Frequency Of Mutations In Patients Research Articles

TP53 mutations in Pap test DNA are a potential biomarker of ovarian cancer risk in high-risk women (226)

<b>Objectives:</b> The use of Pap tests as a molecular diagnostic for high-grade serous ovarian carcinoma (HGSOC) is a promising concept, but studies to detect tumor DNA report limited sensitivity. <i>TP53</i> somatic mutations from clonal expansions in non-neoplastic tissue can be detected in Pap tests and blood and could potentially be utilized for cancer risk assessment. We aimed to determine whether <i>TP53</i> somatic mutations in blood and Pap test DNA are associated with HGSOC in women with and without germline <i>BRCA1</i> or <i>BRCA2 (BRCA)</i> mutations. <b>Methods:</b> Peripheral blood and Pap samples were collected from 30 women with HGSOC (10 with a germline <i>BRCA</i> mutation) and 40 women without cancer (20 with a germline <i>BRCA</i> mutation) who underwent gynecologic surgery at the University of Washington. Genomic DNA from buffy coats and Pap cell pellets was used for ultra-deep sequencing of the <i>TP53</i> coding region (mean depth ~3300x) using duplex sequencing for error correction. Mutations were characterized based on pathogenicity and presence in the UMD <i>TP53</i> Cancer Database. Mutation frequencies (total coding mutations divided by nucleotides sequenced) were compared between groups using t-tests. Fitted linear regression models were used to explore age-related trends, and logistic regression models were used to predict cancer with adjustments for age. <b>Results:</b> Total 436 coding <i>TP53</i> mutations were identified in DNA from Pap tests, and 262 mutations were identified in the DNA from blood. Pap tests demonstrated an overall higher <i>TP53</i> mutation frequency in patients with HGSOC than in those without cancer (2.0x10^-6 vs 1.4x10^-6, p=0.03), but this effect was driven by and limited to patients with <i>BRCA</i> mutations (2.4x10^-6 vs 1.4x10^-6, p=0.01). Women with <i>BRCA</i> mutations and HGSOC also demonstrated a greater frequency of mutations affecting the DNA-binding domain, predicted to be pathogenic, and frequently found in cancer (referred to as ‘cancerlike') (all p<0.05). Cancer-like mutations increased with age in Pap test samples from women without cancer (p<0.01, R²=0.23) but not in patients with HGSOC. Age-adjusted logistic regression confirmed that cancer-like <i>TP53</i> mutation frequency was associated with HGSOC in patients with germline <i>BRCA</i> mutations (OR: 4.2, 95% CI: 1.2-14.3). There were no significant differences between HGSOC and non-cancer cases when examining <i>TP53</i> mutations in blood samples. Among 22 cases with known <i>TP53</i> tumor mutations, the tumor mutation was identified in six Pap samples (27%) and zero blood samples. <b>Conclusions:</b> The identification of HGSOC-specific mutations in Pap tests, even with highly accurate DNA sequencing methods, has limited sensitivity for cancer detection. However, Pap tests can detect abundant low-frequency cancer-like <i>TP53</i> mutations at a higher rate in women with germline <i>BRCA</i> mutations and HGSOC compared to women without cancer. Somatic <i>TP53</i> mutation frequency using age-related thresholds should be further explored as a biomarker for ovarian cancer risk in high-risk women.

Correlation Analysis and Prognostic Impacts of Biological Characteristics in Elderly Patients with Acute Myeloid Leukemia.

BackgroundThe significant heterogeneity of elderly AML patients’ biological features has caused stratification difficulties and adverse prognosis. This paper did a correlation study between their genetic mutations, clinical features, and prognosis to further stratify them.Methods90 newly diagnosed elderly acute myeloid leukemia (AML) patients (aged ≥60 years) who detected genetic mutations by next-generation sequencing (NGS) were enrolled between April 2015 and March 2021 in our medical center.ResultsA total of 29 genetic mutations were identified in 82 patients among 90 cases with a frequency of 91.1%. DNMT3A, BCOR, U2AF1, and BCORL1 mutations were unevenly distributed among different FAB classifications (p < 0.05). DNMT3A, IDH2, NPM1, FLT3-ITD, ASXL1, IDH1, SRSF2, BCOR, NRAS, RUNX1, U2AF1, MPO, and WT1 mutations were distributed differently when an immunophenotype was expressed or not expressed (p<0.05). NPM1 and FLT3-ITD had higher mutation frequencies in patients with normal chromosome karyotypes than abnormal chromosome karyotypes (p<0.001, p=0.005). DNMT3A and NRAS mutations predicted lower CR rates. DNMT3A, TP53, and U2AF1 mutations were related to unfavorable OS. TET2 mutation with CD123+, CD11b+ or CD34- predicted lower CR rate. IDH2+/CD34- predicted lower CR rate. ASXL1+/CD38+ and SRSF2+/CD123- predicted shorter OS.ConclusionThe study showed specific correlations between elderly AML patients’ genetic mutations and clinical features, some of which may impact prognosis.

