Targeted Next-Generation Sequencing for Molecular Diagnosis of Endometriosis -Associated

Targeted next-generation sequencing for molecular diagnosis of endometriosis -associated ovarian cancer, Er et al, Journal of Molecular Medicine 2016

Table S1. List of mutations detected by deep sequencing after applying the relevant filters in six patients with four types of specimens including normal endometrium, ectopic endometriotic lesion, atypical endometriosis, and carcinoma.

Case 2

GENE / Protein level
Change / Type / DNA level
Change / Chr / Mutation frequency
Normal / Ectopic / Atypical / Tumor
AKT1 / - / splice_region / c.958-6G>A / chr14 / 0.0% / 4.1% / 24.6% / 28.9%
ALK / p.E1434D / missense / c.4302G>T / chr2 / 0.0% / 0.0% / 0.0% / 16.4%
AMER1 / p.A1128V / missense / c.3383C>T / chrX / 0.0% / 3.9% / 19.0% / 24.9%
ARID1A / p.C2163fs / InDel / c.6488delG / chr1 / 0.0% / 5.0% / 16.5% / 23.7%
ARID2 / p.Q1112* / nonsense / c.3334C>T / chr12 / 0.0% / 2.7% / 21.3% / 24.8%
BCL11A / p.A664V / missense / c.1991C>T / chr2 / 0.0% / 7.7% / 26.7% / 26.5%
CCNE1 / p.V352I / missense / c.1054G>A / chr19 / 0.0% / 6.0% / 27.8% / 38.1%
CDH5 / p.E737K / missense / c.2209G>A / chr16 / 0.0% / 0.0% / 14.7% / 31.0%
CHEK1 / p.C168R / missense / c.502T>C / chr11 / 0.0% / 0.0% / 0.0% / 10.3%
CREBBP / p.A206V / missense / c.617C>T / chr16 / 0.0% / 6.5% / 8.8% / 27.1%
CTNNA1 / p.A192T / missense / c.574G>A / chr5 / 0.0% / 0.0% / 13.3% / 22.5%
ERG / p.C77Y / missense / c.230G>A / chr21 / 0.0% / 0.0% / 2.1% / 5.5%
ETS1 / p.I402del / InDel / c.1204_1206delATC / chr11 / 0.0% / 2.9% / 15.4% / 17.7%
EXT1 / p.S395Y / missense / c.1184C>A / chr8 / 0.0% / 0.0% / 8.7% / 11.9%
EXT1 / p.C152R / missense / c.454T>C / chr8 / 0.0% / 0.0% / 28.0% / 47.9%
FANCD2 / p.P158S / missense / c.472C>T / chr3 / 0.0% / 4.0% / 9.8% / 16.2%
FGFR4 / p.A60V / missense / c.179C>T / chr5 / 0.0% / 3.4% / 18.2% / 30.9%

Case 2-continued

GENE / Protein level
Change / Type / DNA level
ID / Change / Chr / Mutation frequency
Normal / Ectopic / Atypical / Tumor
FN1 / p.T370M / missense / NM_002026,
NM_212478 / c.1109C>T / chr2 / 0.0% / 6.1% / 17.5% / 21.0%
HNF1A / p.P310T / missense / NM_000545 / c.928C>A / chr12 / 0.0% / 0.0% / 0.0% / 7.5%
HNF1A / p.A174V / missense / NM_000545 / c.521C>T / chr12 / 0.0% / 4.9% / 24.6% / 28.3%
IL7R / - / splice_region / NM_002185 / c.379+2T>C / chr5 / 0.0% / 2.4% / 21.1% / 27.0%
MBD1 / p.R282Q / missense / NM_001204139 / c.845G>A / chr18 / 0.0% / 0.0% / 17.9% / 23.7%
MBD1 / - / splice_region / NM_001204139 / c.978+6T>C / chr18 / 0.0% / 4.5% / 8.4% / 18.6%
MLH1 / p.D450fs / InDel / NM_001258273,
NM_000249 / c.1349delA / chr3 / 49.6% / 52.6% / 62.3% / 69.3%
MYH9 / - / splice_region / NM_002473 / c.5765+7C>T / chr22 / 0.0% / 4.9% / 20.3% / 29.1%
NF1 / p.F1275fs / InDel / NM_001042492 / c.3818_3819delCT / chr17 / 0.0% / 7.5% / 14.4% / 22.1%
NFKB1 / p.K95N / missense / NM_001165412,
NM_003998 / c.285G>T / chr4 / 0.0% / 0.0% / 8.1% / 12.4%
NIN / p.R839C / missense / NM_182946,
NM_016350 / c.2515C>T / chr14 / 0.0% / 0.0% / 0.0% / 6.1%
NOTCH1 / p.L372P / missense / NM_017617 / c.1115T>C / chr9 / 0.0% / 8.4% / 27.7% / 25.2%
NOTCH2 / p.R2105Q / missense / NM_024408 / c.6314G>A / chr1 / 0.0% / 2.5% / 17.8% / 21.0%
NUMA1 / p.R1967Q / missense / NM_006185 / c.5900G>A / chr11 / 0.0% / 0.0% / 28.5% / 34.1%
PARP1 / p.R591H / missense / NM_001618 / c.1772G>A / chr1 / 0.0% / 0.0% / 12.5% / 18.6%
PDGFRA / p.G898S / missense / NM_006206 / c.2692G>A / chr4 / 0.0% / 2.9% / 11.6% / 21.8%

