101
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Lan J, Lu Y, Guan Y, Chang L, Yu Z, Qian H. Identification of circulating tumor DNA using a targeted 545-gene next generation sequencing panel in patients with gastric cancer. Oncol Lett 2020; 19:2251-2257. [PMID: 32194723 PMCID: PMC7039113 DOI: 10.3892/ol.2020.11305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 06/05/2019] [Indexed: 12/26/2022] Open
Abstract
Gastric cancer (GC) is characterized by unique genetic aberrations. Some of these mutations may be used to predict tumor prognosis or to guide patient therapy. Cell-free circulating tumor DNA (ctDNA) has been considered a promising alternative to biopsy to identify genome aberrations. However, no standardized methods to detect ctDNA variations in patients with GC are currently available. In the present study, the targeted sequencing of 545 genes was used to identify somatic alterations in tissues and matched plasma samples of nine patients with GC. Driver gene mutations were detected in matched tissues and plasma ctDNA. The mutated reads concordance rate of ctDNA in GC tissues with matched tissues was 45%. A true positive copy number gain of human epidermal growth factor receptor 2 in plasma from patients with GC was identified. Furthermore, the ctDNA fraction in plasma cell-free DNA (cfDNA) was positively correlated with metastasis lymph node number and with lactate dehydrogenase level. In conclusion, results from the present study suggested that targeted sequencing of plasma ctDNA may be considered a potential option for the clinical monitoring of GC.
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Affiliation(s)
- Jing Lan
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Yaping Lu
- Research and Development Department, Geneplus-Beijing Institute, Beijing 102206, P.R. China
| | - Yanfang Guan
- Research and Development Department, Geneplus-Beijing Institute, Beijing 102206, P.R. China
| | - Lianpeng Chang
- Research and Development Department, Geneplus-Beijing Institute, Beijing 102206, P.R. China
| | - Zhengyuan Yu
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Haixin Qian
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
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102
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Brondani VB, Montenegro L, Lacombe AMF, Magalhães BM, Nishi MY, Funari MFDA, Narcizo ADM, Cardoso LC, Siqueira SAC, Zerbini MCN, Denes FT, Latronico AC, Mendonca BB, Almeida MQ, Lerario AM, Soares IC, Fragoso MCBV. High Prevalence of Alterations in DNA Mismatch Repair Genes of Lynch Syndrome in Pediatric Patients with Adrenocortical Tumors Carrying a Germline Mutation on TP53. Cancers (Basel) 2020; 12:E621. [PMID: 32156018 PMCID: PMC7139318 DOI: 10.3390/cancers12030621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/13/2022] Open
Abstract
Adrenocortical cancer is a rare malignant neoplasm associated with a dismal prognosis. Identification of the molecular pathways involved in adrenal tumorigenesis is essential for a better understanding of the disease mechanism and improvement of its treatment. The aim of this study is to define the prevalence of alterations in DNA mismatch repair (MMR) genes in Lynch syndrome among pediatric patients with adrenocortical neoplasia from southern Brazil, where the prevalence of a specific TP53 germline mutation (p.Arg337His) is quite high. Thirty-six pediatric patients were retrospectively evaluated. Immunohistochemistry (IHC) for the MMR enzymes MLH1, MSH2, MSH6, and PMS2, as well as next-generation sequencing (NGS) were performed. For IHC, 36 pediatric tumors were tested. In all of them, the expression of all evaluated MMR proteins was well-preserved. For NGS, 35 patients with pediatric tumor were tested. Three patients (8.57%) with the TP53 p.Arg337His germline mutation presented pathogenic and likely pathogenic variants in the MMR genes (two in MLH1 and one in MSH6). The prevalence of altered MMR genes among pediatric patients was elevated (8.57%) and higher than in colorectal and endometrial cancer cohorts. Pediatric patients with adrenocortical tumors should, thus, be strongly considered as at genetic risk for Lynch syndrome.
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Affiliation(s)
- Vania Balderrama Brondani
- Laboratório de Hormônios e Genética Molecular LIM/42, Unidade de Suprarrenal, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil; (A.M.F.L.); (B.M.M.); (A.C.L.); (B.B.M.); (M.Q.A.)
| | - Luciana Montenegro
- Laboratório de Hormônios e Genética Molecular LIM/42, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil (M.F.d.A.F.)
| | - Amanda Meneses Ferreira Lacombe
- Laboratório de Hormônios e Genética Molecular LIM/42, Unidade de Suprarrenal, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil; (A.M.F.L.); (B.M.M.); (A.C.L.); (B.B.M.); (M.Q.A.)
| | - Breno Marchiori Magalhães
- Laboratório de Hormônios e Genética Molecular LIM/42, Unidade de Suprarrenal, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil; (A.M.F.L.); (B.M.M.); (A.C.L.); (B.B.M.); (M.Q.A.)
| | - Mirian Yumie Nishi
- Laboratório de Hormônios e Genética Molecular LIM/42, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil (M.F.d.A.F.)
| | - Mariana Ferreira de Assis Funari
- Laboratório de Hormônios e Genética Molecular LIM/42, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil (M.F.d.A.F.)
| | - Amanda de Moraes Narcizo
- Laboratório de Sequenciamento em Larga Escala (SELA), Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil; (A.d.M.N.); (L.C.C.)
| | - Lais Cavalca Cardoso
- Laboratório de Sequenciamento em Larga Escala (SELA), Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil; (A.d.M.N.); (L.C.C.)
| | - Sheila Aparecida Coelho Siqueira
- Departamento de Anatomia Patológica, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil; (S.A.C.S.); (M.C.N.Z.)
| | - Maria Claudia Nogueira Zerbini
- Departamento de Anatomia Patológica, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil; (S.A.C.S.); (M.C.N.Z.)
| | - Francisco Tibor Denes
- Serviço de Urologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil;
| | - Ana Claudia Latronico
- Laboratório de Hormônios e Genética Molecular LIM/42, Unidade de Suprarrenal, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil; (A.M.F.L.); (B.M.M.); (A.C.L.); (B.B.M.); (M.Q.A.)
