriers aged 30–69 years. ResultsOverall, 144, 79, and 517 carriers underwent risk-reducing hysterectomy, BSO, or both combined, respectively. Two-thirds of procedures before 50 years of age were combined hysterectomy and BSO, and 81% of all procedures included BSO. Risk-reducing hysterectomy was performed before age 50 years in 28%, 25%, 15%, and 9%, and BSO in 26%, 25%, 14% and 13% of path_MLH1, path_MSH2, path_MSH6, and path_PMS2 carriers, respectively. Before 50 years of age, 107 of 188 (57%) BSO and 126 of 204 (62%) hysterectomies were performed in women without any prior cancer, and only 5% (20/392) were performed simultaneously with colorectal cancer (CRC) surgery. ConclusionUptake of RRS before 50 years of age was low, and RRS was rarely undertaken in association with surgical treatment of CRC. Uptake of RRS aligned poorly with gene- and age-associated risk estimates for endometrial or ovarian cancer that were published recently from PLSD and did not correspond well with current clinical guidelines. The reasons should be clarified. Decision-making on opting for or against RRS and its timing should be better aligned with predicted risk and mortality for endometrial and ovarian cancer in Lynch syndrome to improve outcomes.

Comparison of suspected Lynch syndrome patients carrying BRCA and BRCA-like variants with Lynch syndrome probands: Phenotypic characteristics and pedigree analyses.

BackgroundColorectal cancer (CRC) patients diagnosed with Lynch syndrome (LS) are recommended genetic testing. Increasing numbers of germline variants involved in homologous recombination have been identified in suspected LS patients. This study compared phenotypic the characteristics of suspected LS patients carrying BRCA and BRCA‐like variants with those of LS patients.MethodsForty‐two patients carrying pathogenic variants of DNA mismatch repair (MMR) genes (MMR group), 9 carrying BRCA variants, and 11 carrying BRCA‐like variants (BRCA/BRCA‐like group) who met LS clinical criteria were enrolled in this study. Clinical characteristics, pedigrees, and survival rates were compared and BRCA variants were analyzed.ResultsThe earliest CRC‐onset age and tumor differentiation were higher in the BRCA/BRCA‐like group than in the MMR group. Metachronous CRCs were more numerous in the MMR group, resulting in a higher progression‐free survival rate in the BRCA/BRCA‐like group. Extra‐colorectal cancers were more frequently observed in the BRCA/BRCA‐like group. BRCA2 and BRCA1 variants were clustered in exons 11 and 4/7, respectively.Conclusion BRCA and BRCA‐like variants in CRC patients with LS showed moderate penetrance. BRCA/BRCA‐like variant carriers had a higher risk for extra‐colorectal cancers. Surveillance of susceptible organs other than the intestine should be performed for probands and affected family members.

Practical Grammar Compression Based on Maximal Repeats

This study presents an analysis of RePair, which is a grammar compression algorithm known for its simple scheme, while also being practically effective. First, we show that the main process of RePair, that is, the step by step substitution of the most frequent symbol pairs, works within the corresponding most frequent maximal repeats. Then, we reveal the relation between maximal repeats and grammars constructed by RePair. On the basis of this analysis, we further propose a novel variant of RePair, called MR-RePair, which considers the one-time substitution of the most frequent maximal repeats instead of the consecutive substitution of the most frequent pairs. The results of the experiments comparing the size of constructed grammars and execution time of RePair and MR-RePair on several text corpora demonstrate that MR-RePair constructs more compact grammars than RePair does, especially for highly repetitive texts.

