Concordance Study Between IBM Watson for Oncology and Clinical Practice for Patients with Cancer in China.

BACKGROUND: IBM Watson for Oncology (WFO), which can use natural language processing to evaluate data in structured and unstructured formats, has begun to be used in China. It provides physicians with evidence-based treatment options and ranks them in three categories for treatment decision support. This study was designed to examine the concordance between the treatment recommendation proposed by WFO and actual clinical decisions by oncologists in our cancer center, which would reflect the differences of cancer treatment between China and the U.S. PATIENTS AND METHODS: Retrospective data from 362 patients with cancer were ingested into WFO from April 2017 to October 2017. WFO recommendations were provided in three categories: recommended, for consideration, and not recommended. Concordance was analyzed by comparing the treatment decisions proposed by WFO with those of the multidisciplinary tumor board. Concordance was achieved when the oncologists' treatment decisions were in the recommended or for consideration categories in WFO. RESULTS: Ovarian cancer showed the highest concordance, which was 96%. Lung cancer and breast cancer obtained a concordance of slightly above 80%. The concordance of rectal cancer was 74%, whereas colon cancer and cervical cancer showed the same concordance of 64%. In particular, the concordance of gastric cancer was very low, only 12%, and 88% of cases were under physicians choice. CONCLUSION: Different cancer types showed different concordances, and only gastric cancers were significantly less likely to be concordant. Incidence and pharmaceuticals may be the major cause of discordance. To be comprehensively and rapidly applied in China, WFO needs to accelerate localization. ClinicalTrials.gov Identifier: NCT03400514. IMPLICATIONS FOR PRACTICE: IBM Watson for Oncology (WFO) has begun to be used in China. In this study, concordance was examined between the treatment recommendation proposed by WFO and clinical decisions for 362 patients in our cancer center, which could reflect the differences of cancer treatment between China and the U.S. Different cancer types showed different concordances, and only gastric cancers were significantly less likely to be concordant. Incidence and pharmaceuticals may be the major causes of discordance. To be comprehensively and rapidly applied in China, WFO needs to accelerate localization. This study may have a significant effect on application of artificial intelligence systems in China.

Clinical characterization and mutation spectrum in patients with familial adenomatous polyposis in China.

BACKGROUND AND AIM: Familial adenomatous polyposis (FAP) is the most common adenomatous polyposis syndrome. Patients with FAP are screened for germline mutations of two genes, APC and MUTYH. However, limited data exist on the clinical characterization and genotypic spectrum of FAP in China. This study was aimed to determine APC and MUTYH mutational status in a small cohort of FAP probands in China and to characterize the genotype-phenotype correlation in mutated patients. METHODS: Mutation screening of 46 unrelated probands was performed using multigene panels by next-generation sequencing. Clinical data of the index were used to assess genotype-phenotype correlations. RESULTS: Overall, 42 out of 46 (91.30%) unrelated probands found mutations, including 35 (76.09%) with APC mutations, 3 (6.52%) with MUTYH mutations, and 4 (8.70%) with both APC and MUTYH mutations. Ten APC genetic alterations variants were novel. The hereditary pattern of the family with both APC and MUTYH mutations was autosomal dominant inheritance. Upper gastrointestinal polyp was the most common extracolonic manifestations. The onset time for patients with both APC and MUTYH mutations was earlier than MUTYH mutation carriers and similar to APC mutation carriers. But the age of carcinogenesis for patients with both APC and MUTYH mutations was later than APC mutation carriers and similar to MUTYH mutation carriers. CONCLUSION: In this study, we show the importance of using multigene panels that allow for a parallel comprehensive screening. We suggest that genetic testing of patients with suspected adenomatous polyposis syndromes should include APC and MUTYH gene mutation analyses simultaneously.

Safety and efficacy of a novel disposable sheathed gastroscopic system in clinical practice.