- Laboratório de Hormônios e Genética Molecular LIM/42, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil (M.F.d.A.F.)
| | - Berenice Bilharinho Mendonca
- Laboratório de Hormônios e Genética Molecular LIM/42, Unidade de Suprarrenal, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil; (A.M.F.L.); (B.M.M.); (A.C.L.); (B.B.M.); (M.Q.A.)
- Laboratório de Hormônios e Genética Molecular LIM/42, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil (M.F.d.A.F.)
| | - Madson Queiroz Almeida
- Laboratório de Hormônios e Genética Molecular LIM/42, Unidade de Suprarrenal, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil; (A.M.F.L.); (B.M.M.); (A.C.L.); (B.B.M.); (M.Q.A.)
- Laboratório de Hormônios e Genética Molecular LIM/42, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil (M.F.d.A.F.)
- Serviço de Endocrinologia, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil
| | - Antonio Marcondes Lerario
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Ibere Cauduro Soares
- Serviço de Anatomia Patológica, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil;
| | - Maria Candida Barisson Villares Fragoso
- Laboratório de Hormônios e Genética Molecular LIM/42, Unidade de Suprarrenal, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil; (A.M.F.L.); (B.M.M.); (A.C.L.); (B.B.M.); (M.Q.A.)
- Laboratório de Hormônios e Genética Molecular LIM/42, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil (M.F.d.A.F.)
- Serviço de Endocrinologia, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, São Paulo 0540396, Brasil
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103
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Wang Y, Han X, Wang X, Sheng W, Chen Z, Shu W, Han J, Zhao S, Dai Y, Wang K, Shi W, Yang Z. Genomic based analyses reveal unique mutational profiling and identify prognostic biomarker for overall survival in Chinese small-cell lung cancer. Jpn J Clin Oncol 2020; 49:1143-1150. [PMID: 31612912 DOI: 10.1093/jjco/hyz131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/03/2019] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE As an aggressive subtype of lung cancer, small-cell lung cancer (SCLC) presents a poor prognosis. Although molecular and clinical characteristics have been established for SCLC, limited investigation has been performed for predicting survival of SCLC patients. METHODS Genomic alterations were profiled in Chinese SCLC patients (N = 37) using targeted sequencing. Clonal mutation burden (CMB) integrated the number of mutations with the clonal structure of the tumor. Specific pathways involving DNA damage repair (DDR) and cell cycle as well as CMB were studied as potential biomarkers for prognosis of SCLC. RESULTS TP53 and RB1 gene mutations were the most common alterations (91.9% and 83.8%, respectively), followed by LRP1B, FAM135B, SPTA1, KMT2D, FAT1, and NOTCH3. Survival analysis revealed that mutation status of the DDR pathway was associated with worse OS in our cohort. Importantly, patients with higher CMB exhibited worse OS in our cohort and this observation was successfully validated in the cBioportal cohort. Moreover, multivariate analysis demonstrated CMB as a promising independent prognostic factor for OS in Chinese SCLC patients. Interestingly, patients with loss of function of RB1, validated by immunohistochemistry staining, appeared to have worse OS. CONCLUSIONS The mutational profiling of Chinese SCLC patients signified an ethnicity dependent component. CMB was firstly found to be associated with OS of Chinese SCLC patients and could be regarded as a prognostic marker for SCLC.
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Affiliation(s)
- Yu Wang
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Xiao Han
- Department of Experiment, Tumor Hospital Affiliated to Guangxi Medical University, Nanning, China
| | - Xingwen Wang
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Wei Sheng
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Zheng Chen
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Weibin Shu
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Junqing Han
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | | | - Yi Dai
- OrigiMed Inc., Shanghai, China
| | | | - Weiwei Shi
- OrigiMed Inc., Shanghai, China.,Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhe Yang
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
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104
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Balachandran P, Beck CR. Structural variant identification and characterization. Chromosome Res 2020; 28:31-47. [PMID: 31907725 PMCID: PMC7131885 DOI: 10.1007/s10577-019-09623-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 10/15/2019] [Accepted: 11/24/2019] [Indexed: 01/06/2023]
Abstract
Structural variant (SV) differences between human genomes can cause germline and mosaic disease as well as inter-individual variation. De-regulation of accurate DNA repair and genomic surveillance mechanisms results in a large number of SVs in cancer. Analysis of the DNA sequences at SV breakpoints can help identify pathways of mutagenesis and regions of the genome that are more susceptible to rearrangement. Large-scale SV analyses have been enabled by high-throughput genome-level sequencing on humans in the past decade. These studies have shed light on the mechanisms and prevalence of complex genomic rearrangements. Recent advancements in both sequencing and other mapping technologies as well as calling algorithms for detection of genomic rearrangements have helped propel SV detection into population-scale studies, and have begun to elucidate previously inaccessible regions of the genome. Here, we discuss the genomic organization of simple and complex SVs, the molecular mechanisms of their formation, and various ways to detect them. We also introduce methods for characterizing SVs and their consequences on human genomes.
