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American Journal of Cancer Research logoLink to American Journal of Cancer Research
. 2011 Mar 30;1(4):562–573.

Multiple gene dysfunctions lead to high cancer-susceptibility: evidences from a whole-exome sequencing study

Ming-Liang He 1, Ying Chen 1, Quan Chen 1,2, Yaqing He 3, Jing Zhao 2, Jun Wang 2, Huanming Yang 2, Hsiang-Fu Kung 1
PMCID: PMC3186053  PMID: 21984973

Abstract

A total of $275 million has been launched to The Cancer Genome Atlas Project for genomic mapping of more than 20 types of cancers. The major challenge is to develop high throughput and cost-effective techniques for human genome sequencing. We developed a targeted exome sequencing technology to routinely determine human exome sequence. As a proof-of-concept, we chose a unique patient, who underwent three high mortalities cancers, i.e., breast, gallbladder and lung cancers, to reveal the genetic cause of high-cancer-susceptibility. Total 24,545 SNPs were detected. 10,868 (44.27%) SNPs were within coding regions, and 1,077 (4.38%) located in the UTRs. 3367 genes were hit by 4480 non-sysnonymous mutations in CDS with truncation of 30 proteins; and 10 mutations occurred at the splice sites that would generate different protein isoforms. Substitutions or premature terminations occurred in 132 proteins encoded by cancer-associated genes. CARD8 was completely loss; ANAPC1 was pre-translationally terminated from the transcripts of one allele. On the Ras-MAPK pathway, 18 genes were homozygously mutated. 15 growth factors/cytokines and their receptors, 9 transcription factors, 6 proteins on WNT signaling pathway, and 16 cell surface and extracellular proteins may be dysfunctioned. Exome sequencing made it possible for individualized cancer therapy.

Keywords: whole-exome sequencing, cancer, genetic variations, high-cancer-susceptibility

Introduction

It has always been bothering physicians to choose correct drugs as the anticancer effects are completely different among patients [1-3]. This is caused by not only the multiple genetic mutations in human cancers but also a wide variety of single nucleotide polymorphisms (SNPs) of individuals [4]. Mutations in exons, such as mutations on H-RAS, p53 and APC genes, are often found to cause human cancers. Up to date, 73 genes with germline mutations and 412 genes with germline or somatic alterations, including amplification, deletion, rearrangement and point mutations, have been shown to be involved in human cancers in the Cancer Gene Census of Cancer Genome Project database (CGC/CGP, www.sanger.ac.uk/genetics/CGP/Census). In the Atlas of Genetics and Cytogenetics Oncology and Haematology (AGCOH) database (atlasgenetics-oncology.org/Indexbychrom/), there are 766 annotated genes that are genetically associated with cancers and other 3,000 other genes are functionally involved in the process of cancer development. Although a great advance has been achieved for early diagnosis of human cancers and anticancer drug development, the mobility of cancer cases is increasing while the average mortality almost remains consistent in the last decades [5, 6]. The random use of anticancer drugs largely neutralized the attempts of anticancer treatment; and cancer is still the second killer of human diseases. Therefore, it is urgently needed to develop genome-based individualized cancer therapy and care.

It is well known that the whole exome constitute only about 1% of the human genome but harbor the major of mutations contribute to cancer development. Therefore, combined with bioinformatics analysis, targeted exome sequencing technology would be a good and practical strategy to largely reduce the cost and labor load. It would also have a great potential to expand our knowledge of rare mutations in cancer development and to accelerate the functional studies of cancer-associated genes. Using high susceptibility of cancers as proof-of-concept, we observed that 132 genes, which have been shown to be important for cancer development, dysfunctioned or functionally alternated. Of them, only 11 genes were germline-mutated according to CGC/CGP database; while the mutations of other 121 genes were newly identified in germline in cancer patient.

Material and methods

Patient

A very unique cancer patient, a Chinese women (YH2), was recruited in this study. She underwent breast cancer, gallbladder adenocacinoma and lung cancer at 41, 63 and 66, respectively. She died of recurrence of gallbladder adenocacinoma in liver at 68. The tumors were removed by surgery at the diagnosis and tumor types were determined by histochemisty assays after surgery. There was no family history of cancers. Informed comment was obtained from the patient for this study, and the study was approved by the ethic committee of The Chinese University of Hong Kong.