BACKGROUND AND AIM: Endoscopic examinations carry a potential risk of cross-infection, and the traditional reprocessing method is time consuming. We evaluated the safety and efficacy of a novel disposable sheathed gastroscope system in clinical practice in comparison with the conventional gastroscope. METHODS: There were two phases in the study. In phase 1, 20 patients with hepatitis B were randomized into two groups: the sheathed group was examined with the novel disposable sheathed gastroscope (n = 10) and the conventional group with the conventional gastroscope (n = 10). Microbiologic tests were performed on each endoscope afterwards. In the second phase, 1120 patients were randomized again into the same two groups with 568 and 552 patients in the sheathed group and the conventional group, respectively. The time duration of the endoscopic procedure and reprocessing were measured. The pathology detection rate of endoscopic examinations, the patients' subjective feelings, and problems occurred during procedures were also recorded. RESULTS: The total instrument turn-around time in the phase 2 sheathed group (9.9 ± 1.3 min) was significantly shorter than the conventional group (39.0 ± 1.4 min, P = 0.000). The mean procedural time was slightly longer in the sheathed group than in the conventional group (4.9 ± 1.4 vs 4.1 ± 1.3 min, P = 0.000). However, the duration of endoscopic reprocessing was much shorter (4.9 ± 0.2 vs 35 ± 0.2 min, P = 0.000). No significant differences were observed in patient discomfort, optical clarity, or pathology detection rate. There were no complications in either group, and no microbial contamination was detected in phase 1 of the study. CONCLUSIONS: Compared with the conventional gastroscope, the novel disposable sheathed gastroendoscope is safe and more efficient in clinical practice.

Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.).

BACKGROUND: MicroRNAs (miRNAs) are a new class of small, endogenous RNAs that play a regulatory role in the cell by negatively affecting gene expression at the post-transcriptional level. miRNAs have been shown to control numerous genes involved in various biological and metabolic processes. There have been extensive studies on discovering miRNAs and analyzing their functions in model species, such as Arabidopsis and rice. Increasing investigations have been performed on important agricultural crops including soybean, conifers, and Phaselous vulgaris but no studies have been reported on discovering peanut miRNAs using a cloning strategy. RESULTS: In this study, we employed the next generation high through-put Solexa sequencing technology to clone and identify both conserved and species-specific miRNAs in peanuts. Next generation high through-put Solexa sequencing showed that peanuts have a complex small RNA population and the length of small RNAs varied, 24-nt being the predominant length for a majority of the small RNAs. Combining the deep sequencing and bioinformatics, we discovered 14 novel miRNA families as well as 75 conserved miRNAs in peanuts. All 14 novel peanut miRNAs are considered to be species-specific because no homologs have been found in other plant species except ahy-miRn1, which has a homolog in soybean. qRT-PCR analysis demonstrated that both conserved and peanut-specific miRNAs are expressed in peanuts. CONCLUSIONS: This study led to the discovery of 14 novel and 22 conserved miRNA families from peanut. These results show that regulatory miRNAs exist in agronomically important peanuts and may play an important role in peanut growth, development, and response to environmental stress.

[Detection of APC gene germline mutation in Chinese familial adenomatous polyposis by direct sequencing in combination with multiplex ligation-dependent probe amplification].

OBJECTIVE: To investigate the characteristics of APC gene germline mutation in Chinese patients with familial adenomatous polyposis (FAP). METHODS: The genomic DNA was extracted from peripheral venous blood drawn from probands of 14 Chinese FAP families from Beijing, Hebei, Henan, Anhui, Inner Mongolia, Shanxi and Fujian. The APC gene was amplified by PCR and underwent direct sequencing. Large fragment deletion was detected by multiplex ligation-dependent probe amplification (MLPA) only in micromutation-negative samples found by sequencing. RESULTS: APC gene micromutations were found in 9 probands and the micromutation detection rate was 64.3%, including 6 frameshift mutations, 2 splicing mutations and 1 nonsense mutation. Large fragment deletions of APC gene were detected in 2 probands (14.3%). The total mutation detection rate of micromutation and large fragment deletion was 78.6%. Four novel micromutations and 2 novel large fragment deletions were found, including c.2336-2337insT, c.3923-3929delAAGAAAA, c.532-2A > T, c.4179-4180GAdelinsT, large fragment deletions of exons 11 and 10A and large fragment deletion of exon 15 start. CONCLUSIONS: In Chinese FAP patients, the germline mutation type of APC gene is variable; the majority is of frameshift mutation. The most common mutation site is exon 15. The mutation detection rate of APC gene can be boosted effectively by direct sequencing in combination with MLPA.

Cloning and sequence analysis of putative type II fatty acid synthase genes from Arachis hypogaea L.