Вариант ремонта элементов фонтанной арматуры импортного производства на Астраханском газоконденсатном месторождении

Вариант ремонта элементов фонтанной арматуры импортного производства на Астраханском газоконденсатном месторождении

Cancer risks by gene, age, and gender in 6350 carriers of pathogenic mismatch repair variants: findings from the Prospective Lynch Syndrome Database

PurposePathogenic variants affecting MLH1, MSH2, MSH6, and PMS2 cause Lynch syndrome and result in different but imprecisely known cancer risks. This study aimed to provide age and organ-specific cancer risks according to gene and gender and to determine survival after cancer. MethodsWe conducted an international, multicenter prospective observational study using independent test and validation cohorts of carriers of class 4 or class 5 variants. After validation the cohorts were merged providing 6350 participants and 51,646 follow-up years. ResultsThere were 1808 prospectively observed cancers. Pathogenic MLH1 and MSH2 variants caused high penetrance dominant cancer syndromes sharing similar colorectal, endometrial, and ovarian cancer risks, but older MSH2 carriers had higher risk of cancers of the upper urinary tract, upper gastrointestinal tract, brain, and particularly prostate. Pathogenic MSH6 variants caused a sex-limited trait with high endometrial cancer risk but only modestly increased colorectal cancer risk in both genders. We did not demonstrate a significantly increased cancer risk in carriers of pathogenic PMS2 variants. Ten-year crude survival was over 80% following colon, endometrial, or ovarian cancer. ConclusionManagement guidelines for Lynch syndrome may require revision in light of these different gene and gender-specific risks and the good prognosis for the most commonly associated cancers.

Validation of an in Vitro Mismatch Repair Assay Used in the Functional Characterization of Mismatch Repair Variants

A significant proportion of DNA-mismatch repair (MMR) variants are classified as of unknown significance, precluding diagnosis. The invitro MMR assay is used to assess their MMR capability, likely the most important function of an MMR protein. However, the robustness of the assay, crucial for its use in the clinical setting, has been rarely evaluated. The aim of the present work was to validate an invitro MMR assay approach to the functional characterization of MMR variants, as a first step to meeting quality standards of diagnostic laboratories. The MMR assay was optimized by testing a variety of reagents and experimental conditions. Reference materials and standard operating procedures were established. To determine the intra- and interexperimental variability of the assay and its reproducibility among centers, independent transfections of six previously characterized MLH1 variants were performed in two independent laboratories. Reagents and conditions optimal for performing the invitro MMR assay were determined. The validated assay demonstrated no significant intra- or interexperimental variability and good reproducibility between centers. We set up a robust invitro MMR assay that can provide relevant invitro functional evidence for MMR variant pathogenicity assessment, eventually improving the molecular diagnosis of hereditary cancer syndromes associated with MMR deficiency.

Quantification and Valuation of Travel Time Costs Due to Road Works in the Integrated System of Road Economic Evaluation

Abstract Software ISEH (Integrated system of road projects economic evaluation) evaluates variants of road repair and maintenance technologies. The economic assessment is based on Cost Benefit Analysis indicators (net present value, internal rate of return, pay-back period and cost benefit ratio). According quantified indicators are determined order of repairs and maintenance of assessed road sections. The road works cause additional negative impacts to road users. The road repairs and maintenance create on road so-called work zones, which negative affect road users. One of the negative impacts is travel time loss of road users. The process of quantification and valuation of travel time costs due to road works, i.e. work zones create a base for implementation to the ISEH software. For implementation it was necessary to suggest changes in current algorithm of the Software - Integrated system of road projects economic evaluation. The aim of the implementation is effective planning road repairs and maintenance not only in terms of choice effective technology but also in terms of reducing negative impacts to road users. A practical example of calculating travel time costs due to work zone has been processed in Excel software.

The influence of polymorphisms of xenobiotic-metabolizing and DNA repair genes in DNA damage, telomere length and global DNA methylation evaluated in open-cast coal mining workers.