Driver mutations and air pollution in advanced non-small cell lung cancer (NSCLC) at two reference hospitals in Mexico City.

e20545 Background: Currently, precision medicine has allowed the classification of NSCLC according to the profile of driver mutations and the development of highly effective treatments. There is evidence to support the relationship between outdoor air pollution, particularly particulate matter (PM) in outdoor air, with lung cancer incidence and mortality. Smoking is a negative predictor of EGFR mutation, but the effect of air pollution has not been stablished. Methods: We perform a retrospective study in two referral hospitals in Mexico City between 2015 to 2020 to determinate the frequency of key driver mutations in patients with advanced NSCLC and the relation with smoking habit, wood smoke exposure and pollution indexes (PM2.5, PM10, SO2, O3, NO2) according to their place of residence. We used WHO air quality thresholds for air pollutants to classify cases with high or low exposure. Results: A total of 1277 cases were analyzed. The median age at diagnosis was 66 years (range 18-97 years), 53% were females and 49.6% had history of smoking habit. According to histology, 61.6% of cases corresponded to adenocarcinoma, 11.7% were squamous, 1.3% large cell, and 25.4% indeterminate. Wood smoke was assessed in 83.1% of cases and 28.5% had exposure history. Air pollutants were measured in half of cases, high level of exposure for PM2.5, PM10, NO2 and SO2 occurred in 63.2%, 30.8%, 15.6%, 53.4%, respectively. EGFR, ALK and KRAS mutations were evaluated in 85%, 16.7% and 8.6% of patients, respectively. The presence of these mutations was: EGFR 17.1%, ALK 11.1%, and KRAS 16.5%. Patients with EGFR-positive NSCLC were more frequently female (65.1% vs 34.9%, OR 1.8 95%CI 1.4-2.5, p &lt; 0.001) and had no history of tobacco use (35% vs 65%, OR 0.49 95%CI 0.36-0.67, p &lt; 0.001). Wood smoke was not statistically significant. High exposure to PM2.5 was most common in patients with non-mutated EGFR NSCLC (65.3% vs 34.7%, OR 1.7 95%CI 1.2-2.5, p = 0.006). Relationship with other air pollutants were not statistically significant. ALK-positive NSCLC patients tend to be females (68% vs 32%, p = 0.07) and had no history of smoking habit (20.8% vs 79.2% OR 0.28 95%CI 0.1-0.78, p = 0.01). High exposure to SO2 was common (78.6% vs 21.4% p = 0.05). Association in KRAS-positive NSCLS patients were not found. Conclusions: A low rate of key driver mutations assessment was found in this Mexican cohort. Clinical profile of NSCLC EGFR positive is according with previous reports in the literature. Exposure to PM2.5 and SO2 were found associated with EGFR and ALK status in this retrospective study and are hypothesis generating information.

DACH1 mutation frequency in endometrial cancer is associated with high tumor mutation burden in a nationwide cohort.

e17634 Background: DACH1 is a novel transcriptional repressor and tumor suppressor gene. DACH1 mutations are associated with poor prognostic features and reduced overall survival in endometrial cancer, with an increased prevalence in the Appalachian region of Kentucky. Preliminary studies have suggested an association with an increase in tumor mutation burden. In this follow up study, we utilized the nationwide Oncology Research Information Exchange Network (ORIEN) to determine the frequency of DACH1 mutations in patients with endometrial cancer through a multi-institution analysis and evaluate its impact on RNA expression, clinical correlates, and outcomes. Methods: We obtained clinical and genomic data for 691 patients with endometrial cancer from nine U.S. institutions within the ORIEN collaborative. We examined the clinical attributes of the cancers with DACH1 status by comparing whole-exome sequencing (WES), RNA Sequencing (RNASeq), microsatellite instability (MSI), and tumor mutational burden (TMB). Results: Appalachian women with endometrial cancer had an increased frequency of DACH1 mutations (6/41 patients, 15%) compared to the non-Appalachian endometrial cancer population (24/581 patients, 4.1%) with p-value = 0.010, with the non-Appalachian DACH1 mutation frequency mirroring the rate of DACH1 gene mutation seen in TCGA at 3.8%. DACH1 mutated patients have a higher tumor mutation burden compared to DACH1 wild-type (32.2 vs. 4.62, p-value = 0.001) though no differences in microsatellite instability between DACH1 mutated and wild-type were present (p-value = 0.350). DACH1 mutations showed significant gene co-occurrence patterns with POLE, MLH1, MSH2, MSH6 and PMS2. Conclusions: DACH1 mutations are prevalent in Kentucky patients with endometrial cancer, particularly those from the Appalachian region. These results were again reflected in the TCGA PanCancer Atlas as well as the ORIEN multi-institution cohort. These mutations are associated with high tumor mutational burden and co-occur with genome destabilizing gene mutations. These findings suggest DACH1 as a candidate biomarker for future trials with immunotherapy, particularly in endometrial cancers.