The cultivated peanut is a valuable source of dietary oil and ranks fifth among the world oil crops. Plant fatty acid biosynthesis is catalysed by type II fatty acid synthase (FAS) in plastids and mitochondria. By constructing a full-length cDNA library derived from immature peanut seeds and homology-based cloning, candidate genes of acyl carrier protein (ACP), malonyl-CoA:ACP transacylase, beta-ketoacyl-ACP synthase (I, II, III), beta-ketoacyl-ACP reductase, beta-hydroxyacyl-ACP dehydrase and enoyl-ACP reductase were isolated. Sequence alignments revealed that primary structures of type II FAS enzymes were highly conserved in higher plants and the catalytic residues were strictly conserved in Escherichia coli and higher plants. Homologue numbers of each type II FAS gene expressing in developing peanut seeds varied from 1 in KASII, KASIII and HD to 5 in ENR. The number of single-nucleotide polymorphisms (SNPs) was quite different in each gene. Peanut type II FAS genes were predicted to target plastids except ACP2 and ACP3. The results suggested that peanut may contain two type II FAS systems in plastids and mitochondria. The type II FAS enzymes in higher plants may have similar functions as those in E. coli.

[Expression of cyclooxygenase-2 and relationship with mismatch repair gene and microsatellite instability in hereditary non-polyposis colorectal cancer].

OBJECTIVE: To investigate the expression of Cyclooxygenase (COX)-2 and the relationship between cox-2, mismatch repair gene (MMR) proteins and microsatellite instability (MSI) in HNPCC. METHODS: Twenty-eight cases of adenomas and 14 cases of carcinomas were collected from 33 HNPCC families patients by colonoscopy. Sporadic adenomas (n = 32) and carcinomas (n = 24) were used as a control group. The expressions of COX-2 and mismatch repair gene hMLH1, hMSH2, hMSH6 proteins were examined by immunohistochemistry. MS1 were analyzed by using PCR with BAT25, BAT26, D2S123, D5S346 and D17S250 loci. RESULTS: The COX-2 high-expression rates were 53.6% (15/28) and 42.9% (6/14) in HNPCC adenomas and carcinomas, and were 62.5% (20/32) and 91.7% (22/24) in sporadic adenomas and carcinomas. COX-2 expression was lower in HNPCC carcinomas than that of sporadic carcinomas (P < 0.05). MMR deficiency rate and positive rate of MSI-H were both 71.4% (10/14) respectively in HNPCC carcinomas. It was higher than that in sporadic colorectal carcinomas [both 12.5% (3/24)]. Eight (80.0%) COX-2 low-expression were observed in 10 HNPCC carcinomas with MMR-deficient system while 4 cox-2 high-expression cases were observed in 4 HNPCC carcinomas with MMR-proficient system. COX-2 expression was lower in HNPCC carcinomas and adenomas, sporadic carcinomas with MMR-deficient system than that of MMR-proficient (P < 0.05). The COX-2 low-expression rates were 80.0% (8/10), 66.7% (12/18) and 66.7% (2/3) in HNPCC adenomas, HNPCC carcinomas and sporadic carcinomas with MSI-H. Cox-2 expression was lower in HNPCC and sporadic carcinomas (adenocarcinomas) with MSI-H than that of MSS (P < 0.05). CONCLUSION: Compared with sporadic carcinomas, the COX-2 expression was lower in HNPCC carcinomas. There was negative correlation between COX-2 expression and MMR-deficient (MSI-H). The detection of COX-2, MMR protein and MSI is of important significance in further studying the pathogenesis and interventional therapy of colorectal neoplasms.

Artificial intelligence system of faster region-based convolutional neural network surpassing senior radiologists in evaluation of metastatic lymph nodes of rectal cancer.

BACKGROUND: An artificial intelligence system of Faster Region-based Convolutional Neural Network (Faster R-CNN) is newly developed for the diagnosis of metastatic lymph node (LN) in rectal cancer patients. The primary objective of this study was to comprehensively verify its accuracy in clinical use. METHODS: Four hundred fourteen patients with rectal cancer discharged between January 2013 and March 2015 were collected from 6 clinical centers, and the magnetic resonance imaging data for pelvic metastatic LNs of each patient was identified by Faster R-CNN. Faster R-CNN based diagnoses were compared with radiologist based diagnoses and pathologist based diagnoses for methodological verification, using correlation analyses and consistency check. For clinical verification, the patients were retrospectively followed up by telephone for 36 months, with post-operative recurrence of rectal cancer as a clinical outcome; recurrence-free survivals of the patients were compared among different diagnostic groups, by methods of Kaplan-Meier and Cox hazards regression model. RESULTS: Significant correlations were observed between any 2 factors among the numbers of metastatic LNs separately diagnosed by radiologists, Faster R-CNN and pathologists, as evidenced by rradiologist-Faster R-CNN of 0.912, rPathologist-radiologist of 0.134, and rPathologist-Faster R-CNN of 0.448 respectively. The value of kappa coefficient in N staging between Faster R-CNN and pathologists was 0.573, and this value between radiologists and pathologists was 0.473. The 3 groups of Faster R-CNN, radiologists and pathologists showed no significant differences in the recurrence-free survival time for stage N0 and N1 patients, but significant differences were found for stage N2 patients. CONCLUSION: Faster R-CNN surpasses radiologists in the evaluation of pelvic metastatic LNs of rectal cancer, but is not on par with pathologists. TRIAL REGISTRATION: www.chictr.org.cn (No. ChiCTR-DDD-17013842).