Coal plants represent one of the main sources of environmental pollution due to the combustion process of this mineral and the consequent release of gases and particles which, in significant quantities, can lead to a potential risk to health and the environment. The susceptibility of individuals to the genotoxic effects of coal mining can be modulated by genetic variations in the xenobiotic detoxification and DNA repair processes. The aim of this study was to evaluate if xenobiotic metabolism polymorphism, base excision repair polymorphisms and non-homologous end joining repair polymorphism, could modify individual susceptibility to genomic instability and epigenetic alterations induced in workers by occupational exposure to coal. In this study, polymerase chain reaction was used to examine the polymorphic sites. The sample population comprising 70 coal mine workers and 71 workers non-exposed to coal. Our results demonstrated the effect of individual genotypes on different biomarkers evaluated. Significant decrease in % of global DNA methylation were observed in CYP1A1 Val/- exposed individuals compared to CYP1A1 Ile/Ile individuals. Coal workers who carried the XRCC4 Ile/Ile genotype showed decrease NBUD frequencies, while the XRCC4 Thr/- genotype was associated with decrease in Buccal micronucleus cells for the group not exposed. No influence of GSTM1 null, GSTT1 null, GSTP1 Ile105Val, hOGG1 Ser326Cys, XRCC1 Arg194Trp polymorphisms was observed. Thus, the current study reinforces the importance of considering the effect of metabolizing and repair variant genotypes on the individual susceptibility to incorporate DNA damage, as these processes act in a coordinated manner to determine the final response to coal exposure.

XRCC1 632 as a candidate for cancer predisposition via a complex interaction with genetic variants of base excision repair and double strand break repair genes.

Aim: The DNA repair system safeguards integrity of DNA. Genetic alterations force the improper repair which in conjugation with other factors ultimately results in carcinogenesis. Materials & methods: PCR-restriction fragment length polymorphismwas used for genotyping, which was followed by statistical analysis using logistic regression analysis, multifactor dimensionality reduction and classification and regression analysis tree, elaborating the association with lung cancer subjects. Results: Combination of XRCC1 632 and OGG1326 showcased a high risk of eightfold (odds ratio: 7.92;95% CI: 2.68-23.4; p=0.0002; false discovery rate (FDR)p=0.002). Similarly, XRCC1 632 and MUTYH 324 (odds ratio: 5.07; 95% CI: 2.6-9.67; p<0.0001; FDRp=0.002) had a high risk. Multifactor dimensionality reduction analysis revealed five factor model as the best model with prediction error of 0.37 (p=0.02). Conclusion: There was a clear indication that high order interactions were major role players in the study.

Profitability Analysis and Assessment of the Possibility of Applying Renovation and Modernization Measures to Improve the Utility Value of Public Buildings

Utility building value depends, among other things, on the renovation and modernization activities undertaken at the maintenance stage. They result from a correct assessment of the building condition. Lack of appropriate methods, which in a comprehensive way, taking into account the utility requirements for these buildings, would allow to assess the condition of buildings is one of the main reasons for negligence in the proper maintenance of public buildings. With this in mind, the author carried out a study aimed at an in-depth analysis and assessment of the possibility of applying renovation and modernization measures in relation to the improvement of the utility value of the building and the cost of their implementation. As part of the research, a mathematical model was first developed, which was used to carry out the research. As part of the development of the model, a set of criteria relating to technical-utility, economic and environmental requirements was selected and a method for their evaluation was developed. Next, proposals of renovation and modernization activities were presented, the aim of which is to improve the utility value ratio of the building. For its evaluation the method based on the theory of fuzzy sets was used, which at the stage of inference uses expert knowledge included in the fuzzy rules database. The calculated utility value of the proposed renovation and modernization activities is the basis for further research analyses. Optimization tasks consisting in the selection of an appropriate repair variant are carried out by means of appropriate optimization methods. The adopted optimization objectives concerned both the possibility of improving the assumed increase in utility value and limitations in their financing. The assessment of utility value of public utility buildings, which has not been carried out yet, taking into account the current legal and utility requirements, will allow to determine the impact of renovation and modernization decisions taken on this basis on the adopted determinants determining the quality of the maintenance process, i.e. the increase in utility value and maintenance cost. The results of these studies may be important in expanding existing knowledge and the knowledge gained may contribute to changes in the way decisions are made and the improvement of the quality of building maintenance.

Germline mismatch repair gene variants analyzed by universal sequencing in Japanese cancer patients.