Identification and Comprehensive Analysis of FREM2 Mutation as a Potential Prognostic Biomarker in Colorectal Cancer.

Gene mutations play an important role in tumor progression. This study aimed to identify genes that were mutated in colorectal cancer (CRC) and to explore their biological effects and prognostic value in CRC patients. We performed somatic mutation analysis using data sets from The Cancer Genome Atlas and International Cancer Genome Consortium, and identified that FREM2 had the highest mutation frequency in patients with colon adenocarcinoma (COAD). COAD patients were divided into FREM2-mutated type (n = 36) and FREM2-wild type (n = 278), and a Kaplan-Meier survival curve was generated to perform prognostic analysis. A FREM2-mutation prognosis model was constructed using random forest method, and the performance of the model was evaluated using receiver operating characteristic curve. Next, the random forest method and Cox regression analysis were used to construct a prognostic model based on the gene expression data of 36 FREM2-mutant COAD patients. The model showed a high prediction accuracy (83.9%), and 13 prognostic model characteristic genes related to overall survival were identified. Then, the results of tumor mutation burden (TMB) and microsatellite instability (MSI) analyses revealed significant differences in TMB and MSI among the risk scores of different prognostic models. Differentially expressed genes were identified and analyzed for functional enrichment and immune infiltration. Finally, 30 samples of CRC patients were collected for immunohistochemical staining to analyze the FREM2 expression levels, which showed that FREM2 was highly expressed in tumor tissues. In conclusion, CRC patients had a high level of FREM2 mutations associated with a worse prognosis, which indicated that FREM2 mutations may be potential prognostic markers in CRC.

Inherited Mutations in Chinese Men With Prostate Cancer.

Although China accounts for 7.8% of worldwide new prostate cancer (PCa) cases and 14.5% of new deaths according to GLOBOCAN 2020, the risk of PCa associated with germline mutations is poorly defined, hampered in part by lack of nationwide evidence. Here, we sequenced 19 PCa predisposition genes in 1,836 Chinese patients with PCa and estimated disease risk associated with inherited mutations. Patients were recruited from 4 tertiary cancer centers (n=1,160) and a commercial laboratory (n=676). Germline DNA was sequenced using a multigene panel, and pathogenic/likely pathogenic (P/LP) mutation frequencies in patients with PCa were compared with populations from the gnomAD (Genome Aggregation Database) and ChinaMAP (China Metabolic Analytics Project) databases. Clinical characteristics and progression-free survival were assessed by mutation status. Of 1,160 patients from hospitals, 89.7% had Gleason scores ≥8, and 65.6% had metastases. P/LP mutations were identified in 8.49% of Chinese patients with PCa. Association with PCa risk was significant for mutations in ATM (odds ratio [OR], 5.9; 95% CI, 3.1-11.1), BRCA2 (OR, 15.3; 95% CI, 10.0-23.2), MSH2 (OR, 15.8; 95% CI, 4.2-59.6), and PALB2 (OR, 5.9; 95% CI, 2.7-13.2). Compared with those without mutations, patients with mutations in ATM, BRCA2, MSH2, or PALB2 showed a poor outcome with treatment using androgen deprivation therapy and abiraterone (hazard ratio, 2.19 [95% CI, 1.34-3.58] and 2.47 [95% CI, 1.23-4.96], respectively) but similar benefit from docetaxel. The present multicenter study confirmed that a significant proportion of Chinese patients with PCa had inherited mutations and identified predisposition genes in this underreported ethnicity. These data provide empirical evidence for precision prevention and prognostic estimation in Chinese patients with PCa.

KAT2B is an immune infiltration-associated biomarker predicting prognosis and response to immunotherapy in non-small cell lung cancer.

