Gene Positive Rate Research Articles

Abstract 11879: The Genetic Characteristics Based on Next Generation Sequencing in Patients With Hypertrophic Cardiomyopathy

Objective: This study aimed to explore the genetic epidemiological characteristics in patients with hypertrophic cardiomyopathy (HCM). Methods: We prospectively enrolled 383 unrelated HCM probands who received genetic testing and 3.0 T cardiac MRI examination, including 118 familial HCM and 265 sporadic HCM. The diagnosis of HCM is based on the diagnostic criteria of the American Heart Association and American College of Cardiology guidelines. Patients with familial HCM underwent targeted next generation sequencing including 117 candidate pathogenic genes associated with cardiomyopathies, while sporadic HCM underwent whole-exome sequencing. The genotypic characteristics were analyzed. Results: Among the 383 unrelated Chinese HCM probands, we reported 56 new pathogenic or likely pathogenic gene site mutations, including 3 new rare non-sarcomeric gene mutations and 53 new sarcomeric gene mutations. According to the analysis of genotypic characteristics, it was found that the frequency of rare genes was 3.4%, and the positive rate of sarcomere protein gene detection was 62.4%. Among them, MYH7 and MYBPC3 are the most common pathogenic genes, accounting for 61.9% of sarcomere protein gene mutations. Additionally, in the included HCM population, there was no significant difference in the positive detection rate of sarcomere protein gene between familial HCM and sporadic HCM (66.1% vs 64%, P = 0.7). The proportion of sporadic HCM carrying polygenic mutations was higher than that of familial HCM (11.2% vs. 1.8%, P = 0.003). Conclusion: We reported 56 new gene mutations, which expanded the gene spectrum of HCM. Additionally, the frequency of rare disease genes in the HCM cohort is 3.4%, and the composition ratio of sarcomere protein gene is similar to that of North American or European HCM populations. However, the gene positive rate of sporadic HCM is similar to that of familial HCM, but the composition ratio of genotypes is different.

Clinical and genetic spectrum of neonatal arrhythmia in a NICU.

BackgroundNeonatal arrhythmia is a common complication that might be life-threatening or serious, but the genetic causes are unclear in most cases. The aim of this study is to investigate the genetic causes of neonatal arrhythmia in a NICU in China.MethodsNewborns who were diagnosed with arrhythmia during the neonatal period were enrolled from Children’s Hospital of Fudan University between January 1st 2016, and December 31st, 2019. A neonatal gene panel was performed for each infant.ResultsIn total, 98 neonatal infants with arrhythmia were enrolled. Fourteen genes and a copy number change were identified and classified as pathogenic/likely pathogenic in 22 patients (22.4%), including 4 genes related to syndrome, 4 related to conduction, 2 related to metabolism, 2 related to structure, 2 related to respiration and immunity, respectively, and trisomy 21. Altogether, 6 genes (6/14, 42.9%) caused original heart structure or conduction abnormalities, leading to arrhythmia. Infants with ventricular tachycardia or fibrillation, atrioventricular block and long-QT syndrome all had positive gene results. The gene positive rate among arrhythmic infants with congenital heart disease or severe heart failure was higher than that of infants without congenital heart disease or severe heart failure.ConclusionsThe genetic disorders associated with neonatal arrhythmia could be syndrome-, conduction-, metabolism-, and structure-related. Infants with non-benign arrhythmia, especially ventricular tachycardia or fibrillation, long-QT syndrome, or high-grade atrioventricular block, have a higher rate of genetic abnormalities and should undergo genetic sequencing. Neonates with hereditary arrhythmias may have a higher risk of congenital heart disease or heart failure.

