SI Appendix - PNAS · 2013-12-04 · SI Appendix Reproducible Copy Number Variation Patterns among Single Circulating Tumor Cells of Lung Cancer Patients Xiaohui Ni, Minglei Zhuo,

SI Appendix

Reproducible Copy Number Variation Patterns among Single Circulating

Tumor Cells of Lung Cancer Patients

Xiaohui Ni, Minglei Zhuo, Zhe Su, Jianchun Duan, Yan Gao, Zhijie Wang, Chenghang Zong, Hua

Bai, Alec Chapman, Jun Zhao, Liya Xu, Tongtong An, Qi Ma, Yuyan Wang, Meina Wu, Yu Sun,

Shuhang Wang, Zhenxiang Li, Xiaodan Yang, Jun Yong, Xiao-Dong Su, Youyong Lu, Fan Bai, X.

Sunney Xie, and Jie Wang

Supporting Materials:

SI Materials and Methods

Figs. S1-S17

Tables S1-S5

SI Materials and Methods

Patient Recruitment and Clinical Information. We enrolled 16 patients that were initially

diagnosed with metastatic lung adenocarcinoma (ADC) or small cell lung cancer (SCLC). A

summary of patient information was listed in Table S1. 10 ml of blood samples were drawn from

each patient, 7.5 ml for CTC analyses and the other 2.5 ml for blood genomic DNA (gDNA)

extraction. Of the 16 participants, 6 patients (Patient 1 – Patient 6) with ADC, 1 patient (Patient

7) with ADC+SCLC, and 4 patients (Patient 8 – Patient 11) with SCLC were chosen for

subsequent sequencing study. The tumor cell content was estimated from haematoxylin and

eosin (H&E)-stained formalin-fixed paraffin-embedded (FFPE) tumor sections. The fraction of

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tumor was estimated to be more than 70% in all FFPE samples by two senior pathologists, which

excluded the possibility of low tumor content in complicating data analyses.

Among the six ADC patients, Patient 1 is a female patient with liver metastasis who never

smoked. She carried EGFR exon 19 deletion mutation. She received palliative resection of her

primary tumor, followed by six cycles of pemetrexed plus carboplatin as a first-line therapy with

partial response (PR). After a 5-month interval without any drug exposure, her liver metastasis

progressed. The patient received erlotinib as the second-line therapy. One month after the start of

the treatment, a response evaluation showed disease progression and erlotinib failure by CT scan

(Fig 1). A 7.5 ml of blood was drawn for CTC isolation and genomic analyses were performed.

The CTCs exhibited genomic characteristic of small cell lung cancer. Biopsy of the liver

metastasis showed histological type of SCLC, which was confirmed by neuroendocrine

immunohistochemical staining with synaptophysin (Fig. 1). To exclude the possibility that

metastatic SCLC in liver derived from the mixture of ADC and SCLC within the primary

pulmonary tumor, serial sections from four paraffin blocks from different regions of resected

samples were examined and the histology was confirmed by H&E staining and tissue-specific

markers such as thyroid transcription factor 1 (TTF-1) to be ADC without visible SCLC

component. Etoposide plus cisplatin was administered for 6 cycles with a dramatic clinical

response. Patients 2, 3 and 5 received pemetrexed or docetaxel plus platinum as first-line

therapy; their CTCs were obtained before initiating first-line chemotherapy. Patient 4’s tumor

tissues were not obtained at the time point of CTC isolation. Sequencing of CTCs revealed

EGFR exon 19 deletion mutation in Patient 4. Patient 6 carried EGFR mutation and her CTCs

were obtained during the first cycle of pemetrexed plus carboplatin.

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Patient 7 was diagnosed as a mixture of ADC and SCLC in the lung. CTCs from Patient 7

were obtained before the start of first-line therapy. Docetaxel plus nedaplatin was administered

for 6 cycles followed by 4 cycles of docetaxel. This patient has PR at cycles 2, 4, 6, 8, and PD at

cycle 10. Biopsy of the liver metastasis showed histological type of SCLC. This patient received

irinotecan as second-line therapy.

Among the 4 SCLC patients with extensive-stage SCLC, Patient 8’s CTCs were isolated at

three time points: before chemotherapy, after partial response to first-line chemotherapy with

etoposide plus platinum for 2 cycles, and after disease progression to second-line chemotherapy

with topotecan. CTCs from the other 3 SCLC patients were isolated before first-line

chemotherapy.

This study was approved by the institutional ethics committee at Peking University Cancer

Hospital & Institute and the Committee on the Use of Human Subjects at Harvard University. All

participants provided written informed consent form.

Copy Number Determination from Whole-genome Sequencing Data. The copy number

variant regions were identified according to the procedure in Ref. 1. Briefly, the likely diploid

regions were determined from the normalized (by total reads) coverage at a bin size of 500 kb

using the hidden Markov model (HMM) with the coverage from single leukocytes from eight

patients as control. A binary array, which indicates whether a single cancer cell has higher

coverage than the normal leukocyte, is taken as emission in our HMM. Three states, one, two, or

three copies, have been assumed to exist in our coverage data.

Two constants, a and b, were empirically chosen to represent the rate per bin for abnormal

copy number to begin and end, respectively. In our HMM, transitions among the three states can

be described with a transition matrix:

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For a state with copy number s, the emission probability for observing more coverage in the

cancer cells is assumed as p(X1*s/2>Xo), where X1 and Xo are random variables retrieved from

the observed distribution of coverage in the normal leukocyte. Given the above parameters, the

likely state path can be solved using Viterbi algorithm, which provides a coverage normalization

factor so that regions determined to be diploid would have a mean coverage of 2.

After the above procedures, we employed a second HMM which allows six hidden states (N

= 0 to 5 copies) for a more precise identification of variations. The emissions of this model are

the coverage of the cancer cells, normalized by normal leukocytes.

The transition matrix for the second HMM is similar to the first one except that all transitions

to an abnormal copy number state have a probability a/N, and transitions from an abnormal state

to the diploid state have a probability b.

The coverage of the diploid regions determined in the previous step was used to represent the

emission probabilities of the two copy state, denoted by p2. The single copy state emission

probabilities p1 was assumed to satisfy p2=p1 p1, where denotes convolution. Once p1 is

solved by deconvolution, the emission probabilities for higher copy states can be determined

from the iterative relation pn=pn-1 p1.

The Viterbi algorithm is again applied to determine the most likely state path. The

determined diploid regions are then used to provide an updated normalization factor for further

repeat. We used twenty iterations to ensure sufficient convergence.

Validation of SNVs and CNVs. Blood genomic DNA and a normal leukocyte from each patient

were sequenced as a control for variant calling.

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Our study yielded 410 non-synonymous mutations across 28 (24 CTCs, 4 FFPE tissues)

samples in four ADC patients (Patients 1-4). We validated 10 SNVs in 10 genes (RB1, PIK3CA,

APC, CNTNAP5, TGFBR2, FOXP1, C9orf91, ZNF473, MORF4L2, FLT3) by PCR amplification

followed by Sanger sequencing or deep sequencing. The distribution of SNVs among CTCs,

primary and metastatic tumors are shown in Fig. 2A and Fig. S1. The genes and primer pairs for

the validation are listed in Table S5. The validation was performed by 38 cycles of PCR reaction

followed by Sanger sequencing. In order to reduce PCR bias, we performed a total of 30 cycles

of two-step PCR reactions with different primer pairs in each step, followed by deep sequencing,

to check RB1 and PIK3CA mutations in the primary tumor.

Of 29 SNVs in CTCs, one was considered to be wild type by Sanger sequencing,

corresponding to a false positive rate of 1/29. Of the 19 wild type CTC samples that SNV was

detected in other CTCs or tumor tissues of the same patient, Sanger sequencing confirmed they

are all true negative (0/19). The false positive rate was 1/7 in tumor tissues. To estimate the rate

of false negative SNV calls in tumors, we checked SNVs that detected in CTCs and/or metastatic

(primary) tumor but not in the primary (metastatic) tumor of the same patient. 3 out of 7 SNVs

were confirmed to exist in the primary (metastatic) tumor. False negatives of SNVs in the tumors

could be due to the low mutation frequency instead of sequencing errors of next-generation

sequencing platforms. We didn’t exclude those false negative findings in Fig. 2 and Fig. S1 for a

better understanding of tumor heterogeneity.

None of the eight leukocytes from four ADC and four SCLC patients have shown distinct

CNVs. We further verified the amplification of c-Myc gene and TERT gene in CTC using the

digital PCR technique. One CTC and one normal leukocyte from the same patient were

respectively lysed and aliquoted to 24 tubes to ensure that multiple copies of DNA were

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distributed into different tubes. The whole genome amplification product of each aliquot was

subjected to PCR reactions targeting c-Myc gene (forward primer,

CCGGCGAGAGAAAGAAGAAA; reverse primer: GGGAGGCAGTCTTGAGTTAAA) and

TERT gene (forward primer, CACTGCTGGCCTCATTCA; reverse primer:

CCCTTTGCAGATGTGGTCT). The PCR products were loaded in a 1.5% agarose gel. The

bands that appeared in the gel were counted (Fig. S11). Six copies (hexaploid) of c-Myc gene and

five copies of TERT gene were found in CTC. Two copies (diploid) of c-Myc gene and TERT

gene were found in the normal leukocyte. This result was consistent with our observation that the

chromosome region containing c-Myc gene was amplified in 19 of 19 CTCs of ADC patients 2-6

and TERT gene was amplified in 17 of 19 CTCs of ADC patients 2-6.

References

1. Zong C, Lu S, Chapman AR, Xie XS (2012) Genome-wide detection of single-nucleotide and

copy-number variations of a single human cell. Science 338(6114):1622-1626.

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A B

WT

Mutant (hetero.)

Mutant (homo.)

C

Fig. S1. Detection of SNVs and INDELs in CTCs and metastatic tumors. (A) Non-synonymousheterozygous (hetero.) and homozygous (homo.) mutations in CTCs and the metastatic (Meta.)tumor of Patient 2 (mutations without coverage in CTCs are excluded). (B) Non-synonymousmutations in CTCs and the metastatic tumor of Patient 3. (C) Non-synonymous mutations inCTCs of Patient 4. Blank region represents no sequence coverage.

CTC

1

CTC

2

CTC

3

CTC

4

CTC

5

CTC

6

Met

a.

ZNF644SLCO2B1SCN3APNLIPPLCB1P4HA2OR11A1LCE2AFLGEIF2B1COL11A1BRCA2BOD1L1ZNF804BZNF804AZNF785ZNF729ZNF717ZNF567ZNF442ZFHX4WDFY3USP9XUBXN11TRHRTRAPPC8TRA2ATPPP2TPCN2TP53TMTC2TMTC1TMPRSS11BTMEM27TMEM176BTMEM14BTEP1TDRD5TCN1TBCCD1TAF1LSLC30A2SHISA3SHANK2SEMA6DSAMD9RTDR1RPTORRNF121RGS1RBP3RB1RAVER2RAMP1PRUNE2PRAMEF12PPWD1PPFIA4POLK(2)POLK(1)PDE4APDCL2PCLOPCDHA6PCDH15PAPPA2OSBPL8OR6M1OR51G2OR4K2OR4C12OR4A16OR2M2ODZ3OBSL1NPHS1NPHP1NOS2NLRP2NDRG1MYH2MS4A14MED16MC5RMAPK9LPOLOC100129520LMX1ALMOD3LAMC1KRT2KLBKIAA1244KIAA0232KERAKDM4CKCNC2IL37IGSF9BIGSF11IGFN1(2)IGFN1(1)HECW1HEATR7B2H1FOOGTPBP3GPR1GPAMGLB1L3GABRR1FSIP2FLT3FGL2FDXRFAT4ETV3ENPP3ENGASEEHD3DYNC1H1DSG3DROSHADOCK2DOCK1DNAJC13DNAH6DMKN(2)DMKN(1)DLATDGKICTNND2CSMD1CPZCPNE2COL6A6COL14A1CEP128CDC42EP1CD1BCCDC129CAPN1C9orf114C2orf77C2orf16C14orf38BPTFBICD1BCORATXN7L2ATXN7L1ATP13A3ARHGAP35AP2M1ALOXE3AGLADPRHL2ADAMTS6ABCB1AAAS

CTC

1

CTC

2

CTC

3

CTC

4

CTC

5

Met

a.

NUP98ZSCAN5B(2)ZSCAN5B(1)ZNF827ZNF614ZNF460ZNF440ZNF285ZNF274ZNF230ZNF175ZFP112WWP1WDR44VWDEUSP6UNC80TTLL6TTC40TTC39ATSHZ3TRPC6TP53TNNC2TMEM14BTIAM1TECTATCTE1TBC1D1TAF1LSYTL3SYNE2STK31STK11IPSPATA18SNAP25SLURP1SLC7A2SLC5A1SLC39A12SLC27A5SGIP1SCPEP1RYR2RTL1RTEL1RPS6KC1RPL35ROS1ROBO4RNMTRMI1RBM42RASGEF1CRALGDSQTRT1PTPRUPSME4PRRC2BPRKDCPREX1PPP1R12BPOTEAPOM121L12POLNPLD1PKHD1L1PIGZPHOSPHO1PGBD1PCDHB11PCDH15PBX2PBRM1PARD3BPAPSS2PAPPA2OTOGLOR52E6OR4K5OR4D9OR4C15OR2AK2OGDHODF1NIF3L1NEK11NDPNCAPG2MYO9BMUC17MRM1MRGPRX3MMP21LRRK2LRRC66LRGUKLMNALGALS3BPLCN1KPRPKLHL14KCNQ2ITPR1INTS2IGFBP7IFIT2HYDIN(2)HYDIN(1)HUWE1HIVEP1HERC3HEPACAMGPR171GLT25D1G6PC2FNIP2FNDC1FLNBFLNAFCHSD2FCHO1FBXO40FAT3(2)FAT3(1)FANK1ERCC5EPHA4EPC1DZIP3DPP10DMXL1(2)DMXL1(1)DGKIDCCDAPK1DAG1DAAM2CSMD1CRAMP1LCOL4A6COL20A1COL11A1CNTNAP5CLEC17ACEP63CAPS2CACNA1EC5orf42C1orf168C12orf51C12orf50C10orf71BTNL3BIVM−ERCC5BIRC6ATXN3ASLANO3(2)ANO3(1)ANKRD5ANKRD50ADRA2CADAMTS18ADAM32ACTRT1ABCD2MYBPC1IKBKAPGPR98ADAM12

CTC

1

CTC

2

CTC

3

CTC

4

CTC

5

DNAH14SEC24AMAGI2KTN1KIFAP3DGKDTP53(1)ANPEPKIF2BWDFY4TP53(2)TBCEPHEXMXRA5HSF5FBN3SAMD8EGFRCOPS3BPTF

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A

B

RB1

chr13:48941648 PIK3CA

chr3:178936091

C>T G>A

6% 3%

Fig. S2. Validation of RB1, PIK3CA

mutations in CTC and the primary tumor of

Patient 1. (A) Validation of RB1 and

PIK3CA mutations in CTC of Patient 1

using PCR amplification followed by

Sanger sequencing. (B) Identification of low

frequency mutation of RB1 (6%) and

PIK3CA (3%) in primary tumor of Patient 1

using PCR amplification followed by deep

sequencing. The deep sequence data is

displayed in the Integrative Genomics

Viewer (IGV).

Patient 1

Fig. S3. Copy number variations in CTCs,

leukocyte, blood DNA and tumor tissues of

Patient 1. Normalized sequence reads are

visualized in a Circos plot

(http://www.circos.ca). CTCs exhibit

reproducible CNV patterns.

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Patient 2

A B

Fig. S4. Copy number variations in Patient 2. Normalized sequence reads and copy

numbers are visualized in a Circos (A) and a linear plot (B). The copy numbers were

segmented (blue and red lines) with HMM (see Materials and Methods).

Patient 3

A B

Fig. S5. Copy number variations in Patient 3. Normalized sequence reads and copy numbers are

visualized in a Circos (A) and a linear plot (B).

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Patient 4

A

B

Fig. S6. Copy number variations in Patient 4.

Normalized sequence reads and copy

numbers are visualized in a Circos (A) and a

linear plot (B).




This patient has a mixture of ADC and SCLC

in the lung.

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q value Fig. S10. Statistical

significance of gain and

loss regions in CTCs of

ADC patients (Patients 2-

6). The gains (red) and

losses (blue) are plotted

across the genome (Y-

axis). The q value (X-axis)

at each chromosome

position is calculated

(Materials and Methods).

A significant level of 10-

4.76 for gains and 10-4.18 for

losses (black lines) are

given according to the q

values of gains and losses

in eight normal

leukocytes. Important

cancer associated genes in

the significant gain or loss

regions are marked.

Normal leukocyte CTC

Normal leukocyte CTC

C-Myc

TERT

Fig. S11. Validation of c-Myc gene and TERT gene amplification in CTC with digital PCR.

One CTC and one normal leukocyte from the same patient were lysed and aliquoted,

respectively, to 24 tubes to ensure that multiple copies of DNA were distributed into different

tubes. The whole genome amplification product of each aliquot was subjected to PCR

reactions targeting c-Myc gene and TERT gene. The bands appeared in the gel were counted.

Two copies (diploid) of c-Myc gene and two copies of TERT gene were found in the normal

leukocyte. Six copies (hexaploid) of c-Myc gene and five copies of TERT gene were found in

the CTC.

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Patient 8

A

B

Fig. S12. Copy number variations in Patient 8

(before chemotherapy). Normalized sequence

reads and copy numbers are visualized in a

Circos (A) and a linear plot (B).