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Affiliation(s)
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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105
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Roca I, González-Castro L, Maynou J, Palacios L, Fernández H, Couce ML, Fernández-Marmiesse A. PattRec: An easy-to-use CNV detection tool optimized for targeted NGS assays with diagnostic purposes. Genomics 2020; 112:1245-1256. [DOI: 10.1016/j.ygeno.2019.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/25/2019] [Accepted: 07/21/2019] [Indexed: 12/17/2022]
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106
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Kuo AJ, Paulson VA, Hempelmann JA, Beightol M, Todhunter S, Colbert BG, Salipante SJ, Konnick EQ, Pritchard CC, Lockwood CM. Validation and implementation of a modular targeted capture assay for the detection of clinically significant molecular oncology alterations. Pract Lab Med 2020; 19:e00153. [PMID: 32123717 PMCID: PMC7038441 DOI: 10.1016/j.plabm.2020.e00153] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/24/2019] [Accepted: 01/16/2020] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES The rapid discovery of clinically significant genetic variants has translated to next-generation sequencing assays becoming out-of-date by the time they are designed, validated, and implemented. UW-OncoPlex addresses this through the adoption of a modular panel capable of redesign as significant alterations are identified. We describe the validation of OncoPlex version 6 (OPXv6) for the detection of single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs), structural variants (SVs), microsatellite instability (MSI), and tumor mutational burden (TMB) in a panel of 340 genes. DESIGN One hundred twelve samples with diverse diagnoses were comprised of formalin-fixed-paraffin-embedded tissue, fresh-frozen tissue, plasma, peripheral blood, bone marrow, saliva, and cell-line DNA. Libraries were prepared from genomic and cell-free DNA, hybridized to a custom panel of xGen Lockdown probes, and sequenced on Illumina platforms. Sequences were processed through a custom bioinformatics pipeline, and variant calls were compared to prior orthogonal clinical results. RESULTS Accuracy was 99% for SNVs ≥5% allele frequency, 98% for indels, 97% for SVs, 99% for CNVs, 100% for MSI, and 100% for TMB (compared to previous OncoPlex versions). Library preparation turnaround time decreased by 40%, and sequencing quality improved with a 2.5-fold increase in average sequencing coverage and 4-fold increase in percent on-target. CONCLUSIONS OPXv6 demonstrates improvements over prior UW-OncoPlex versions including reduced capture cost, improved sequencing quality, and decreased time to results. The modular capture probe design also provides a nimble laboratory response in addressing the expansions necessary to meet the needs of the continuously evolving field of molecular oncology.
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107
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Han E, Yoo J, Chae H, Lee S, Kim DH, Kim KJ, Kim Y, Kim M. Detection of BRCA1/2 large genomic rearrangement including BRCA1 promoter-region deletions using next-generation sequencing. Clin Chim Acta 2020; 505:49-54. [PMID: 32092317 DOI: 10.1016/j.cca.2020.02.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 02/03/2020] [Accepted: 02/20/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND Germline mutations in BRCA1 and BRCA2 (BRCA1/2) have been conventionally analyzed by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). Nowadays, next-generation sequencing (NGS) is increasingly being used in clinical genetics. The aim of this study was to evaluate the performance of NGS BRCA1/2 assays by comparing them with the conventional method. MATERIALS AND METHODS We did BRCA1/2 NGS assays of 108 breast and/or ovarian cancer patients whose BRCA1/2 mutation had been previously analyzed by Sanger sequencing and MLPA using TruSeq Custom Amplicon Design AFP2. Single-nucleotide variations (SNVs) and small insertions or deletions (InDels) were evaluated. In addition, we analyzed large genomic rearrangements (LGRs) using a coverage-based algorithm as well as a revised BRCA1/2 NGS assay (BRCAaccuTest PLUS), which additionally covered a BRCA1 promoter region. RESULTS The NGS BRCA1/2 assay detected all 20 SNVs and 21 small InDels in 56 patients. Among seven LGRs detected by MLPA, six exonic LGRs were well identified by both NGS BRCA1/2 assays. One pathogenic LGR, located on a BRCA1 promoter region, was successfully identified using revised BRCAaccuTestPLUS. CONCLUSIONS These results indicated that an NGS BRCA1/2 assay could detect most LGRs including BRCA1 promoter-region deletion as well as SNVs and small InDels. Therefore, it was applicable to clinical BRCA1/2 mutation tests.
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Affiliation(s)
- Eunhee Han
- Department of Laboratory Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Jaeeun Yoo
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea; Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Hyojin Chae
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea; Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Seungok Lee
- Department of Laboratory Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Do-Hoon Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Republic of Korea
| | | | - Yonggoo Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea; Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea; Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea.
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108
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Li L, Rao X, Wen Z, Ding X, Wang X, Xu W, Meng C, Yi Y, Guan Y, Chen Y, Wang J, Jun L. Implications of driver genes associated with a high tumor mutation burden identified using next-generation sequencing on immunotherapy in hepatocellular carcinoma. Oncol Lett 2020; 19:2739-2748. [PMID: 32218826 PMCID: PMC7068659 DOI: 10.3892/ol.2020.11372] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 12/19/2019] [Indexed: 02/06/2023] Open
Abstract
Immune checkpoint blockade (ICB) therapy is a treatment strategy for hepatocellular carcinoma (HCC); however, its clinical efficacy is limited to a select subset of patients. Next-generation sequencing has identified the value of tumor mutation burden (TMB) as a predictor for ICB efficacy in multiple types of tumor, including HCC. Specific driver gene mutations may be indicative of a high TMB (TMB-H) and analysis of such mutations may provide novel insights into the underlying mechanisms of TMB-H and potential therapeutic strategies. In the present study, a hybridization-capture method was used to target 1.45 Mb of the genomic sequence (coding sequence, 1 Mb), analyzing the somatic mutation landscape of 81 HCC tumor samples. Mutations in five genes were significantly associated with TMB-H, including mutations in tumor protein 53 (TP53), Catenin®1 (CTNNB1), AT-rich interactive domain-containing protein 1A (ARID1A), myeloid/lymphoid or mixed-lineage leukemia (MLL) and nuclear receptor co-repressor 1 (NCOR1). Further analysis using The Cancer Genome Atlas Liver Hepatocellular Carcinoma database showed that TP53, CTNNB1 and MLL mutations were positively correlated with TMB-H. Meanwhile, mutations in ARID1A, TP53 and MLL were associated with poor overall survival of patients with HCC. Overall, TMB-H and associated driver gene mutations may have potential as predictive biomarkers of ICB therapy efficacy for treatment of patients with HCC.
