24. WHOLE EXOME SEQUENCING META-ANALYSIS OF DEPRESSION SUGGESTS SUBTLE ROLE FOR FUNCTIONAL VARIANTS IN KNOWN GENETIC ASSOCIATION LOCI

AbstractBackgroundCarcinogenesis is a severe consequence of chronic ulcerative colitis. We investigated the somatic mutations and pathway alterations in ulcerative colitis–associated colorectal cancer (CRC) in Chinese patients compared with sporadic CRCs to reveal potential therapeutic targets in ulcerative colitis–associated CRC.MethodsWhole exome sequencing was performed on archival tumor tissues and paired adjacent nondysplastic mucosa from 10 ulcerative colitis–associated CRC patients at a high risk of carcinogenesis. Genomic alteration profiles from 223 primary CRCs from The Cancer Genome Atlas served as sporadic CRC controls. A meta-analysis was performed to investigate differences in major genetic mutations between ulcerative colitis–associated and Crohn’s disease–associated CRCs.ResultsWe identified 44 nonsilent recurrent somatic mutations via whole exome sequencing, including 25 deleterious mutations involved in apoptosis and the PI3K-Akt pathway (COL6A3, FN1), autophagy (ULK1), cell adhesion (PODXL, PTPRT, ZFHX4), and epigenetic regulation (ARID1A, NCOR2, KMT2D, NCOA6, MECP2, SUPT6H). In total, 11 of the 25 mutated genes significantly differed between ulcerative colitis–associated CRC and sporadic CRC (APC, APOB, MECP2, NCOR2, NTRK2, PODXL, RABGAP1, SIK3, SUPT6H, ULK1, USP48). Somatic TP53 mutations occurred in 33% of ulcerative colitis–associated CRCs. Subsequent meta-analysis revealed distinct mutation profiles for Crohn’s disease– and ulcerative colitis–associated CRCs. Mutations involving the NF-kB pathway and epigenetic regulation were more common in ulcerative colitis–associated CRCs than in sporadic CRCs.ConclusionDistinct genomic alteration profiles of deleterious somatic mutations were found in ulcerative colitis–associated and sporadic CRCs. Mutations of epigenetic regulators, such as KMT2D and NCOA6, were common, suggesting an epigenetic pathomechanism for colitis-associated carcinoma in Chinese patients.

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Whole-Exome Sequencing in Korean Children with Acute Lymphoblastic Leukemia

Blood ◽

10.1182/blood.v126.23.4994.4994 ◽

2015 ◽

Vol 126 (23) ◽

pp. 4994-4994

Author(s):

Ye Jee Shim ◽

Jung-Sook Ha ◽

Young-Rok Do ◽

Heung Sik Kim

Keyword(s):

Acute Lymphoblastic Leukemia ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Lymphoblastic Leukemia ◽