Over the past few years, dramatic breakthroughs in the field of tumor immunotherapy with immune checkpoint inhibitors (ICIs) have made a therapeutic revolution for non-small cell lung cancer (NSCLC). While only some patients present a favorable response to this treatment. It is urgent to explore the potential molecular mechanisms underlying the regulation of tumor immune microenvironment in the process of immunotherapy. Lysine acetyltransferase 2B (KAT2B) plays a crucial role in the regulation of gene expression at the post-transcriptional level by acetylation, and is associated with many types of cancer. RNA-sequencing data,genetic mutation data,and corresponding clinical information were extracted from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, then subjected to immune characteristics, gene expression, survival, genetic alteration, enrichment analyses. KAT2B expression correlated positively with infiltrating levels of multiple immune cells and mRNA expression levels of immune checkpoint genes in NSCLC. Furthermore, KAT2B expressionwas downregulated in tumor tissues, and low KAT2B expression was associated with unsatisfactory efficacy of immune checkpoint blockade (ICB) and poor prognosis of patients with lung adenocarcinoma. Moreover, there were higher somatic genes mutation frequency in patients with low expression of KAT2B. Finally, functional enrichment analysis suggested that KAT2B was mainly linked to the regulation of immune cells and interferon - gamma (IFN-γ) mediated signaling pathways, response to IFN-γ, antigen processing and presentation. This is the first comprehensive study to disclose that KAT2B is correlated with immune infiltrates and may serve as a novel biomarker predicting prognosis and response to immunotherapy in NSCLC.

Detection of S-HBsAg Mutations in Patients with Hematologic Malignancies.

Multiple studies of hepatitis B virus (HBV) genetic variability and its relationship with the disease pathogenesis are currently ongoing, stemming from growing evidence of the clinical significance of HBV mutations. It is becoming increasingly evident that patients with hematologic malignancies may be particularly prone to a higher frequency of such mutations. The present report is the first extensive study of the prevalence of escape mutations in S-HBsAg, performed using isolates from 59 patients from hospital hematology departments with diagnoses of leukemia (n = 32), lymphoma (n = 20), multiple myeloma (n = 3), and non-tumor blood diseases (n = 4). The isolates were serologically examined for the presence of HBV markers and sequenced using either next-generation sequencing (NGS) or Sanger sequencing. Occult hepatitis B was found in 5.1% of cases. Genetic analysis of the region corresponding to S-HBsAg demonstrated an exceptionally high mutation frequency in patients with leukemias (93.4%) and lymphomas (85.0%), along with the prominent mutation heterogeneity. Additionally, more than 15 mutations in one sample were found in patients with leukemias (6.3% of cases) and lymphomas (5.0% of cases). Most of the mutations were clinically significant. The study analyzes the mutation profile of HBV in different oncohematological diseases and the frequency of individual mutations. The data strongly suggest that the NGS method, capable of detecting minor populations of HBV mutations, provides a diagnostic advantage, lays the foundation for the development of screening methods, and allows for the study of the virological and pathogenetic aspects of hepatitis B.

Molecular genetic testing for BRAF V600 gene mutations in melanoma in the Republic of Kazakhstan

Along with other diagnostic methods, all current recommendations and protocols for malignant tumors’ diagnostics and treatment require mandatory molecular genetic testing at the initial diagnosis and in case of disease progression.&#x0D; The discovery of the BRAF gene mutation in skin melanoma allows the treatment with tyrosine kinase inhibitors, so-called BRAF inhibitors. This increases the probability of tumor response by half and opens up new therapeutic options.&#x0D; The study aimed to identify the BRAF V600E gene mutation frequency in patients with stage III-IV melanoma in the Republic of Kazakhstan to determine the need for targeted therapy.&#x0D; Results: 2251 persons are currently registered with melanoma in the Republic of Kazakhstan, with 355 new primary melanoma cases in 2019. Of them, 54% were diagnosed at stages III-IV and were subject to molecular genetic testing. 278 of 2251 patients were sent for BRAF mutations testing. The mutations were detected in 105 (37.7%) patients.&#x0D; Conclusion: The introduction of molecular genetic testing for malignant neoplasms under the Comprehensive Cancer Control Plan framework for 2018-2022 will increase the use of molecular genetic methods in the Republic of Kazakhstan. Molecular genetic testing is an important step in diagnosing melanoma and choosing the appropriate therapy to personalize cancer treatment.

Molecular genetic testing for BRAF V600 gene mutations&#x0D; in melanoma in the Republic of Kazakhstan