Abstract A089: Detection of circulating tumor cells (CTC) by microfluidic technology based on lateral magnetophoresis and CTC-based multigene profiling analysis in prostate cancer patient

Abstract Introduction By using the circulating tumor cells (CTCs), we can get useful genomic information that enable monitoring of patient’s prognosis or selecting of appropriate treatment over time by repeat biopsy. Despite their usefulness, current CTC separation techniques are limited in terms of their ability to separate high recovery and purity CTCs from peripheral blood. We aimed to separate CTCs from prostate cancer patients using microfluidic technique that based on disposable lateral magnetophoretic microseparator (named ‘assembly-disposable CTC-μChip’) and assess the gene expression that are specific for prostate cancer using mRNA from isolated CTCs measured by droplet digital PCR (ddPCR) method. Patients and Methods Total 54 samples of 45 patients who underwent treatment for prostate cancer between 06/2018 and 03/2019 were prospectively enrolled for CTC collection. Approximately 10 ml of whole blood was drawn from prostate cancer patients; Group A, 12 samples (22.2%) with localized stage II-III cancer, Group B, 5 samples (9.3%) with stage IV, Group C, 6 samples (11.1%) with metastatic hormone-sensitive prostate cancer (mHSPC) and Group D, 31 samples (57.4%) with metastatic castration-resistant prostate cancer (mCRPC). CTCs were positively isolated by using Assembly-disposable CTC-μChip. CTCs from 5 mL of blood were used for counting to identify isolated CTC numbers with immunofluorescence detection procedure. CTCs from the remaining 5 mL of blood were used for gene analysis by ddPCR. For the gene expression analysis, selected 13 patient’s samples were examined for 6 prostate cancer-related genes, such as androgen receptor (AR), androgen receptor splice variant 7 (AR-V7), prostate specific membrane antigen (PSMA), prostate specific antigen (PSA), cytokeratin-19 (CK-19) and epithelial cell adhesion molecule (EpCAM). Results We identified the average of 3, 16, 14 and 26 CTCs per 1ml in group A, B, C and D, respectively (P< 0.01). Background contaminated white blood cells are indispensably isolated with CTCs that counted on average 2245.4 cells, thereby CTC purity rate was 2.56 %. The gene positive rate of AR, AR-V7, PSA, PSMA, KRT-19, and EpCAM were 2.3 % (12/13), 15.4 % (2/13), 38.5 % (5/13), 69.2 % (9/13), and 100 % (13/13), respectively. Especially, the copy number of PSA, PSAM and CK-19 increased in proportion as the clinical stage increased. All samples showed EpCAM positive, whereas AR-V7 was rare events, with only in 2 out 5 patients positive with mCRPC, but not in other stages. Conclusions This study demonstrates that assembly-disposable CTC-μChip is a suitable for CTC isolation from prostate cancer patients. Our data also showed that CTC-based multigene profiling can be analyzed using ddPCR, making it a clinically relevant biomarker. Interrogating tumor expression via CTCs isolation may allow for enhancing precision-based treatment. Citation Format: Hyungseok Cho, Ki-Ho Han, Jae-Seung Chung. Detection of circulating tumor cells (CTC) by microfluidic technology based on lateral magnetophoresis and CTC-based multigene profiling analysis in prostate cancer patient [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 A089.

Comparison of EML4-ALK fusion gene positive rate in different detection methods and samples of non-small cell lung cancer.