Exome sequencing

The strategy for exome sequencing was similar as described by Ng et al [7]. In brief, shotgun libraries were generated from 10 ug of blood leukocytes purified genomic DNA (gDNA) using the standard Illumina protocols [8]. The fragments of size 150-200 bp were isolated after electrophoresis on 6% PAGE and hybridized with NimbleGen 2.1M-probe sequence capture array (http://www.nimblegen.com/products/seqcap), in which oligos were fixed to cover the human exomes (RefSeq, NCBI 36.3, 33.92 Mb). The captured exomes were applied for direct single-end sequencing on an Illumina Genome Analyzer II. The average read for each probe is 75 bases. Sequences were then aligned to the reference (RefSeq, hg18, 19 and YH1) [9] using SOAPaligner, and the mapped bases, depth, coverage and the base distribution were analyzed.

Substitution detection

SNPs were called by SOAPsnp based on the alignments with HapMap database (www.hapmap.org). For each site within the exome targeted region, only copy number <1.5 of the surrounding area was allowed and the depth should range from 10X to 200X. Finally, a Q20 threshold was used to filter unreliable SNPs. After excluding known substitutions from the potential mutations available, the SNPs were annotated and the genes involved in cancer development were revealed by comparison of our data with CGC/CGP and the AGCOH database.

Insertion and deletion detection

For the single reads we produced, the short in-dels <4 bp were also identified by S0APaligner2 in a gap tolerable mode. Local alignments were performed with our custom perl scripts.

Results

Exome sequences

Our sequencing strategy was similar to the one published by Ng et al recently but with a larger coverage (33.92 instead of 26.6 megabases) [7]. The average sequencing depth was 21.1 (Figure 1). The total reads were about 1.97 Gagabases (GBs) which covered 97.36% of the reference. With SOAPaligner software, 87.92% of bases were aligned to the reference (build 131,10/03/26, hg18 and hg19) and YH genome sequence [9]. The mismatch rate was 0.65%, indicating the data was in high sequencing quality. We detected total 24,545 SNPs. Among them, 10,874 (44.3%) SNPs located in the coding regions and 142 (0.6%) SNPs located in the UTRs. There were 23,604 SNPs were shared among YH1 and dbSNPs, while 941 SNPs were newly identified in the patient after comparative analysis of SNPs in the captured exome. Among them, 8091 SNPs (42.81%) were homozygous. 3058 genes were hit by 4480 non-synonymous mutations in the coding sequences (CDS). 10 mutations displayed at spice sites, and 8 small in/dels were identified.

Figure 1.

Figure 1

Targeted capture exome sequencing. A. Chromosome depth and GC distribution in targeted capture exome regions. X axis stands for each chromosome, Y1 axis presents the sequencing depth and YH2 axis is the GC proportion in exon capture region of each chromosome. B. Nu-cleotide distribution under different depth in exon capture region. Y axis stands for the proportion of bases under each depth in exon capture region.

Nonsense mutations

We detected 33 nonsense mutations that caused truncation of 30 proteins (Table 1). We found only 3 proteins (PTPN11, MAGEE2 and IL17RB) have been recorded to have genetic associations with cancer [10-12]; while 11 other cancer-associated proteins, for the first time, were observed to be mutated in the germline. Particularly, MAGEE2, which has been shown genetic association in melanoma and hepato-cellular carcinoma, was truncated at N-terminal by homozygous mutations. CARD8, a key factor for the recruitment of caspase in apoptosis pathway[13], was almost completely loss in the patient. ANAPC1, a key components of ana-phase promoting complex that play crucial roles in cell mitosis and protection of the integration of chromosomes from separation [14-17], truncated >70% by a heterozygous mutation at Gln465. Some important proteins on the RAS-MAPK signaling pathway, including G protein coupled receptor 1 (GRP1), tyrosine kinase (MAP2K3), and protein tyrosine phosphatase (PTPN11), also prematurely terminated.

Table 1.

Nonsense mutations (ST, stop; JMML, juvenile myelomonocytic leukemia; AML, acute myelogenous leukemia; MDS, myelodysplastic syndrome)

Name type mutation Position (stop) full length (aa) function Genetic association with disease(s)
Functional associated with cancers