Relevance: Along with other diagnostic methods, all current recommendations and protocols for malignant tumors’&#x0D; diagnostics and treatment require mandatory molecular&#x0D; genetic testing at the initial diagnosis and in case of disease&#x0D; progression. The discovery of the BRAF gene mutation in skin&#x0D; melanoma allows the treatment with tyrosine kinase inhibitors, so-called BRAF inhibitors. This increases the probability of&#x0D; tumor response by half and opens up new therapeutic options.&#x0D; The study aimed to identify the BRAF V600E gene mutation frequency in patients with stage III-IV melanoma in the&#x0D; Republic of Kazakhstan to determine the need for targeted&#x0D; therapy.&#x0D; Results: 2251 persons are currently registered with melanoma in the Republic of Kazakhstan, with 355 new primary&#x0D; melanoma cases in 2019. Of them, 54% were diagnosed at&#x0D; stages III-IV and were subject to molecular genetic testing.&#x0D; 278 of 2251 patients were sent for BRAF mutations testing.&#x0D; The mutations were detected in 105 (37.7%) patients.&#x0D; Conclusion: The introduction of molecular genetic&#x0D; testing for malignant neoplasms under the Comprehensive&#x0D; Cancer Control Plan framework for 2018-2022 will increase&#x0D; the use of molecular genetic methods in the Republic of Kazakhstan. Molecular genetic testing is an important step in&#x0D; diagnosing melanoma and choosing the appropriate therapy to personalize cancer treatment.

FNDC1 Promotes the Invasiveness of Gastric Cancer via Wnt/β-Catenin Signaling Pathway and Correlates With Peritoneal Metastasis and Prognosis.

BackgroundGastric cancer (GC) has a high morbidity and mortality rate, with peritoneal metastasis (PM) identified as the main site of metastasis. Our previous study found that FNDC1 has a higher frequency of mutations in patients with PM by high-throughput sequencing assay, suggesting that it may be associated with GC invasion and PM, however the specific mechanism remains unclear.MethodsFirst, the correlation between FNDC1 and PM and prognosis of GC was clarified by bioinformatics and clinicopathological analysis. Next, the effect of FNDC1 expression on the invasion and metastasis ability of GC was investigated in vivo and in vitro. Finally, the signaling pathways involved in the regulation of FNDC1 were explored.ResultsFNDC1 was highly expressed in GC and was associated with PM and poor prognosis. FNDC1 was also associated with epithelial-mesenchymal transition (EMT) in GC cells. Through in vivo and in vitro experiments, it was clarified that knockdown of FNDC1 could inhibit the proliferation, invasion, and migration of GC cells. In addition, it was elucidated that FNDC1 promotes EMT through the Wnt/β-catenin signaling pathway.ConclusionFNDC1 may be associated with the invasion of GC and PM after surgery. FNDC1 was highly expressed in GC tissues and cell lines, while significantly associated with poor DFS and OS in GC patients. Both univariate and multivariate analyses suggested that the expression of FNDC1 was an independent factor for GC. Knockdown of FNDC1 also significantly inhibited the proliferation, migration, and activity of GC cells. FNDC1 may promote EMT in GC cells through the regulation of Wnt/β-catenin signaling pathway. FNDC1 has the potential to be used as a predictor of PM and may also be studied in depth as a therapeutic target for GC, which has potential clinical utility and is worthy of further validation.

Frequency of DNMT3A Mutations in Patients with Acute Leukemia in Mashhad

Background and Aims: DNA methyltransferase3A (DNMT3A) is necessary for the adjustment of gene expression, and the mutations in the DNMT3A gene are reported in a variety of leukemia cases. DNMT3A mutations are during cancer progression and cause poor prognosis in many leukemias. Thus, this gene can be a target for new treatments. This study aimed to examine the distribution of DNMT3A mutations in Iranian acute leukemia patients. Materials and Methods: In this study, diagnostic samples from 45 patients with de novo acute leukemia, including 22 acute myeloid leukemia (AML) patients, and 23 acute leukemia lymphoblastic (ALL) patients were screened, from April 2017 to March 2018 for the incidence of DNMT3A mutations by polymerase chain reaction and direct sequencing. Results: A total of 2 (9.1%) AML cases and 1 (4.34%) ALL cases were found to have the DNMT3A R882H mutation. It was found that a total of 22.7% and 21.7% of patients with AML and ALL had polymorphism rs368516543, respectively. DNMT3A mutations were considerably associated with higher age in AML patients. Conclusions: The findings suggest that the DNMT3A mutations are probably a new biomarker in the early examination and treatment of acute leukemia, even though further studies are needed.

Mutation analysis of MFSD8 in an amyotrophic lateral sclerosis cohort from mainland China.

Recent studies have suggested that rare variants in MFSD8 contribute to risk for frontotemporal dementia (FTD). Considering the common underlying pathogenesis and the shared genetic risk between amyotrophic lateral sclerosis (ALS) and FTD, we screened the coding region of MFSD8 in 551 unrelated patients with ALS (510 unrelated sporadic ALS and 41 familial ALS probands) from mainland China by whole-exome sequencing to assess its mutation frequency in patients with ALS and evaluate its association. Two rare deleterious variants, c.343G>A (p. V115M) and c.695T>C (p.L232P), were identified in this study. The variant c.695T>C (p.L232P) has not been previously reported and the carrier of this variant exhibits a relatively younger age of disease onset. Our studies provide some independent evidence showing that the rare variant p.L232P in MFSD8 might be a candidate risk factor for ALS. However, the relatively small sample sizeand the lack of patient-derived cells limit the power of the genetic exploration of this study, further robust multicenter studies with larger sizes and biological experiments with patient-derived cells are needed to elucidate the pathogenesis of the rare variant in MFSD8 in ALS.

