新一代分子诊断技术在肿瘤精准医学中应用课件

1、新一代分子诊断技术在肿瘤精准医学中应用新一代分子诊断技术在肿瘤精准医学中应用新一代分子诊断技术在肿瘤精准医学中应用新一代分子诊断技术在肿瘤精准医学中应用新一代分子诊断技术在肿精准医学（肿瘤领域）检测方案设计和质控基于新一代测序（NGS）的肿瘤精准医学检测产品设计全球多中心数据整合和数据质控2精准医学（肿瘤领域）检测方案设计和质控2新一代测序平台互补融合性不同测序仪平台可以使用不同基因富集方法PCR捕获PCR捕获IonIonIlluminaIllumina3新一代测序平台互补融合性不同测序仪平台可以使用不同基因富集方基因变异类型检测 I：突变基因全长（全外显子）的所有点突变影响因素：基因富集覆盖

2、度（90%）影响因素：测序深度（200X）报告中的突变 %灵敏度：1%4基因变异类型检测 I：突变基因全长（全外显子）的所有点突变4临床研究发现癌组织中CNV及Mutation共存肿瘤分型新概念（C型肿瘤，M型肿瘤）2015年CSCO年会厦门 基因变异类型检测 II：拷贝数变异（Copy Number Variation, CNV）5临床研究发现癌组织中CNV及Mutation共存肿瘤分基因变异类型检测 III：融合基因NGS检测融合基因RNA转录混合法NCI-MATCH Sample Test -Oncomine Comprehensive Panel6基因变异类型检测 III：融合基因NG

3、S检测融合基因NCI-肿瘤发病机制学说肿瘤的器官发生学说肿瘤的血液发生学说肿瘤的泛感染发生学说及诊疗进展50例接受缬更昔洛韦（Valcyte）治疗的胶质母细胞瘤患者2年生存率为62%，对照组为18%（P0.001）。治疗周期长的亚组预后更好，2年生存率可达70%和90%上海xx医院使用xxx抗病毒药物治疗xxx瘤获得突破性进展N Engl J Med 2013 Sep 5;369(10):985-67肿瘤发病机制学说肿瘤的器官发生学说N Engl J Med基于iFISH-CTC技术的单细胞测序临床应用肿瘤早期检测肿瘤个体化诊疗方案8基于iFISH-CTC技术的单细胞测序临床应用8iFISH-

4、CTC技术助力肿瘤精准医学研究9iFISH-CTC技术9肿瘤早期iFISH-CTC检测数据（2014.1-2015.8）5363例统计癌种灵敏度乳腺癌 95.93%结直肠癌93.18%肝癌81%胰腺癌 97.73%肺癌91.67%胃癌92.59%甲状腺癌87%食管癌81.8%10肿瘤早期iFISH-CTC检测数据（2014.1-2015年CSCO年会厦门 癌症早期筛查受检者信息检测路径病理检查结果：低分化腺癌手术切除腺癌112015年CSCO年会厦门 癌症早期筛查受检者信息检测路径肿瘤早期综合检测及预防案例 -福建x州xx医院循环肿瘤细胞检测体内存在肿瘤细胞提示癌组织特征及用药指导发现 22

5、个肿瘤细胞影像学显示右肺弥漫状阴影（纤维化/癌变）激光显微切割单个CTC肿瘤细胞单细胞全基因组测序分析12345定期随访和复查6癌标NSE ：72.6（ 99%每份样本测序深度10000X19靶向基因捕获技术（设计报告）xxx个基因外显子及重点区域1Phase 1 results1,262 HCC related somatic mutations from original file (3,000,381 somatic mutations in total, for all phenotypes).425 non-redundant HCC related somatic mutation

6、s, with unique genomic coordinates.These 425 mutations reside in 36 exons (covering 28 genes).Results would also be shown in figures later.20Phase 1 results1,262 HCC relatPhase 1 resultsThe covered 28 genes are (by official symbol):AACS,ADAM22,AKAP13,ARVCF,ATR,CDKN2A,CLCC1,CUL3,DMGDH,EGFR,ERBB2,GABB

7、R1,GIF,GTPBP2,HNF1A,JAK2,LITAF,MET,MFSD8,MUC5B,MYCL,NOVA1,NTRK2,PCDH7,PLEKHG5,PSTK,RAF1,USP25.OR (by ensembl ID):ENSG00000008277.10,ENSG00000036257.8,ENSG00000081760.12,ENSG00000096968.8,ENSG00000099889.9,ENSG00000105976.10,ENSG00000116990.9,ENSG00000117983.13,ENSG00000121940.11,ENSG00000132155.7,EN

8、SG00000132837.10,ENSG00000134812.3,ENSG00000135100.13,ENSG00000139910.15,ENSG00000141736.9,ENSG00000146648.11,ENSG00000147889.12,ENSG00000148053.11,ENSG00000155313.11,ENSG00000164073.5,ENSG00000169851.11,ENSG00000170776.15,ENSG00000171680.16,ENSG00000172432.14,ENSG00000175054.10,ENSG00000179988.9,EN

9、SG00000189067.8,ENSG00000204681.621Phase 1 resultsThe covered 28 Phase 1 ResultsThese 36 exons covered 12,415bp in total, including:chr1 2061bpchr2 97bpchr3 201bpchr4 3218bpchr5 249bpchr6 322bpchr7 621bpchr8 0bpchr9 1986bpchr10 282bpchr11 350bpchr12 540bpchr13 0bpchr14 1400bpchr15 136bpchr16 157bpch

10、r17 342bpchr18 0bpchr19 0bpchr20 0bpchr21 325bpchr22 128bpchrX 0bpchrY 0bp22Phase 1 ResultsThese 36 exons 6-phase selectorMethod description:Phase 2: max coverage “For each exon with SNVs covering 5 patients in LUAD and SCC, we selected the exon with highest RI that identified at least 1 new patient

11、 when compared to the prior phase.” original paperData required: TCGA maf files (somatic mutation)236-phase selectorMethod descrip6-phase selectorMethod description:Phase 3: RI = 30 & =3 patients “For each remaining exon with an RI 30 and with SNVs covering 3 patients in LUAD and SCC, we identified

12、the exon that would result in the largest reduction in patients with only 1 SNV.” original paperData required: TCGA maf files (somatic mutation)246-phase selectorMethod descrip6-phase selectorMethod description:Phase 4: RI = 20 & = 3 patients “Same procedure as phase 3, but using RI 20.” original pa

13、perData required: TCGA maf files (somatic mutation)256-phase selectorMethod descrip6-phase selectorMethod description:Phase 5: Predicted drivers “We included all exons from additional genes previously predicted to harbor driver mutations in NSCLC.” original paperData required: predicted driver gene

14、in HCC (from publication, 15 genes in reference paper)266-phase selectorMethod descrip6-phase selectorMethod description:Phase 6: Add fusions “For recurrent rearrangements in NSCLC involving the receptor tyrosine kinases ALK, ROS1, and RET, the introns most frequently implicated in the fusion event

15、and the flanking exons were included.” original paperNot included (not under our consideration by far).276-phase selectorMethod descripResultsThis panel includes:604 genes (not necessarily have all exons of this gene included in panel)782 exons 120.1 kb in total, 154 bp per exon202 patients in total

16、199 patients covered by this panel199 (99%), 181 (90%), 158 (78%) patients with at least 1, 2, 3 SNVsMean RI is 22.67 (Recurrence Index, the higher this number the more chance a SNV is found in patients)RI is 2.23, 68.85, 38.47, 23.52, 1.04 for phase 1, 2, 3, 4, 528ResultsThis panel includes:28Results shown by figure