黃其晟1 塗昭江1 張景年1 黃清水2 1天主教輔仁大學附設醫院乳房外科 2國泰綜合醫院外科部

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Presentation transcript:

黃其晟1 塗昭江1 張景年1 黃清水2 1天主教輔仁大學附設醫院乳房外科 2國泰綜合醫院外科部目標基因定序方法改善台灣乳癌預後 Targeted sequencing of actionable genes to refine the prognostication of Taiwanese breast cancers 黃其晟1 塗昭江1 張景年1 黃清水2 1天主教輔仁大學附設醫院乳房外科 2國泰綜合醫院外科部

Purpose The aim of the study is to use targeted sequencing to refine the prognostication of Taiwanese breast cancers. Somatic mutations with clinical significance will be revealed. SureSelectXT HS Target Enrichment

Materials and methods Consecutive breast cancer samples (n=61) were assayed by targeted sequencing of actionable genes. Target-enrichment sequencing was performed with Illumina SolexaTM technology with read length of 150 PE and was analyzed with Agilent SureCallTM, Partek® Flow ®, and Ion ReporterTM software. There were 56 targets comprising 990 regions with a total regional size of 173.999 kbp, resulting in a coverage rate of 99.75%.

Analytic Flow Chart

Coverage Report

Post-Alignment Alignments breakdowns Average alignments per read

Average Base Quality Per position Per read

Coverage

Variant Detection and Annotation SAM Tools 1.4.1

Sankey Plot (I)

Sankey Plot (II)

Variant Impact

TNBC (n=9)

IRGV

Chromosome View

Variant Impact INDEL SNV ERBB2 (frameshift: 1), DAB2IP (frameshift: 2), FGFR2 (frameshift: 3), BRCA2 (frameshift: 1), FANCA (frameshift: 1), IDH1 (frameshift: 1), ATM1 (frameshift: 6), FGFR1 (frameshift: 6), WT1 (frameshift: 5), PDGFRA (frameshift: 2), TP53 (frameshift: 1), SMO (frameshift: 1), STK11 (frameshift: 2), FGFR1 (frameshift: 1), NOTCH1 (frameshift: 1), PIK3R1 (frameshift: 1), IDH2 (frameshift: 2), AR (frameshift: 2, non-frameshift: 2), ERBB4 (missense: 2), RUNX1 (frameshift: 1), HRAS (no-frameshift: 1) SNV BRCA1 (splicesite_5: 6), TP53 (nonsense: 2, missense: 3), FGFR3 (missense: 1), NOTCH1 (missense: 1), AKT1 (missense: 1), CTNNB1 (missense: 1), RET (missense: 3), JAK3 (splicesite_3: 3), KRAS (missense: 1), SRC (missense: 2), PIK3R1 (missense: 1), FLT3 (missense: 4), CSF1R (missense: 3), IDH2 (missense: 1), SH3GLB2 (missense:4), MAP2K2 (missense:2), ERBB4 (missense:1), RUNX1 (missense: 1), HIF1A (missense: 2), VHL (missense: 2), SMAD4 (missense: 1), RUNX3 (missense: 1)

FGFR2

ATM1

BRCA1

HR-/HER2+ (n=10) INDEL SNP Frameshift: BRCA2 (1), ATM, FGFR1(10), WT1 (7), PIK3R1 (4), PDGFRA (3), RUNX1(3), NRAS(1), Non-frameshift: CDKN2A (1), AR(4) SNP Splice: BRCA1 (10) Missense: ERBB2, FANCA, IDH1, DAB21P, FGFR2, MET, EGFR, RB1, FANCG, JAG2 (10), BRCA2 (9), DAB2, KIT (8), CDKN2A, FLT3, SH3GLB2 (7), ABL1, FNACC, PIK3CA, TP53 (6), ALK (5), PDGFRA (3), RET(1), CTNNB1(1), JAK3(2), BSG(1), CSF1R(3), FANCF(1),

HR+/HER2+ (n=11) INDELS SNP Frameshift: ATM, FGFR1(10), WT1(7), RUNX1(5), PDGFRA, PIK3R1, NRAS(3), DAB2IP, FGFR2, NOTCH1, AKT1, BSG, ALK, IDH2, AR, ERBB4(1) Non-frameshift: ABL1(1), RET(1), AR(2) SNP Splice: BRCA1 (9), JAK3(1), Stop loss: SMAD4(1) Missense: ATM, FGFR1, BRCA1, PDGFRA(2), DAB2, RB1, DH1(9), BRCA2, FANCG, FANCA, EGFR, MET(10), DAB2IP(9), FGFR2(8), PIK3CA, JAK2, ERBB2 (9), ABL1(7), CDK2NA, KIT(8), FANCC, TP53(7), RET, SMO, FGFR3, NOTCH1(1), JAK3, BSG(2), STK11(1), ALK(3), SH3GLB2, FLT3(5), MAP2K2, CSF1R(1), HIF1A(2), NPM1(1)

HR+/HER2-(n=31) INDELS SNP Frameshift: ATM, FGFR1(20), WT1(16), PDGFRA(10), PIK3R1(8), FANCA(1), DAB2IP(7), FGFR2(9), BRCA2(5), ERBB2(3), FANCG(1), RB1, ALK(2), AKT1(5), NOTCH1(3), SMO, RET(1), FGFR3(2), STK11(5), BSG, CSF1R, CDKN2A(1), ERBB4(6), AR(4), RUNX1(7), IDH2(5), NRAS(3), Non-frameshift: FGFR1(1), NOTCH1(1), RET(1), ABL1(9), CDKN2A(1), AR(16), HRAS(1) SNP Splice: BRCA1(20), JAK3(9) Missense: SMAD4, MAP2K4(1), ATM(7), FGFR1, WT1(2), BRCA(8), PDGFRA(5), PIK3R1(6), EGFR(28), FANCA(28), DAB2IP(21), FGFR2(18), ERBB2(25), FANCG(27), MET(26), RB1(23), JAK2(24), FLT3(22), ALK(21), PIK3CA(22), DAB2(20), KIT, IDH1(19), TP53(18), SRC(2), KRAS(1), NOTCH1(5), SMO, JAK3(2), RET(7), FGFR3(2), STK11(6), CTNNB1(3), BSG(5), CSF1R(13), ABL1(10), MAP2K2(4) CDKN2A(12), FANCA(13), ERBB4(4), RUNX1(3), SH3GLB2(12), IHD2(1), HF1A(6), NRAS(1), FANCF(1), RUNX3(4), VHL(2), MAP2K1(1), NPM1(1) Nonsense: ATM(2), ERBB2(1), MET(1), BRAF(2), CTNNB1(1), PTEN(2)

Which Target? Cancer Hotspot v.1

Conclusion Targeted sequencing of actionable genes is believed to provide clinical applicability and substantial benefits for Taiwanese breast cancer patients. The most difficult part is functional annotation, reproducibility, and clinical implications of sequencing findings. Ongoing with additional samples….. Integrated with WE sequencing…..