[Mutation of hMLH1 and hMSH2 genes in hereditary nonpolyposis colorectal cancer: analysis of 76 probands].

OBJECTIVE: To investigate the mutations of the mismatch repair genes hMLH1 and hMSH2 in hereditary nonpolyposis colorectal cancer (HNPCC). METHODS: The DNA samples of 76 probands of HNPCC families underwent PCR amplification and sequencing on 35 exons in hMLH1 and hMSH2 genes. RESULTS: (1) The overall mutation rate of the hMLH1 and hMSH2 genes was 33% (25/76). (2) 22 mutations were found, 16 in the hMLH1 gene and 6 in the hMSH2 gene. (3) The spectrum of mutation type included frame shift, nonsense, splice site, and missense mutations. Missense mutation was the most common mutation type. CONCLUSION: The hMLH1 and hMSH2 mutations in Chinese HNPCC families show a wide spectrum. It seems that hMLH1 gene is involved more frequently than hMSH2 gene. A certain number of HNPCC families can be benefited from the genetic screening for mutation of the mismatch repair genes.

Predictive Value of Stemness Factor Sox2 in Gastric Cancer Is Associated with Tumor Location and Stage.

Cancer stem cells (CSCs) are thought to be the "root" of cancer. Although stemness-related factors ALDH1A1 and Sox2 have been used as markers to identify gastric CSCs, the expression pattern and significance of these factors in gastric cancer have not been sufficiently demonstrated. In this study, the expressions of ALDH1A1 and Sox2 were detected by immunohistochemistry in 122 gastric cancer specimens. And the correlation between Sox2 or ALDH1A1 expression and clinicopathological parameters and overall survival data were analyzed. The positive rate of ALDH1A1 expression was 60%, but there was no significant difference between survival rates of ALDH1A1-positive and ALDH1A1-negative patients. Sox2 was expressed in 42% of specimens and was associated with poor prognosis of patients (P = 0.015). Stratified analysis showed that Sox2 expression correlated with shorter lifespan only in patients with cardiac gastric cancers (P = 0.002) or stage I or II gastric cancers (P = 0.002); but not in patients with non-cardiac cancers (P = 0.556) or stage III or IV gastric cancers (P = 0.121). Analysis on a database cohort validated the correlation between Sox2 expression and poor prognosis in stage II cancer. Also, expression of Sox2 was associated with lymphnode metastasis in patients with cardiac gastric cancer (P = 0.037). A multivariate analysis revealed that Sox2 was an independent prognostic factor in cardiac gastric cancer. Our results indicate that predictive value of Sox2 in gastric cancer is associated with cardiac cancer location and with early cancer stages (I and II).

[Detection of large intragenic mismatch repair genes deletions in Chinese hereditary nonpolyposis colorectal cancer families with multiplex ligation-dependent probe amplification technique].

OBJECTIVE: To gain an insight into the large intragenic hMSH2 and hMLH1 deletions in Chinese hereditary nonpolyposis colorectal cancer (HNPCC) families. METHOD: The large intragenic hMSH2 and hMLH1 deletions in 17 probands of HNPCC families were detected with multiplex ligation-dependent probe Three large intragenic hMSH2 deletions of examplification (MLPA) and GeneMapper techniques. RESULTS: on 8, exon 1-6, and exon 1-7 were found in three families respectively, and no hMLH1 deletion was found. The deletions accounted for 19% of the total hMSH2 and hMLHI germline pathogenic mutations. CONCLUSIONS: The incidence of large intragenic mismatch repair (MMR) genes deletions is relatively higher in Chinese families, and hMSH2 deletions may be more common. It is necessary to detect the large intragenic MMR genes deletions in the molecular detection of HNPCC.