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Patient 9

A B

Fig. S13. Copy number variations in Patient 9. Normalized sequence reads and copy numbers

are visualized in a Circos (A) and a linear plot (B).

Patient 10

A B

Fig. S14. Copy number variations in Patient 10. Normalized sequence reads and copy numbers

are visualized in a Circos (A) and a linear plot (B).

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Patient 11

A

B

Fig. S15. Copy number variations in Patient

11. Normalized sequence reads and copy

numbers are visualized in a Circos (A) and a

linear plot (B).

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WT Mutant (hetero.) Mutant (homo.)

Before chemo. First-line chemo. Second-line chemo.

Fig. S16. Detection of SNVs and INDELs in CTCs and metastatic tissue of Patient 8. Non-synonymous heterozygous (hetero.) and homozygous (homo.) mutations in CTCs before, andduring first-line and second-line chemotherapy were shown (mutations with low coverage inCTCs are excluded). Blank region represents no sequence coverage.

CTC

1

CTC

2

CTC

3

CTC

4

CTC

5

CTC

6

CTC

7

CTC

8

CTC

9

CTC

10

CTC

11

CTC

12

CTC

13

CTC

14

CTC

15

CTC

16

CTC

17

CTC

18

CTC

19

CTC

20

CTC

21

CTC

22

CTC

23

CTC

24

CTC

25

Met

a.

ZMYM3UPP1UHRF1BP1SYTL5SFSWAPPIGRPDGFRBMYH11LAMA1KATNA1JAM2GON4LGNAQ(2)GNAQENDOUCARD14ARHGAP32CCDC171ZNF157EXTL1ARL8AVLDLRST3GAL5MUC17GOLM1COL16A1ADAMTS9NCOA6MYCBP2OR6C76COL12A1AHI1PRIMA1PLXNA4DNAH11NINEIF4G1TCF20GOLGB1HHLA1ISG20L2ZNF780ACOL14A1ZIC1KLHL1CSMD3ESCO1CHD8TRIOBPC2orf71TDRD1GALNT1KCNH7AGTR1CTSZRIF1ZNF331SCYL3RYR2GPR87ABCC10NBEAVPS37BRPGRIP1LHABP2U2AF1MLL2BZRAP1FER1L6DBC1(2)CLEC4EGPR98CACNA1CZNF700PARD3BPIK3C2BPPIP5K2ITGB1LRRC4CDAAM2LARP4C4BPAMXRA5F5CYP11B1TTN(2)ATG2BAGTR1(2)OR5D18C16orf58SLC27A6C6orf221DBC1SHISA5DCAF8L1STX8RPE65PHF3ZFATHIPK2OR2W1TMEM132CC22orf23SRGAP1HYDINPRRC2CASXL1RIMS1CILPANKRD34CCOL25A1OR8K5ITGB7GAS2CUL7C10orf137RNF31TTN(3)DSCAMDPP6KCNAB1PLA2G4BJMJD7−PLA2G4BMKS1CSMD3(3)NRASAAK1KLKB1ATXN1LTTLL2TMPRSS12TP53MAP1BGLRA1GRIK2MMEC14orf133MYH7GPA33LRP1BKIF16BMUC2CCDC158ITGA11OR2G3OXR1PAK2CNOT1CRISPLD1SPTA1ZMYM1CSMD3(2)SOX5FAM75E1SLC5A1C2orf77ALPK2ASAP1NR3C2DHX57C1orf173SV2CTTNUSP39MMRN1KIAA1671BCAT1TTC23LUBR4

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Seco

nd

-lin

e c

he

mo

the

rap

y

Fir

st-

lin

e c

he

mo

the

rap

y

Fig. S17. Copy number variations in CTCs of Patient 8 during the first- and second-line

chemotherapy.

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Table S1. Patient information summary.

Sixteen patients with stage IV lung adenocarcinoma (ADC) or small cell lung cancer (SCLC)

were recruited in this study. The tumor cell content was estimated from haematoxylin and eosin

(H&E)-stained formalin-fixed paraffin-embedded (FFPE) tissue sections by two senior

pathologists. 27 CTCs from 6 patients with ADC, 2 CTCs from 1 patient with a mixture of ADC

and SCLC, and 39 CTCs from 4 patients with SCLC in the lung were selected to continue the

whole genome (WGS) and/or exome sequencing study. *Patient whose CTCs were captured at

multiple time points during the course of treatment.

Patient

#

Age

(yrs) Sex

Tumor

type

Tumor

stage at

diagnosis

Sites of FFPE

collection

Estimated

tumor

content in

FFPE

CTC

Isolated

# of CTCs

sequenced

Sequencing

type

1 52 F ADC IV Lung / Liver >70%-90% 24 9 Exome/WGS

2 59 M ADC IV

Superclavian

Lymph Node/Liver >80% 14 6 Exome/WGS

3 52 M ADC IV

Superclavian

Lymph Node >90% 17 5 Exome/WGS

4 54 F ADC IV Lung / Liver 6 5 Exome/WGS

5 54 M ADC IV Lung 6 2 WGS

6 61 F ADC IV Lung 1 1 WGS

7 52 F ADC+

SCLC IV Lung / Liver 17 2 WGS

8* 58 M SCLC IV Lung / Liver >90% 40 11 Exome/WGS

20 8 Exome/WGS

17 9 Exome/WGS

9 62 F SCLC IV Lung/Liver >85% 7 4 WGS

10 53 M SCLC IV Lung/Liver >80% 24 4 WGS

11 61 M SCLC IV Lung >80% 7 6 WGS

12 60 M ADC IV Lung / Liver >80% 3 0 0

13 62 F ADC IV Lung >70% 0 0 0

14 43 F ADC IV

Superclavian

Lymph Node >90% 0 0 0

15 46 F ADC IV Lung >75% 0 0 0

16 78 M SCLC IV Lung >75% 2 0 0

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Chr Start(Mb) End(Mb) Band Type High Risk Genes in the region*chr1 1.0 1.5 1p36.33 gain DVL1chr1 153.5 157.0 1q21.3-1q23.1 gain MUC1 NTRK1 PRCC TPM3 CKS1Bchr1 200.0 201.0 1q32.1 gainchr1 202.5 206.0 1q32.1 gain ELK4 MDM4 SLC45A3chr2 235.5 242.0 2q37.1-2q37.3 gainchr2 86.5 87.0 2p11.2 gainchr3 126.0 129.0 3q21.3 gain GATA2 RPN1chr3 131.0 150.5 3q22.1-3q25.1 gain FOXL2 WWTR1 PIK3CBchr3 153.0 157.5 3q25.2-3q25.32 gain GMPSchr3 162.0 164.0 3q26.1 gainchr3 165.0 198.0 3q26.1 gain BCL6 EIF4A2 ETV5 LPP PIK3CA SOX2 TFRC DVL3 FGF12 MECOM PLD1chr5 0.0 17.5 5p15.33-5p15.1 gain TERTchr5 31.0 40.0 5p13.3-5p13.1 gain IL7R LIFR SKP2

chr6 0.0 57.5 6p25.3-6p11.2 gainCCND3 DAXX DEK FANCE HIST1H4I HMGA1 IRF4 PIM1 POU5F1 SFRS3 TFEB TRIM27 CDKN1A E2F3 HSP90AB1 PPARD RXRB VEGFA HLA-A HLA-B HLA-C

chr6 168.0 169.5 6q27 gain MLLT4chr6 171.0 171.1 6q27 gainchr7 44.0 45.5 7p13-7p12.3 gainchr8 107.0 109.0 8q23.1 gainchr8 109.5 111.0 8q23.1-8q23.2 gainchr8 113.0 122.0 8q23.3-8q24.12 gain EXT1chr8 124.5 146.4 8q24.13-8q24.3 gain MYC NDRG1 RECQL4 PTK2chr8 48.5 49.5 8q11.21 gainchr8 53.5 55.0 8q11.23 gain TCEA1chr8 98.5 105.0 8q22.1-8q22.3 gain COX6C FZD6chr9 115.5 118.0 9q32-9q33.1 gainchr9 122.5 124.5 9q33.2 gain TRAF1chr9 133.0 135.0 9q34.11-9q34.13 gain ABL1 NUP214 LAMC3chr9 136.5 138.0 9q34.2-9q34.3 gain BRD3 RXRAchr10 0.0 3.5 10p15.3-10p15.2 gainchr11 0.0 2.5 11p15.5 gain HRASchr12 104.5 106.0 12q23.3 gainchr12 131.5 132.5 12q24.33 gainchr12 95.5 97.0 12q22-12q23.1 gainchr1 35.5 44.5 1p34.3-1p34.1 gain MPL MYCL1 SFPQ THRAP3 CSF3R SLC2A1chr14 37.0 38.5 14q13.3-14q21.1 gainchr14 56.0 57.5 14q22.3 gain KTN1

chr16 0.0 15.0 16p13.3-16p13.11 gainC16orf75 CIITA CREBBP ERCC4 RUNDC2A SOCS1 TNFRSF17 TSC2 AXIN1 TCEB2

chr17 25.5 49.5 17q11.1-17q21.33 gainBRCA1 CDK12 COL1A1 ERBB2 ETV4 LASP1 MLLT6 NF1 SUZ12 TAF15 FZD2 ITGA2B ITGA3 JUP NOS2 RARA STAT3 STAT5A STAT5B TRAF4 WNT3 WNT9B

chr17 52.5 79.0 17q22-17q25.3 gain BRIP1 CANT1 CD79B CLTC DDX5 HLF MSI2 PRKAR1A AXIN2 BIRC5 GRB2 PRKCA

chr17 79.5 81.2 17q25.3 gain ASPSCR1 RAC3chr18 12.5 14.5 18p11.21 gainchr19 33.5 37.0 19q13.11-19q13.12 gain CEBPAchr19 38.5 40.0 19q13.13-19q13.2 gainchr20 0.5 11.5 20p13-20p12.2 gain BMP2chr20 20.5 23.5 20p11.23-20p11.21 gainchr20 30.0 52.5 20q11.21-20q13.2 gain ASXL1 MAFB SDC4 TOP1 BCL2L1 E2F1 MMP9 PLCG1 STK4chr20 55.0 60.5 20q13.31-20q13.33 gain GNASchr20 62.5 63.0 20q13.33 gainchr21 45.0 47.5 21q22.3 gainchr10 42.0 43.0 10q11.1-10q11.21 losschr17 22.0 22.5 17p11.2-17p11.1 losschr21 11.0 11.5 21p11.1 loss

Table S2. Common chromosome regions with gain or loss in CTCs of ADC patients 2-6.

Common gain regions were found in more than 16 CTCs and loss regions were found in more than 7 CTCs. *Genes in these regions with most frequent CNVs or genes that listed in Cancer Gene Census (http://www.sanger.ac.uk/genetics/CGP/Census), or Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway in Cancer.

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Target and Flanking Target Target Flanking Target Flanking 1x 4x 10x 20x

1 gDNA 5,356.94 89.90% 66.50% 69.62 17.9 99.40% 92.10% 99.40% 97.90% 93.70% 89.20%

Leukocyte 4,163.07 90.10% 67.00% 54.5 13.77 56.00% 43.90% 56.00% 44.90% 38.00% 31.70%

Pri. 7,949.17 92.40% 74.80% 116.2 20.01 99.70% 85.30% 99.70% 99.10% 97.40% 92.60%

CTC1 3,658.68 88.50% 69.90% 49.94 9.76 76.80% 60.10% 76.80% 66.90% 55.90% 44.50%

CTC2 3,341.48 89.20% 67.40% 43.99 10.43 59.10% 49.20% 59.10% 51.50% 43.40% 35.00%

CTC3 3,319.48 87.90% 66.30% 43.01 10.25 61.10% 49.60% 61.10% 53.00% 44.40% 35.60%

CTC4 4,649.20 88.40% 67.60% 61.44 13.85 53.40% 43.40% 53.40% 46.90% 40.70% 34.30%

CTC5 2,840.74 85.10% 63.90% 35.46 8.65 63.70% 48.30% 63.70% 48.00% 39.40% 30.80%

CTC6 3,092.17 88.90% 67.60% 40.83 9.45 66.60% 51.70% 66.60% 55.70% 44.80% 34.60%

CTC7 4,404.31 87.90% 66.50% 57.23 13.49 55.10% 43.10% 55.10% 46.40% 39.20% 32.60%

CTC8 3,720.92 89.30% 67.50% 49.03 11.65 59.60% 40.50% 59.60% 41.40% 34.10% 28.00%

Meta. 6,539.35 93.00% 75.80% 96.88 16.03 99.50% 80.90% 99.50% 98.60% 95.90% 89.20%

2 gDNA 3,649.50 89.40% 67.00% 47.75 11.7 99.40% 89.30% 99.40% 97.20% 90.10% 74.10%

Leukocyte 3,163.24 78.20% 62.90% 38.85 6.96 56.70% 44.00% 56.70% 48.90% 40.90% 32.70%

CTC 1 4,565.80 84.50% 65.60% 58.51 12.34 62.70% 50.20% 62.70% 53.40% 45.70% 38.00%

CTC 2 5,270.73 82.80% 64.10% 66.04 14.13 65.20% 52.80% 65.20% 55.10% 47.40% 39.80%

CTC 3 3,977.64 82.10% 62.70% 48.75 11.04 65.40% 55.00% 65.40% 57.20% 48.40% 39.00%

CTC 4 3,593.64 84.10% 68.00% 47.72 8.31 67.90% 52.80% 67.90% 59.30% 50.00% 40.00%

CTC 5 5,100.83 81.80% 63.50% 63.25 13.39 72.10% 61.20% 72.10% 64.80% 55.90% 46.10%

CTC 6 4,072.62 86.00% 69.70% 55.48 9.49 74.40% 56.30% 74.40% 65.10% 54.90% 44.20%

Meta. 9,970.98 93.90% 84.30% 164.18 13.79 99.80% 62.80% 99.80% 99.00% 96.40% 90.00%

3 gDNA 4,781.80 90.00% 67.60% 63.15 15.35 99.60% 91.70% 99.60% 98.10% 93.60% 82.40%

Leukocyte 2,931.47 78.50% 63.70% 36.47 6.22 47.20% 35.60% 47.20% 39.60% 33.30% 27.10%

CTC1 3,722.87 84.50% 68.20% 49.63 8.65 70.60% 54.30% 70.60% 61.40% 51.50% 41.20%

CTC2 3,236.98 81.70% 66.00% 41.76 7.25 66.80% 50.80% 66.80% 57.40% 47.50% 37.50%

CTC3 4,037.88 89.40% 66.90% 52.79 13.01 77.00% 62.90% 77.00% 67.50% 56.10% 44.30%

CTC4 3,056.03 88.30% 65.60% 39.19 9.91 57.60% 45.20% 57.60% 49.40% 40.60% 31.80%

CTC5 4,236.88 89.50% 66.50% 55.07 13.94 59.40% 48.50% 59.40% 52.50% 44.90% 36.90%

Meta. 4,666.53 93.80% 80.70% 73.53 8.8 99.60% 70.40% 99.60% 97.90% 92.10% 79.60%

4 gDNA 6,167.17 91.40% 74.40% 89.63 15 99.70% 91.00% 99.70% 98.90% 96.60% 90.20%

Leukocyte 4,157.36 78.70% 63.60% 51.62 9.05 85.20% 55.50% 85.20% 60.50% 46.10% 37.20%

CTC1 4,753.38 84.40% 67.80% 62.95 11.28 64.80% 51.90% 64.80% 57.90% 50.00% 41.50%

CTC2 4,595.64 87.50% 71.60% 64.26 10.46 68.20% 52.40% 68.20% 61.00% 52.60% 43.70%

CTC3 3,757.48 83.50% 68.20% 50.07 8.22 65.40% 49.50% 65.40% 57.50% 48.50% 39.20%

CTC4 4,425.78 81.30% 66.10% 57.13 9.66 54.00% 42.50% 54.00% 47.90% 41.40% 34.60%

CTC5 5,286.46 84.90% 69.50% 71.76 11.67 80.50% 62.00% 80.50% 71.90% 61.30% 50.00%

gDNA 4,045.32 90.40% 66.40% 52.48 13.91 99.60% 94.30% 99.60% 97.80% 91.90% 77.80%

Leukocyte 2,816.17 86.60% 64.30% 35.35 9 58.00% 46.60% 58.00% 48.50% 39.40% 30.80%