BackgroundLynch syndrome (LS) is the commonest inherited cancer syndrome caused by pathogenic variants of germline DNA mismatch repair (g.MMR) genes. Genome‐wide sequencing is now increasingly applied for tumor characterization, but not for g.MMR. The aim of this study was to evaluate the incidence and pathogenicity of g.MMR variants in Japanese cancer patients.MethodsFour g.MMR genes (MLH1, MSH2, MSH6, and PMS2) were analyzed by next generation sequencing in 1058 cancer patients (614 male, 444 female; mean age 65.6 years) without past diagnosis of LS. The g.MMR variant pathogenicity was classified based on the ClinVar 2015 database. Tumor MMR immunohistochemistry, microsatellite instability (MSI), and BRAF sequencing were also investigated in specific cases.ResultsOverall, 46 g.MMR variants were detected in 167 (15.8%) patients, 17 likely benign variants in 119 patients, 24 variants of uncertain significance (VUSs) in 68 patients, two likely pathogenic variants in two patients, and three pathogenic variants in three (0.3%) patients. The three pathogenic variants included two colorectal cancers with MLH1 loss and high MSI and one endometrial cancer with MSH6 loss and microsatellite stability. Two likely pathogenic variants were shifted to VUSs by ClinVar (2018). One colon cancer with a likely benign variant demonstrated MLH1 loss and BRAF mutation, but other nonpathogenic variants showed sustained MMR and microsatellite stability.ConclusionsUniversal sequencing of g.MMR genes demonstrated sundry benign variants, but only a small proportion of cancer patients had pathogenic variants. Pathogenicity evaluation using the ClinVar database agreed with MSI, MMR immunohistochemistry, and BRAF sequencing.

Thyroid Cancer: The Quest for Genetic Susceptibility Involving DNA Repair Genes

The incidence of thyroid cancer (TC), particularly well-differentiated forms (DTC), has been rising and remains the highest among endocrine malignancies. Although ionizing radiation (IR) is well established on DTC aetiology, other environmental and genetic factors may also be involved. DNA repair single nucleotide polymorphisms (SNPs) could be among the former, helping in explaining the high incidence. To further clarify the role of DNA repair SNPs in DTC susceptibility, we analyzed 36 SNPs in 27 DNA repair genes in a population of 106 DTCs and corresponding controls with the aim of interpreting joint data from previously studied isolated SNPs in DNA repair genes. Significant associations with DTC susceptibility were observed for XRCC3 rs861539, XPC rs2228001, CCNH rs2230641, MSH6 rs1042821 and ERCC5 rs2227869 and for a haplotype block on chromosome 5q. From 595 SNP-SNP combinations tested and 114 showing relevance, 15 significant SNP combinations (p < 0.01) were detected on paired SNP analysis, most of which involving CCNH rs2230641 and mismatch repair variants. Overall, a gene-dosage effect between the number of risk genotypes and DTC predisposition was observed. In spite of the volume of data presented, new studies are sought to provide an interpretability of the role of SNPs in DNA repair genes and their combinations in DTC susceptibility.

Lack of association between screening interval and cancer stage in Lynch syndrome may be accounted for by over-diagnosis; a prospective Lynch syndrome database report