ANAPC1 HET CAG>TAG Q465 1926 anaphase promoting complex

GPR1 HET CGA>TGA R236 355 signal transduction

ASCC3 HET CAG>TAG Q87 111 signal transduction

MAP2K3 HET CAG>TAG Q73 318 tyrosine kinase, signal transduction

PTPN11 HET TAT>TAG Y197 593 protein tyrosine phosphatases JMML, AML, MDS

MAGEE2 HOM GAG>TAG E120 523 signal transduction melanoma, HCC

CARD8 HOM TGT>TGA C10 432 caspase recruitment rheumatoid arthritis

ABCA10 HET CGA>TGA R1322 1544 drug transport

CYP2C18 HET TAT>TAA Y68 490 drug metabolism

IL17RB HET CAG>TAG Q484 502 cytokine receptor intestinal inflammation

UBE2NL HET TTA>TGA L89 153 ubiquitin ligation

FTHL17 HET GAG>TAG E148 183 ferritin heavy polypeptide-like protein

TP53RK HET CGA>TGA R152 254 TP53-regulating kinase

Others

SPATA21 HET CGA>TGA R467 470 spermatogenesis

PZP HET CAA>TAA Q598 1483 proteinase inhibitor

UNC5CL HET CAG>TAG Q12 519 NF-kB inhibitor

TCTE1 HET CAG>TAG Q460 502 t-complex-associated-testis-expressed 1

ASCC3 HET CAG>TAG Q87 2203 RNA helicase

ZNF75D HET CGA>TGA R331 511 transcriptional factor

DKFZp547 HOM TGG>TGA W141 150 unknown

LOC149643 HET CGA>TGA R37 98 unknown

MS4A12 HET CAA>TAA Q71 267 membrane protein

OR2T5 HET CGA>TGA R24 315 olfactory receptor

PZP HET CAA>TAA Q598 1483 pregnancy-zone protein

SLC6A18 HET TAC>TAG Y319 628 unknown

SPATA21 HET CGA>TGA R467 470 spermatogenesis

ZNF75 HET CGA>TGA R331 510 zinc finger protein

ZNF80 HET TAT>TAG Y245 273 zinc finger protein

PTCHD3 HET TAA>CAA ST768Q 767 spermatogenesis

Missense mutations

Missensense mutations hit over 3,000 proteins. After aligned with the CGC/CGP and AGCOH databases, we observed important substitutions (most likely causing function alterations) occurred in 132 proteins, which strongly associated with cancer development (Table 3). Among them, 45 have been recorded as somatic mutations and only 11 recorded as germline mutations in cancer patients in the CGC/CGP database. Totally 121 cancer-associated genes were newly found to display mutations in germline; some mutations would cause significant function alterations.

Table 3.

Mutations in the genes strongly associated with human cancers

Gene type FL (aa)1 mutation Somatic germline
ACSL3 Het 719 L641H prostic cancer

ADAM12 Hom 1593 G48R

ADAM8 Hom 823 W35R, F657L

ADAMST5 Het 929 R614H,L692P

ADAMTS4 Het 837 Q626R

AFF3 Hom 1226 S538N

AKAP12 Het 1683 K118Q,K1218I multiple cancers, anti-angiogenesis

AKR1C4 Hom 324 S145C*, Q250R, L311V*

ALOX12 Hom 662 N322S

ANAPC1 Het 1926 Q465ST(GAC->TAC)

APC Hom 2843 V1288D colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS cancers the same cancers as somatic mutations

ASNS Het 561 V210E

ASXL1 Hom 1541 L815P MDS, CMML

ATF6 Het 670 A145P, P157S leukemia, lymphoma, medulloblastoma, glioma

ATM Hom 3056 N1983S T-PLL

BCAS1 Hom 584 Q24K, V163A*

BCL2A1 Het 174 C19Y, N39K, G82D

BCL2L2 Hom 193 Q133R

BCL9 Het 1426 A218V B-ALL, Hodgkin lymphoma colon/breast/ovary cancer, AML, leukemia, rhabdomyosarcama

BMPR1A Het 531 P2T breast cancer AML, leukemia, breast cancer

BRIP1 Hom 1249 S919P

BUB1B Hom 1049 R349Q colorectal cancer, breast cancer gastrointestinal neoplasia, rhabdomyosarcoma

CABC1 Het 647 H85Q

CARD8 Hom 432 C10st (TGT->TGA)