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Affiliation(s)
- Li Li
- Department of Oncology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Xiaosong Rao
- Department of Pathology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Zhaohong Wen
- Geneplus-Beijing Institute, Beijing 102206, P.R. China
| | - Xiaosheng Ding
- Department of Oncology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Xiangyi Wang
- Department of Oncology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Weiran Xu
- Department of Oncology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Chao Meng
- Department of Oncology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Yuting Yi
- Geneplus-Beijing Institute, Beijing 102206, P.R. China
| | - Yanfang Guan
- Geneplus-Beijing Institute, Beijing 102206, P.R. China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P.R. China
| | - Yongshen Chen
- Geneplus-Beijing Institute, Beijing 102206, P.R. China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P.R. China
| | - Jiayin Wang
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P.R. China
| | - Liang Jun
- Department of Oncology, Peking University International Hospital, Beijing 102206, P.R. China
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109
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Luo J, Zhang S, Tan M, Li J, Xu H, Tan Y, Huang Y. Targeted molecular profiling of genetic alterations in colorectal cancer using next-generation sequencing. Oncol Lett 2020; 19:1137-1144. [PMID: 31966042 PMCID: PMC6955650 DOI: 10.3892/ol.2019.11203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 10/10/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is a major contributor to cancer-associated mortality in China and remains a vast challenge worldwide. Although the genetic basis of CRC has been investigated, the uncommonly mutated genes in CRC remain unknown, in particular in the Asian population. In the present study, targeted region sequencing on 22 CRC and 10 paired non-cancerous tissues was performed to determine the genetic pattern of CRC samples in the Chinese population. Driver genes were detected by three distinct softwares, including MutSigCV, oncodriveFM and iCAGES. A total of 1,335 reliable somatic mutations were identified in tumour samples compared with normal samples. Furthermore, mismatch repair (MMR) mutant patients presented significantly higher mutation density compared with MMR wild-type patients. The results from MutSigCV, oncodriveFM and iCAGES analyses simultaneously detected 29 unique driver genes. In addition, the genes APC regulator of WNT signaling pathway, SMAD family member 4, neurofibromin 1, AT-rich interaction domain 5B and nuclear receptor corepressor 1 were the top five most frequently mutated genes in CRC samples, with mutation rates of 68, 36, 36, 32 and 27%, respectively. The findings from the present study may therefore serve as a basis for future investigation on the diagnosis and oncogenesis of CRC.
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Affiliation(s)
- Jia Luo
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Shengjun Zhang
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Meihua Tan
- BGI Education Center, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jia Li
- Department of Thyroid and Breast, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Shanghai 200072, P.R. China
| | - Huadong Xu
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
| | - Yanfei Tan
- Institute of Stem Cell Medicine, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China
| | - Yue Huang
- Department of Gastroenterology, The Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian 365000, P.R. China
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110
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Wu R, Shi C, Chen Q, Wu F, Li Q. Detection of circulating tumor cell DNA for monitoring advanced gastric cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:203-211. [PMID: 32211100 PMCID: PMC7061790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Circulating tumor DNA (ctDNA) for monitoring the effects of chemotherapy and predicting prognosis in advanced gastric cancer have not been thoroughly investigated. METHODS We performed next-generation sequencing (NGS) of ctDNA from 23 gastric cancer patients. Then the genetic information and clinical information were statistically analyzed. RESULTS In this study, the frequency of TP53 was significantly different between the effective and ineffective groups (P = 0.040), and the number of TP53 mutations was more frequent in the ineffective group. Missense mutation was a significant difference between the treatment effect groups (P = 0.026). The number of gene mutations and the change in copy number levels were related to therapeutic effect. Among the ineffective group, there was a significant difference in the number of gene mutations (P = 0.0006). We further divided the number of gene mutations into an increase group and a decrease group, and found that there was a significant difference between the effective and ineffective groups (P = 0.038). Finally, it was found that patients with high mutation abundance of gastric cancer had a shorter overall survival than patients with low mutation abundance (P<0.05). CONCLUSION ctDNA can be used as an effective tool to monitor the efficacy of chemotherapy and predict prognosis in advanced gastric cancer.
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Affiliation(s)
- Riping Wu
- Department of Medical Oncology, Fujian Medical University Union HospitalFuzhou, Fujian Province, People’s Republic of China
| | - Chunmei Shi
- Department of Medical Oncology, Fujian Medical University Union HospitalFuzhou, Fujian Province, People’s Republic of China
| | - Qiang Chen
- Department of Medical Oncology, Fujian Medical University Union HospitalFuzhou, Fujian Province, People’s Republic of China
- Stem Cell Research Institute, Fujian Medical UniversityFuzhou, Fujian Province, People’s Republic of China
| | - Fan Wu
- Fujian Medical UniversityFuzhou, Fujian Province, People’s Republic of China
| | - Qiaolian Li
- Fujian Medical UniversityFuzhou, Fujian Province, People’s Republic of China
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111
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Tertiary lymphoid structures improve immunotherapy and survival in melanoma. Nature 2020; 577:561-565. [DOI: 10.1038/s41586-019-1914-8] [Citation(s) in RCA: 698] [Impact Index Per Article: 174.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 12/04/2019] [Indexed: 02/06/2023]
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112
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Nie Q, Omerza G, Chandok H, Prego M, Hsiao MC, Meyers B, Hesse A, Uvalic J, Soucy M, Bergeron D, Peracchio M, Burns S, Kelly K, Rowe S, Rueter J, Reddi HV. Molecular profiling of gynecologic cancers for treatment and management of disease - demonstrating clinical significance using the AMP/ASCO/CAP guidelines for interpretation and reporting of somatic variants. Cancer Genet 2020; 242:25-34. [PMID: 31992506 DOI: 10.1016/j.cancergen.2019.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/17/2019] [Accepted: 11/02/2019] [Indexed: 10/25/2022]
Abstract
Molecular features of gynecologic cancers have been investigated in comprehensive studies, but correlation of these molecular signatures with clinical significance for precision medicine is yet to be established. Towards this end, we evaluated 95 gynecologic cancer cases submitted for testing using The JAX ActionSeq™ NGS panel. Molecular profiles were studied and compared to TCGA datasets to identify similarities and distinguishing features among subtypes. We identified 146 unique clinically significant variants (Tier I and II) across 45 of the 212 genes (21%), in 87% (83/95) of cases. TP53, PTEN, ARID1A, PIK3CA and ATM were the most commonly mutated genes; CCNE1 and ERBB2 amplifications were the most frequently detected copy-number alterations. PARP inhibitors were among the most commonly reported drug class with clinical trials, consistent with the frequency of DNA damage-response pathway mutations in our cohort. Overall, our study provides additional insight into the molecular profiles of gynecologic cancers, highlighting regulatory pathways involved, raising the potential implications for targeted therapeutic options currently available.