Diagnostic Information ◽

Cancer Gene ◽

Korean Children ◽

Functional Variants ◽

Hla Dr ◽

Whole Exome

Abstract Purpose: Next-generation sequencing methods recently have been applied for leukemia patients to discover genetic variants. In this study, we conducted whole-exome sequencing (WES) in Korean acute lymphoblastic leukemia (ALL) children to identify putative genetic drivers of leukemia. Methods: Four Korean ALL children were included for WES. For two of them, we also conducted WES after remission, considered as germline control. The characteristics of subjects and the diagnostic information are described in Table 1. Genomic DNA was extracted from the subject¡¯s bone marrow aspirates at diagnosis of leukemia and/or after remission. Whole-exome was captured by SureSelect Human All Exon V4 (Agilent Technologies, California, USA). Sequencing was performed using HiSeq2000 (Illumina, California, USA). Variants in dbSNP135 and TIARA database were excluded. Variants with minor allele frequencies > 0.5% of 1000g were filtered out. Functional variants (gain of stop codon, frameshifts and nonsynonymous SNVs) were selected as pathogenic mutations and were scanned for the 571 cancer gene set using ¡°Cancer gene Census¡± in COSMIC website. The finally selected variants were verified by PROVEAN, SIFT and PolyPhen-2. This research was approved by The Institutional Review Board in Keimyung University Dongsan Medical Center (Approval No., 2015-05-029-002). Results: After comparison between WES at diagnosis and WES after remission, p.W112C in PAX5 in patient 1 andp.G315C in KMT2C, p.T311P in NOTCH1, p.G11A in HOXD13 in patient 2 were considered as pathogenic, respectively. In patient 3 and 4, p.R293C in FNBP1, p.R254H in PCSK7, p.E11Q in TP53, p.R806Q in MYO5A, p.R108G in PPFIBP1, p.C1785R in RNF213, and p.A963P in WRN were suspected as putative drivers of leukemia. The respective variants are shown in Table 2. Conclusions: This is the first attempt of WES in Korean children with leukemia. WES is a valuable method to identify genomics of childhood ALL. Table 1. Characteristics and diagnostic information of four Korean acute lymphoblastic leukemia children. No. Diagnosis BMblast Karyotype Hemavision FISH Immunophenotype WESAt diagnosis WESAfter remission 1 B-ALL 88.4% 44,XX,der(2)t(2;?),-4,-9,der(9)t(2;9),der(16)t(9;16)(q13;q12) Negative . CD10, D19, CD20, CD22, cCD22,cCD79a, CD34, CD45 Yes Yes 2 Pre B-ALL 95.0% No mitosis t(1;19)(q23;p13) . CD38, CD138, CD10, CD19, CD22,cCD79a, HLA-DR, CD45 Yes Yes 3 B-ALL 88.6% 46,XX Negative . CD10, CD19, CD22, cCD79a, CD34,TdT, HLA-DR, CD45, CD38 Yes No 4 B-ALL 94.3% Hypotriploidywith structural abnormality/46,XY Negative Trisomy 5, 11, 12Tetrasomy 21 CD10, CD19, CD22, cCD79a, CD34,TdT, HLA-DR Yes No Table 2. Identified putative genetic drivers in four Korean acute lymphoblastic leukemia children by whole-exome sequencing. No. Gene Chr:Position Variant PROVEAN (score) SIFT (score) Polyphen-2 (score) Germline or somatic 1 PAX5 9:37015068 exon3:c.G336T:p.W112C Deleterious (-11.12) Damaging (0.000) Probably damaging (0.998) Somatic 2 KMT2C 7:151970859 exon7:c.G943T:p.G315C Deleterious (-7.05) Damaging (0.001) Probably damaging (1.000) Somatic NOTCH1 9:139413211 exon6:c.A931C:p.T311P Deleterious (-4.82) Damaging (0.012) Benign (0.033) Somatic HOXD13 2:176957650 exon1:c.G32C:p.G11A Neutral (-0.88) Tolerated (0.118) Possibly damaging (0.953) Somatic 3 FNBP1 9:132687349 exon9:c.C877T:p.R293C Deleterious (-6.03) Damaging (0.001) Probably damaging (1.000) Somatic PCSK7 11:117097881 exon5:c.G761A:p.R254H Deleterious (-3.30) Damaging (0.007) Probably damaging (0.991) Somatic 4 TP53 17:7579882 exon2:c.G31C:p.E11Q Neutral (0.42) Damaging (0.000) Probably damaging (0.996) Germline/somatic MYO5A 15:52668547 exon19:c.G2417A:p.R806Q Deleterious (-3.12) Damaging (0.003) Possibly damaging (0.575) Somatic PPFIBP1 12:27799046 exon5:c.C322G:p.R108G Deleterious (-5.76) Damaging (0.000) Probably damaging (1.000) Somatic RNF213 17:78313373 exon27:c.T5353C:p.C1785R Deleterious (-10.45) Damaging (0.000) Probably damaging (1.000) Somatic WRN 8:30989942 exon24:c.G2887C:p.A963P Deleterious (-3.90) Damaging (0.003) Probably damaging (0.988) Germline Disclosures No relevant conflicts of interest to declare.

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