BackgroundRecent epidemiological evidence shows that colorectal cancer (CRC) continues to occur in carriers of pathogenic mismatch repair (path_MMR) variants despite frequent colonoscopy surveillance in expert centres. This observation conflicts with the paradigm that removal of all visible polyps should prevent the vast majority of CRC in path_MMR carriers, provided the screening interval is sufficiently short and colonoscopic practice is optimal.MethodsTo inform the debate, we examined, in the Prospective Lynch Syndrome Database (PLSD), whether the time since last colonoscopy was associated with the pathological stage at which CRC was diagnosed during prospective surveillance. Path_MMR carriers were recruited for prospective surveillance by colonoscopy. Only variants scored by the InSiGHT Variant Interpretation Committee as class 4 and 5 (clinically actionable) were included. CRCs detected at the first planned colonoscopy, or within one year of this, were excluded as prevalent cancers.ResultsStage at diagnosis and interval between last prospective surveillance colonoscopy and diagnosis were available for 209 patients with 218 CRCs, including 162 path_MLH1, 45 path_MSH2, 10 path_MSH6 and 1 path_PMS2 carriers. The numbers of cancers detected within < 1.5, 1.5–2.5, 2.5–3.5 and at > 3.5 years since last colonoscopy were 36, 93, 56 and 33, respectively. Among these, 16.7, 19.4, 9.9 and 15.1% were stage III–IV, respectively (p = 0.34). The cancers detected more than 2.5 years after the last colonoscopy were not more advanced than those diagnosed earlier (p = 0.14).ConclusionsThe CRC stage and interval since last colonoscopy were not correlated, which is in conflict with the accelerated adenoma-carcinoma paradigm. We have previously reported that more frequent colonoscopy is not associated with lower incidence of CRC in path_MMR carriers as was expected. In contrast, point estimates showed a higher incidence with shorter intervals between examinations, a situation that may parallel to over-diagnosis in breast cancer screening. Our findings raise the possibility that some CRCs in path_MMR carriers may spontaneously disappear: the host immune response may not only remove CRC precursor lesions in path_MMR carriers, but may remove infiltrating cancers as well. If confirmed, our suggested interpretation will have a bearing on surveillance policy for path_MMR carriers.

Prevalence of Germline Variants in Prostate Cancer and Implications for Current Genetic Testing Guidelines

Prostate cancer is the third leading cause of cancer-related death in men in the United States. Although serious, most of these diagnoses are not terminal. Inherited risk for prostate cancer is associated with aggressive disease and poorer outcomes, indicating a critical need for increased genetic screening to identify disease-causing variants that can pinpoint individuals at increased risk for metastatic castration-resistant prostate cancer. To identify positive (pathogenic, likely pathogenic, and increased risk) germline variants in a large prostate cancer cohort and to evaluate the usefulness of current practice guidelines in recognizing individuals at increased risk for prostate cancer who would benefit from diagnostic genetic testing. Cross-sectional study of data from 3607 men with a personal history of prostate cancer who underwent germline genetic testing between 2013 and 2018 and were unselected for family history, stage of disease, or age at diagnosis. Referral-based testing was performed at a Clinical Laboratory Improvement Amendments/College of American Pathologists-certified diagnostic laboratory. All analysis took place between February 2017 and August 2018. The frequency and distribution of positive germline variants, and the percentage of individuals with prostate cancer who met National Comprehensive Cancer Network (NCCN) guidelines for germline genetic testing. Of 3607 men (mean [SD] age at testing, 67 [9.51] years; mean age at diagnosis, 60 [9.05] years) with a personal diagnosis of prostate cancer who were referred for genetic testing, 620 (17.2%) had positive germline variants, of which only 30.7% were variants in BRCA1/2. Positive variants in HOXB13, a gene associated only with prostate cancer risk, were identified in 30 patients (4.5%). DNA mismatch repair variants with substantial known therapeutic implications were detected in 1.74% of variants in the total population tested. Examination of self-reported family histories indicated that 229 individuals (37%) with positive variants in this cohort would not have been approved for genetic testing using the NCCN genetic/familial breast and ovarian guidelines for patients with prostate cancer. Current NCCN guidelines and Gleason scores cannot reliably stratify patients with prostate cancer for the presence or absence of pathogenic germline variants. Most positive genetic test results identified in this study have important management implications for patients and their families, which underscores the need to revisit current guidelines.

Use of Big Data to Estimate Prevalence of Defective DNA Repair Variants in the US Population