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Affiliation(s)
- Qian Nie
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Gregory Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Harshpreet Chandok
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Matthew Prego
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Meng-Chang Hsiao
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Bridgette Meyers
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Andrew Hesse
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Jasmina Uvalic
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Melissa Soucy
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Daniel Bergeron
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Michael Peracchio
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Shelbi Burns
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Shannon Rowe
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Jens Rueter
- The Maine Cancer Genomics Initiative, The Jackson Laboratory, Augusta, ME 04330, United States.
| | - Honey V Reddi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States.
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113
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Yang H, Zhu D. Combinatorial Detection Algorithm for Copy Number Variations Using High-throughput Sequencing Reads. INT J PATTERN RECOGN 2019. [DOI: 10.1142/s0218001419500228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Copy number variation (CNV) is a prevalent kind of genetic structural variation which leads to an abnormal number of copies of large genomic regions, such as gain or loss of DNA segments larger than 1[Formula: see text]kb. CNV exists not only in human genome but also in plant genome. Current researches have testified that CNV is associated with many complex diseases. In this paper, guanine-cytosine (GC) bias, mappability and their effect on read depth signals in sequencing data are discussed first. Subsequently, a new correction method for GC bias and an improved combinatorial detection algorithm for CNV using high-throughput sequencing reads based on hidden Markov model (CNV-HMM) are proposed. The corrected read depth signals have lower correlation with GC content, mappability of reads and the width of analysis window. Then we create a hidden Markov model which maps the reads onto the reference genome and records the unmapped reads. The unmapped reads are counted and normalized. The CNV-HMM detects the abnormal signal of read count and gains the candidate CNVs using the expectation maximization (EM) algorithm. Finally, we filter the candidate CNVs using split reads to promote the performance of our algorithm. The experiment result indicates that the CNV-HMM algorithm has higher accuracy and sensitivity for CNVs detection than most current detection algorithms.
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Affiliation(s)
- Hai Yang
- School of Computer Science and Technology, Shandong University, Qingdao 266237, P. R. China
| | - Daming Zhu
- School of Computer Science and Technology, Shandong University, Qingdao 266237, P. R. China
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Mutation Profiling of Premalignant Colorectal Neoplasia. Gastroenterol Res Pract 2019; 2019:2542640. [PMID: 31781186 PMCID: PMC6875414 DOI: 10.1155/2019/2542640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023] Open
Abstract
Accumulation of allelic variants in genes that regulate cellular proliferation, differentiation, and apoptosis may result in expansion of the aberrant intestinal epithelium, generating adenomas. Herein, we compared the mutation profiles of conventional colorectal adenomas (CNADs) across stages of progression towards early carcinoma. DNA was isolated from 17 invasive adenocarcinomas (ACs) and 58 large CNADs, including 19 with low-grade dysplasia (LGD), 21 with LGD adjacent to areas of high-grade dysplasia and/or carcinoma (LGD-H), and 28 with high-grade dysplasia (HGD). Ion AmpliSeq Comprehensive Cancer Panel libraries were prepared and sequenced on the Ion Proton. We identified 956 unique allelic variants; of these, 499 were considered nonsynonymous variants. Eleven genes (APC, KRAS, SYNE1, NOTCH4, BLNK, FBXW7, GNAS, KMT2D, TAF1L, TCF7L2, and TP53) were mutated in at least 15% of all samples. Out of frequently mutated genes, TP53 and BCL2 had a consistent trend in mutation prevalence towards malignancy, while two other genes (HNF1A and FBXW7) exhibited the opposite trend. HGD adenomas had significantly higher mutation rates than LGD adenomas, while LGD-H adenomas exhibited mutation frequencies similar to those of LGD adenomas. A significant increase in copy number variant frequency was observed from LGD through HGD to malignant samples. The profiling of advanced CNADs demonstrated variations in mutation patterns among colorectal premalignancies. Only limited numbers of genes were repeatedly mutated while the majority were altered in single cases. Most genetic alterations in adenomas can be considered early contributors to colorectal carcinogenesis.
