Objective The study of loss of heterozygosity (LOH) on chromosome 1p36 was performed to locate the deletion areas probably harboring tumor suppressor genes in invasive ductal breast carcinoma not otherwise specified (IDC NOS).Methods Eighty paired breast cancer/normal tissue DNA samples were examined for LOH on chromosome lp36 using eight polymorphic microsatellite (MS) loci.The PCR products were electrophoresed on 8％ denatured polyacrylamide gel and stained using silver staining.Finally,the data were analysed and compared with the clinicopathological parameters using statistical analysis.Results In 80 IDC NOS,LOH was identified in 45 cases (56.3 ％) at least in one MS locus.MS locus D1S1310 showed the highest rate of LOH [35.7％ (25/70)].Conclusion Chromosome 1p36 might be the highly deleted region.The results of this study indicate that the chromosomal regions 1p36.23-33 might contain tumor suppressor genes associated with human breast carcinomas.

Objective To study the relationship between mutations of well-known driver genes and clinicopathologic characteristics of non-small cell lung cancers ( NSCLC ) . Methods Scorpions amplification refractory mutation system ( scorpions ARMS) fluorescence quantitative PCR was performed to investigate 205 driver gene mutation status in NSCLC in correlation with clinicopathological characteristics of the patients.Results Driver gene mutations were detected in 146 of 205 (71.2%) patients with NSCLC, including 81.7%( 138/169 ) adenocarcinomas, in which mutations of nine genes were found:EGFR (63.3%,107/169), KRAS (5.9%,10/169), PIK3CA (4.1%,7/169), ALK (4.1%,7/169), ROS1 (3.0%,5/169), RET (3.6%,6/169), HER2 (1.8%,3/169), NRAS (0.6%,1/169) and BRAF (0.6%,1/169).The frequencies of driver gene mutations were higher in adenocarcinomas, female patients and non-smokers (P<0.01, P=0.003, P<0.01, respectively).Driver gene mutation status showed no correlation with either the age or the clinical stage (P=0.281, P=0.490, respectively).However, EGFR mutations tended to occur in adenocarcinoma, female, non-smokers, and patients of≥62 years of age ( P<0.01, P<0.01, P=0.002, P=0.012, respectively) .The frequency of EGFR mutation was positively correlated with the tumor histology of lepidic, acinar, papillary and micropapillary predominant growth patterns.There was no relationship between EGFR mutation and the clinical stage ( P =0.237 ) .The frequency of KRAS mutation was higher in solid predominant and invasive mucinous adenocarcinomas ( P=0.015); that of PIK3CA mutation was higher in patients of ≥62 years of age, invasive mucinous adenocarcinoma and fetal adenocarcinoma ( P =0.015, P =0.006, respectively) .ALK, ROS1 or RET mutation positive NSCLC tended to occur in nonsmokers and have solid predominant tumors and invasive mucinous adenocarcinoma ( P=0.012, P=0.017 respectively).The frequency of EML4-ALK mutation was higher in the early stage patients with solid predominant tumors and invasive mucinous adenocarcinomas ( P=0.025, P =0.014, respectively ); that of ROS1 rearrangement was higher in invasive mucinous adenocarcinomas (P=0.049).NRAS, BRAF and HER2 gene mutations were infrequent and their clinical significance remained to be elucidated.Conclusions The relationship between mutations of well-known driver genes and clinicopathological characteristics in patients with NSCLC has diversity, the rate of mutations is higher in non-smoking female patients with adenocarcinoma.

Objective: To study the characteristics of lung adenocarcinoma driver gene variants detected by next generation sequencing (NGS) and quantitative fluorescence PCR. Methods: NGS was performed on 372 surgical resections from primary lung adenocarcinoma patients to detect 10 driver gene mutations, single-nucleotide variants(SNV), insertion/deletion and gene fusions; and quantitative fluorescence PCR were performed on 169 surgical resections from primary lung adenocarcinoma patients to detect nine driver gene hotspot mutations. Variants of VAF (variant allele frequency)≥1.0% were classified into 1 of 4 levels according to the guidelines and the precision oncology knowledge base of OncoKB, and the characteristics were investigated. Results: Sixty seven variants(leve1-4) were found by NGS, the positive rate of total mutations was 86.6% (322/372), in which variants at four levels were detected: levelⅠvariant, which was recognized as biomarker predictive of response to an FDA/NMPA approved drug in non-small cell lung cancer (NSCLC), was 71.2% (265/372);level Ⅱ variant, which was recognized as being standard care by the NCCN or other expert panels, was 3.0% (11/372); levelⅢA, a variant with compelling clinical evidence supports the biomarker as being predictive of response to a drug in this indication 3.0% (11/372); levelⅢB, a variant with compelling clinical evidence supports the biomarker as being predictive of response to a drug in another indication, was 4.3% (16/372); and level Ⅳ, a variant with compelling biological evidence supports the biomarker as being predictive of response to a drug, was 8.1% (30/372). The positive rate of unknown clinical significance and/or benign/likely benign variants was 18.8% (70/372). The positive rate of mutations detected by quantitative fluorescence PCR was 81.7% (138/169). Eighteen of the 20 samples showed concordance between NGS and quantitative fluorescence PCR. The two discordant cases could be due to the lack of coverage of two mutation sites in fluorescence PCR: EGFR c. 2571_2573delinsTCG(p. L858R), and HIP1-ALK_H19:A20 fusion. Conclusions Lung adenocarcinoma driver gene variants occur mainly in hotspot region, and NGS can comprehensively detect the driver gene variants of significant and potential clinical significance. NGS should be recommended when multiple genes need to be tested.