ImportanceWide use of genomic sequencing to diagnose disease has raised concern about the extent of genotype-phenotype correlations.ObjectiveTo correlate disease-associated allele frequencies with expected and reported prevalence of clinical disease.Design, Setting, and ParticipantsXeroderma pigmentosum (XP), a recessive, cancer-prone, neurocutaneous disorder, was used as a model for this study. From January 1, 2017, to May 4, 2018, the Human Gene Mutation Database and a cohort of patients at the National Institutes of Health were searched and screened to identify reported mutations associated with XP. The clinical phenotype of these patients was confirmed from reports in the literature and National Institutes of Health medical records. The genetically predicted prevalence of disease based on frequency of known pathogenic mutations was compared with the prevalence of patients clinically diagnosed with phenotypic XP. Exome sequencing of more than 200 000 alleles from the Genome Aggregation Database, the National Cancer Institute Division of Cancer Epidemiology and Genetics database of healthy controls, and an Inova Hospital Study database was used to investigate the frequencies of these mutations in the general population.Main Outcomes and MeasuresListing of all reported mutations associated with XP, their frequencies in 3 large exome sequence databases, determination of the number of patients in the United States with XP using modeling equations, and comparison of the observed and reported numbers of patients with XP with specific mutations.ResultsA total of 156 pathogenic missense and nonsense mutations associated with XP were identified in the National Institutes of Health cohort and the Human Gene Mutation Database. The Genome Aggregation Database provided frequency data for 65 of these mutations, with a total allele frequency of 1.13%. The XPF (ERCC4) mutation, p.P379S, had an allele frequency of 0.4%, and the XPC mutation, p.P334H, had an allele frequency of 0.3%. With the Hardy-Weinberg equation, it was determined that there should be more than 8000 patients who are homozygous for these mutations in the United States. In contrast, only 3 patients with XP were reported as having the XPF mutation, and 1 patient was reported as having the XPC mutation.Conclusions and RelevanceThe findings from this study suggest that clinicians should approach large genomic databases with caution when trying to correlate the clinical implications of genetic variants with the prevalence of disease risk. Unsuspected mutations in known genes with a predisposition for skin cancer may be responsible for some of the high frequency of skin cancers in the general population.

DNA Repair Genes May Influence Cognitive Outcomes in Adult Patients with Hematologic Malignancies (HM) Treated with Blood or Marrow Transplantation (BMT)

Introduction: We recently demonstrated that cognitive impairment (CI) is prevalent and persistent in HM patients treated with BMT (Sharafeldin et al., J Clin Oncol, 2018). While the impact of genetic factors on cognition in the non-oncology realm is well-recognized, limited information exists in HM patients treated with BMT. We tested the hypothesis that genetic variants in blood-brain barrier (BBB), drug transporter, telomere homeostasis, neurotransmission, neural repair and DNA repair are associated with CI in HM patients treated with BMT. We previously presented preliminary results of the Discovery cohort (Sharafeldin et al., Blood, 2016); here we present additional analyses (at the gene level) on the Discovery cohort, and replication of salient findings in an independent Validation cohort.Methods: The Discovery cohort consisted of prospective, longitudinally-assessed patients undergoing autologous or allogeneic BMT for HM at a single center. Cognitive function was assessed objectively using a battery of standardized tests prior to BMT, and at 6mo, 1y, 2y, and 3y post-BMT; germline DNA was collected pre-BMT. Global Deficit Score (GDS) was used as an indicator of CI (GDS ≥0.5 indicated CI). We employed a candidate gene approach, relying on biologically-plausible hypotheses for gene selection. Standard quality control procedures yielded 985 SNPs in 68 genes with a total genotyping call rate of 99% in 277 BMT recipients. Generalized estimating equation models were fitted to examine association of individual SNPs with CI. Linkage disequilibrium-based pruning yielded 326 independent tests, with an overall p-value threshold of 1.53x10-4 using Bonferroni correction for multiple testing. We also conducted gene-level analysis considering each gene as a SNP-set using the machine learning approach of logic regression, with cross-validation, to identify SNP-SNP interactions at the gene-level (Bonferroni p ≤ 7.94x10-4). An independent Validation case-control set from the BMT Survivor Study was used to replicate significant findings from the Discovery cohort, using conditional logistic regression models. Cases (n=141) were BMT survivors who reported: i) presence of memory/learning problems; and ii) severity of memory/learning problems. Controls (n=258) were BMT survivors without cognitive problems, matched (1-2/case) on race/ethnicity, HM, and time from BMT.Results:Discovery: Among the 277 patients in the Discovery cohort, mean age at BMT was 50y, 59% were males, 69% were non-Hispanic whites and 47% received an allogeneic BMT. Male sex (OR=3.2, 95%CI, 1.5-6.7, p=0.002) and lower pre-BMT cognitive reserve (OR=4.6, 95%CI, 2.2-9.6, p <0.0001) were associated with CI. Risk of CI was increased in the younger patients (<50y) if they received TBI (age*TBI interaction OR=3.86, 95%CI, 1.0-15.1, p=0.05). Final genetic models were adjusted for relevant variables with significant independent main effects including BMT type, age at BMT, sex, race/ethnicity, and cognitive reserve. We identified significant associations between CI and BBB, telomere homeostasis and DNA repair SNPs using the single-SNP (Fig 1) and gene-level analyses. Replication: The mean age at BMT was 44y, 54% were males, 88% were non-Hispanic whites and 5% received an allogeneic BMT. Replication models were adjusted for age at BMT, sex, race, and education and income levels. Of the 69 SNPs identified for replication, DNA repair SNPs from the single-SNP analysis rs13006837 on XRCC5 (OR=5.8, 95%CI, 2.7-12.3, p=2.0 x 10-5) and rs293796 on OGG1 gene (OR=11.4, 95%CI, 4.6-28.5, p-value=1.08 x 10-6) were successfully replicated. Five SNPs on DNA repair genes from the gene-level analysis showed individual statistically-significant associations in the Validation cohort: rs238417 on ERCC2 (OR=0.48, 95%CI, 0.25-0.91, p=0.03); rs2526698 on EXO1 (OR=0.57, 95%CI: 0.33-0.98, p=0·04); rs3793906 on MGMT (OR=1.96, 95%CI: 1.2-3.3, p=0.01); rs4725016 on RPA3 (OR=0.20, 95%CI, 0.05-0.92, p=0.04); and rs1479569 on XRCC4 (OR=2.3, 95%CI, 1.3-4.1, p=0.005).Conclusion: Our study provides genetic characterization of adult HM patients at increased risk of cognitive impairment following BMT; associations with DNA repair variants were independently replicated. These findings could have implications towards the personalized management of patients undergoing BMT. DisclosuresForman:Mustang Therapeutics: Other: Licensing Agreement, Patents & Royalties, Research Funding.