CTC1 6,515.90 90.80% 74.50% 94.84 15.25 65.60% 53.00% 65.60% 60.20% 54.30% 48.00%

CTC2 3,995.39 90.50% 68.30% 53.33 12.67 56.30% 47.60% 56.30% 49.20% 42.40% 35.30%

CTC3 5,652.52 86.10% 70.20% 77.52 12.9 77.20% 62.70% 77.20% 70.80% 62.80% 53.70%

CTC4 5,401.02 87.80% 71.40% 75.35 12.64 59.20% 49.40% 59.20% 54.40% 49.20% 43.30%

CTC5 3,918.17 87.50% 71.30% 54.56 9.12 69.00% 52.90% 69.00% 61.40% 52.40% 42.70%

CTC6 5,436.91 89.20% 72.80% 77.29 12.81 66.30% 52.60% 66.30% 59.90% 53.00% 45.60%

CTC7 5,119.24 84.80% 68.80% 68.77 11.76 73.50% 58.00% 73.50% 66.10% 57.70% 48.70%

CTC8 2,535.86 89.60% 66.90% 33.14 8.24 70.30% 53.80% 70.30% 57.10% 44.30% 32.70%

CTC9 4,353.09 90.20% 68.00% 57.86 13.79 58.00% 47.90% 58.00% 49.80% 42.60% 35.40%

CTC10 4,990.54 90.30% 73.30% 71.49 12.14 55.80% 45.30% 55.80% 50.20% 44.30% 37.80%

CTC11 3,262.88 89.80% 67.60% 43.09 10.38 71.40% 57.70% 71.40% 60.60% 49.70% 38.80%

CTC12 3,930.51 89.40% 72.40% 55.6 9.57 57.80% 46.40% 57.80% 52.20% 45.40% 38.00%

CTC13 4,219.84 86.80% 64.80% 53.39 13.31 58.00% 49.60% 58.00% 51.30% 44.30% 36.70%

CTC14 4,665.48 90.00% 65.30% 59.5 16.54 60.10% 53.30% 60.10% 53.60% 46.40% 38.80%

CTC15 3,993.72 86.70% 70.40% 54.89 9.37 67.50% 53.10% 67.50% 60.60% 52.10% 42.60%

CTC16 5,895.18 89.60% 73.10% 84.19 13.9 66.40% 52.20% 66.40% 59.80% 52.90% 45.70%

CTC17 4,423.86 84.50% 68.30% 59 10.3 55.30% 40.20% 55.30% 44.90% 38.70% 32.90%

CTC18 5,710.40 90.30% 73.70% 82.25 13.53 69.70% 57.60% 69.70% 64.20% 57.70% 50.30%

CTC19 5,056.23 77.90% 63.00% 62.27 10.74 58.30% 45.60% 58.30% 51.50% 44.50% 37.40%

CTC20 4,229.79 79.30% 64.20% 53.04 9.15 58.70% 45.00% 58.70% 50.90% 43.50% 35.90%

CTC21 4,085.05 80.80% 65.40% 52.19 9.04 56.50% 43.90% 56.50% 49.70% 42.50% 35.10%

CTC22 4,596.35 82.70% 67.30% 60.43 10.17 68.10% 51.90% 68.10% 60.20% 51.30% 42.00%

CTC23 5,614.43 88.20% 71.80% 78.78 13.21 72.60% 59.60% 72.60% 66.60% 59.60% 51.60%

CTC24 6,440.24 86.40% 70.10% 88.15 15.05 77.60% 65.30% 77.60% 71.80% 64.80% 56.50%

CTC25 6,561.42 90.50% 73.90% 94.67 15.63 61.80% 51.70% 61.80% 56.80% 51.60% 46.00%

Meta. 7,835.58 93.10% 76.10% 116.45 19.1 99.60% 83.50% 99.60% 98.90% 96.70% 91.50%

Percentage of coverage for target and its flanking (200 bp outside the target region boundaries) regions for individual CTCs, normalleukocytes, primary (Pri.) and/or metastastic (Meta.) tumors from each patient. The percentage of target regions that were covered at>1x, >4x, >10x, >20x were shown.

8

Table S3. Exome capture sequence coverage.

Target regions at x Fold Coverage (%)Mean Depth

Patient

Coverage(%)

SampleYield bases

(Mb)

Mapped Bases(%)

19 of 30

Chr PositionWild

typeMutant

Change

typeGene name Trancript_ID

Exon

RankEffect

old_AA/

new_AA

Old_codon/

New_codonCodon# Dist.

1 19415329 C T SNP UBR4 NM_020765 98 NON_SYNONYMOUS R/H cGc/cAc 4785 C/M

1 26671625 A G SNP AIM1L NM_001039775 2 SYNONYMOUS S/S tcT/tcC 508 P/M

1 35824705 A G SNP ZMYM4 NM_005095 3 NON_SYNONYMOUS N/D Aat/Gat 89 C/M

1 177133576 G A SNP ASTN1 NM_207108 1 SYNONYMOUS V/V gtC/gtT 79 C/M

1 186275982 C T SNP PRG4 NM_005807 7 SYNONYMOUS T/T acC/acT 377 C

1 199997039 G A SNP NR5A2 NM_003822 1 NON_SYNONYMOUS V/M Gtg/Atg 22 M

1 204378887 C T SNP PPP1R15B NM_032833 1 SYNONYMOUS E/E gaG/gaA 551 C/M

2 74007164 C T SNP DUSP11 NM_003584 1 NON_SYNONYMOUS E/K Gag/Aag 27 P/C/M

2 112933344 G A SNP FBLN7 NM_153214 4 NON_SYNONYMOUS G/R Gga/Aga 154 M

2 125521689 T C SNP CNTNAP5 NM_130773 16 NON_SYNONYMOUS L/P cTt/cCt 832 M

2 179423113 C A SNP TTN NM_003319 155 NON_SYNONYMOUS D/Y Gac/Tac 19960 P/C/M

2 179596666 T C SNP TTN NM_133378 55 NON_SYNONYMOUS I/V Att/Gtt 4402 C

2 179612324 T C SNP TTN NM_133379 46 NON_SYNONYMOUS I/V Atc/Gtc 4935 P/C/M

2 200813085 A T SNP TYW5 NM_001039693 2 SYNONYMOUS A/A gcT/gcA 63 C/M

2 206869847 C T SNP INO80D NM_017759 11 NON_SYNONYMOUS E/K Gag/Aag 777 P

2 209212646 C T SNP PIKFYVE NM_015040 35 NON_SYNONYMOUS S/F tCt/tTt 1758 C/M

2 220366721 C T SNP GMPPA NM_013335 5 STOP_GAINED R/* Cga/Tga 131 C/M

3 27431460 T A SNP SLC4A7 NM_003615 22 NON_SYNONYMOUS I/L Ata/Tta 1099 P

3 30691922 G A SNP TGFBR2 NM_003242 3 NON_SYNONYMOUS E/K Gag/Aag 142 C/M

3 51907931 G A SNP IQCF5 NM_001145059 2 NON_SYNONYMOUS R/C Cgt/Tgt 89 C/M

3 118906753 C T SNP UPK1B NM_006952 3 SYNONYMOUS I/I atC/atT 67 C/M

3 127298688 G C SNP TPRA1 NM_016372 2 SYNONYMOUS L/L ctC/ctG 51 P/C/M

3 142274740 * +T INS ATR NM_001184 10 FRAME_SHIFT -/? -/A 774 C

3 155615734 A G SNP GMPS NM_003875 3 SYNONYMOUS G/G ggA/ggG 76 C

3 178936091 G A SNP PIK3CA NM_006218 10 NON_SYNONYMOUS E/K Gag/Aag 545 C/M

4 183651411 G A SNP ODZ3 NM_001080477 14 NON_SYNONYMOUS V/I Gta/Ata 882 C/M

5 112179782 C T SNP APC NM_000038 16 NON_SYNONYMOUS P/S Cct/Tct 2831 C/M

5 127647024 T C SNP FBN2 NM_001999 39 NON_SYNONYMOUS Y/C tAc/tGc 1681 P/C

5 140209662 G A SNP PCDHA6 NM_018909 1 SYNONYMOUS T/T acG/acA 662 M

5 141353167 A T SNP RNF14 NM_001201365 3 NON_SYNONYMOUS D/V gAt/gTt 5 C/M

5 159680609 G A SNP CCNJL NM_024565 7 STOP_GAINED Q/* Cag/Tag 362 C/M

6 12015758 G A SNP HIVEP1 NM_002114 SPLICE_SITE_ACCEPTOR C/M

6 28542592 G A SNP SCAND3 NM_052923 3 SYNONYMOUS P/P ccC/ccT 630 C

6 31473633 A C SNP MICB NM_005931 2 NON_SYNONYMOUS K/Q Aag/Cag 104 P/C/M

6 34835056 C A SNP UHRF1BP1 NM_017754 16 NON_SYNONYMOUS A/D gCt/gAt 1156 P

6 35423973 G A SNP FANCE NM_021922 2 NON_SYNONYMOUS R/K aGa/aAa 233 C/M

6 52996883 C A SNP GCM1 NM_003643 4 NON_SYNONYMOUS K/N aaG/aaT 121 M

6 133767828 A G SNP EYA4 NM_004100 4 SYNONYMOUS P/P ccA/ccG 48 C/M

7 11446018 C T SNP THSD7A NM_015204 21 SYNONYMOUS V/V gtG/gtA 1382 C

7 55242465 *

-GGAATTAAGAGAAGC

DEL EGFR NM_005228 19CODON_CHANGE_PLUS_C

ODON_DELETIONKELREA/K

aaggaattaagagaagca/

aaa745 P/C/M

7 64439463 T C SNP ZNF117 NM_015852 4 SYNONYMOUS E/E gaA/gaG 162 C/M

7 110763611 T A SNP LRRN3 NM_018334 2 NON_SYNONYMOUS N/K aaT/aaA 261 M

7 142881465 G C SNP TAS2R39 NM_176881 1 SYNONYMOUS L/L ctG/ctC 318 P/C/M

8 73480124 C T SNP KCNB2 NM_004770 2 NON_SYNONYMOUS T/M aCg/aTg 52 C/M

9 15203853 G A SNP TTC39B NM_152574 7 NON_SYNONYMOUS L/F Ctc/Ttc 243 C/M

9 88284462 T C SNP AGTPBP1 NM_015239 8 SYNONYMOUS G/G ggA/ggG 200 C

10 94835050 C T SNP CYP26A1 NM_057157 4 NON_SYNONYMOUS R/W Cgg/Tgg 215 C/M

10 100174885 G A SNP PYROXD2 NM_032709 1 NON_SYNONYMOUS A/V gCa/gTa 3 P

10 116093049 C T SNP AFAP1L2 NM_032550 3 NON_SYNONYMOUS D/N Gat/Aat 51 C/M

11 1094855 C T SNP MUC2 NM_002457 32 SYNONYMOUS Y/Y taC/taT 1977 P

11 5221097 G A SNP OR51V1 NM_001004760 1 SYNONYMOUS S/S tcC/tcT 278 C/M

11 30928186 C T SNP DCDC5 NM_020869 11 SYNONYMOUS L/L ctG/ctA 442 C/M

11 64677277 G A SNP ATG2A NM_015104 14 SYNONYMOUS G/G ggC/ggT 661 C/M

11 100863155 C G SNP TMEM133 NM_032021 1 NON_SYNONYMOUS P/R cCc/cGc 39 C/M

11 123484217 C T SNP GRAMD1B NM_020716 15 NON_SYNONYMOUS S/F tCt/tTt 550 P/C/M

11 125888323 A G SNP CDON NM_016952 5 NON_SYNONYMOUS V/A gTa/gCa 181 P/C/M

12 11174534 T C SNP TAS2R19 NM_176888 1 NON_SYNONYMOUS S/G Agc/Ggc 213 P/C

12 57642536 C T SNP STAC3 NM_145064 4 NON_SYNONYMOUS E/K Gaa/Aaa 129 P

12 81762589 G A SNP PPFIA2 NM_003625 13 NON_SYNONYMOUS S/L tCg/tTg 466 M

12 100478342 A C SNP UHRF1BP1L NM_015054 10 SYNONYMOUS V/V gtT/gtG 400 P

12 105600927 G A SNP APPL2 NM_018171 8 NON_SYNONYMOUS S/F tCc/tTc 178 C/M

13 48941648 C T SNP RB1 NM_000321 10 STOP_GAINED R/* Cga/Tga 320 C/M

13 95095801 T C SNP DCT NM_001922 7 NON_SYNONYMOUS I/V Att/Gtt 424 C

13 96743296 G A SNP HS6ST3 NM_153456 1 SYNONYMOUS A/A gcG/gcA 60 M

14 20711536 G T SNP OR11H4 NM_001004479 1 NON_SYNONYMOUS A/S Gct/Tct 196 C/M

14 20760258 G A SNP TTC5 NM_138376 9 NON_SYNONYMOUS P/S Cct/Tct 363 C/M

14 21875094 C T SNP CHD8 NM_020920 14 NON_SYNONYMOUS R/H cGt/cAt 664 C/M

15 80445418 G A SNP FAH NM_000137 1 NON_SYNONYMOUS E/K Gag/Aag 8 M

16 89805613 G A SNP FANCA NM_000135 41 SYNONYMOUS V/V gtC/gtT 1365 P

17 7578466 G A SNP TP53 NM_000546 5 NON_SYNONYMOUS T/I aCc/aTc 155 C/M

17 10204904 G A SNP MYH13 NM_003802 40 SYNONYMOUS S/S agC/agT 1928 P

17 33316621 T A SNP LIG3 NM_002311 4 NON_SYNONYMOUS N/K aaT/aaA 276 C

17 33884155 G A SNP SLFN14 NM_001129820 1 SYNONYMOUS V/V gtC/gtT 309 M

17 42957991 T C SNP EFTUD2 NM_004247 8 NON_SYNONYMOUS T/A Act/Gct 184 C

17 43181196 G A SNP NMT1 NM_021079 10 SYNONYMOUS Q/Q caG/caA 428 C

17 56663238 G T SNP TEX14 NM_031272 18 SYNONYMOUS G/G ggC/ggA 998 P

17 80202688 G A SNP CSNK1D NM_001893 9 NON_SYNONYMOUS S/F tCc/tTc 406 P

18 30847211 A G SNP C18orf34 NM_198995 13 SYNONYMOUS S/S agT/agC 409 P

Table S4. Summary of non-synonymous and synonymous SNVs and INDELs identified in CTCs and tumor tissues from five patients.