"Analysis of the Associated Mutations of DJ-1 Gene to Parkinson’s Patients in Vietnam"

The exact causes of Parkinson's disease (PD) are currently unknown, but studies have shown that the environment and genetics are the two factors that play the biggest role in Parkinson's disease. DJ-1 gene (belong to the PARK genes) is known as the main cause of Parkinson's disease in populations. In Vietnam, the evaluation of DJ-1 gene mutation frequency in patients is necessary to clarify the pathogenesis and genetic mechanisms of this disease. In this research, we identified the frequency mutations of the DJ-1 gene in Vietnamese PD patients. The results showed that we detected some DJ-1 mutations at exon 5 and exon 7. Interestingly, Ala86Gly and Gln95Leu mutations of exon 5 and His138Pro of exon 7 are found, which leads to a change in amino acid sequence and possibly a change in a functional protein. In addition, out of more than 20 heterozygous or homozygous mutations occurring in the intron regions 4 and 5, we found that 3 homozygous mutations occurred frequently in both patient and control. The data of mutation analysis has shown the ambiguous and unforeseeable meanings; however, they possibly associated with the mutation of PD. Therefore, the study of our next will focus on the relationship between these mutations with some clinical symptoms in patients.

Spectrum and frequency of BRCA1, BRCA2, CHEK2, PALB2, RAD50 mutations in breast cancer patients in the Republic of Bashkortostan

Aim. To assess the spectrum and frequency of mutations in patients with hereditary breast cancer from the Republic of Bashkortostan.&#x0D; Methods. The material for the study was sections of fresh frozen, formalin-fixed and paraffin-embedded tumor tissue from 100 unrelated patients with a histologically confirmed diagnosis of breast cancer. The study was carried out using two methods: real-time polymerase chain reaction and next-generation sequencing-NGS.&#x0D; Results. By using real-time polymerase chain reaction (PCR), the 5382insC mutation in the BRCA1 gene was detected in 12 cases. By using a next-generation sequencing method (NGS), highly penetrant mutations in BRCA1, BRCA2, CHEK2, PALB2 and RAD50 were revealed in 16 patients. In total, these methods detected mutations in 28 patients. Out of a total of probands in the BRCA1 gene, mutations were detected in 13 patients, that included 12 patients with the 5382insC mutation, and 1 patient with c.3143delG. In the BRCA2 gene, mutations were revealed in 3 patients, of which c.6621_6622del in 2 patients and c.-39-1_-39delGA in 1 patient. Mutations in CHEK2 were detected in 5 patients: c.470TC in 3 patients, c.444+1GA in 2 patients. The 1592delT mutation in PALB2 was found in 4 patients. The c.2157delA mutation in RAD50 was detected in 3 patients.&#x0D; Conclusion. Pathogenic mutations in BRCA1/2, CHEK2, PALB2 and RAD50 were found in 28 patients with a hereditary feature of the disease; the identification of highly penetrant mutations in probands allowed us to determine their relatives, probable carriers of mutations, which were referred for genetic counselling.

Andquot;Analysis of the Associated Mutations of DJ-1 Gene to Parkinsonandrsquo;s Patients in Vietnamandquot;

The exact causes of Parkinson's disease (PD) are currently unknown, but studies have shown that the environment and genetics are the two factors that play the biggest role in Parkinson's disease. DJ-1 gene (belong to the PARK genes) is known as the main cause of Parkinson's disease in populations. In Vietnam, the evaluation of DJ-1 gene mutation frequency in patients is necessary to clarify the pathogenesis and genetic mechanisms of this disease. In this research, we identified the frequency mutations of the DJ-1 gene in Vietnamese PD patients. The results showed that we detected some DJ-1 mutations at exon 5 and exon 7. Interestingly, Ala86Gly and Gln95Leu mutations of exon 5 and His138Pro of exon 7 are found, which leads to a change in amino acid sequence and possibly a change in a functional protein. In addition, out of more than 20 heterozygous or homozygous mutations occurring in the intron regions 4 and 5, we found that 3 homozygous mutations occurred frequently in both patient and control. The data of mutation analysis has shown the ambiguous and unforeseeable meanings; however, they possibly associated with the mutation of PD. Therefore, the study of our next will focus on the relationship between these mutations with some clinical symptoms in patients.