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Bewicke-Copley F, Arjun Kumar E, Palladino G, Korfi K, Wang J. Applications and analysis of targeted genomic sequencing in cancer studies. Comput Struct Biotechnol J 2019; 17:1348-1359. [PMID: 31762958 PMCID: PMC6861594 DOI: 10.1016/j.csbj.2019.10.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022] Open
Abstract
Next Generation Sequencing (NGS) has dramatically improved the flexibility and outcomes of cancer research and clinical trials, providing highly sensitive and accurate high-throughput platforms for large-scale genomic testing. In contrast to whole-genome (WGS) or whole-exome sequencing (WES), targeted genomic sequencing (TS) focuses on a panel of genes or targets known to have strong associations with pathogenesis of disease and/or clinical relevance, offering greater sequencing depth with reduced costs and data burden. This allows targeted sequencing to identify low frequency variants in targeted regions with high confidence, thus suitable for profiling low-quality and fragmented clinical DNA samples. As a result, TS has been widely used in clinical research and trials for patient stratification and the development of targeted therapeutics. However, its transition to routine clinical use has been slow. Many technical and analytical obstacles still remain and need to be discussed and addressed before large-scale and cross-centre implementation. Gold-standard and state-of-the-art procedures and pipelines are urgently needed to accelerate this transition. In this review we first present how TS is conducted in cancer research, including various target enrichment platforms, the construction of target panels, and selected research and clinical studies utilising TS to profile clinical samples. We then present a generalised analytical workflow for TS data discussing important parameters and filters in detail, aiming to provide the best practices of TS usage and analyses.
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Key Words
- BAM, Binary Alignment Map
- BWA, Burrows-Wheeler Aligner
- Background error
- CLL, Chronic Lymphocytic Leukaemia
- COSMIC, Catalogue of Somatic Mutations in Cancer
- Cancer genomics
- Clinical samples
- ESP, Exome Sequencing Project
- FF, Fresh Frozen
- FFPE, Formalin Fixed Paraffin Embedded
- FL, Follicular Lymphoma
- GATK, Genome Analysis Toolkit
- ICGC, International Cancer Genome Consortium
- MBC, Molecular Barcode
- NCCN, the National Comprehensive Cancer Network®
- NGS, Next Generation Sequencing
- NHL, Non-Hodgkin Lymphoma
- NSCLC, Non-Small Cell Lung Carcinoma
- PCR duplicates
- QC, Quality Control
- SAM, Sequence Alignment Map
- TCGA, The Cancer Genome Atlas
- TS, Targeted Sequencing
- Targeted sequencing
- UMI, Unique Molecular Identifiers
- VAF, Variant Allele Frequency
- Variant calling
- WES, Whole Exome Sequencing
- WGS, Whole Genome Sequencing
- tFL, Transformed Follicular Lymphoma
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Affiliation(s)
- Findlay Bewicke-Copley
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Emil Arjun Kumar
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Giuseppe Palladino
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Koorosh Korfi
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jun Wang
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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Bartha Á, Győrffy B. Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology. Cancers (Basel) 2019; 11:E1725. [PMID: 31690036 PMCID: PMC6895801 DOI: 10.3390/cancers11111725] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 12/17/2022] Open
Abstract
Whole exome sequencing (WES) enables the analysis of all protein coding sequences in the human genome. This technology enables the investigation of cancer-related genetic aberrations that are predominantly located in the exonic regions. WES delivers high-throughput results at a reasonable price. Here, we review analysis tools enabling utilization of WES data in clinical and research settings. Technically, WES initially allows the detection of single nucleotide variants (SNVs) and copy number variations (CNVs), and data obtained through these methods can be combined and further utilized. Variant calling algorithms for SNVs range from standalone tools to machine learning-based combined pipelines. Tools for CNV detection compare the number of reads aligned to a dedicated segment. Both SNVs and CNVs help to identify mutations resulting in pharmacologically druggable alterations. The identification of homologous recombination deficiency enables the use of PARP inhibitors. Determining microsatellite instability and tumor mutation burden helps to select patients eligible for immunotherapy. To pave the way for clinical applications, we have to recognize some limitations of WES, including its restricted ability to detect CNVs, low coverage compared to targeted sequencing, and the missing consensus regarding references and minimal application requirements. Recently, Galaxy became the leading platform in non-command line-based WES data processing. The maturation of next-generation sequencing is reinforced by Food and Drug Administration (FDA)-approved methods for cancer screening, detection, and follow-up. WES is on the verge of becoming an affordable and sufficiently evolved technology for everyday clinical use.
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Affiliation(s)
- Áron Bartha
- Semmelweis University, Department of Bioinformatics and 2nd Department of Pediatrics, H-1094 Budapest, Hungary.
- TTK Cancer Biomarker Research Group, Institute of Enzymology, Magyar tudósokkörútja 2., H-1117 Budapest, Hungary.
| | - Balázs Győrffy
- Semmelweis University, Department of Bioinformatics and 2nd Department of Pediatrics, H-1094 Budapest, Hungary.
- TTK Cancer Biomarker Research Group, Institute of Enzymology, Magyar tudósokkörútja 2., H-1117 Budapest, Hungary.
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Yang H, Zhang J, Zhang L, Wen X, Luo Y, Yao D, Cheng T, Cheng H, Wang H, Lou F, Guo J, Liang X, Cao S, Chen J. Comprehensive analysis of genomic alterations detected by next-generation sequencing-based tissue and circulating tumor DNA assays in Chinese patients with non-small cell lung cancer. Oncol Lett 2019; 18:4762-4770. [PMID: 31611986 PMCID: PMC6781496 DOI: 10.3892/ol.2019.10791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 07/03/2019] [Indexed: 11/30/2022] Open
Abstract
While tumor genotyping is the standard treatment for patients with non-small cell lung cancer (NSCLC), spatial and temporal tumor heterogeneity and insufficient specimens can lead to limitations in the use of tissue-based sequencing. Circulating tumor DNA (ctDNA) fully encompasses tumor-specific sequence alterations and offers an alternative to tissue sample biopsies. However, few studies have evaluated whether the frequency of multiple genomic alterations observed following ctDNA sequencing is similar to that observed following tissue sequencing in NSCLC. Therefore, in the present study, targeted next-generation sequencing (NGS) was performed on tissue and plasma ctDNA samples in 99 patients with NSCLC. Overall, the frequencies of genetic alterations detected in ctDNA were positively correlated with those detected via tissue profiling (r=0.812; P=0.022). Genomic data revealed significant mutual exclusivity between alterations in epidermal growth factor receptor (EGFR) and tumor protein 53 (TP53; P=0.020), and between alterations in EGFR and KRAS (P=0.008), as well as potential mutual exclusivity between alterations in EGFR and Erb-B2 receptor tyrosine kinase 2 (P=0.059). Furthermore, the EGFR mutant allele frequency (MAF) was positively correlated with the TP53 MAF in individual tumors (r=0.773; P=0.005), and there was a marked difference in the EGFR MAF between patients with and without the TP53 mutation (P=0.001). Levels of the tumor serum marker CA242 in patients with ctDNA-detectable mutations were higher compared with those in patients without ctDNA-detectable mutations. The data from the present study highlight the importance of tissue and plasma ctDNA screening by NGS to guide personalized therapy and promote the clinical management of patients with NSCLC.