CARS Het 879 A774T ALCL

CBLB Het 981 N466D AML

CCND3 Het 292 S259A MM

CD97 Hom 785 R318Q

CDH11 Hom 795 T255M*, M275I*,S373A aneurismal bone cycs

CDX2 Hom 313 P293S AML

CENPF Hom 3113 R2729Q, R2943G, N3106K

COL1A1 Hom 1465 T1075A

COL1A2 Hom 1365 P549A dermatofibrosarcoma protuberans

DDX43 Hom 647 K625E

DKK2 Hom 259 R146Q

DKK3 Hom 349 R335G gastric/lung/breast/prostate/ovary cancer, glioma

EML4 Hom 980 K283E NSCLC

ENPP2 Hom 865 S493E

EPHA1 Hom 976 V160A

ERCC2 Het 759 K751N skin basal cell, melanoma, SKC,

ERCC5 Hom 1186 G1053R, G1080R, D1104H skin basal cell, SKC, melanoma

FANCA Hom 1453 T266A, A412V*, G501S, P643A*, G809D, T1328A* AML, leukemia

FGFR2 Het 820 M186T gastric, endometrial cancer, NSCLC

FGFR4 Hom 802 V10I

FLT3 Het 992 T227M, D358V AML, ALL

FNIP1 Hom 1165 G76C, Q648R

FTHL17 Het 183 E148st (GAG->TAG)

FXYD5 Hom 178 S35A, R176H*

GATA2 Hom 479 A146T AML

GGH Het 317 C6R

GOLGA5 Hom 730 A67G*,P350L papillary thyroid

GPR1 Het 355 R236st (CGA->TGA)

GPR103 Hom 431 L344S

GPR112 Hom 3080 I276M*, P368H*,T1213N, S1540P, F1791L

GPR116 Hom 1345 T604M

GPR142 Hom 462 H132N

GPRC6A Hom 925 P91S

GRP115 Hom 694 K541N

GRP56 Hom 692 S281R

HTATIP2 Hom 276 S231R

IGF2R Hom 2491 R1619G, N2020S

IL23R Hom 628 Q3H, L310P

JAG2 Het 1237 E501K

KLK10 Hom 275 S50A, L149P*

KLK4 Hom 250 S22A*, H179Q

KLK5 Hom 292 N153D

LCP1 Hom 626 K553E NHL

LIFR Hom 1097 D578N salivary adenoma

LOX Hom 417 R158Q

LOXL2 Hom 773 M570L

LOXL4 Hom 755 R154Q

MAP2K3 Het 317 Q73st (CAG->TAG)

MAP3K7IP1 Het 503 C235W

MEN1 Hom 614 T546A parathyroid tumors parathyroid/pituitary/pancreatic/characinoid adenoma

MGC34647 Het 266 Y213st (TAC->TAG)

MMP10 Het 475 D81Y

MMP11 Hom 486 A38V

MMP17 Hom 602 A182T

MMP20 Hom 482 K18T*, V275A,T281N

MMP26 Hom 260 K43E

MMP27 Hom 512 M30V

MMP8 Hom 467 K87E

MMP9 Het 706 Q279R

MST1 Het 724 R108Q, R122Q breast cancer

MST1R Hom 1399 Q523R/E, S1195G, R1135G/E

MTHFR Het 655 A222V

MYEOV Het 312 V159A, R198Q, G271R

MYH11 Het 1937 N1899S AML

MYST3 Het 2003 L134S

NBN Het 753 E185Q

NIN Hom 2045 Q1125P, G1320E MPD

NOTCH2NL Het 235 S67P, P133L, T158I, S181R, P188H marginal zone lymphoma, DLBCL

NQO1 Het 239 Q139W

NSD1 Het 2695 S726P AML

NUP214 Het 2090 P754S AML

NUT Hom 1131 P22L lethal midline carcinoma

OPTN Hom 576 M98K*, K322E

P2RX7 Hom 594 Y155H*, R270H*, E496A*, N568I

PBX1 Het 429 G21S Pre B-ALL

PDE4DIP Hom 2345 R25L*, A167T*, R681H*, C708R, R1504Q* MPD

PDGFRA Het S361R, T474M,S478P GIST, idiopathic hyperosinophilic syndrome

PLAG1 Het 500 S443R salivary adenoma, pleomorphic adenoma

PML Het 828 S722G APL

PMS2 Hom 861 P470S*, T485K*, K541E colorectal, endometrial, ovarian, medulloblastoma, glioma