Abstract A001: Improving cancer germline testing in rural Appalachian populations with ORIEN

Abstract Background: Reduced access to treatment advances in rural populations contributes to increased cancer mortality. Rural Appalachian Kentucky is a geographically isolated population with a unique carcinogen exposure and a low frequency guideline-recommended germline testing. To improve testing rates, a return of germline results program for patients enrolled in the Total Cancer Care (TCC) protocol at Markey Cancer Center (MCC) was initiated. Methods: Pre-intervention testing rates were obtained from the electronic health record. Patient and physician focus groups were conducted to assess barriers to germline testing. Whole exome germline data from TCC patients enrolled in the Avatar subset is analyzed using standard bioinformatics pipeline for known, clinically significant mutations in the 59 American College of Medical Genetics (ACMG) genes where return of incidental germline findings is recommended and 21 pharmacogenetic genes. Results are reviewed by our Molecular Tumor Board and a recommendation for confirmatory clinical testing, if needed, is made to the treating physician. Results: Baseline rates of guideline recommended germline testing at MCC in 2018 was 20% of ovarian, 15% of breast, 9% of colon, 3% of pancreas and no metastatic prostate patients. Testing was infrequent in rural communities. Almost all patients who had testing recommended by their physician, had testing performed. Unaffected family members were also rarely tested. Physician focus groups at MCC identified lack of time and low perceived value of the testing as barriers. Rural physicians also identified lack of access to genetic counselors. Patient focus groups in the Appalachian region demonstrated poor quality internet and low knowledge and self- efficacy as major barriers to patients discussing genetic testing with family members. To overcome patient barriers, a preloaded audio card was developed to facilitate discussion with family members. The preloaded audio card was tested in a rural Appalachian community, demonstrating significantly improved knowledge and self-efficacy. To overcome physician barriers, a genetic counselor telemedicine clinic and standing order were initiated. To improve physician perception of test value, the ORIEN return of germline results project was initiated. Of the more than 2000 patients enrolled on TCC at MCC, approximately 40% are from Appalachia, 173 have appropriate consent and specimen availability for germline sequencing and 5 have had results returned. Data describing the first 3 months of this initiative, including frequency of mutations in patients and unaffected family members and acceptance of genetic counselor referrals by physicians, patients and family members will be presented. Conclusion: Rural Appalachian communities identified significant barriers to guideline recommended germline testing, however, ORIEN and the TCC protocol are novel methods to reduce these barriers and improve the rates of testing in both patients and their family members. Citation Format: Jill Kolesar, Micheal Cavnar, Rachel Miller, Justine Pickarski, Shulin Zhang, Kannabiran Nandakumar, Marissa Schuh, Elizabeth Belcher, Eric Durbin, Ming Poi, Fred Ueland, Isaac Hands, Therese Bocklage, JC Jeong, Susanne Arnold, Mark Evers. Improving cancer germline testing in rural Appalachian populations with ORIEN [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr A001.

Abstract P6-10-07: Activating HER2 missense mutations in HER2-negative metastatic breast cancer