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Affiliation(s)
- Hua Yang
- Department of Thoracic Internal Medicine, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya Medical School of Central South University, Changsha, Hunan 410013, P.R. China
| | - Junjie Zhang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Lemeng Zhang
- Department of Thoracic Internal Medicine, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya Medical School of Central South University, Changsha, Hunan 410013, P.R. China
| | - Xiaoping Wen
- Department of Thoracic Internal Medicine, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya Medical School of Central South University, Changsha, Hunan 410013, P.R. China
| | - Yongzhong Luo
- Department of Thoracic Internal Medicine, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya Medical School of Central South University, Changsha, Hunan 410013, P.R. China
| | - Dingquan Yao
- Department of Thoracic Internal Medicine, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya Medical School of Central South University, Changsha, Hunan 410013, P.R. China
| | - Tianli Cheng
- Department of Thoracic Internal Medicine, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya Medical School of Central South University, Changsha, Hunan 410013, P.R. China
| | - Huanqing Cheng
- Acornmed Biotechnology Co., Ltd., Beijing 100176, P.R. China
| | - Huina Wang
- Acornmed Biotechnology Co., Ltd., Beijing 100176, P.R. China
| | - Feng Lou
- Acornmed Biotechnology Co., Ltd., Beijing 100176, P.R. China
| | - Jing Guo
- Acornmed Biotechnology Co., Ltd., Beijing 100176, P.R. China
| | - Xiayuan Liang
- Acornmed Biotechnology Co., Ltd., Beijing 100176, P.R. China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd., Beijing 100176, P.R. China
| | - Jianhua Chen
- Department of Thoracic Internal Medicine, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya Medical School of Central South University, Changsha, Hunan 410013, P.R. China
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Zare F, Nabavi S. Copy Number Variation Detection Using Total Variation. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2019; 2019:423-428. [PMID: 32515750 PMCID: PMC7278034 DOI: 10.1145/3307339.3342181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Next-generation sequencing (NGS) technologies offer new opportunities for precise and accurate identification of genomic aberrations, including copy number variations (CNVs). For high-throughput NGS data, using depth of coverage has become a major approach to identify CNVs, especially for whole exome sequencing (WES) data. Due to the high level of noise and biases of read-count data and complexity of the WES data, existing CNV detection tools identify many false CNV segments. Besides, NGS generates a huge amount of data, requiring to use effective and efficient methods. In this work, we propose a novel segmentation algorithm based on the total variation approach to detect CNVs more precisely and efficiently using WES data. The proposed method also filters out outlier read-counts and identifies significant change points to reduce false positives. We used real and simulated data to evaluate the performance of the proposed method and compare its performance with those of other commonly used CNV detection methods. Using simulated and real data, we show that the proposed method outperforms the existing CNV detection methods in terms of accuracy and false discovery rate and has a faster runtime compared to the circular binary segmentation method.
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Affiliation(s)
| | - Sheida Nabavi
- Corresponding author. This study was supported by a grant from the National Institutes of Health (NIH, R00LM011595, PI: Nabavi).
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119
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Phi JH, Sun CH, Lee SH, Lee S, Park I, Choi SA, Park SH, Lee JY, Wang KC, Kim SK, Yun H, Park CK. NPM1 as a potential therapeutic target for atypical teratoid/rhabdoid tumors. BMC Cancer 2019; 19:848. [PMID: 31462227 PMCID: PMC6714307 DOI: 10.1186/s12885-019-6044-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 08/16/2019] [Indexed: 01/10/2023] Open
Abstract
Background Atypical teratoid/rhabdoid tumors (AT/RTs) are highly malignant brain tumors with inactivation of the SMARCB1 gene, which play a critical role in genomic transcriptional control. In this study, we analyzed the genomic and transcriptomic profiles of human AT/RTs to discover new druggable targets. Methods Multiplanar sequencing analyses, including whole exome sequencing (WES), single nucleotide polymorphism (SNP) arrays, array comparative genomic hybridization (aCGH), and whole transcriptome sequencing (RNA-Seq), were performed on 4 AT/RT tissues. Validation of a druggable target was conducted using AT/RT cell lines. Results WES revealed that the AT/RT genome is extremely stable except for the inactivation of SMARCB1. However, we identified 897 significantly upregulated genes and 523 significantly downregulated genes identified using RNA-Seq, indicating that the transcriptional profiles of the AT/RT tissues changed substantially. Gene set enrichment assays revealed genes related to the canonical pathways of cancers, and nucleophosmin (NPM1) was the most significantly upregulated gene in the AT/RT samples. An NPM1 inhibitor (NSC348884) effectively suppressed the viability of 7 AT/RT cell lines. Network analyses showed that genes associated with NPM1 are mainly involved in cell cycle regulation. Upon treatment with an NPM1 inhibitor, cell cycle arrest at G1 phase was observed in AT/RT cells. Conclusions We propose that NPM1 is a novel therapeutic target for AT/RTs. Electronic supplementary material The online version of this article (10.1186/s12885-019-6044-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ji Hoon Phi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea.,Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Choong-Hyun Sun
- Genome opinion Co., Ltd. 7, Yeonmujang 5ga-gil, Seongdong-gu, Seoul, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seungmook Lee
- Graduated, Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | - Inho Park
- SD Genomics, Seoul, Republic of Korea
| | - Seung Ah Choi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ji Yeoun Lee
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea.,Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea.,Department of Anatomy, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyu-Chang Wang
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea.,Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea. .,Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea.
| | - Hongseok Yun
- Center for Precision Medicine, Seoul National University Hospital, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea.