Patient 1

20 of 30

18 61649004 T C SNP SERPINB8 NM_002640 4 NON_SYNONYMOUS L/S tTg/tCg 119 C

18 67365812 C T SNP DOK6 NM_152721 5 SYNONYMOUS F/F ttC/ttT 194 P/C

19 11036381 C T SNP YIPF2 NM_024029 5 SYNONYMOUS R/R cgG/cgA 116 P

19 49867931 G A SNP DKKL1 NM_014419 2 NON_SYNONYMOUS D/N Gat/Aat 35 P

19 50361847 G A SNP PTOV1 NM_017432 10 SYNONYMOUS Q/Q caG/caA 326 P/C/M

19 50550285 G A SNP ZNF473 NM_015428 5 NON_SYNONYMOUS R/H cGt/cAt 862 C/M

19 53572491 T C SNP ZNF160 NM_033288 6 SYNONYMOUS K/K aaA/aaG 432 C/M

20 62195987 G C SNP PRIC285 NM_033405 3 NON_SYNONYMOUS F/L ttC/ttG 827 P

21 46032482 C T SNP KRTAP10-8 NM_198695 1 SYNONYMOUS C/C tgC/tgT 155 P/C/M

22 19504166 G A SNP CDC45 NM_003504 16 SYNONYMOUS K/K aaG/aaA 519 C/M

22 38710124 C T SNP CSNK1E NM_001894 2 SYNONYMOUS R/R cgG/cgA 13 C/M

X 55479352 G C SNP MAGEH1 NM_014061 1 NON_SYNONYMOUS R/T aGg/aCg 182 C/M

X 77913105 A T SNP ZCCHC5 NM_152694 2 SYNONYMOUS T/T acT/acA 271 M

X 101972299 G A SNP GPRASP2 NM_138437 4 SYNONYMOUS V/V gtG/gtA 834 C/M

X 102931628 C T SNP MORF4L2 NM_012286 4 NON_SYNONYMOUS E/K Gaa/Aaa 110 C/M

X 123519644 C T SNP ODZ1 NM_014253 28 NON_SYNONYMOUS E/K Gag/Aag 1980 C/M

X 132887970 C T SNP GPC3 NM_004484 3 NON_SYNONYMOUS A/T Gcc/Acc 191 M

X 148797710 C G SNP MAGEA11 NM_005366 5 NON_SYNONYMOUS I/M atC/atG 188 C/M

Chr Position WT MutantChange


Exon

RankEffect

old_AA/

new_AA

Old_codon/


1 12835964 C T SNP PRAMEF12 NM_001080830 2 NON_SYNONYMOUS A/V gCc/gTc 189 C/M

1 26369939 G T SNP SLC30A2 NM_032513 3 NON_SYNONYMOUS D/E gaC/gaA 125 C/M

1 26608819 A C SNP UBXN11 NM_183008 16 NON_SYNONYMOUS C/G Tgt/Ggt 512 M

1 36557425 A T SNP ADPRHL2 NM_017825 3 NON_SYNONYMOUS K/M aAg/aTg 172 C/M

1 65247070 A G SNP RAVER2 NM_018211 4 NON_SYNONYMOUS Q/R cAg/cGg 265 C/M

1 89323019 C T SNP GTF2B NM_001514 6 SYNONYMOUS Q/Q caG/caA 229 C/M

1 91382527 C A SNP ZNF644 NM_201269 6 NON_SYNONYMOUS R/L cGa/cTa 1271 C

1 100342070 A G SNP AGL NM_000645 9 NON_SYNONYMOUS H/R cAt/cGt 430 C/M

1 103352545 T C SNP COL11A1 NM_080630 61 NON_SYNONYMOUS E/G gAa/gGa 1443 C

1 110033758 T C SNP ATXN7L2 NM_153340 10 NON_SYNONYMOUS C/R Tgc/Cgc 525 C/M

1 152279848 T C SNP FLG NM_002016 3 NON_SYNONYMOUS H/R cAt/cGt 2505 C

1 152325783 T G SNP FLG2 NM_001014342 3 SYNONYMOUS T/T acA/acC 1493 M

1 152671515 *

-

CAGCTCTGGGGG

CTGCTGCGGC

TCCAGCTCTGGG

GGCTGCTG

DEL LCE2A NM_178428 2 CODON_DELETIONPSSGGCCG

SSSGGCC/P

cccagctctgggggctgctg

cggctccagctctgggggct

gctgc/ccc

46 C

1 157095030 T A SNP ETV3 NM_001145312 5 NON_SYNONYMOUS K/M aAg/aTg 381 M

1 158300811 A G SNP CD1B NM_001764 2 NON_SYNONYMOUS S/P Tcc/Ccc 35 C/M

1 158607978 A T SNP SPTA1 NM_003126 36 SYNONYMOUS T/T acT/acA 1678 C/M

1 165324772 C T SNP LMX1A NM_177398 2 NON_SYNONYMOUS E/K Gag/Aag 9 M

1 176564502 C A SNP PAPPA2 NM_021936 3 NON_SYNONYMOUS P/T Ccc/Acc 588 M

1 179561979 A C SNP TDRD5 NM_173533 2 NON_SYNONYMOUS K/Q Aaa/Caa 77 M

1 183086480 G C SNP LAMC1 NM_002293 9 NON_SYNONYMOUS Q/H caG/caC 530 C/M

1 192548318 C A SNP RGS1 NM_002922 5 NON_SYNONYMOUS P/T Cca/Aca 166 C/M

1 201178637 C G SNP IGFN1 NM_001164586 12 NON_SYNONYMOUS A/G gCa/gGa 1539 C/M

1 201178768 A G SNP IGFN1 NM_001164586 12 NON_SYNONYMOUS S/G Agt/Ggt 1583 C/M

1 203036843 T A SNP PPFIA4 NM_015053 13 NON_SYNONYMOUS I/N aTc/aAc 518 M

1 248263328 T C SNP OR2L13 NM_175911 3 SYNONYMOUS C/C tgT/tgC 217 M

1 248343406 T C SNP OR2M2 NM_001004688 1 NON_SYNONYMOUS M/T aTg/aCg 40 M

2 27800497 G C SNP C2orf16 NM_032266 1 NON_SYNONYMOUS G/A gGg/gCg 353 C/M

2 31467243 G A SNP EHD3 NM_014600 2 NON_SYNONYMOUS G/R Ggg/Agg 111 C/M

2 84848361 G T SNP DNAH6 NM_001370 25 NON_SYNONYMOUS W/L tGg/tTg 1280 C/M

2 110922728 T G SNP NPHP1 NM_207181 7 NON_SYNONYMOUS Y/S tAt/tCt 210 C/M

2 113676198 T C SNP IL37 NM_173205 4 NON_SYNONYMOUS Y/H Tat/Cat 131 M

2 165984491 T C SNP SCN3A NM_001081676 18 NON_SYNONYMOUS I/V Att/Gtt 966 C

2 170518915 T A SNP C2orf77 NM_001085447 5 NON_SYNONYMOUS R/W Agg/Tgg 232 M

2 185803724 A T SNP ZNF804A NM_194250 4 NON_SYNONYMOUS T/S Act/Tct 1201 M

2 186657513 A T SNP FSIP2 NM_173651 16 NON_SYNONYMOUS T/S Acc/Tcc 1973 C/M

2 207041328 T C SNP GPR1 NM_005279 3 NON_SYNONYMOUS Y/C tAt/tGt 215 C/M

2 220416251 C A SNP OBSL1 NM_015311 20 NON_SYNONYMOUS G/C Ggc/Tgc 1895 C/M

2 238820348 G T SNP RAMP1 NM_005855 3 NON_SYNONYMOUS V/L Gtg/Ttg 124 M

3 40286080 C G SNP MYRIP NM_015460 13 SYNONYMOUS V/V gtC/gtG 748 C/M

3 69171510 G C SNP LMOD3 NM_198271 1 NON_SYNONYMOUS Q/E Caa/Gaa 10 M

3 75787989 G C SNP ZNF717 NM_001128223 5 NON_SYNONYMOUS P/R cCa/cGa 262 C/M

3 118623523 C A SNP IGSF11 NM_152538 8 STOP_GAINED E/* Gaa/Taa 275 C/M

3 129267887 C A SNP H1FOO NM_153833 3 NON_SYNONYMOUS A/D gCc/gAc 141 M

3 130289707 G A SNP COL6A6 NM_001102608 6 NON_SYNONYMOUS S/N aGc/aAc 816 C/M

3 132233509 C T SNP DNAJC13 NM_015268 46 NON_SYNONYMOUS P/L cCa/cTa 1827 C/M

3 183898893 G T SNP AP2M1 NM_004068 7 NON_SYNONYMOUS V/L Gtg/Ttg 196 C/M

3 186269006 G T SNP TBCCD1 NM_018138 7 NON_SYNONYMOUS T/K aCa/aAa 536 C/M

3 194140670 A T SNP ATP13A3 NM_024524 30 NON_SYNONYMOUS L/I Tta/Ata 1114 C/M

4 6865741 T C SNP KIAA0232 NM_014743 7 NON_SYNONYMOUS L/S tTg/tCg 1211 M

4 8621087 C T SNP CPZ NM_003652 10 NON_SYNONYMOUS P/S Ccc/Tcc 557 M

4 13604215 C T SNP BOD1L1 NM_148894 10 NON_SYNONYMOUS G/S Ggc/Agc 1437 C

4 39439550 A T SNP KLB NM_175737 3 NON_SYNONYMOUS T/S Acg/Tcg 514 C/M

4 42403241 A C SNP SHISA3 NM_001080505 2 NON_SYNONYMOUS T/P Aca/Cca 164 C/M

4 56448304 C A SNP PDCL2 NM_152401 2 NON_SYNONYMOUS R/L cGt/cTt 36 C/M

4 69097014 C T SNP TMPRSS11B NM_182502 7 STOP_GAINED W/* tGg/tAg 198 C/M

4 85747991 G A SNP WDFY3 NM_014991 10 NON_SYNONYMOUS A/V gCa/gTa 367 M

4 126371409 A G SNP FAT4 NM_024582 9 NON_SYNONYMOUS T/A Act/Gct 3080 M

4 183659631 G T SNP ODZ3 NM_001080477 17 STOP_GAINED E/* Gaa/Taa 1105 C/M

5 11364920 T C SNP CTNND2 NM_001332 8 NON_SYNONYMOUS I/M atA/atG 420 C/M

5 31464430 * -C DEL DROSHA NM_013235 19 FRAME_SHIFT -/- -/- 829 C/M

5 37206328 C A SNP C5orf42 NM_023073 17 SYNONYMOUS L/L ctG/ctT 1040 M

Patient 2

21 of 30

5 41065541 C T SNP HEATR7B2 NM_173489 4 NON_SYNONYMOUS A/T Gca/Aca 85 C/M

5 64520228 C G SNP ADAMTS6 NM_197941 SPLICE_SITE_ACCEPTOR C/M

5 64881830 T A SNP PPWD1 NM_015342 10 NON_SYNONYMOUS F/Y tTt/tAt 540 M

5 74872683 C G SNP POLK NM_016218 6 NON_SYNONYMOUS H/D Cac/Gac 207 C/M

5 74872699 * -A DEL POLK NM_016218 6 FRAME_SHIFT -/- -/- 212 C/M

5 131552997 T C SNP P4HA2 NM_004199 4 NON_SYNONYMOUS D/G gAt/gGt 75 C

5 140208397 A T SNP PCDHA6 NM_031848 1 NON_SYNONYMOUS T/S Act/Tct 241 C/M

5 140475439 C T SNP PCDHB2 NM_018936 1 SYNONYMOUS I/I atC/atT 355 M

5 169174471 T A SNP DOCK2 NM_004946 23 NON_SYNONYMOUS L/Q cTg/cAg 780 C/M

5 179663443 C T SNP MAPK9 NM_139070 12 NON_SYNONYMOUS A/T Gcc/Acc 406 C/M

6 10756728 C T SNP TMEM14B NM_030969 6 NON_SYNONYMOUS R/C Cgt/Tgt 108 M

6 29394815 T A SNP OR11A1 NM_013937 1 NON_SYNONYMOUS I/F Att/Ttt 202 C

6 30545211 G A SNP ABCF1 NM_001090 2 SYNONYMOUS K/K aaG/aaA 33 C/M

6 89891746 G A SNP GABRR1 NM_002042 8 NON_SYNONYMOUS T/M aCg/aTg 276 C/M

6 131973792 A G SNP ENPP3 NM_005021 4 NON_SYNONYMOUS K/E Aag/Gag 130 C/M

6 138655277 A T SNP KIAA1244 NM_020340 33 NON_SYNONYMOUS Q/L cAg/cTg 1765 C/M

7 23552613 T C SNP TRA2A NM_013293 4 NON_SYNONYMOUS Y/C tAt/tGt 142 M

7 31682758 C T SNP CCDC129 NM_194300 11 NON_SYNONYMOUS H/Y Cac/Tac 592 C/M

7 43531763 T A SNP HECW1 NM_015052 18 NON_SYNONYMOUS H/Q caT/caA 1108 C/M

7 57528803 T C SNP ZNF716 NM_001159279 4 SYNONYMOUS S/S tcT/tcC 212 C/M

7 76825796 A G SNP FGL2 NM_006682 2 NON_SYNONYMOUS Y/H Tac/Cac 374 C/M

7 82451871 C T SNP PCLO NM_014510 20 NON_SYNONYMOUS D/N Gat/Aat 4911 C/M

7 87160768 G T SNP ABCB1 NM_000927 22 NON_SYNONYMOUS L/I Ctt/Att 843 C/M

7 88389380 G T SNP ZNF804B NM_181646 1 NON_SYNONYMOUS K/N aaG/aaT 30 M

7 92732120 C G SNP SAMD9 NM_017654 3 NON_SYNONYMOUS K/N aaG/aaC 1097 C/M

7 105278986 T C SNP ATXN7L1 NM_138495 5 NON_SYNONYMOUS H/R cAc/cGc 215 C/M

7 105283436 G A SNP ATXN7L1 NM_138495 3 SYNONYMOUS T/T acC/acT 113 M

7 137341232 A T SNP DGKI NM_004717 4 NON_SYNONYMOUS C/S Tgc/Agc 221 C/M

7 150488674 T C SNP TMEM176B NM_014020 7 NON_SYNONYMOUS N/S aAt/aGt 253 C/M

8 2966139 A T SNP CSMD1 NM_033225 44 NON_SYNONYMOUS V/D gTc/gAc 2247 C/M

8 61732610 G A SNP CHD7 NM_017780 9 SYNONYMOUS R/R cgG/cgA 886 C/M

8 77764425 G T SNP ZFHX4 NM_024721 10 NON_SYNONYMOUS L/F ttG/ttT 1756 C/M

8 110100165 G A SNP TRHR NM_003301 1 NON_SYNONYMOUS A/T Gcc/Acc 142 C/M

8 121279099 C G SNP COL14A1 NM_021110 25 NON_SYNONYMOUS P/R cCa/cGa 1017 C/M

8 134274336 C A SNP NDRG1 NM_006096 5 NON_SYNONYMOUS V/L Gtg/Ttg 94 C/M

9 7011808 G T SNP KDM4C NM_015061 13 STOP_GAINED E/* Gag/Tag 633 C/M

9 32633381 C A SNP TAF1L NM_153809 1 NON_SYNONYMOUS A/S Gca/Tca 733 C/M