Abstract Background: Activating HER2 missense mutations can develop in HER2-negative metastatic breast cancer, particularly in ER-positive disease. These mutations may be targeted with anti-HER2-directed therapy, providing a novel therapeutic option for women with HER2-negative metastatic breast cancer. The clinical behavior and significance of these mutations in the era of cyclin-dependent kinase 4 and 6 inhibitors (CDK4/6i) for ER-positive breast cancer are unknown. Methods: We examined patients enrolled onto an ongoing single institution prospective study entitled Individualized Molecular Analyses Guide Efforts (IMAGE) II. The purpose of IMAGE II was to identify potentially targetable tumor genetic alterations, and the purpose of this analysis was to identify HER2 missense mutations. Patients eligible for IMAGE II had metastatic breast cancer of any subtype that had progressed on at least one standard-of-care therapy. Genetic profiling of blood was performed using the FoundationOne Liquid platform; metastatic tumor tissue profiling was performed using one of several commercially available next-generation sequencing platforms. All assays were capable of detecting common point mutations in the ERBB2 gene. Results: As of June 1, 2019, 54 patients were enrolled onto IMAGE II and had available genetic profiling results. Approximately half had ER+HER2- disease (n=29, 54%), one-third had triple negative breast cancer-TNBC (n=18, 33%), and the rest had HER2-positive disease (n=7, 13%). Six patients had activating HER2 missense mutations, with the same mutation(s) found in both tissue and blood in all patients. Five of these patients had ER+HER2- disease and the prevalence of HER2 mutations among patients with ER+HER2- disease was 17% (5/29) in our cohort. All five patients had received CDK4/6i with endocrine therapy in the metastatic setting prior to enrollment on IMAGE II. Four patients had markedly rapid tumor progression with this therapy. The median time to progression on CDK4/6i and endocrine therapy was 3.7 months (range 2.4-14.7) among patients with ER+HER2- disease and a HER2 missense mutation, compared to 9.4 months (range 2.3-40.9) among patients with ER+HER2- disease without a missense mutation. A summary of the patients with a HER2 missense mutation is shown in Table 1. Three patients with a HER2 missense mutation received HER2-directed therapy with trastuzumab and pertuzumab. One patient has an ongoing clinical response at 9.4 months, one patient has a clinical response after 1.8 months of therapy, and one patient recently began treatment with no follow-up data available yet. Conclusions: The frequency of HER2 missense mutations in patients with ER+HER2- metastatic breast cancer in our small cohort was higher than previously reported, and patients with this mutation had early tumor progression on CDK4/6i therapy regardless of endocrine therapy pairing. We hypothesize that activating HER2 missense mutations may be important drivers of resistance to CDK4/6i therapy. Testing patients who progress rapidly on CDK4/6i therapy for activating HER2 missense mutations may provide a novel therapeutic option. PatientSubtypeHER2 Mutation(s)Found whereReceived CDK4/6iLineWith which endocrine therapyTime to progression (in months)1ER+HER2-L755STissue/bloodYes2ndfulvestrant14.82ER+HER2-V777LTissue/bloodYes1sttamoxifen3.73ER+HER2-L755PTissue/bloodYes1stfulvestrant3.34ER+HER2-L755S, V697LTissue/bloodYes2ndfulvestrant4.15ER+HER2-L869RTissue/bloodYes1stletrozole2.46TNBCD769YTissue/bloodNoNANANA Citation Format: Mirat Shah, Jennifer Ensminger, Chenguang Wang, Siraj Ali, Jon Chung, Josh Lauring, Ben Ho Park, Vered Stearns. Activating HER2 missense mutations in HER2-negative metastatic breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-10-07.

P4633The frequency of mutations in patients with familial hypercholesterolemia who underwent acute coronary syndrome and patients with stable ischemic heart disease

Abstract Introduction Familial hypercholesterolemia (FH) is the most common genetically inherited disease in the world, which leads to a significant increase in blood cholesterol and an increased risk of early atherosclerosis and, consequently, an increase in mortality from ischemic heart disease (IHD). The actual prevalence of genetic variants causing FH in every population remains unknown. Purpose To compare the frequency of mutations in patients with FH who underwent acute coronary syndrome (ACS) and patients with stable IHD. Material and methods We included 120 patients (male-79, female-41) who had a clinical diagnosis of FH based on the Dutch Lipid Clinic Network (DLCN) score and Simon Broome criteria. The men and women included in the study were ≤55 and ≤60 years of age, respectively. 40 of them were patients with ACS; the remaining 80 were patients with stable IHD. Genetic studies were performed using a multiple approach based on targeted Next Generation Sequencing (NGS) in the Health in code and the ReadSense laboratories. Results Variants of the three “classic” genes implicated in FH were detected in 46 patients (38,3%). The frequency of mutations was detected in 32.5% of cases, and in patients with stable IHD in 41.25% of cases (p=0.35). In the group of participants with stable IHD, a mutation in the LDLR gene was obtained in 85% of cases; mutations in the APOB, PCSK9 genes were detected in 15% of cases. The same rate of mutations in the APOB and LDLR genes (38.5% each) was detected in patients with ACS. One patient had a mutation in the PCSK9 gene. In two patients there were mutations at once in two genes responsible for the development of FH: in one case, mutations were determined in the APOB and LDLR genes, in the other - LDLR and PCSK9. All patients who carried variants of the studied genes were heterozygous. Patients with clinically established FH had mutations in other genes involved in lipid metabolism, such as APOE, which turned to be mutant in 20 participants (16,6%). This variant defines the apoE4 isoform (also called ε4 allele), which is one of the three common genetic isoforms (apoE2, apoE3, and apoE4) of the APOE gene. It has been shown that the choice of apoE4 isoform have TC and LDL levels and increased risk of cardiovascular events related to atherosclerosis. Two patients had LPA mutations. This variant is a genetic polymorphism that has been previously published in association with elevated lipoprotein (a) (Lp(a)) levels and increased risk of IHD. Three patients were found to have ABCG8 mutations thought to be associated with sitosterolemia: two were pathogenic and another one of uncertain significance. Conclusion Thus, the frequency of mutations in patients with FH does not depend on the presence or absence of ACS. Both groups of patients are patients of a very high risk of developing both primary and repeated cardiovascular events.

Type and frequency of genetic mutations in patients suffering from recurrent and chronic pancreatitis

Type and frequency of genetic mutations in patients suffering from recurrent and chronic pancreatitis