Functional Interaction Between BRCA1 and DNA Repair in Yeast May Uncover a Role of RAD50, RAD51, MRE11A, and MSH6 Somatic Variants in Cancer Development.

In this study, we determined if BRCA1 partners involved in DNA double-strand break (DSB) and mismatch repair (MMR) may contribute to breast and ovarian cancer development. Taking advantage the functional conservation of DNA repair pathways between yeast and human, we expressed several BRCA1 missense variants in DNA repair yeast mutants to identify functional interaction between BRCA1 and DNA repair in BRCA1-induced genome instability. The pathogenic p.C61G, pA1708E, p.M775R, and p.I1766S, and the neutral pS1512I BRCA1 variants increased intra-chromosomal recombination in the DNA-repair proficient strain RSY6. In the mre11, rad50, rad51, and msh6 deletion strains, the BRCA1 variants p.C61G, pA1708E, p.M775R, p.I1766S, and pS1215I did not increase intra-chromosomal recombination suggesting that a functional DNA repair pathway is necessary for BRCA1 variants to determine genome instability. The pathogenic p.C61G and p.I1766S and the neutral p.N132K, p.Y179C, and p.N550H variants induced a significant increase of reversion in the msh2Δ strain; the neutral p.Y179C and the pathogenic p.I1766S variant induced gene reversion also, in the msh6Δ strain. These results imply a functional interaction between MMR and BRCA1 in modulating genome instability. We also performed a somatic mutational screening of MSH6, RAD50, MRE11A, and RAD51 genes in tumor samples from 34 patients and identified eight pathogenic or predicted pathogenic rare missense variants: four in MSH6, one in RAD50, one in MRE11A, and two in RAD51. Although we found no correlation between BRCA1 status and these somatic DNA repair variants, this study suggests that somatic missense variants in DNA repair genes may contribute to breast and ovarian tumor development.