Case2-continued

GENE / Protein level
Change / Type / DNA level
ID / Change / Chr / Mutation frequency
Normal / Ectopic / Atypical / Tumor
PER1 / p.Q1167* / nonsense / NM_002616 / c.3499C>T / chr17 / 0.0% / 0.0% / 14.2% / 26.5%
PIK3CB / p.G195fs / InDel / NM_006219 / c.584delG / chr3 / 0.0% / 0.0% / 12.3% / 19.8%
PLCG1 / p.D770E / missense / NM_002660 / c.2310C>G / chr20 / 0.0% / 0.0% / 20.4% / 34.5%
PRDM1 / p.P270S / missense / NM_001198 / c.808C>T / chr6 / 0.0% / 0.0% / 0.0% / 5.1%
PRKDC / p.Q3036R / missense / NM_006904 / c.9107A>G / chr8 / 0.0% / 5.6% / 7.5% / 10.5%
PTPRT / p.R721C / missense / NM_007050 / c.2161C>T / chr20 / 0.0% / 2.5% / 12.2% / 17.0%
RNF213 / p.D437N / missense / NM_001256071 / c.1309G>A / chr17 / 0.0% / 0.0% / 0.0% / 14.2%
RNF213 / p.D790N / missense / NM_001256071 / c.2368G>A / chr17 / 0.0% / 0.0% / 16.3% / 26.2%
RNF213 / p.R2572* / nonsense / NM_001256071 / c.7714C>T / chr17 / 0.0% / 0.0% / 0.0% / 6.0%
ROS1 / p.L1470M / missense / NM_002944 / c.4408C>A / chr6 / 0.0% / 0.0% / 9.0% / 14.8%
ROS1 / p.Y1239C / missense / NM_002944 / c.3716A>G / chr6 / 0.0% / 2.1% / 9.4% / 13.5%
SAMD9 / p.T60A / missense / NM_001193307,
NM_017654 / c.178A>G / chr7 / 0.0% / 0.0% / 6.9% / 19.9%
SGK1 / p.Q55L / missense / NM_005627 / c.164A>T / chr6 / 0.0% / 0.0% / 11.5% / 12.9%
SUFU / p.A416T / missense / NM_016169 / c.1246G>A / chr10 / 0.0% / 0.0% / 8.8% / 28.9%
SYNE1 / p.M5327V / missense / NM_182961
_Identities_99% / c.15979A>G / chr6 / 0.0% / 0.0% / 14.6% / 30.7%
TCF3 / p.R561W / missense / NM_003200 / c.1681C>T / chr19 / 0.0% / 10.0% / 26.3% / 25.2%
TRIP11 / p.K479R / missense / NM_004239 / c.1436A>G / chr14 / 0.0% / 0.0% / 0.0% / 8.7%

Case 3

GENE / Protein level
Change / Type / DNA level
ID / Change / Chr / Mutation frequency
Normal / Ectopic / Atypical / Tumor
ARID1A / p.Q1493fs / InDel / NM_006015 / c.4478delA / chr1 / 0.0% / 2.7% / 12.8% / 45.6%
DDR2 / p.T335M / missense / NM_001014796 / c.1004C>T / chr1 / 0.0% / 8.8% / 3.6% / 58.1%
KRAS / p.G13D / missense / NM_004985 / c.38G>A / chr12 / 0.0% / 4.8% / 4.6% / 43.8%
PIK3CA / p.K111E / missense / NM_006218 / c.331A>G / chr3 / 0.0% / 0.0% / 2.5% / 35.1%
PPP2R1A / p.P179H / missense / NM_014225 / c.536C>A / chr19 / 0.0% / 0.0% / 11.4% / 35.2%

Case 4

GENE / Protein level
Change / Type / DNA level
ID / Change / Chr / Mutation frequency
Normal / Ectopic / Atypical / Tumor
PIK3CA / p.H1047R / missense / NM_006218 / c.3140A>G / chr3 / 0.0% / 0.0% / 0.0% / 28.2%
ERCC1 / p.G4R / missense / NM_202001 / c.10G>A / chr19 / 0.0% / 0.0% / 2.2% / 13.2%
GUCY1A2 / p.T299I / missense / NM_000855 / c.896C>T / chr11 / 0.0% / 0.0% / 0.0% / 5.7%
PBRM1 / p.Q1522H / missense / NM_018313 / c.4566G>T / chr3 / 0.0% / 0.0% / 0.0% / 7.3%

Case 5

GENE / Protein level
Change / Type / DNA level
ID / Change / Chr / Mutation frequency
Normal / Ectopic / Atypical / Tumor
PIK3CA / p.H1047R / missense / NM_006218 / c.3140A>G / chr3 / 0.0% / - / 7.5% / 45.3%
TAF1L / p.E1570D / missense / NM_153809 / c.4710G>T / chr9 / 0.0% / - / 0.0% / 8.3%
TP53 / p.R282W / missense / NM_001276760,
NM_001276761,
NM_001126118,
NM_000546,
NM_001126112 / c.844C>T / chr17 / 0.0% / - / 0.0% / 38.2%

Case 6

GENE / Protein level
Change / Type / DNA level
ID / Change / Chr / Mutation frequency
Normal / Ectopic / Atypical / Tumor
RB1 / p.Y790* / nonsense / NM_000321 / c.2370C>A / chr13 / 0.0% / 0.0% / 2.1% / 9.0%