POU6F2 Hom 691 P191L

PPARGC1A Hom 797 G482S

PTPN11 Het 592 S189A, Y197st (TAT->TAG) JMML, AML, MDS

PTPN21 Het 1173 L385F, V936A

PVRL4 Het 509 F53L

REL Het 618 N424S many cancers and other disease

RHOD Hom 210 C134R

RHOT2 Het 617 A88T, R245Q

ROS1 Het 2347 T145P

SDC1 Hom 310 L136Q

SELE Het 371 S303R

SERPINB5 Het 374 S176P, I319V

SFRP4 Het 345 P320T, R340K

STEAP2 Hom 489 F17C*, R456Q*, M475I

TCF3 Het 653 P479L pre B-ALL

TEK Hom 1123 I148T*, Q346P

TFEB Het 475 V130M renal (childhood) epithelioid

TFRC Het 760 G142S NHL

THBS4 Hom 1538 I192T, I598T, S1055G

TMPRSS2 Het 491 V160M prostate

TNC Hom 2200 V295M*, Q539R, V605I, E2008Q* glioma, lung/colon/breast cancer

TNFRSF10A Hom 467 H141R, R209T, R441K

TNFRSF17 Hom 183 N81S intestinal T-cell lymphoma

TRAF3 Hom 568 M129T

TSC1 Het 365 M322T

USP6 Het 234 Y162H, W475R, Y484H aneurysmal bone cysts

WISP3 Het 331 Q34H, E100K, E141K colon cancer hamartoma, renal cell carcinoma

ALCL, anaplastic large-cell lymphoma; ALL, acute lymphocytic leukemia; AML, acute myelogenous leukemia; APL, acute promyelocytic leukemia; B-ALL, B-cell acute lymphocytic leukaemia; CMML, chronic myelomonocytic leukemia; CNS, central nervous system; DLBL, diffuse large B-cell lymphoma; DLCL, diffuse large-cell lymphoma; GIST, gastrointestinal stromal tumour; JMML, juvenile myelomonocytic leukemia; MDS, myelodysplastic syndrome; MLCLS, mediastinal large cell lymphoma with sclerosis; MM, multiple myeloma; MPD, Myeloproliferative disorder; NHL, non-Hodgkin lymphoma; NSCLC, non small cell lung cancer; pre-B All, pre-B-cell acute lymphoblastic leukaemia; SKC, skin squamous cell; T-PLL, T cell prolymphocytic leukaemia.

*

listed as heterozyous mutation.

Homozygous mutations displayed in 58 genes that may contribute to high susceptibility of cancers in this patient. Homozygous missense mutations occurred in 18 genes on RAS-MARK pathway, including G-protein coupled receptors (GPRs), tyrosine kinases and phosphatases (Table 2). On this pathway, heterozygous mutations hit 9 other genes, including AKAP12, CBLB, MAP2K3, MAP3K7IP1, PTPN11, PTPN21, TCL1B and USP6 (Table 3). Although the proteins encoded by these genes play critical roles in cells response to extracellular signalings [18, 19]; however, only EML4 and NIN were recorded somatic mutations in tumors in the CGC/CGP database. The second largest group (10 genes), which were hit by homozygous mutations, were growth factors/cytokines and their receptors. Although only mutation of TNFRSF17 was shown in the intestinal T-cell lymphoma in the database, the products of these genes are important to control cell growth and immune responses to infection and other human diseases including carcinogenesis. On the Wnt signaling pathway, besides APC, homozygous mutations of CD97, DKK2 and DKK3 most likely cause significant alteration of protein functions. The genetic alterations in tumors have not yet recorded. Apart from DDX43, the other homozy-gously mutated genes (ATM, BUB1B, ERCC5 and FANCA) for cell cycle control and DNA/RNA process were shown genetic association with cacinogenesis (Table 2). Besides function association, the germline mutations of transcription factors (AFF3 and POU6F2) have not yet recorded. All 3 apoptotic/anti-apoptotic genes (CARD8, BCL2L2 and OPTN) were newly observed genetic alterations in cancer patients. This would enhance the somatic cells escaping from apoptosis during carcinogenesis.

Table 2.

Homozygous mutation(s) in genes strongly (either genetically or functionally) associated with carcinogenesis (*, heterozygous mutation)

Name Full length (FL, aa) mutations Name FL (aa) mutations
RAS-MAPK signaling pathway Wnt signaling pathway

EML4 981 K283E APC 2843 V1822D

ENPP2 865 S493P CD97 786 R318Q

EPHA1 976 M900V DKK2 259 R146Q

FNIP1 1166 G76C, Q648R DKK3 350 R335G

GPR103 431 L344S Growth factors/cytokines and their receptors/signal transducers

GPR112 3080 T1213N.S1540P, F1791L, I276M*, P368H* FGFR4 802 V10I, P136L

GPR116 1346 T604M IGF2R 2491 R1619G, N2020S *

GPR142 462 H132N IL23R 629 Q3H, L310P

GPRC6A 926 P91S MST1R 1400 Q523R(E), S1195G, R1335G(E)