9 79323743 A C SNP PRUNE2 NM_015225 8 NON_SYNONYMOUS S/R agT/agG 1149 C/M

9 131588714 T G SNP C9orf114 NM_016390 SPLICE_SITE_ACCEPTOR M

10 48386022 * -CTT DEL RBP3 NM_002900 2CODON_CHANGE_PLUS_C

ODON_DELETIONEV/V gaagta/gta 1023 C/M

10 55568837 T A SNP PCDH15 NM_001142769 36 NON_SYNONYMOUS N/I aAc/aTc 1663 C/M

10 113920626 C A SNP GPAM NM_020918 16 STOP_GAINED G/* Gga/Tga 499 M

10 114154789 T C SNP ACSL5 NM_016234 2 SYNONYMOUS L/L Ttg/Ctg 85 C/M

10 118306915 C A SNP PNLIP NM_000936 3 NON_SYNONYMOUS N/K aaC/aaA 52 C

10 128823013 A T SNP DOCK1 NM_001380 15 NON_SYNONYMOUS Q/L cAa/cTa 485 M

11 4936446 C A SNP OR51G2 NM_001005238 1 NON_SYNONYMOUS G/C Ggc/Tgc 150 C/M

11 50003461 G A SNP OR4C12 NM_001005270 1 NON_SYNONYMOUS L/F Ctt/Ttt 193 C/M

11 55111217 C T SNP OR4A16 NM_001005274 1 NON_SYNONYMOUS P/S Cca/Tca 181 M

11 59629013 G C SNP TCN1 NM_001062 4 NON_SYNONYMOUS S/R agC/agG 181 M

11 60183312 A T SNP MS4A14 NM_032597 5 NON_SYNONYMOUS T/S Acc/Tcc 291 M

11 64956073 T G SNP CAPN1 NM_005186 10 NON_SYNONYMOUS F/V Ttc/Gtc 341 M

11 68853993 G A SNP TPCN2 NM_139075 23 STOP_GAINED W/* tGg/tAg 669 C/M

11 70821058 C T SNP SHANK2 NM_012309 5 NON_SYNONYMOUS R/H cGc/cAc 174 M

11 71706536 A T SNP RNF121 NM_018320 8 STOP_GAINED K/* Aag/Tag 268 M

11 74880272 C T SNP SLCO2B1 NM_007256 5 NON_SYNONYMOUS P/L cCa/cTa 168 C

11 111896471 A G SNP DLAT NM_001931 1 NON_SYNONYMOUS Q/R cAg/cGg 92 C/M

11 123676367 G T SNP OR6M1 NM_001005325 1 NON_SYNONYMOUS R/S Cgt/Agt 231 C/M

11 124743268 C T SNP ROBO3 NM_022370 10 SYNONYMOUS S/S agC/agT 533 C/M

11 133796885 T A SNP IGSF9B NM_014987 13 NON_SYNONYMOUS Y/F tAc/tTc 578 M

11 134184223 G T SNP GLB1L3 NM_001080407 SPLICE_SITE_ACCEPTOR M

12 29936562 G T SNP TMTC1 NM_001193451 1 STOP_GAINED Y/* taC/taA 41 C/M

12 32481238 G T SNP BICD1 NM_001714 5 NON_SYNONYMOUS D/Y Gac/Tac 617 C/M

12 53040696 G T SNP KRT2 NM_000423 7 NON_SYNONYMOUS H/N Cat/Aat 433 C/M

12 53702580 T C SNP AAAS NM_015665 11 NON_SYNONYMOUS D/G gAt/gGt 339 C/M

12 75444283 G A SNP KCNC2 NM_139137 3 NON_SYNONYMOUS P/L cCt/cTt 501 C/M

12 76791598 T G SNP OSBPL8 NM_020841 8 NON_SYNONYMOUS K/T aAa/aCa 183 C/M

12 83360710 G T SNP TMTC2 NM_152588 7 NON_SYNONYMOUS V/L Gta/Tta 628 C/M

12 91449994 C T SNP KERA NM_007035 2 NON_SYNONYMOUS S/N aGt/aAt 22 C/M

12 124114789 A G SNP EIF2B1 NM_001414 4 NON_SYNONYMOUS L/P cTt/cCt 99 C

13 28622413 T G SNP FLT3 NM_004119 9 NON_SYNONYMOUS S/R Agc/Cgc 402 C/M

13 32913000 T C SNP BRCA2 NM_000059 11 NON_SYNONYMOUS L/P cTa/cCa 1503 C

13 48881511 G A SNP RB1 NM_000321 2 STOP_GAINED W/* tGg/tAg 78 C/M

14 20344848 G A SNP OR4K2 NM_001005501 1 NON_SYNONYMOUS C/Y tGt/tAt 141 C/M

14 20841967 C A SNP TEP1 NM_007110 45 NON_SYNONYMOUS E/D gaG/gaT 2158 C/M

14 21500064 T C SNP TPPP2 NM_173846 4 NON_SYNONYMOUS V/A gTg/gCg 114 C/M

14 60035036 T C SNP C14orf38 NM_001164399 4 NON_SYNONYMOUS T/A Aca/Gca 140 C/M

14 70989750 C A SNP ADAM20 NM_003814 2 SYNONYMOUS L/L ctG/ctT 625 C/M

14 81259208 C A SNP CEP128 NM_152446 13 NON_SYNONYMOUS A/S Gct/Tct 486 C/M

14 102478332 G T SNP DYNC1H1 NM_001376 33 NON_SYNONYMOUS V/L Gtg/Ttg 2247 C/M

15 48062892 G C SNP SEMA6D NM_153618 19 NON_SYNONYMOUS S/T aGt/aCt 711 M

15 65993507 A T SNP DENND4A NM_005848 19 SYNONYMOUS P/P ccT/ccA 861 C/M

15 74751056 G A SNP UBL7 NM_032907 2 SYNONYMOUS L/L ctC/ctT 51 M

15 77473522 G A SNP PEAK1 NM_024776 5 SYNONYMOUS H/H caC/caT 249 M

15 86198716 G A SNP AKAP13 NM_006738 11 SYNONYMOUS L/L ctG/ctA 1481 M

22 of 30

16 30593945 A G SNP ZNF785 NM_152458 3 NON_SYNONYMOUS L/S tTg/tCg 385 M

16 57151441 A T SNP CPNE2 NM_152727 5 NON_SYNONYMOUS I/F Atc/Ttc 157 C/M

17 7576852 C T SNP TP53 NM_000546 SPLICE_SITE_DONOR C/M

17 8006799 * -C DEL ALOXE3 NM_021628 15 FRAME_SHIFT -/- -/- 600 C/M

17 10430374 C A SNP MYH2 NM_017534 SPLICE_SITE_ACCEPTOR C/M

17 26087764 G T SNP NOS2 NM_000625 24 NON_SYNONYMOUS S/R agC/agA 965 C/M

17 56342101 T G SNP LPO NM_006151 10 NON_SYNONYMOUS Y/D Tac/Gac 429 C/M

17 65850151 A G SNP BPTF NM_182641 2 NON_SYNONYMOUS M/V Atg/Gtg 237 M

17 65972045 A G SNP BPTF NM_004459 29 SYNONYMOUS V/V gtA/gtG 2882 C/M

17 72858986 C T SNP FDXR NM_024417 12 NON_SYNONYMOUS E/K Gag/Aag 477 M

17 77079946 A G SNP ENGASE NM_001042573 10 NON_SYNONYMOUS H/R cAc/cGc 452 C/M

17 78829298 T G SNP RPTOR NM_020761 12 NON_SYNONYMOUS L/W tTg/tGg 450 C/M

17 79163570 C T SNP AZI1 NM_014984 26 SYNONYMOUS_STOP */* tGa/tAa 1081 M

18 13826342 T C SNP MC5R NM_005913 1 NON_SYNONYMOUS M/T aTg/aCg 193 M

18 29044164 C T SNP DSG3 NM_001944 9 STOP_GAINED R/* Cga/Tga 364 C/M

18 29412098 C G SNP TRAPPC8 NM_014939 28 NON_SYNONYMOUS C/S tGt/tCt 1341 C/M

18 61310665 A G SNP SERPINB4 NM_002974 2 SYNONYMOUS T/T acT/acC 49 M

18 74637227 G T SNP ZNF236 NM_007345 22 SYNONYMOUS T/T acG/acT 1246 C/M

19 889709 C T SNP MED16 NM_005481 4 NON_SYNONYMOUS V/M Gtg/Atg 126 M

19 2115598 G A SNP AP3D1 NM_003938 19 SYNONYMOUS T/T acC/acT 696 M

19 10561301 A T SNP PDE4A NM_001111309 5 NON_SYNONYMOUS T/S Acc/Tcc 154 C/M

19 12461915 A C SNP ZNF442 NM_030824 6 NON_SYNONYMOUS F/V Ttc/Gtc 162 C/M

19 12911669 A G SNP PRDX2 NM_181738 3 SYNONYMOUS S/S agT/agC 106 C/M

19 17449775 G T SNP GTPBP3 NM_133644 5 NON_SYNONYMOUS V/L Gtg/Ttg 202 C/M

19 22497126 G T SNP ZNF729 NM_001242680 4 NON_SYNONYMOUS G/W Ggg/Tgg 303 C/M

19 36002356 * -TTGCCA DEL DMKN NM_033317 5CODON_CHANGE_PLUS_C

ODON_DELETIONSGN/S agtggcaac/agc 290 C/M

19 36002368 * -CCA DEL DMKN NM_033317 5CODON_CHANGE_PLUS_C

ODON_DELETIONGG/G ggtggc/ggc 287 C/M

19 36332683 G A SNP NPHS1 NM_004646 20 NON_SYNONYMOUS L/F Ctc/Ttc 917 M

19 37210273 A G SNP ZNF567 NM_152603 4 NON_SYNONYMOUS E/G gAg/gGg 185 C/M

19 47422356 G T SNP ARHGAP35 NM_004491 1 STOP_GAINED E/* Gag/Tag 142 C/M

19 52569539 C T SNP ZNF841 NM_001136499 7 SYNONYMOUS Q/Q caG/caA 532 C/M

19 55485883 C T SNP NLRP2 NM_017852 3 NON_SYNONYMOUS S/F tCc/tTc 99 C/M

19 58199491 G A SNP ZNF551 NM_138347 3 SYNONYMOUS E/E gaG/gaA 600 C/M

20 8862344 G C SNP PLCB1 NM_015192 32 NON_SYNONYMOUS E/Q Gaa/Caa 1167 C

22 23406153 C A SNP RTDR1 NM_014433 5 NON_SYNONYMOUS V/F Gtc/Ttc 194 C/M

22 37964273 A C SNP CDC42EP1 NM_152243 3 NON_SYNONYMOUS S/R Agc/Cgc 208 C/M

X 14625311 T G SNP GLRA2 NM_002063 6 SYNONYMOUS V/V gtT/gtG 212 C/M

X 15682462 C A SNP TMEM27 NM_020665 2 NON_SYNONYMOUS A/S Gca/Tca 39 C/M

X 39933437 G A SNP BCOR NM_017745 4 NON_SYNONYMOUS L/F Ctc/Ttc 388 M

X 41073859 A G SNP USP9X NM_001039591 34 NON_SYNONYMOUS D/G gAc/gGc 1743 C/M

X 124454740 G A SNP LOC100129520NM_001195272 1 NON_SYNONYMOUS A/T Gca/Aca 258 C/M



Exon

RankEffect

old_AA/

new_AA

Old_codon/


1 29581810 A G SNP PTPRU NM_133178 2 NON_SYNONYMOUS S/G Agt/Ggt 33 C/M

1 51756267 C T SNP TTC39A NM_001144832 15 NON_SYNONYMOUS V/M Gtg/Atg 437 C/M

1 57257894 T C SNP C1orf168 NM_001004303 2 NON_SYNONYMOUS K/E Aag/Gag 198 C/M

1 67000053 T A SNP SGIP1 NM_032291 SPLICE_SITE_DONOR C/M

1 103352378 G C SNP COL11A1 NM_080630 61 NON_SYNONYMOUS P/A Cct/Gct 1499 C/M

1 152732091 C G SNP KPRP NM_001025231 2 NON_SYNONYMOUS C/W tgC/tgG 9 C/M

1 156106081 G C SNP LMNA NM_170708 7 NON_SYNONYMOUS G/R Ggg/Cgg 412 C/M

1 176671754 C T SNP PAPPA2 NM_020318 9 NON_SYNONYMOUS P/L cCt/cTt 1083 C/M

1 181548336 C T SNP CACNA1E NM_000721 5 STOP_GAINED R/* Cga/Tga 249 C/M

1 202407112 C G SNP PPP1R12B NM_002481 10 STOP_GAINED S/* tCa/tGa 473 C/M

1 213415478 G A SNP RPS6KC1 NM_012424 11 NON_SYNONYMOUS E/K Gag/Aag 887 C/M

1 235346011 C T SNP ARID4B NM_016374 20 SYNONYMOUS L/L ttG/ttA 741 C/M

1 237794757 G C SNP RYR2 NM_001035 42 NON_SYNONYMOUS Q/H caG/caC 2157 C/M

1 248129286 G A SNP OR2AK2 NM_001004491 1 NON_SYNONYMOUS G/E gGa/gAa 218 C/M

2 32673892 C T SNP BIRC6 NM_016252 22 NON_SYNONYMOUS P/L cCa/cTa 1505 M

2 36764640 C T SNP CRIM1 NM_016441 14 SYNONYMOUS P/P ccC/ccT 858 C/M

2 54131295 T C SNP PSME4 NM_014614 SPLICE_SITE_ACCEPTOR C/M

2 116548656 G T SNP DPP10 NM_020868 SPLICE_SITE_ACCEPTOR C/M

2 125521722 G T SNP CNTNAP5 NM_130773 16 NON_SYNONYMOUS S/I aGc/aTc 843 C/M

2 169759049 T A SNP G6PC2 NM_021176 2 NON_SYNONYMOUS C/S Tgt/Agt 105 C/M

2 173451101 C T SNP PDK1 NM_002610 9 SYNONYMOUS S/S tcC/tcT 347 C/M

2 201756935 T G SNP NIF3L1 NM_021824 2 NON_SYNONYMOUS L/R cTc/cGc 63 C/M

2 205829945 G T SNP PARD3B NM_205863 3 NON_SYNONYMOUS R/L cGg/cTg 98 C/M

2 210682658 G A SNP UNC80 NM_182587 11 NON_SYNONYMOUS E/K Gaa/Aaa 559 C/M

2 220480058 G C SNP STK11IP NM_052902 24 NON_SYNONYMOUS D/H Gat/Cat 1049 M

2 222347354 A C SNP EPHA4 NM_004438 5 NON_SYNONYMOUS L/V Ttg/Gtg 346 C/M

3 4725141 C T SNP ITPR1 NM_002222 26 NON_SYNONYMOUS T/M aCg/aTg 1054 C/M

3 49570604 G T SNP DAG1 NM_004393 3 NON_SYNONYMOUS R/L cGg/cTg 887 C/M

3 52643561 G A SNP PBRM1 NM_018313 17 STOP_GAINED Q/* Caa/Taa 779 C/M

3 58062863 G A SNP FLNB NM_001457 2 STOP_GAINED W/* tGg/tAg 128 C/M