Objective: To evaluate differences of EML4-ALK positive rates in tissues samples between immunohistochemistry, reverse transcriptase polymerase chain reaction and the next-generation sequencing method. Besides, to compare the differences of EML4-ALK positive rates in blood samples and tissue samples by next-generation sequencing. The results provide a basis for the selection of a suitable EML4-ALK fusion gene detection method.Methods: Immunohistochemistry analysis of EML4-ALK in tumors was performed on samples from 2631 patients with non-small cell lung cancer. The mutation of EML4-ALK in the tissue samples of 399 patients with non-small cell lung cancer was detected by reverse transcription polymerase chain reaction. Next-generation sequencing was used to detect the mutation of EML4-ALK in 1505 non-small cell lung cancer patients, including 1208 tissue samples and 297 blood samples.Results: The positive incidence of EML4-ALK by immunohistochemistry was 7.11% (187/2631). Histologically, 9.51% (170/1787) of the samples were lung adenocarcinomas, and 2.01% (17/844) were squamous cell carcinomas. The positive rate of EML4-ALK was 8.52% (34/399) in 399 patients with non-small cell lung cancer, as detected by reverse transcription polymerase chain reaction; the mutation rate of adenocarcinoma was 11.62% (33/284), and the mutation rate of squamous cell carcinoma was 0.86% (1/115). In 1208 patients with non-small cell lung cancer with tissue samples, the positive rate of EML4-ALK was 4.88% (59/1208), as determined by next-generation sequencing, the mutation rate of adenocarcinoma was 5.84% (58/994), and the mutation rate of squamous cell carcinoma was 0.47% (1/214). The positive rate of EML4-ALK detected by reverse transcription polymerase chain reaction was higher than that detected by immunohistochemistry. Compared with the next-generation sequencing results, the positive rates of EML4-ALK detected by immunohistochemistry and reverse transcription polymerase chain reaction were higher, and the differences were significant (p<0.05). In blood samples from 297 patients with non-small cell lung cancer, the positive rate of EML4-ALK detected by next-generation sequencing was 3.70% (11/297), the mutation rate of adenocarcinoma was 3.82% (10/262), and the mutation rate of squamous cell carcinoma was 2.86% (1/35). The EML4-ALK positive rate of the tissue samples was thus higher than that of the blood biopsy samples.Conclusion: Among the three methods for detecting EML4-ALK, reverse transcription polymerase chain reaction has the highest positive rate, followed by immunohistochemistry, and next-generation sequencing has the lowest positive rate. The positive detection rate of EML4-ALK in tissue samples by next-generation sequencing was higher than that in blood samples.

Expressions of transmembrane protease serine 2-E26 transformation specific fusion gene and its related proteins in prostate cancer and their significances

Objective To study the expressions of transmembrane protease serine 2-E26 transformation specific (TMPRSS2-ETS) fusion gene and ETS related gene (ERG), ETS variant 1 (ETV1), phosphatase and tensin homolog deleted on chromosome 10 (PTEN), androgen receptor (AR) in prostate cancer. Methods A total of 50 cases of prostate cancer paraffin specimens and 30 cases of benign prostatic hyperplasia as the controls in the same period from the Third People's Hospital of Datong between December 2016 and October 2017 were collected. TMPRSS2-ERG, TMPRSS2-ETV1 and TMPRSS2-ETV4 gene fusion status were detected by using fluorescence in situ hybridization. Immunohistochemistry was used to detect the expressions of ERG, ETV1, PTEN and AR protein. Results In prostate cancer tissues, TMPRSS2-ETS fusion gene positive rate was 70% (35/50), and TMPRSS2-ETS fusion gene was not detected in benign prostatic hyperplasia. The expression of TMPRSS2-ETS fusion gene in prostate cancer patients with different age, serum prostate specific antigen level and whether distant metastasis had no statistically significant differences (all P > 0.05). The expression of TMPRSS2-ETS fusion gene in Gleason score > 7 patients was higher than that in Gleason score≤7 patients (P 0.05). The expressions of TMPRSS2-ETS fusion gene and ERG in prostate cancer were positively correlated (r=0.302, P 0.05). Conclusions The expressions of TMPRSS2-ETS fusion gene and ERG, ETV1 protein are upregulated in prostate cancer, which may involve in the occurrence and development of prostate cancer. The detection of TMPRSS2-ETS fusion genes and ERG protein can provide a reference for the diagnosis of prostate cancer. Key words: Prostatic neoplasms; Transmembrane protease serine 2; E26 transformation specific; Gene fusion; Fluorescence in situ hybridization

CD9 expression indicates a poor outcome in acute lymphoblastic leukemia.

We undertook a single-center retrospective study to determine the relationship between CD9 and acute lymphoblastic leukemia (ALL). In total, 112 newly diagnosed patients in our center were enrolled in the study. Their clinical information was collected and the patients werefollowed over the course of the study. Flow cytometry was used to detect the expression of CD9. CD9 expression was more common in B cell acute lymphoblastic leukemia (B-ALL) and patients > 40 years old. CD9-positive patients exhibited a higher BCR-ABL fusion gene positive rate and higher neutrophil counts than CD9 negative patients (P= 0.004 and P= 0.004, respectively). Response to induction chemotherapy was not dependent on CD9 expression. CD9-positive patients had a lower 2-year overall survival rate than CD9-negative patients. CD9 expression predicts some clinical characteristics and indicates an unfavorable prognosis in ALL patients.