Purpose To study the consistency of NTRK fu-sion gene in the thyroid carcinoma detected by four technology platforms:immunohistochemistry,DNA-based NGS,FISH and qRT-PCR.Methods NTRK fusion gene was detected by FISH,immunohistochemical(IHC),DNA-based NGS and qRT-PCR in a same group of 40 clinical cases(among them,31 cases were thyroid cancer samples).Results In a group of 31 thyroid cancer cases detected by four techniques,compared with FISH,the sensitivity,specificity,positive predictive value(PPV),negative predictive value(NPV)and total coincidence rate(TCR)of IHC was 100%(9/9),90.9%(20/22),81.8%(9/11),100%(20/20),93.5%(29/31),respectively.The PPV of IHC was poor.The sensitivity,specificity,PPV,NPV and TCR of DNA-based NGS was 44.4%(4/9),100%(22/22),100%(4/4),81.5%(22/27),83.9%(26/31),respectively,and the sensitivity was poor.The TCR of qRT-PCR was 100%(31/31).Compared with FISH,Kappa value of IHC,DNA-based NGS and qRT-PCR was 0.853,0.532 and 1.000,respectively.Of the 40 clinical cases,the concordance between qRT-PCR and FISH was observed for 39 samples,for the qRT-PCR assay did not cover the NTRK fusion type(LM-NA:exon4-NTRK1:exon10).Compared with FISH,the coinci-dence rate of qRT-PCR was highest.Conclusion The RNA-based assay of qRT-PCR does have the advantages of high sensi-tivity and high specificity,and may be an optimal scheme for routine clinical detection of NTRK fusion variation in thyroid cancer in pathology department.

Objective To study the characteristics of lung adenocarcinoma driver gene variants detected by next generation sequencing (NGS) and quantitative fluorescence PCR. Methods NGS was performed on 372 surgical resections from primary lung adenocarcinoma patients to detect 10 driver gene mutations, single?nucleotide variants(SNV), insertion / deletion and gene fusions; and quantitative fluorescence PCR were performed on 169 surgical resections from primary lung adenocarcinoma patients to detect nine driver gene hotspot mutations. Variants of VAF (variant allele frequency)≥1.0% were classified into 1 of 4 levels according to the guidelines and the precision oncology knowledge base of OncoKB, and the characteristics were investigated. Results Sixty seven variants(leve1?4) were found by NGS, the positive rate of total mutations was 86.6% (322/372), in which variants at four levels were detected: levelⅠvariant, which was recognized as biomarker predictive of response to an FDA/NMPA approved drug in non?small cell lung cancer (NSCLC), was 71.2% (265/372);levelⅡvariant, which was recognized as being standard care by the NCCN or other expert panels, was 3.0% (11/372); levelⅢA, a variant with compelling clinical evidence supports the biomarker as being predictive of response to a drug in this indication 3.0% (11/372); levelⅢB, a variant with compelling clinical evidence supports the biomarker as being predictive of response to a drug in another indication, was 4.3% (16/372); and levelⅣ, a variant with compelling biological evidence supports the biomarker as being predictive of response to a drug, was 8.1% (30/372). The positive rate of unknown clinical significance and/or benign/likely benign variants was 18.8% (70/372). The positive rate of mutations detected by quantitative fluorescence PCR was 81.7% (138/169). Eighteen of the 20 samples showed concordance between NGS and quantitative fluorescence PCR. The two discordant cases could be due to the lack of coverage of two mutation sites in fluorescence PCR: EGFR c. 2571_2573delinsTCG(p. L858R), and HIP1?ALK_H19:A20 fusion. Conclusions Lung adenocarcinoma driver gene variants occur mainly in hotspot region, and NGS can comprehensively detect the driver gene variants of significant and potential clinical significance. NGS should be recommended when multiple genes need to be tested.