GRP115 695 K541N PPARGC1A 798 G482S

GRP56 693 S281R TNC 2201 V295M*, Q539R, V605I, E2008Q*

KLK4 251 S22A*, H197Q TNFRSF10A 468 H141R, R209T, R441K

KLK5 293 N153D TNFRSF17 184 N81S

KLK10 276 S50A, L149P* TRAF3 568 M129T

KLK11 250 G17E PLEK2 354 S217C

NIN 2046 Q1125P, G1320E Cell cycle control

RHOD 210 C134R ATM 3056 N1983S

TEK 1124 I148T*, Q346P BUB1B 1050 R349Q

Apoptosis/anti-apoptosis Others

CARD8 432 C10ST ASXL1 1541 L815P

BCL2L2 194 Q133R CDH11 796 T255M*, M275I*,S373A

OPTN 577 M98K*, K322E BRIP1 1249 S919P

DNA repair/RNA synthesis COL1A1 1464 T1075A

ERCC5 1186 G1053R, G1080R, D1104H GOLGA5 731 A67G*,P350L

FANCA 1454 T266A,A412V*,G501S,P643A*,G809D, T1328A* LCP1 627 K533E

DDX43 648 K625E, Q629R LIFR 1098 D578N

ATM 3056 N1983S MAGEE2 523 E120ST(GAG>TAG)

BUB1B 1049 R349Q MEN1 615 T546A

Transcription factors NUT 1132 P22L

AFF3 1226 S538N PDE4DIP 2346 R25L*, A167T*, R681H*, C708R, R1504Q*

CDX2 313 P293S PMS2 862 P470S*, T485K*, K541E

GATA2 480 A146T P0U6F2 691 P191L

Discussion

The Cancer Genome Atlas project is currently the central task of genome-related research. It remains largely unknown how germline mutations in global contribute to cancer-susceptibility, although it is well known some germline mutations in a special gene would cause human cancers (e.g., mutaions in pRB gene leads to retinoblastoma in children). The major challenge is to develop a high throughput and cost-effective techniques for genome sequencing. Supported with extensive bioinformatic assays, a US group [7] and us have independently developed cost-effective targeted capture exome sequencing technology to routinely reveal the genetic variations of individuals. However, to our knowledge, the whole exome sequencing on high-cancer-susceptible patient has not yet been studied. In this study, we independently developed a similar technology for the whole exome sequencing. As a pilot study, we showed that homozygous mutations of CARD8 may contribute to the high-cancer-susceptibility in a patient, who underwent three high mortality cancers (breast cancer, gallbladder cancer and lung cancer) in the last three decades.

CARD8 was reported to inhibit apoptosis and caspase activation induced by Apaf-1/caspase-9-dependent stimili [20]; however, it was also showed to induce apoptosis in certain cells [13]. It is unclear how the loss of CARD8 contributes the high-cancer-susceptibility in this patient. The mutations in other genes, such as genes on RAS-MARK signaling pathway, may also play important roles in high-cancer-susceptibility. However, as some mutations may neutralize or antagonize the other mutations, the exact roles of these mutations are very complicated in the patient. For example, the truncation of MAGEE2 and PTPN11 may neutralize the mutations of tyrosine kinases and GPRs. The roles of these mutations in cancer-susceptibility would be further investigated by identification of more high-cancer-susceptibility patients or direct sequencing the tumor samples and paired germline genomes.

In summary, we developed targeted exome capture sequencing technology to characterize the whole-exome of human genome and applied to a high-cancer-susceptible patient. We showed that the truncations of CARD8, MAGEE2, ANAPC1, GPR1, ASCC3, MAP2K3 and PTPN11 be an important reasons for high-cancer-susceptiblity. The non-synonymous mutations in 132 cancer-associated genes, in which most of them have not been reported as germline variations in tumors, may positively or negatively contribute to cancer development. This exome sequencing technology makes it possible for routine dissection of important genes for carcinogenesis and individualized medicine, as the total cost is just less than US$10,000 per sample. The targeted exome capture sequencing would be a new era of individualized cancer therapy.

Acknowledgments

This study was supported in partial by Shenzhen -Hong Kong Collaborative Research Grant of Shenzhen Science and Technology Bureau (08DF-23, to ML He and Y He) and Research Grant Council, The Government of Hong Kong Special Administration Region (CUHK4428/ 06M,toMLHe).

Declaration

No conflicts of interest.

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