Molecular characteristics of Staphylococcus aureus isolated from intensive care units of children's hospital

Objective To study the molecular characteristics of the Staphylococcus aureus isolated from the intensive care units (ICUs) of children's hospital. Methods From January 2016 to December 2016, a total of 39 S. aureus strains were collected and identified from various clinical specimens that were obtained from patients who were confined in the neonatal and pediatric ICUs of Beijing Children's Hospital. Methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) were identified using the cefoxitin disc method and the detection of the mecA gene. Multilocus sequence typing (MLST) and spa typing were analyzed using the PCR, and the staphylococcal chromosomal cassette mec (SCCmec) type was analyzed for the MRSA isolates. Twenty-one superantigen genes and the Panton-Valentine leukocidin (pvl) gene were also detected by PCR. Their susceptibility to 12 antibiotics was evaluated using the E-test method. The differences in prevalence of virulence genes and antimicrobial resistance were compared between the MRSA and MSSA isolates by Fisher's exact test. Results All the S. aureus strains were isolated from secretion inside the airway of pneumonia (including severe pneumonia), the blood of patients with bacteremia, and exudate of skin and soft tissue infections. ST59-SCCmecⅣa-t437 (55.6%) and ST398-t571 (28.6%) were the most predominant clones of MRSA and MSSA, respectively. Of the 39 isolates, 26 strains (66.7%) had at least one superantigen gene, and seb (38.5%), sek (30.8%), and seq (20.5%) were the most common genes; seb-sek-seq (18.0%) was the main virulence genotype. The pvl gene's positive rate was 25.6%, and no significant difference between MRSA and MSSA was observed (P>0.05). Notably, 79.9% of the S. aureus isolates were multidrug resistant, and 94.9%, 53.8%, and 51.3% of the isolates were resistant to erythromycin, clindamycin, and chloramphenicol, respectively. The tested isolates were susceptible to trimethoprim/sulfamethoxazole, rifampicin, and vancomycin. Conclusions The S. aureus strains from the ICUs of children's hospital were isolated from the secretion inside the airway of pneumonia (including severe pneumonia), the blood of patients with bacteremia, and exudate of skin and soft tissue infections. ST59-SCCmecⅣa-t437 (55.6%) and ST398-t571 (28.6%) were the common clones of MRSA and MSSA, respectively. The prevalence of superantigen genes and the multidrug resistant rate were relatively high. Key words: Staphylococcus aureus; Methicillin-resistant Staphylococcus aureus; Pediatric; Intensive care unit; Molecular characteristics; Virulence; Antimicrobial susceptibility; Multidrug resistance

Clinicopathologic features of patients with non-small cell lung cancer harboring the EML4-ALK fusion gene: a meta-analysis.

BackgroundThe frequencies of EML4-ALK fusion gene in non-small cell lung cancer (NSCLC) with different clinicopathologic features described by previous studies are inconsistent. The key demographic and pathologic features associated with EML4-ALK fusion gene have not been definitively established. This meta-analysis was conducted to compare the frequency of the EML4-ALK fusion gene in patients with different clinicopathologic features and to identify an enriched population of patients with NSCLC harboring EML4-ALK fusion gene.MethodsThe Pubmed and Embase databases for all studies on EML4-ALK fusion gene in NSCLC patients were searched up to July 2014. A criteria list and exclusion criteria were established to screen the studies. The frequency of the EML4-ALK fusion gene and the clinicopathologic features, including smoking status, pathologic type, gender, and EGFR status were abstracted.ResultsSeventeen articles consisting of 4511 NSCLC cases were included in this meta-analysis. A significant lower EML4-ALK fusion gene positive rate was associated with smokers (pooled OR = 0.40, 95% CI = 0.30–0.54, P<0.00001). A significantly higher EML4-ALK fusion gene positivity rate was associated with adenocarcinomas (pooled OR = 2.53, 95% CI = 1.66–3.86, P<0.0001) and female (pooled OR = 0.61, 95% CI = 0.41–0.90, P = 0.01). We found that a significantly lower EML4-ALK fusion gene positivity rate was associated with EGFR mutation (pooled OR = 0.07, 95% CI = 0.03–0.19, P<0.00001). No publication bias was observed in any meta-analysis (all P value of Egger's test >0.05); however, because of the small sample size, no results were in the meta-analysis regarding EGFR gene status.ConclusionThis meta-analysis revealed that the EML4-ALK fusion gene is highly correlated with a never/light smoking history, female and the pathologic type of adenocarcinoma, and is largely mutually exclusive of EGFR.