3 86010658 A G SNP CADM2 NM_153184 7 SYNONYMOUS L/L ttA/ttG 270 M

3 108407498 A T SNP DZIP3 NM_014648 30 NON_SYNONYMOUS Q/L cAg/cTg 1110 C/M

3 121341322 C A SNP FBXO40 NM_016298 3 NON_SYNONYMOUS T/N aCc/aAc 349 C/M

3 130852733 G T SNP NEK11 NM_145910 7 STOP_GAINED G/* Gga/Tga 194 C/M

3 134264544 G T SNP CEP63 NM_025180 8 NON_SYNONYMOUS E/D gaG/gaT 224 C/M

3 150916447 G A SNP GPR171 NM_013308 3 STOP_GAINED R/* Cga/Tga 243 C/M

3 171452677 T C SNP PLD1 NM_002662 5 NON_SYNONYMOUS E/G gAa/gGa 173 C/M

3 174814716 T C SNP NAALADL2 NM_207015 2 SYNONYMOUS G/G ggT/ggC 60 C/M

Patient 3

23 of 30

3 196674692 *

-

GCACCCAGTGCC

C

DEL PIGZ NM_025163 3 FRAME_SHIFT -/- -/- 355 C/M

4 2129852 A C SNP POLN NM_181808 17 NON_SYNONYMOUS L/R cTg/cGg 657 C/M

4 3769622 G A SNP ADRA2C NM_000683 1 NON_SYNONYMOUS S/N aGc/aAc 430 M

4 38037319 G T SNP TBC1D1 NM_015173 8 NON_SYNONYMOUS Q/H caG/caT 471 C/M

4 46994900 G C SNP GABRA4 NM_000809 2 SYNONYMOUS R/R cgC/cgG 50 C/M

4 52869484 A T SNP LRRC66 NM_001024611 2 NON_SYNONYMOUS F/I Ttt/Att 191 C/M

4 52938102 C A SNP SPATA18 NM_145263 6 NON_SYNONYMOUS Q/K Cag/Aag 180 C/M

4 57899421 G T SNP IGFBP7 NM_001553 3 NON_SYNONYMOUS D/E gaC/gaA 214 C/M

4 70350927 A G SNP UGT2B4 NM_021139 5 SYNONYMOUS L/L Tta/Cta 437 C/M

4 89627967 G C SNP HERC3 NM_014606 26 NON_SYNONYMOUS Q/H caG/caC 1003 C/M

4 118975965 C T SNP NDST3 NM_004784 2 SYNONYMOUS S/S tcC/tcT 300 M

4 125591691 C G SNP ANKRD50 NM_020337 4 NON_SYNONYMOUS R/T aGa/aCa 914 C/M

4 146823651 C G SNP ZNF827 NM_178835 2 NON_SYNONYMOUS A/P Gcc/Ccc 254 C/M

4 159791539 T A SNP FNIP2 NM_020840 14 NON_SYNONYMOUS M/K aTg/aAg 956 C/M

4 175598367 G A SNP GLRA3 NM_006529 7 SYNONYMOUS P/P ccC/ccT 263 M

5 14749338 C T SNP ANKH NM_054027 6 SYNONYMOUS R/R cgG/cgA 255 M

5 37182864 T C SNP C5orf42 NM_023073 26 NON_SYNONYMOUS K/E Aag/Gag 1807 C/M

5 90086741 A T SNP GPR98 NM_032119 70 NON_SYNONYMOUS T/S Acc/Tcc 4699 C/M

5 118500301 C G SNP DMXL1 NM_005509 20 NON_SYNONYMOUS S/C tCt/tGt 1601 C/M

5 118580123 G C SNP DMXL1 NM_005509 42 NON_SYNONYMOUS G/A gGt/gCt 2904 M

5 140480524 C A SNP PCDHB3 NM_018937 1 SYNONYMOUS G/G ggC/ggA 97 C/M

5 140580331 * -TG DEL PCDHB11 NM_018931 1 FRAME_SHIFT -/- -/- 328 M

5 140772638 C A SNP PCDHGA8 NM_014004 1 SYNONYMOUS T/T acC/acA 86 C/M

5 146781171 T C SNP DPYSL3 NM_001387 9 SYNONYMOUS A/A gcA/gcG 300 C/M

5 150407556 C T SNP GPX3 NM_002084 5 SYNONYMOUS N/N aaC/aaT 182 M

5 156590091 C A SNP FAM71B NM_130899 2 SYNONYMOUS V/V gtG/gtT 395 C/M

5 179565042 G A SNP RASGEF1C NM_175062 2 NON_SYNONYMOUS T/M aCg/aTg 4 C/M

5 180432717 G T SNP BTNL3 NM_197975 8 NON_SYNONYMOUS G/W Ggg/Tgg 416 C/M

6 10756728 C T SNP TMEM14B NM_030969 6 NON_SYNONYMOUS R/C Cgt/Tgt 108 C/M

6 12125987 G C SNP HIVEP1 NM_002114 4 NON_SYNONYMOUS A/P Gct/Cct 1987 M

6 28251876 C A SNP PGBD1 NM_032507 2 NON_SYNONYMOUS L/M Ctg/Atg 96 C/M

6 32154667 A G SNP PBX2 NM_002586 7 NON_SYNONYMOUS S/P Tct/Cct 346 M

6 39835422 C A SNP DAAM2 NM_015345 6 NON_SYNONYMOUS Q/K Cag/Aag 189 C/M

6 44253796 C T SNP TCTE1 NM_182539 3 NON_SYNONYMOUS D/N Gac/Aac 251 C/M

6 109752405 G A SNP PPIL6 NM_173672 3 SYNONYMOUS D/D gaC/gaT 125 M

6 117665305 G C SNP ROS1 NM_002944 27 NON_SYNONYMOUS T/S aCc/aGc 1481 C/M

6 159134898 A T SNP SYTL3 NM_001242394 9 NON_SYNONYMOUS T/S Acc/Tcc 195 C/M

6 159659679 G C SNP FNDC1 NM_032532 13 NON_SYNONYMOUS D/H Gat/Cat 1388 C/M

7 12412602 C A SNP VWDE NM_001135924 SPLICE_SITE_DONOR C/M

7 23830450 * +GAGCCT INS STK31 NM_032944 22 STOP_GAINED R/RA* cga/cGAGCCTga 859 C/M

7 44737344 G T SNP OGDH NM_002541 17 NON_SYNONYMOUS G/V gGc/gTc 774 C/M

7 45124795 C T SNP NACAD NM_001146334 2 SYNONYMOUS P/P ccG/ccA 328 M

7 53103936 G A SNP POM121L12 NM_182595 1 NON_SYNONYMOUS R/K aGg/aAg 191 C/M

7 65557756 C A SNP ASL NM_000048 17 NON_SYNONYMOUS P/T Ccc/Acc 418 C/M

7 100352874 C T SNP ZAN NM_003386 15 SYNONYMOUS Y/Y taC/taT 1050 C/M

7 100681322 A T SNP MUC17 NM_001040105 3 NON_SYNONYMOUS S/C Agc/Tgc 2209 C/M

7 133868605 G T SNP LRGUK NM_144648 11 NON_SYNONYMOUS G/V gGg/gTg 445 C/M

7 137284636 G A SNP DGKI NM_004717 11 STOP_GAINED Q/* Cag/Tag 395 C/M

7 139090464 G T SNP LUC7L2 NM_016019 5 SYNONYMOUS G/G ggG/ggT 147 C/M

7 158449008 G C SNP NCAPG2 NM_017760 19 NON_SYNONYMOUS L/V Ctc/Gtc 778 C/M

8 3226776 C T SNP CSMD1 NM_033225 19 NON_SYNONYMOUS G/R Gga/Aga 967 C/M

8 6783465 T C SNP DEFA6 NM_001926 1 SYNONYMOUS A/A gcA/gcG 31 M

8 17412098 G T SNP SLC7A2 NM_001008539 7 NON_SYNONYMOUS R/L cGt/cTt 362 C/M

8 39027452 G C SNP ADAM32 NM_145004 10 NON_SYNONYMOUS R/P cGt/cCt 284 M

8 43197329 G A SNP POTEA NM_001002920 SPLICE_SITE_ACCEPTOR C/M

8 48766668 G A SNP PRKDC NM_006904 51 NON_SYNONYMOUS H/Y Cac/Tac 2290 M

8 80965549 G A SNP TPD52 NM_005079 3 SYNONYMOUS A/A gcC/gcT 84 C/M

8 87393834 G T SNP WWP1 NM_007013 5 NON_SYNONYMOUS A/S Gct/Tct 104 C/M

8 103564038 T C SNP ODF1 NM_024410 1 NON_SYNONYMOUS I/T aTc/aCc 28 C/M

8 110408354 G A SNP PKHD1L1 NM_177531 11 NON_SYNONYMOUS V/I Gtt/Att 304 C/M

8 110505895 T C SNP PKHD1L1 NM_177531 63 SYNONYMOUS N/N aaT/aaC 3414 C/M

8 143823792 * -GC DEL SLURP1 NM_020427 1 FRAME_SHIFT -/- -/- 4 C/M

9 32635371 * +G INS TAF1L NM_153809 1 FRAME_SHIFT -/? -/C 69 C/M

9 86616030 G C SNP RMI1 NM_024945 3 NON_SYNONYMOUS L/F ttG/ttC 43 C/M

9 90301581 * -G DEL DAPK1 NM_004938 21 FRAME_SHIFT -/- -/- 780 C/M

9 111640303 A G SNP IKBKAP NM_003640 35 NON_SYNONYMOUS L/P cTt/cCt 1276 C/M

9 127620232 G C SNP RPL35 NM_007209 4 NON_SYNONYMOUS L/V Ctg/Gtg 113 M

9 134348946 G C SNP PRRC2B NM_013318 14 NON_SYNONYMOUS R/P cGc/cCc 720 C/M

9 135982605 G A SNP RALGDS NM_006266 7 NON_SYNONYMOUS A/V gCg/gTg 427 C/M

9 138415729 G A SNP LCN1 NM_002297 4 NON_SYNONYMOUS G/E gGg/gAg 99 C/M

10 18250630 A T SNP SLC39A12 NM_152725 3 NON_SYNONYMOUS I/F Atc/Ttc 128 C/M

10 32575917 C A SNP EPC1 NM_025209 8 NON_SYNONYMOUS E/D gaG/gaT 393 C/M

10 50533342 A T SNP C10orf71 NM_001135196 3 NON_SYNONYMOUS T/S Aca/Tca 918 C/M

10 55568754 T C SNP PCDH15 NM_001142769 36 NON_SYNONYMOUS K/E Aaa/Gaa 1691 C/M

10 76788686 A G SNP KAT6B NM_012330 18 SYNONYMOUS E/E gaA/gaG 1368 C/M

10 89487103 C G SNP PAPSS2 NM_004670 8 NON_SYNONYMOUS L/V Ctg/Gtg 310 C/M

10 91066795 T C SNP IFIT2 NM_001547 2 NON_SYNONYMOUS F/S tTc/tCc 361 C/M

10 101643775 G A SNP DNMBP NM_015221 15 SYNONYMOUS D/D gaC/gaT 1330 C/M

10 127464375 T C SNP MMP21 NM_147191 1 NON_SYNONYMOUS I/V Atc/Gtc 6 C/M

10 127697999 G A SNP FANK1 NM_145235 11 NON_SYNONYMOUS V/I Gtc/Atc 344 C/M

10 127806615 * -C DEL ADAM12 NM_021641 6 FRAME_SHIFT -/- -/- 202 C/M

10 134748355 T A SNP TTC40 NM_001200049 8 NON_SYNONYMOUS Q/L cAa/cTa 256 C/M

11 3704668 T C SNP NUP98 NM_139132 29 NON_SYNONYMOUS I/M atA/atG 1486 C

11 5862816 G C SNP OR52E6 NM_001005167 1 NON_SYNONYMOUS F/L ttC/ttG 104 C/M

11 18158799 G T SNP MRGPRX3 NM_054031 3 NON_SYNONYMOUS G/V gGa/gTa 17 M

11 19251145 C T SNP E2F8 NM_024680 10 SYNONYMOUS L/L ctG/ctA 583 C/M

24 of 30

11 22281109 C A SNP ANO5 NM_213599 15 SYNONYMOUS R/R cgC/cgA 484 C/M

11 26529708 A G SNP ANO3 NM_031418 5 NON_SYNONYMOUS I/V Att/Gtt 164 C/M

11 26669263 G C SNP ANO3 NM_031418 24 NON_SYNONYMOUS W/C tgG/tgC 812 C/M

11 55322295 G T SNP OR4C15 NM_001001920 1 NON_SYNONYMOUS M/I atG/atT 171 C/M

11 59282879 C T SNP OR4D9 NM_001004711 1 NON_SYNONYMOUS P/L cCa/cTa 165 C/M

11 64606195 A G SNP CDC42BPG NM_017525 8 SYNONYMOUS Y/Y taT/taC 352 C/M

11 72554367 T A SNP FCHSD2 NM_014824 16 NON_SYNONYMOUS N/Y Aat/Tat 512 C/M

11 76895695 G A SNP MYO7A NM_000260 27 SYNONYMOUS R/R cgG/cgA 1146 C/M

11 82643769 G T SNP C11orf82 NM_145018 6 SYNONYMOUS V/V gtG/gtT 463 C/M

11 92086384 G C SNP FAT3 NM_001008781 1 NON_SYNONYMOUS R/T aGa/aCa 369 C/M

11 92543053 G A SNP FAT3 NM_001008781 12 NON_SYNONYMOUS V/M Gtg/Atg 3098 M

11 101353860 C A SNP TRPC6 NM_004621 5 NON_SYNONYMOUS V/L Gta/Tta 444 M

11 121033077 G T SNP TECTA NM_005422 15 NON_SYNONYMOUS C/F tGc/tTc 1757 C/M

11 124766445 A T SNP ROBO4 NM_019055 3 NON_SYNONYMOUS D/E gaT/gaA 174 C/M

11 124793876 G T SNP HEPACAM NM_152722 3 NON_SYNONYMOUS A/D gCt/gAt 153 C/M

12 39994460 A G SNP ABCD2 NM_005164 6 NON_SYNONYMOUS L/P cTc/cCc 520 C/M

12 40702327 G T SNP LRRK2 NM_198578 29 NON_SYNONYMOUS V/L Gtg/Ttg 1340 C/M

12 55846609 A T SNP OR6C2 NM_054105 1 SYNONYMOUS A/A gcA/gcT 204 C/M

12 75698598 T C SNP CAPS2 NM_032606 9 NON_SYNONYMOUS I/V Atc/Gtc 259 C/M

12 80760387 A G SNP OTOGL NM_173591 52 NON_SYNONYMOUS S/G Agt/Ggt 2092 C/M

12 88379795 A G SNP C12orf50 NM_152589 11 NON_SYNONYMOUS Y/H Tat/Cat 320 C/M

12 102067385 G A SNP MYBPC1 NM_206821 23 NON_SYNONYMOUS D/N Gac/Aac 907 C/M

12 112622399 G C SNP C12orf51 NM_001109662 61 SYNONYMOUS P/P ccC/ccG 3323 M

12 112646359 G C SNP C12orf51 NM_001109662 51 NON_SYNONYMOUS P/R cCt/cGt 2514 C/M