[Abnormalities of microsatellite in transitional cell carcinoma of urinary bladder related with aromatic amine exposure].

OBJECTIVE: To study the microsatellite abnormalities of the aromatic amine exposure-associated transitional cell carcinoma (TCC) and sporadic TCC of urinary bladder, and to evaluate the potential of microsatellite analysis on detection of this diseases. METHODS: Based on our previous investigations, 5 microsatellite markers (D17S695, D9S162, D3S1295, DBH and D3S1234) that had high frequencies of loss of heterozygosity (LOH) in sporadic TCC, were selected for analysis with the bladder lesions derived from 16 patients with aromatic amine exposure history. The microsatellite analysis with urine sediments from the post-operated patients was also carried out. RESULTS: There was at least one informative marker out of the 5 microsatellite foci showed polymorphism in the DNA derived from 16 patients examined. Within 87.50% (14/16) patients, LOH was detected in the bladder lesions at least with one microsatellite marker. The LOH frequency of D3S1295 was higher in occupational TCC patients than that in sporadic TCC patients. The diagnostic accordance rate of patients showed LOH in at least one microsatellite marker with patients diagnosed by pathology was 81.25% (13/16). In the urine sediments from 8 TCC post-operated patients, LOH was found at least with one microsatellite marker. CONCLUSION: There could be a different LOH pattern in aromatic amine exposure-associated TCC, and genes near D3S1295 might play a role in the occupational exposure-associated TCC.

Factors for Endoscopic Submucosal Dissection in Early Colorectal Neoplasms: A Single Center Clinical Experience in China.

BACKGROUND/AIMS: Early colorectal (CR) neoplasm can be cured by endoscopic submucosal dissection (ESD), but clinical experience and factors associated with complications from ESD for CR neoplasms in China have not been reported. METHODS: Seventy-eight cases of early CR neoplasm treated with endoscopic resection performed between December 2012 and December 2013 at Beijing Military General Hospital were included. Factors associated with ESD complications and procedure times were evaluated. RESULTS: The en bloc resection rate was 88.5% (69/78), tumor size was 32.1±10.7 mm, and procedure time was 71.8±49.5 minutes. The major complication was perforation, which occurred in 8.97% of the ESD procedures. Multivariate logistic regression analysis indicated that only tumor size (p=0.022) was associated with ESD perforation. Tumor size (p<0.001) and the non-lifting sign (p=0.017) were independent factors for procedure time, and procedure time (p=0.016) was a key factor for en bloc resection. After a median 10 months (range, 4 to 16) of follow-up, no patients had local recurrence. CONCLUSIONS: This study indicated that ESD is an applicable method for large early CR neoplasm in the colon and rectum. Tumor size and the non-lifting sign might be considerable factors for increased complication rate and procedural time of ESD.

[Oral candida species distribution in patients receiving radiotherapy for head and neck cancer].

PURPOSE: To investigate the distribution of oral candida species in head and neck cancer (HNC) patients treated with radiation therapy, and provide the basis for planning of clinical preventive measures. METHODS: Saliva was sampled from 60 HNC patients before, during and after radiation. Concomitantly, 60 healthy individuals whose age and sex matched that of the patient group were selected as control group. Oral candida carriages were quantitatively detected and the different candida species were identified by multiple measures such as CHROMagar candida culture medium and API 20C AUX yeast identification system. Then the differences between the two groups in terms of the candida detection rate and the distribution of each species of candida were analyzed with SPSS 17.0 software package. RESULTS: Xerostomia and dysphagia was found in 54 HNC patients during radiotherapy, radiation-induced oral mucotitis(RIOM) was found in 50 HNC patients,and oral candidiasis was found in 18 HNC patients; In radiation group, the detection rate of candida colonization during radiation was 56.7%, 63.3% postradiation, which showed significant differences compared with pre-radiation (X² =18.320,P<0.001 ); Among the 54 identified clinical isolates, candida albicans (n=42) was the most frequent, followed by candida parapsilosis (n=6), candida tropicalis (n=4) and candida glabrata (n=2). In radiation group, the oral candida pathogens detection rate was 30%, and candida colonization was 46.7%. CONCLUSIONS: The oral candida colonization rate was significantly higher in HNC patients after radiotherapy, which indicated that the candida infection may be closely related to RIOM.