Correlation between the biofilm-forming ability, biofilm-related genes and antimicrobial resistance of Acinetobacter baumannii

To study the biofilm-forming ability and the distribution of biofilm-related genes in Acinetobacter baumannii clinical isolates as well as antimicrobial resistance, to analyze their relationships with the bacterial resistance phenotype. A prospective study was conducted. Biofilm models of 70 strains Acinetobacter baumannii collected in Chengwu County People's Hospital from October 2012 to October 2013 were constructed using 96-well polystyrene plate. In order to analyze the biofilm-forming ability, a qualitative and quantitative analysis was conduct by crystal violet staining assay. And the antimicrobial resistance of different biofilm-forming ability strains was compared including imipenem, amikacin, meropenem, cefepime, sulbactam cefoperazone, trimethoprim, levofloxacin, gentamicin, ciprofloxacin, cefotaxime, ceftizoxime, aztreonam, piperacillin, ceftriaxone, cefuroxime. In addition, the expressions of biofilm-related gene Bap, bfs and intI1 were tested with polymerase chain reaction (PCR) assay. Among 70 strains Acinetobacter baumannii, 40 strains were multi-drug resistant (57.14%) and 6 strains were pan-drug resistant (8.57%); 68 strains had biofilm-forming ability (97.14%), 14 of which were weakly positive, 20 were positive and 34 were strongly positive. The antimicrobial resistant rate of Acinetobacter baumannii to imipenem, amikacin, meropenem and cefepime was decreased, it was 30.00%, 32.86%, 38.57% and 41.43%, respectively. However, the antimicrobial resistant rates to other commonly used antibiotics were all higher than 50%. The drug resistance of Acinetobacter baumannii to levofloxacin (85.71%, 45.00%, 38.24%, χ² = 9.225, P=0.010), cefepime (71.43%, 45.00%, 29.41%, χ² = 7.222, P=0.027), gentamicin (78.57%, 55.00%, 38.24%, χ² = 6.601, P=0.037) was significantly decreased when biofilm-forming ability reinforced (weakly positive, positive, hadropositive). Bap gene positive rate of weakly positive, positive and strong positive biofilm-forming strains Acinetobacter baumannii was 50.00%, 65.00% and 79.41% (χ² = 4.244, P=0.120), respectively. Bfs gene positive rate was 35.71%, 65.00% and 88.24% , respectively (χ² = 13.602, P=0.001) and intI1 gene positive rate was 42.86%, 75.00% and 91.18%, respectively (χ² = 12.902, P=0.002). Moreover, the antimicrobial resistances of biofilm-related gene positive strains were higher than the negative, of which the drug resistance of intI1 positive group to amikacin was significantly higher than the negative group (40.38% vs. 11.11%, χ² = 5.194, P=0.023). The Acinetobacter baumannii collected from the hospital had strong multi-drug resistance as well as strong biofilm-forming ability. The drug resistance of Acinetobacter baumannii decreased when biofilm-forming ability reinforced. In addition, genes, such as Bap, bfs, and intI1, contributed to biofilm formation.

273 Molecular Characteristics of Methicillin Resistant Staphylococcus Aureus Isolated from Chinese Children

ObjectiveThe present study aim to investigate the molecular characteristics of methicillin-resistant Staphylococcus aureus (MRSA) isolates from Chinese children in seven city.MethodA total of 134 MRSA isolats were collected from eight...