12 116457746 C A SNP MED13L NM_015335 6 SYNONYMOUS T/T acG/acT 219 C/M

12 129100781 G T SNP TMEM132C NM_001136103 4 SYNONYMOUS T/T acG/acT 402 C/M

13 103514596 G T SNP BIVM-ERCC5 NM_001204425 16 NON_SYNONYMOUS R/L cGa/cTa 820 C/M

13 103514596 G T SNP ERCC5 NM_000123 8 NON_SYNONYMOUS R/L cGa/cTa 366 C/M

14 20389240 C A SNP OR4K5 NM_001005483 1 NON_SYNONYMOUS Q/K Cag/Aag 159 C/M

14 64486727 T G SNP SYNE2 NM_182914 35 NON_SYNONYMOUS H/Q caT/caG 1689 C/M

14 68229446 T C SNP ZFYVE26 NM_015346 33 SYNONYMOUS A/A gcA/gcG 2034 C/M

14 92563122 T C SNP ATXN3 NM_004993 2 NON_SYNONYMOUS S/G Agc/Ggc 29 C/M

14 101348596 A G SNP RTL1 NM_001134888 1 NON_SYNONYMOUS Y/H Tac/Cac 844 C/M

15 22383156 A T SNP OR4N4 NM_001005241 1 SYNONYMOUS A/A gcA/gcT 228 C/M

15 50154553 C A SNP ATP8B4 NM_024837 27 SYNONYMOUS L/L ctG/ctT 1062 C/M

16 1712787 A T SNP CRAMP1L NM_020825 12 NON_SYNONYMOUS K/M aAg/aTg 874 C/M

16 70893971 C A SNP HYDIN NM_032821 71 NON_SYNONYMOUS E/D gaG/gaT 4042 C/M

16 71196455 A T SNP HYDIN NM_032821 6 NON_SYNONYMOUS V/E gTa/gAa 232 C/M

16 77317885 G T SNP ADAMTS18 NM_199355 23 NON_SYNONYMOUS Q/K Caa/Aaa 1212 M

17 5036274 C A SNP USP6 NM_004505 5 NON_SYNONYMOUS H/N Cac/Aac 89 C/M

17 7577574 T C SNP TP53 NM_000546 7 NON_SYNONYMOUS Y/C tAc/tGc 236 C/M

17 34964765 * -C DEL MRM1 NM_024864 5 FRAME_SHIFT -/- -/- 326 C/M

17 46846440 C T SNP TTLL6 NM_173623 8 NON_SYNONYMOUS A/T Gca/Aca 556 C/M

17 47302230 G T SNP PHOSPHO1 NM_178500 3 NON_SYNONYMOUS A/D gCc/gAc 61 C/M

17 55058497 C T SNP SCPEP1 NM_021626 2 NON_SYNONYMOUS T/M aCg/aTg 44 C/M

17 59945367 A G SNP INTS2 NM_020748 24 NON_SYNONYMOUS L/S tTa/tCa 1091 C/M

17 76970889 A T SNP LGALS3BP NM_005567 4 NON_SYNONYMOUS I/N aTc/aAc 86 C/M

18 13746323 T C SNP RNMT NM_003799 9 NON_SYNONYMOUS M/T aTg/aCg 415 C/M

18 30260470 T C SNP KLHL14 NM_020805 6 NON_SYNONYMOUS Y/C tAt/tGt 444 C/M

18 50451626 G T SNP DCC NM_005215 5 NON_SYNONYMOUS G/C Ggt/Tgt 291 C/M

19 10812210 G A SNP QTRT1 NM_031209 1 NON_SYNONYMOUS R/H cGc/cAc 25 M

19 11941451 G T SNP ZNF440 NM_152357 3 NON_SYNONYMOUS Q/H caG/caT 50 C/M

19 14693994 A C SNP CLEC17A NM_207390 1 NON_SYNONYMOUS T/P Act/Cct 8 M

19 17213125 G T SNP MYO9B NM_004145 2 NON_SYNONYMOUS V/L Gtg/Ttg 200 C/M

19 17691647 G C SNP GLT25D1 NM_024656 11 NON_SYNONYMOUS A/P Gct/Cct 512 M

19 17883303 T A SNP FCHO1 NM_015122 10 NON_SYNONYMOUS M/K aTg/aAg 211 C/M

19 31769455 G T SNP TSHZ3 NM_020856 2 NON_SYNONYMOUS T/N aCc/aAc 415 M

19 36124671 C G SNP RBM42 NM_024321 7 NON_SYNONYMOUS A/G gCg/gGg 256 M

19 44514778 C G SNP ZNF230 NM_006300 5 NON_SYNONYMOUS S/C tCt/tGt 196 M

19 44832442 C G SNP ZFP112 NM_013380 4 NON_SYNONYMOUS R/T aGa/aCa 623 C/M

19 44890932 C T SNP ZNF285 NM_152354 4 NON_SYNONYMOUS C/Y tGc/tAc 492 C/M

19 46417823 C T SNP NANOS2 NM_001029861 1 SYNONYMOUS P/P ccG/ccA 43 C/M

19 51857740 C A SNP ETFB NM_001014763 1 SYNONYMOUS L/L ctG/ctT 51 C/M

19 52091082 G A SNP ZNF175 NM_007147 5 NON_SYNONYMOUS E/K Gag/Aag 500 C/M

19 52519263 G C SNP ZNF614 NM_025040 5 NON_SYNONYMOUS Q/E Caa/Gaa 530 C/M

19 56701209 G C SNP ZSCAN5B NM_001080456 4 NON_SYNONYMOUS T/S aCc/aGc 492 M

19 56702337 T C SNP ZSCAN5B NM_001080456 3 NON_SYNONYMOUS H/R cAc/cGc 203 C/M

19 57802385 T G SNP ZNF460 NM_006635 3 NON_SYNONYMOUS V/G gTt/gGt 159 M

19 58724017 G A SNP ZNF274 NM_133502 8 NON_SYNONYMOUS G/E gGa/gAa 490 M

19 59010935 A T SNP SLC27A5 NM_012254 7 NON_SYNONYMOUS Y/N Tac/Aac 531 C/M

20 10033870 * -G DEL ANKRD5 NM_198798 8 FRAME_SHIFT -/- -/- 661 C/M

20 10280039 G T SNP SNAP25 NM_130811 7 NON_SYNONYMOUS Q/H caG/caT 177 C/M

20 17434533 C T SNP PCSK2 NM_002594 9 SYNONYMOUS D/D gaC/gaT 344 C/M

20 44453265 G A SNP TNNC2 NM_003279 3 NON_SYNONYMOUS A/V gCc/gTc 23 C/M

20 47282822 *

-

GTGGTGCATGAA

GCCATT

DEL PREX1 NM_020820 15 CODON_DELETION NGFMHH/- aatggcttcatgcaccac/- 574 C/M

20 56137148 C T SNP PCK1 NM_002591 3 SYNONYMOUS P/P ccC/ccT 82 C/M

20 57767964 G A SNP ZNF831 NM_178457 1 SYNONYMOUS R/R agG/agA 630 M

20 61939442 G C SNP COL20A1 NM_020882 7 NON_SYNONYMOUS G/R Ggc/Cgc 259 M

20 62059760 G C SNP KCNQ2 NM_172108 10 NON_SYNONYMOUS L/V Ctg/Gtg 393 C/M

20 62292654 G C SNP RTEL1 NM_032957 3 NON_SYNONYMOUS V/L Gtg/Ctg 36 C/M

21 32624336 G A SNP TIAM1 NM_003253 6 NON_SYNONYMOUS A/V gCg/gTg 378 C/M

22 32482314 G C SNP SLC5A1 NM_001256314 9 NON_SYNONYMOUS G/R Gga/Cga 250 M

X 43817854 *

-

AGCATAGAAAAG

GATGC

DEL NDP NM_000266 2 FRAME_SHIFT -/- -/- 8 C/M

X 53675225 T C SNP HUWE1 NM_031407 5 NON_SYNONYMOUS K/R aAa/aGa 25 C/M

25 of 30

X 107434698 G A SNP COL4A6 NM_001847 19 NON_SYNONYMOUS R/C Cgt/Tgt 417 C/M

X 117575503 G A SNP WDR44 NM_019045 15 NON_SYNONYMOUS C/Y tGt/tAt 716 C/M

X 127185119 A G SNP ACTRT1 NM_138289 1 NON_SYNONYMOUS M/T aTg/aCg 356 C/M

X 153588868 C A SNP FLNA NM_001456 22 NON_SYNONYMOUS G/C Ggc/Tgc 1099 C/M



Exon

RankEffect

old_AA/

new_AA

Old_codon/


1 43915842 G A SNP SZT2 NM_015284 70 SYNONYMOUS T/T acG/acA 3328 C

1 169951990 C A SNP KIFAP3 NM_014970 14 NON_SYNONYMOUS A/S Gca/Tca 509 C

1 225525151 * +A INS DNAH14 NM_001373 65 FRAME_SHIFT -/? -/A 3329 C

1 235612073 G T SNP TBCE NM_003193 17 NON_SYNONYMOUS W/L tGg/tTg 527 C

2 105900796 G A SNP TGFBRAP1 NM_004257 5 SYNONYMOUS F/F ttC/ttT 366 C

2 234354291 T C SNP DGKD NM_003648 10 NON_SYNONYMOUS L/P cTc/cCc 362 C

3 113721342 G A SNP KIAA1407 NM_020817 12 SYNONYMOUS I/I atC/atT 674 C

5 59899290 C T SNP DEPDC1B NM_018369 9 SYNONYMOUS Q/Q caG/caA 390 C

5 134044567 C G SNP SEC24A NM_021982 18 NON_SYNONYMOUS L/V Ctc/Gtc 906 C

6 66053931 C T SNP EYS NM_198283 9 SYNONYMOUS E/E gaG/gaA 533 C

7 55242466 *

-

GAATTAAGAGAA

GCA

DEL EGFR NM_005228 19 CODON_DELETION ELREA/- gaattaagagaagca/- 746 C

7 77973104 * +T INS MAGI2 NM_012301 9 FRAME_SHIFT -/? -/A 467 C

10 50174653 C G SNP WDFY4 NM_020945 55 NON_SYNONYMOUS P/R cCt/cGt 2840 C

10 76935975 G A SNP SAMD8 NM_144660 5 NON_SYNONYMOUS C/Y tGt/tAt 315 C

14 56083271 C T SNP KTN1 NM_004986 3 NON_SYNONYMOUS P/L cCa/cTa 187 C

15 90349267 * -T DEL ANPEP NM_001150 2 FRAME_SHIFT -/- -/- 183 C

17 7578449 C T SNP TP53 NM_000546 5 NON_SYNONYMOUS A/T Gcc/Acc 161 C

17 7579373 C A SNP TP53 NM_000546 4 NON_SYNONYMOUS G/V gGc/gTc 105 C

17 17150464 * +CT INS COPS3 NM_003653 12 FRAME_SHIFT -/? -/AG 407 C

17 51901040 G C SNP KIF2B NM_032559 1 NON_SYNONYMOUS V/L Gtc/Ctc 216 C

17 56540288 G C SNP HSF5 NM_001080439 4 NON_SYNONYMOUS T/R aCa/aGa 466 C

17 62272306 C T SNP TEX2 NM_018469 3 SYNONYMOUS K/K aaG/aaA 598 C

17 65941651 *

-

CAGCTCAGCCCC

AGCCCC

AAACCCAGCCCC

AGTCCC

DEL BPTF NM_182641 21 CODON_DELETIONSAQPQPQT

QPQSP/S

tcagctcagccccagcccca

aacccagccccagtcccca/

tca

2276 C

19 8138142 C G SNP FBN3 NM_032447 61 NON_SYNONYMOUS S/T aGc/aCc 2581 C

19 8536235 G A SNP HNRNPM NM_005968 10 SYNONYMOUS G/G ggG/ggA 307 C

19 36575639 A T SNP WDR62 NM_173636 12 SYNONYMOUS P/P ccA/ccT 545 C

21 46086732 A G SNP KRTAP12-2 NM_181684 1 SYNONYMOUS C/C tgT/tgC 24 C

X 3240731 C A SNP MXRA5 NM_015419 5 NON_SYNONYMOUS A/S Gca/Tca 999 C

X 22132603 C T SNP PHEX NM_000444 11 NON_SYNONYMOUS P/S Cct/Tct 401 C

X 48673392 A T SNP HDAC6 NM_006044 14 SYNONYMOUS A/A gcA/gcT 361 C



Exon

RankEffect

old_AA/

new_AA

Old_codon/


1 100203795 C T SNP FRRS1 NM_001013660 7 SYNONYMOUS K/K aaG/aaA 202 C/M

1 115256530 G T SNP NRAS NM_002524 3 NON_SYNONYMOUS Q/K Caa/Aaa 61 C/M

1 155823200 * -GT DEL GON4L NM_032292 2 FRAME_SHIFT -/- -/- 124 C

1 156694023 * -G DEL ISG20L2 NM_030980 2 FRAME_SHIFT -/- -/- 289 C

1 158614072 C A SNP SPTA1 NM_003126 30 NON_SYNONYMOUS D/Y Gac/Tac 1437 C/M

1 159170643 G A SNP CADM3 NM_021189 10 SYNONYMOUS A/A gcG/gcA 410 C/M

1 160268752 T A SNP COPA NM_004371 19 SYNONYMOUS L/L ctA/ctT 620 C

1 167042733 G C SNP GPA33 NM_005814 2 NON_SYNONYMOUS D/E gaC/gaG 29 C/M

1 169511671 A G SNP F5 NM_000130 13 NON_SYNONYMOUS L/P cTa/cCa 886 C/M

1 169847882 T A SNP SCYL3 NM_020423 3 NON_SYNONYMOUS T/S Act/Tct 82 C/M

1 171526988 *

-

GCCCCAGCCCCA

GCCCCTACCCCA

GTCTCAGCCCCA

AATCCTGCCCCAC

CT DEL PRRC2C NM_015172 19 CODON_DELETION APAPAPTPVSAPNPAPP/-

gccccagccccagccccta

ccccagtctcagccccaaat

cctgccccacct/- 1911 C

1 175365834 C A SNP TNR NM_003285 5 SYNONYMOUS T/T acG/acT 362 C/M

1 180832857 G A SNP XPR1 NM_004736 12 SYNONYMOUS S/S tcG/tcA 505 C/M

1 19432242 A T SNP UBR4 NM_020765 84 NON_SYNONYMOUS L/Q cTg/cAg 4163 C

1 202104346 T C SNP ARL8A NM_001256129 5 SYNONYMOUS E/E gaA/gaG 125 C

1 202104346 T C SNP ARL8A NM_138795 6 NON_SYNONYMOUS N/S aAt/aGt 148 C

1 204433664 C G SNP PIK3C2B NM_002646 5 NON_SYNONYMOUS S/T aGc/aCc 368 C/M

1 207108852 C T SNP PIGR NM_002644 5 NON_SYNONYMOUS V/M Gtg/Atg 453 C

1 207317961 G T SNP C4BPA NM_000715 12 NON_SYNONYMOUS V/L Gtg/Ttg 565 C/M

1 237753125 C T SNP RYR2 NM_001035 30 STOP_GAINED Q/* Caa/Taa 1211 C/M

1 247588857 G T SNP NLRP3 NM_004895 3 SYNONYMOUS V/V gtG/gtT 704 C/M

1 247769541 T A SNP OR2G3 NM_001001914 1 STOP_GAINED Y/* taT/taA 218 C/M

1 248487805 G T SNP OR2M7 NM_001004691 1 SYNONYMOUS P/P ccC/ccA 22 C/M

1 26349533 * -CCT DEL EXTL1 NM_004455 1 CODON_DELETION CL/C tgcctc/tgc 132 C/M

1 32133776 * -G DEL COL16A1 NM_001856 51 FRAME_SHIFT -/- -/- 1098 C

1 35563038 A G SNP ZMYM1 NM_024772 4 NON_SYNONYMOUS Q/R cAg/cGg 97 C/M

1 53729843 T C SNP LRP8 NM_004631 10 SYNONYMOUS R/R cgA/cgG 551 C

1 55565462 C T SNP USP24 NM_015306 45 SYNONYMOUS Q/Q caG/caA 1784 C/M

1 55631573 T C SNP USP24 NM_015306 7 SYNONYMOUS E/E gaA/gaG 304 C

1 68906556 T G SNP RPE65 NM_000329 6 NON_SYNONYMOUS K/T aAg/aCg 208 C/M

1 75038611 * -G DEL C1orf173 NM_001002912 14 FRAME_SHIFT -/- -/- 928 C/M

2 1168848 G A SNP SNTG2 NM_018968 8 SYNONYMOUS L/L ctG/ctA 190 C

2 121043593 G A SNP RALB NM_002881 3 SYNONYMOUS G/G ggG/ggA 86 C

Patient 8

Patient 4

26 of 30

2 136566611 G T SNP LCT NM_002299 8 SYNONYMOUS A/A gcC/gcA 1102 C

2 141806595 C A SNP LRP1B NM_018557 11 NON_SYNONYMOUS Q/H caG/caT 583 C/M

2 152319972 A G SNP RIF1 NM_018151 30 NON_SYNONYMOUS N/S aAt/aGt 1313 C/M

2 163279914 G C SNP KCNH7 NM_033272 9 NON_SYNONYMOUS L/V Ctg/Gtg 696 C/M

2 170505693 A G SNP C2orf77 NM_001085447 8 NON_SYNONYMOUS M/T aTg/aCg 439 C/M

2 179401092 A G SNP TTN NM_003319 185 NON_SYNONYMOUS L/P cTt/cCt 24396 C

2 179419780 G A SNP TTN NM_003319 159 NON_SYNONYMOUS A/V gCg/gTg 20404 C/M

2 179587978 G T SNP TTN NM_133378 72 SYNONYMOUS T/T acC/acA 6008 C/M

2 179611791 C A SNP TTN NM_133379 46 NON_SYNONYMOUS E/D gaG/gaT 5112 C/M

2 197008375 G A SNP STK17B NM_004226 5 SYNONYMOUS L/L ctC/ctT 172 C/M

2 200233401 T A SNP SATB2 NM_015265 7 SYNONYMOUS T/T acA/acT 209 C/M

2 205969149 G C SNP PARD3B NM_057177 SPLICE_SITE_ACCEPTOR C/M

2 21230656 C T SNP APOB NM_000384 26 SYNONYMOUS K/K aaG/aaA 3028 C/M

2 27016114 G C SNP CENPA NM_001809 4 SYNONYMOUS R/R cgG/cgC 130 C/M

2 29295647 T C SNP C2orf71 NM_001029883 1 NON_SYNONYMOUS E/G gAa/gGa 494 C

2 39053683 C A SNP DHX57 NM_198963 15 NON_SYNONYMOUS D/Y Gat/Tat 930 C/M

2 69746214 C A SNP AAK1 NM_014911 12 NON_SYNONYMOUS A/S Gcc/Tcc 457 C/M

2 85875073 A G SNP USP39 NM_001256726 11 NON_SYNONYMOUS N/S aAt/aGt 483 C

2 86075292 C A SNP ST3GAL5 NM_003896 4 NON_SYNONYMOUS K/N aaG/aaT 118 C

2 95753114 T C SNP MRPS5 NM_031902 12 SYNONYMOUS R/R agA/agG 427 C/M

3 121417544 T C SNP GOLGB1 NM_004487 13 NON_SYNONYMOUS E/G gAg/gGg 604 C

3 133654659 T G SNP SLCO2A1 NM_005630 13 SYNONYMOUS R/R cgA/cgC 591 C

3 147131162 G T SNP ZIC1 NM_003412 3 NON_SYNONYMOUS G/C Ggc/Tgc 390 C/M

3 148459594 A T SNP AGTR1 NM_000685 3 NON_SYNONYMOUS I/L Ata/Tta 258 C/M

3 148459734 T A SNP AGTR1 NM_000685 3 NON_SYNONYMOUS F/L ttT/ttA 304 C/M

3 151012421 T A SNP GPR87 NM_023915 3 NON_SYNONYMOUS T/S Acg/Tcg 205 C/M

3 154884739 C A SNP MME NM_000902 18 NON_SYNONYMOUS S/Y tCc/tAc 570 C/M

3 156175263 A G SNP KCNAB1 NM_003471 4 NON_SYNONYMOUS I/V Atc/Gtc 116 C/M

3 184039616 T C SNP EIF4G1 NM_004953 3 NON_SYNONYMOUS L/S tTa/tCa 219 C

3 196529902 G C SNP PAK2 NM_002577 4 NON_SYNONYMOUS Q/H caG/caC 101 C

3 20167447 A G SNP KAT2B NM_003884 10 SYNONYMOUS E/E gaA/gaG 488 C

3 48510931 G A SNP SHISA5 NM_016479 5 NON_SYNONYMOUS P/S Cct/Tct 158 C/M

3 64587762 A G SNP ADAMTS9 NM_182920 26 NON_SYNONYMOUS M/T aTg/aCg 1292 C

3 9413196 C T SNP THUMPD3 NM_015453 4 SYNONYMOUS A/A gcC/gcT 261 C/M

4 109782101 A G SNP COL25A1 NM_032518 22 SYNONYMOUS S/S tcT/tcC 408 C/M

4 109784480 G T SNP COL25A1 NM_032518 20 NON_SYNONYMOUS P/T Cca/Aca 383 C/M

4 149075770 A G SNP NR3C2 NM_000901 5 NON_SYNONYMOUS L/P cTc/cCc 766 C

4 187172958 G T SNP KLKB1 NM_000892 10 NON_SYNONYMOUS G/W Ggg/Tgg 363 C/M

4 77288825 C G SNP CCDC158 NM_001042784 11 NON_SYNONYMOUS L/F ttG/ttC 484 C/M

4 90857374 T C SNP MMRN1 NM_007351 6 NON_SYNONYMOUS L/P cTa/cCa 848 C

5 102487020 G A SNP PPIP5K2 NM_015216 8 NON_SYNONYMOUS G/S Ggc/Agc 324 C/M

5 128320910 G A SNP SLC27A6 NM_014031 3 NON_SYNONYMOUS G/D gGt/gAt 189 C/M

5 140769593 A G SNP PCDHGB4 NM_003736 1 SYNONYMOUS R/R cgA/cgG 714 C/M

5 140857924 G T SNP PCDHGC3 NM_002588 1 SYNONYMOUS V/V gtG/gtT 747 C/M

5 149515117 C T SNP PDGFRB NM_002609 SPLICE_SITE_DONOR C/M

5 151266343 * -G DEL GLRA1 NM_000171 3 FRAME_SHIFT -/- -/- 64 C/M

5 23527873 G A SNP PRDM9 NM_020227 11 SYNONYMOUS E/E gaG/gaA 892 C/M

5 34863002 G T SNP TTC23L NM_144725 SPLICE_SITE_ACCEPTOR C

5 54721046 A G SNP PPAP2A NM_003711 6 SYNONYMOUS N/N aaT/aaC 281 C

5 55081288 A G SNP DDX4 NM_024415 12 SYNONYMOUS S/S tcA/tcG 229 C/M

5 71492271 G T SNP MAP1B NM_005909 5 NON_SYNONYMOUS R/I aGa/aTa 1030 C/M

5 75581116 T G SNP SV2C NM_014979 5 NON_SYNONYMOUS L/W tTg/tGg 348 C/M

5 80521509 T C SNP RASGRF2 NM_006909 27 SYNONYMOUS L/L Ttg/Ctg 1212 C/M

5 89918476 C G SNP GPR98 NM_032119 5 NON_SYNONYMOUS I/M atC/atG 172 C/M

6 102069941 A G SNP GRIK2 NM_021956 2 NON_SYNONYMOUS Y/C tAt/tGt 78 C/M

6 10796273 C G SNP MAK NM_005906 9 SYNONYMOUS P/P ccG/ccC 367 C

6 135776915 A G SNP AHI1 NM_017651 9 NON_SYNONYMOUS L/P cTt/cCt 434 C

6 149916313 G C SNP KATNA1 NM_007044 11 NON_SYNONYMOUS I/M atC/atG 445 C/M

6 167754279 G C SNP TTLL2 NM_031949 3 NON_SYNONYMOUS L/F ttG/ttC 297 C/M

6 29012357 A G SNP OR2W1 NM_030903 1 NON_SYNONYMOUS V/A gTt/gCt 199 C/M

6 34840126 G C SNP UHRF1BP1 NM_017754 21 NON_SYNONYMOUS E/Q Gaa/Caa 1412 C/M

6 36336802 G T SNP ETV7 NM_016135 6 SYNONYMOUS T/T acC/acA 237 C/M

6 39838209 A T SNP DAAM2 NM_015345 8 NON_SYNONYMOUS I/F Atc/Ttc 323 C/M

6 43013992 C T SNP CUL7 NM_014780 12 NON_SYNONYMOUS R/H cGc/cAc 881 C/M

6 43400136 G T SNP ABCC10 NM_033450 1 NON_SYNONYMOUS A/S Gcc/Tcc 97 C/M

6 64408179 * -C DEL PHF3 NM_015153 6 FRAME_SHIFT -/- -/- 916 C/M

6 69758213 G T SNP BAI3 NM_001704 14 SYNONYMOUS P/P ccG/ccT 748 C/M

6 73000448 T G SNP RIMS1 NM_014989 25 NON_SYNONYMOUS I/M atT/atG 1207 C/M

6 74073443 G T SNP C6orf221 NM_001017361 3 NON_SYNONYMOUS V/L Gtg/Ttg 172 C/M

6 75893231 T A SNP COL12A1 NM_004370 10 NON_SYNONYMOUS R/W Agg/Tgg 476 C

7 100685790 C T SNP MUC17 NM_001040105 3 NON_SYNONYMOUS T/I aCt/aTt 3698 C

7 103275919 A G SNP RELN NM_005045 19 SYNONYMOUS T/T acT/acC 806 C

7 123303062 A G SNP LMOD2 NM_207163 2 SYNONYMOUS Q/Q caA/caG 474 C

7 131825499 A G SNP PLXNA4 NM_020911 30 NON_SYNONYMOUS I/T aTc/aCc 1766 C

7 139268602 C A SNP HIPK2 NM_022740 13 NON_SYNONYMOUS A/S Gcc/Tcc 976 C/M

7 139746728 G A SNP PARP12 NM_022750 5 SYNONYMOUS N/N aaC/aaT 314 C/M

7 154593106 C G SNP DPP6 NM_001936 13 NON_SYNONYMOUS F/L ttC/ttG 385 C/M

7 156526947 C G SNP LMBR1 NM_022458 10 SYNONYMOUS L/L ctG/ctC 254 C/M

7 21805101 T C SNP DNAH11 NM_003777 56 NON_SYNONYMOUS F/S tTc/tCc 3006 C

7 48147859 C T SNP UPP1 NM_003364 9 STOP_GAINED Q/* Cag/Tag 280 C/M

8 103266719 T C SNP UBR5 NM_015902 59 SYNONYMOUS P/P ccA/ccG 2737 C/M

8 107696550 C T SNP OXR1 NM_018002 6 NON_SYNONYMOUS S/L tCa/tTa 163 C/M

8 113318359 C A SNP CSMD3 NM_052900 50 NON_SYNONYMOUS V/L Gta/Tta 2546 C/M

8 113678576 T C SNP CSMD3 NM_052900 16 NON_SYNONYMOUS K/E Aaa/Gaa 812 C/M

8 114326909 C G SNP CSMD3 NM_052900 2 NON_SYNONYMOUS E/Q Gaa/Caa 98 C/M

8 121357692 *

-

CTGGGGAGCCTG

GGAGG DEL COL14A1 NM_021110 45 FRAME_SHIFT -/- -/- 1656 C

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8 125109581 T A SNP FER1L6 NM_001039112 36 NON_SYNONYMOUS S/T Tct/Act 1589 C/M

8 131072896 A C SNP ASAP1 NM_018482 28 NON_SYNONYMOUS S/A Tct/Gct 1041 C/M

8 133076246 A G SNP HHLA1 NM_001145095 16 NON_SYNONYMOUS V/A gTg/gCg 531 C/M

8 135614641 C A SNP ZFAT NM_020863 6 NON_SYNONYMOUS A/S Gcc/Tcc 441 C/M

8 143955827 T A SNP CYP11B1 NM_000497 9 NON_SYNONYMOUS S/C Agc/Tgc 492 C/M

8 75926334 C A SNP CRISPLD1 NM_031461 5 NON_SYNONYMOUS P/Q cCa/cAa 208 C/M

8 77767221 G A SNP ZFHX4 NM_024721 10 SYNONYMOUS S/S tcG/tcA 2688 C/M

9 121971073 G T SNP DBC1 NM_014618 7 NON_SYNONYMOUS Q/K Caa/Aaa 357 C/M

9 121971150 T G SNP DBC1 NM_014618 7 NON_SYNONYMOUS H/P cAc/cCc 331 C/M

9 125424309 A G SNP OR1L1 NM_001005236 1 SYNONYMOUS L/L ttA/ttG 105 C

9 127715125 A G SNP SCAI NM_173690 19 SYNONYMOUS V/V gtT/gtC 617 C

9 15778969 A G SNP CCDC171 NM_173550 20 NON_SYNONYMOUS S/G Agc/Ggc 968 C

9 2643642 C T SNP VLDLR NM_003383 6 STOP_GAINED R/* Cga/Tga 279 C

9 27172687 T C SNP TEK NM_000459 5 SYNONYMOUS H/H caT/caC 234 C/M

9 71549819 A T SNP PIP5K1B NM_003558 13 SYNONYMOUS S/S tcA/tcT 405 C/M

9 79461468 A T SNP PRUNE2 NM_015225 4 SYNONYMOUS P/P ccT/ccA 157 C/M

9 80537095 G T SNP GNAQ NM_002072 2 STOP_GAINED Y/* taC/taA 101 C/M

9 80537112 T A SNP GNAQ NM_002072 2 NON_SYNONYMOUS T/S Aca/Tca 96 C/M

9 88692394 A G SNP GOLM1 NM_016548 3 NON_SYNONYMOUS L/P cTt/cCt 81 C

9 90502324 G T SNP FAM75E1 NM_178828 4 NON_SYNONYMOUS R/S agG/agT 974 C/M

9 96002138 C A SNP WNK2 NM_006648 6 SYNONYMOUS I/I atC/atA 474 C/M

10 115348112 G C SNP HABP2 NM_004132 13 NON_SYNONYMOUS S/T aGt/aCt 556 C/M

10 115985839 * -G DEL TDRD1 NM_198795 22 FRAME_SHIFT -/- -/- 1013 C/M

10 116417744 C A SNP ABLIM1 NM_002313 1 SYNONYMOUS G/G ggG/ggT 72 C/M

10 127429626 C A SNP C10orf137 NM_015608 16 NON_SYNONYMOUS Q/K Caa/Aaa 709 C/M

10 17107571 C A SNP CUBN NM_001081 22 SYNONYMOUS V/V gtG/gtT 1025 C/M

10 33212521 G A SNP ITGB1 NM_002211 7 NON_SYNONYMOUS H/Y Cat/Tat 312 C/M

10 75558061 T C SNP KIAA0913 NM_015037 20 SYNONYMOUS P/P ccT/ccC 1342 C/M

10 84745172 C A SNP NRG3 NM_001010848 9 SYNONYMOUS V/V gtC/gtA 634 C/M

11 1099375 *

-

CCCAGCCCCACC

CCACCTGTCTGAC

AATGCCCTCCCGC

CCCCAGCTCCT DEL MUC2 NM_002457 40 FRAME_SHIFT -/- -/- 2416 C

11 128856531 A G SNP ARHGAP32 NM_014715 4 NON_SYNONYMOUS L/P cTg/cCg 81 C/M

11 22747869 C T SNP GAS2 NM_005256 3 NON_SYNONYMOUS T/I aCc/aTc 100 C/M

11 28058012 A G SNP KIF18A NM_031217 14 SYNONYMOUS N/N aaT/aaC 716 C

11 32954910 G A SNP QSER1 NM_001076786 4 SYNONYMOUS Q/Q caG/caA 573 C/M

11 40137007 A C SNP LRRC4C NM_020929 2 NON_SYNONYMOUS L/R cTa/cGa 279 C/M

11 55563094 T C SNP OR5D14 NM_001004735 1 SYNONYMOUS D/D gaT/gaC 21 C/M

11 55587715 G T SNP OR5D18 NM_001001952 1 NON_SYNONYMOUS A/S Gcc/Tcc 204 C/M

11 55703403 G T SNP OR5I1 NM_006637 1 SYNONYMOUS S/S tcC/tcA 158 C/M

11 55927367 C T SNP OR8K5 NM_001004058 1 NON_SYNONYMOUS V/I Gta/Ata 143 C/M

11 64875183 C A SNP C11orf2 NM_013265 3 SYNONYMOUS R/R cgC/cgA 163 C/M

12 103699849 G A SNP C12orf42 NM_198521 5 SYNONYMOUS H/H caC/caT 178 C/M

12 123355587 T C SNP VPS37B NM_024667 2 NON_SYNONYMOUS K/E Aaa/Gaa 45 C/M

12 129190764 G T SNP TMEM132C NM_001136103 9 NON_SYNONYMOUS W/L tGg/tTg 1084 C/M

12 132262839 C A SNP SFSWAP NM_004592 14 NON_SYNONYMOUS S/Y tCt/tAt 791 C/M

12 1741842 G T SNP WNT5B NM_030775 3 SYNONYMOUS P/P ccG/ccT 33 C/M

12 24048862 G C SNP SOX5 NM_006940 2 NON_SYNONYMOUS D/E gaC/gaG 45 C/M

12 25002862 G A SNP BCAT1 NM_005504 6 NON_SYNONYMOUS P/S Cct/Tct 178 C

12 2659199 C A SNP CACNA1C NM_000719 10 NON_SYNONYMOUS A/D gCc/gAc 494 C/M

12 48105426 G A SNP ENDOU NM_006025 8 NON_SYNONYMOUS P/S Cca/Tca 328 C/M

12 49426353 C A SNP MLL2 NM_003482 39 NON_SYNONYMOUS Q/H caG/caT 4045 C/M

12 50855088 C G SNP LARP4 NM_052879 11 NON_SYNONYMOUS S/C tCc/tGc 431 C/M

12 51237672 A G SNP TMPRSS12 NM_182559 2 NON_SYNONYMOUS I/V Ata/Gta 79 C/M

12 53586676 C T SNP ITGB7 NM_000889 13 NON_SYNONYMOUS C/Y tGt/tAt 582 C/M

12 55820740 T C SNP OR6C76 NM_001005183 1 NON_SYNONYMOUS F/L Ttt/Ctt 235 C

12 64502818 G T SNP SRGAP1 NM_020762 SPLICE_SITE_DONOR C/M

12 8688764 A C SNP CLEC4E NM_014358 5 NON_SYNONYMOUS F/C tTt/tGt 137 C/M

13 103399006 T C SNP CCDC168 NM_001146197 4 SYNONYMOUS K/K aaA/aaG 1347 C

13 108518918 C A SNP FAM155A NM_001080396 1 SYNONYMOUS R/R cgG/cgT 9 C/M

13 35864536 T A SNP NBEA NM_015678 35 STOP_GAINED C/* tgT/tgA 1929 C/M

13 70456499 C G SNP KLHL1 NM_020866 5 NON_SYNONYMOUS M/I atG/atC 381 C/M

13 77700553 T C SNP MYCBP2 NM_015057 53 NON_SYNONYMOUS K/R aAg/aGg 2595 C

14 20851414 C T SNP TEP1 NM_007110 27 SYNONYMOUS E/E gaG/gaA 1322 C/M

14 21853995 *

-

TGGTGATGGTGG

TGATGGTGGGGG

TGGGGGTGGTGG

TGG DEL CHD8 NM_020920 38 CODON_CHANGE_PLUS_CODON_DELETIONHHHHPHPHHHHHHH/H

caccaccaccacccccacc

cccaccatcaccaccatcac

cat/cat 2216 C

14 23896878 T A SNP MYH7 NM_000257 16 NON_SYNONYMOUS N/Y Aat/Tat 602 C/M

14 24629617 G T SNP RNF31 NM_017999 SPLICE_SITE_DONOR C/M

14 51204979 A G SNP NIN NM_016350 26 NON_SYNONYMOUS L/P cTt/cCt 1172 C

14 77901718 C A SNP C14orf133 NM_022067 15 STOP_GAINED E/* Gaa/Taa 311 C/M

14 94203679 * +C INS PRIMA1 NM_178013 4 FRAME_SHIFT -/? -/G 89 C

14 96773172 G A SNP ATG2B NM_018036 30 NON_SYNONYMOUS S/F tCc/tTc 1462 C/M

15 42139599 G T SNP JMJD7-PLA2G4BNM_005090 24 NON_SYNONYMOUS S/I aGc/aTc 902 C/M

15 42139599 G T SNP PLA2G4B NM_001114633 19 NON_SYNONYMOUS S/I aGc/aTc 671 C/M

15 65496862 G T SNP CILP NM_003613 6 STOP_GAINED C/* tgC/tgA 221 C/M

15 68620455 * -G DEL ITGA11 NM_001004439 16 FRAME_SHIFT -/- -/- 683 C/M

15 79585643 C G SNP ANKRD34C NM_001146341 2 NON_SYNONYMOUS T/S aCt/aGt 6 C/M

16 15826566 C A SNP MYH11 NM_002474 SPLICE_SITE_ACCEPTOR C/M

16 31505025 G T SNP C16orf58 NM_022744 8 NON_SYNONYMOUS T/N aCc/aAc 286 C/M

16 53636074 C A SNP RPGRIP1L NM_015272 27 NON_SYNONYMOUS G/C Ggt/Tgt 1288 C/M

16 58570934 C A SNP CNOT1 NM_016284 39 NON_SYNONYMOUS G/C Ggc/Tgc 1869 C/M

16 71065780 C A SNP HYDIN NM_017558 19 NON_SYNONYMOUS G/V gGc/gTc 857 C/M

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16 71885022 T C SNP ATXN1L NM_001137675 3 NON_SYNONYMOUS I/T aTt/aCt 460 C

16 77323246 C T SNP ADAMTS18 NM_199355 22 SYNONYMOUS R/R cgG/cgA 1155 C/M

17 26906821 A G SNP SPAG5 NM_006461 17 SYNONYMOUS S/S agT/agC 944 C

17 56289790 A C SNP MKS1 NM_017777 9 STOP_GAINED Y/* taT/taG 288 C/M

17 56382773 * -C DEL BZRAP1 NM_004758 29 FRAME_SHIFT -/- -/- 1803 C/M

17 7577144 * +A INS TP53 NM_000546 8 FRAME_SHIFT -/? -/T 265 C/M

17 78155323 G C SNP CARD14 NM_024110 2 NON_SYNONYMOUS R/T aGg/aCg 29 C/M

17 9471762 G C SNP STX8 NM_004853 2 NON_SYNONYMOUS Q/E Caa/Gaa 15 C/M

18 19153927 T C SNP ESCO1 NM_052911 4 NON_SYNONYMOUS E/G gAg/gGg 293 C/M

18 33271049 C T SNP GALNT1 NM_020474 7 NON_SYNONYMOUS P/L cCt/cTt 351 C/M

18 56204012 C T SNP ALPK2 NM_052947 5 NON_SYNONYMOUS G/E gGg/gAg 1136 C/M

18 6975969 A T SNP LAMA1 NM_005559 45 NON_SYNONYMOUS D/E gaT/gaA 2152 C/M

19 12060263 A C SNP ZNF700 NM_144566 4 NON_SYNONYMOUS E/A gAa/gCa 475 C/M

19 307307 C T SNP MIER2 NM_017550 13 SYNONYMOUS L/L ctG/ctA 476 C/M

19 40580491 T C SNP ZNF780A NM_001010880 6 NON_SYNONYMOUS K/E Aag/Gag 620 C

19 46120944 G A SNP EML2 NM_012155 13 SYNONYMOUS R/R cgC/cgT 422 C

19 52919068 A G SNP ZNF528 NM_032423 7 SYNONYMOUS G/G ggA/ggG 321 C

19 54081138 A T SNP ZNF331 NM_018555 7 STOP_GAINED K/* Aag/Tag 442 C/M

20 16486772 C A SNP KIF16B NM_024704 8 STOP_GAINED G/* Gga/Tga 255 C/M

20 31024581 T A SNP ASXL1 NM_015338 12 NON_SYNONYMOUS W/R Tgg/Agg 1356 C/M

20 33338161 G A SNP NCOA6 NM_014071 9 NON_SYNONYMOUS P/S Ccc/Tcc 613 C

20 57572801 G T SNP CTSZ NM_001336 4 NON_SYNONYMOUS D/E gaC/gaA 165 C/M

21 27084668 T C SNP JAM2 NM_021219 9 NON_SYNONYMOUS S/P Tct/Cct 280 C/M

21 41427696 C T SNP DSCAM NM_001389 29 NON_SYNONYMOUS R/K aGg/aAg 1664 C/M

21 44515595 C A SNP U2AF1 NM_006758 5 NON_SYNONYMOUS V/F Gtc/Ttc 101 C/M

22 25424172 A G SNP KIAA1671 NM_001145206 1 NON_SYNONYMOUS K/R aAa/aGa 69 C

22 32464567 T C SNP SLC5A1 NM_000343 5 NON_SYNONYMOUS Y/H Tac/Cac 153 C

22 36657688 A G SNP APOL1 NM_003661 5 SYNONYMOUS K/K aaA/aaG 78 C

22 38119801 A G SNP TRIOBP NM_001039141 7 NON_SYNONYMOUS K/R aAa/aGa 413 C

22 38340486 C T SNP C22orf23 NM_032561 6 NON_SYNONYMOUS D/N Gac/Aac 174 C/M

22 42610776 * -TGC DEL TCF20 NM_005650 1 CODON_CHANGE_PLUS_CODON_DELETIONQQ/Q cagcaa/caa 178 C

22 46627925 C T SNP PPARA NM_005036 8 SYNONYMOUS A/A gcC/gcT 316 C/M

X 149680506 C T SNP MAMLD1 NM_001177465 5 SYNONYMOUS G/G ggC/ggT 720 C

X 27998922 C G SNP DCAF8L1 NM_001017930 1 NON_SYNONYMOUS C/S tGt/tCt 177 C/M

X 3240739 T A SNP MXRA5 NM_015419 5 NON_SYNONYMOUS D/V gAc/gTc 996 C/M

X 37984652 T C SNP SYTL5 NM_138780 16 NON_SYNONYMOUS I/T aTc/aCc 648 C/M

X 47269700 C A SNP ZNF157 NM_003446 2 NON_SYNONYMOUS A/D gCt/gAt 33 C

X 69420245 C T SNP DGAT2L6 NM_198512 4 SYNONYMOUS P/P ccC/ccT 136 C/M

X 70462862 T C SNP ZMYM3 NM_005096 22 NON_SYNONYMOUS N/D Aac/Gac 1169 C/M

Column "Dist." gives the distribution of the SNVs/INDELs among CTCs ("C"), primary ("P") and metastatic ("M") tumors.

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Gene Primer Sequence (5'-3') Chr Position WT MT

RB1* forward GCATGCGAACTCAGTGTAT

Chr13 48941648 C T reverse CCATGTGCAATACCTGTCTAT

RB1** forward TTATATTGCATGCGAACTC

Chr13 48941648 C T reverse CTAAAGGTCACTAAGCTAAAG

PIK3CA* forward ATGTCTTAGATTGGTTCTTTCC

Chr3 178936091 G A reverse CACTTACCTGTGACTCCATAG

PIK3CA** forward CACTACCATCCTCTAGTA

Chr3 178936091 G A reverse GAGATCAGCCAAATTCA

APC forward AGTTCACCTAGTGGGACTGTTGCT

Chr5 112179782 C T reverse TCACAAGGTAAGACCCAGAATGGC

CNTNAP5 forward GAAAGAAGCTTTCTCTCTGCATTAC

Chr2 125521689 T C reverse TACAAATGCCCACTAGTGACTG

TGFBR2 forward TCCAGATTGCCTTTCTGTCTG

Chr3 30691922 G A reverse GAGCTCCTAATCCACTGTATGC

FOXP1 forward AGTGCACTAGACCTTGTGATTTA

Chr3 71064784 G A reverse TCTGGTGGAATGGTTCTTGG

C9orf91 forward CAGTAGTGTCTGAAAGGTGTCC

Chr9 117390415 C G reverse GCTTACGGGCTAGTGTGAAT

ZNF473 forward GCCTTACTCCTGTAATGTGTGT

Chr19 50550285 G A reverse CGTTGTACAGCTTCTCCACTT

MORF4L2 forward ACTCCTCCAGAATTGCATCTAC

ChrX 102931628 C T reverse GCTGGTCCACAGCAGAAA

FLT3 Forward ACTGTATCCTCACATCTGCTTATT

Chr13 28622413 T G Reverse ATCTTCTCAATACGTTTCCCTATGA

Table S5. Primer pairs used for validation of SNVs.

For each primer pairs, the oligonucleotide sequences, the position (hg19) of SNV in the

chromosome, the wild type (WT) and mutant (MT) nucleotide sequences are listed. *Primer pair

for the first PCR reaction. **Primer pair for the second PCR reaction in a two-step PCR

reaction.

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Documents

SI Appendix - PNAS · 2013-12-04 · SI Appendix Reproducible Copy Number Variation Patterns among Single Circulating Tumor Cells of Lung Cancer Patients Xiaohui Ni, Minglei Zhuo,