Molecular characteristics of methicillin resistant Staphylococcus aureus isolated from Chinese children

To investigate the molecular characteristics of methicillin-resistant Staphylococcus aureus (MRSA) isolates from Chinese children in seven cities. A total of 134 MRSA isolates were collected from nine hospitals. Multilocus sequence typing and spa typing were analyzed by polymerase chain reaction (PCR), and staphylococcal chromosomal cassette mec (SCCmec) type was analyzed by multiplex PCR. The Panton-Valentine leukocidin (pvl) gene was also detected. Most MRSA strains were isolated from pneumonia and skin and soft tissue infection (SSTIs) patients, accounting for 82.1%. Overall, 16 sequence types (STs) were obtained, and CC59 (51.7%) was found to be the most prevalent, which included ST 59 and ST 338, followed by ST239 (16.4%). SCCmec types II, III, IV, and V were also identified in the current study. SCCmec type IV was the most predominant type at 50.0%, followed by SCCmec type V at 23.9% and III at 23.9%. SCCmec subtypes IVa, IVc, and IVg were found among SCCmec type IV strains, whereas IVa was the main subtype at 77.6%. Twenty-six spa types were also identified, among which the predominant type was t437 (47.8%). The prevalence of pvl genes and the SCCmec type of strain was relevant, and the pvl gene positive rate was higher in SCCmec type IV and V-type strains than in SCCmec type II and III strains (58.6% vs. 14.3%, P < 0.05); there was a significant difference between them. In the strains isolated from pneumonia and SSTIs, ST59-MRSA-IVa(t437) was the predominant clone. There were five clones detected from the strains isolated from septicemia, with ST59-MRSA-IVa(t437) and ST59-MRSA-V(t437) as the main clones (57.1%). Various predominant clones existed in different regions. ST59-MRSA-IVa(t437) was the prevalent clone in the Guangzhou, Beijing, Chongqing, and Shenzhen areas, whereas ST239-MRSA-III(t037) was the prevalent clone in the Shanghai area. Fifty percent of the isolates from the Wenzhou area belonged to ST910-MRSA-V(t318), whereas three clinical strains isolated from the Shenyang region belonged to three different types. The results indicate that MRSA isolates from Chinese children are largely associated with the ST59-MRSA-IV(t437) and ST239-MRSA-III(t037) clones. These two may belong to community-acquired MRSA and hospital-acquired ones, respectively. Different prevalent clones were detected in different diseases and different regions. Therefore, there is a need to conduct further research on clinical isolates, which can guide the choice of antibiotic treatment and the examination of MRSA prevalence.

HLA‐DR genotypes in Chinese patients with ulcerative colitis

OBJECTIVE: To study HLA‐DR genotypes and to analyze the relationship between HLA‐DR genotypes, antineutrophil cytoplasmic antibodies (ANCA) and clinical classification of ulcerative colitis (UC) in Chinese patients.METHODS: Eighty UC patients and 123 healthy subjects were enrolled in the study. Serum ANCA was detected by using indirect immunofluorescence and HLA‐DR was genotyped by using the polymerase chain reaction with sequence‐specific primers (PCR‐SSCP).RESULTS: The positive rate of ANCA in UC patients was 55%, but 0.0% in the controls. The HLA‐DR2 and DR15 positive rates in the UC patients were 58.8 and 40%, respectively, which were significantly greater than 30.1 and 17.9% in the controls (P &lt; 0.05). In the UC patients, the DR15‐positive rate was significantly higher, but the DR16‐positive rate was significantly lower in the ANCA‐positive group than in the ANCA‐negative group (52.3 vs 25.0%; 9.1 vs 30.6%, P &lt; 0.05). The HLA‐DR2 and DR15‐positive rates in chronic persistent UC patients were significantly greater than those in the incipient or chronic recrudescent type of UC (84.2 vs 50.0 or 51.4%; 63.2 vs 29.2 or 35.1%, P &lt; 0.05).CONCLUSIONS: In Chinese UC patients, the positive rates of HLA‐DR2 and ANCA were significantly higher compared with healthy controls. The increase in the DR2‐positive rate was associated with the increase in the DR15‐positive rate in ANCA‐positive UC patients, and was associated with the increase in the DR16 gene positive rate in ANCA‐negative UC patients. In general, HLA‐DR genotypes are related to the clinical classification of ulcerative colitis.