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea.
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Ried T, Meijer GA, Harrison DJ, Grech G, Franch-Expósito S, Briffa R, Carvalho B, Camps J. The landscape of genomic copy number alterations in colorectal cancer and their consequences on gene expression levels and disease outcome. Mol Aspects Med 2019; 69:48-61. [PMID: 31365882 DOI: 10.1016/j.mam.2019.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022]
Abstract
Aneuploidy, the unbalanced state of the chromosome content, represents a hallmark of most solid tumors, including colorectal cancer. Such aneuploidies result in tumor specific genomic imbalances, which emerge in premalignant precursor lesions. Moreover, increasing levels of chromosomal instability have been observed in adenocarcinomas and are maintained in distant metastases. A number of studies have systematically integrated copy number alterations with gene expression changes in primary carcinomas, cell lines, and experimental models of aneuploidy. In fact, chromosomal aneuploidies target a number of genes conferring a selective advantage for the metabolism of the cancer cell. Copy number alterations not only have a positive correlation with expression changes of the majority of genes on the altered genomic segment, but also have effects on the transcriptional levels of genes genome-wide. Finally, copy number alterations have been associated with disease outcome; nevertheless, the translational applicability in clinical practice requires further studies. Here, we (i) review the spectrum of genetic alterations that lead to colorectal cancer, (ii) describe the most frequent copy number alterations at different stages of colorectal carcinogenesis, (iii) exemplify their positive correlation with gene expression levels, and (iv) discuss copy number alterations that are potentially involved in disease outcome of individual patients.
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Affiliation(s)
- Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD, USA.
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - David J Harrison
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK
| | - Godfrey Grech
- Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Sebastià Franch-Expósito
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain
| | - Romina Briffa
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK; Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain; Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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121
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Ma F, Guan Y, Yi Z, Chang L, Li Q, Chen S, Zhu W, Guan X, Li C, Qian H, Xia X, Yang L, Zhang J, Husain H, Liao Z, Futreal A, Huang J, Yi X, Xu B. Assessing tumor heterogeneity using ctDNA to predict and monitor therapeutic response in metastatic breast cancer. Int J Cancer 2019; 146:1359-1368. [PMID: 31241775 DOI: 10.1002/ijc.32536] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/18/2019] [Accepted: 06/12/2019] [Indexed: 12/12/2022]
Abstract
Tumor heterogeneity was associated with treatment outcome of metastatic cancers but few studies have examined whether tumor heterogeneity in circulating tumor DNA (ctDNA) can be used to predict treatment outcome. ctDNA analysis was performed in 37 HER2-positive metastatic breast cancer patients treated with pyrotinib. Patients with high tumor heterogeneity had significantly worse PFS outcomes, with a median PFS of 30.0 weeks vs. 60.0 weeks for patients with low tumor heterogeneity (hazard ratio [HR], 2.9; p = 0.02). Patients with trunk resistance mutations receiving pyrotinib monotherapy had worse outcomes (HR, 4.5; p = 0.03), with a median PFS of 7.8 weeks vs. 27.4 weeks for those with branch resistance mutations or without any resistance mutations in baseline ctDNA. Longitudinal monitoring of 21 patients during treatment showed that the molecular tumor burden index ([mTBI] a measure of the percentage of ctDNA in samples) was positively correlated with tumor size as evaluated by computed tomography (p < 0.0001, Pearson r = 0.52) and detected disease progression 8-16 weeks earlier. Our current findings suggested that ctDNA could be used to assess tumor heterogeneity and predict treatment outcomes. Furthermore, the mTBI is better for assessing therapeutic response than single gene mutations and might supplement the current therapeutic response evaluation system.
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Affiliation(s)
- Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanfang Guan
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Zongbi Yi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lianpeng Chang
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Qiao Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanshan Chen
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenjie Zhu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiuwen Guan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chunxiao Li
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuefeng Xia
- Houston Methodist Research Institute, Weill Cornell School of Medicine, Houston, TX
| | - Ling Yang
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hatim Husain
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Zhongxing Liao
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Yi
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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122
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Funari MFA, de Barros JS, Santana LS, Lerario AM, Freire BL, Homma TK, Vasques GA, Mendonca BB, Nishi MY, Jorge AAL. Evaluation of SHOX defects in the era of next-generation sequencing. Clin Genet 2019; 96:261-265. [PMID: 31219618 DOI: 10.1111/cge.13587] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 01/15/2023]
Abstract
Short stature homeobox (SHOX) haploinsufficiency is a frequent cause of short stature. Despite advances in sequencing technologies, the identification of SHOX mutations continues to be performed using standard methods, including multiplex ligation-dependent probe amplification (MLPA) followed by Sanger sequencing. We designed a targeted panel of genes associated with growth impairment, including SHOX genomic and enhancer regions, to improve the resolution of next-generation sequencing for SHOX analysis. We used two software packages, CONTRA and Nexus Copy Number, in addition to visual analysis to investigate the presence of copy number variants (CNVs). We evaluated 15 patients with previously known SHOX defects, including point mutations, deletions and a duplication, and 77 patients with idiopathic short stature (ISS). The panel was able to confirm all known defects in the validation analysis. During the prospective evaluation, we identified two new partial SHOX deletions (one detected only by visual analysis), including an intragenic deletion not detected by MLPA. Additionally, we were able to determine the breakpoints in four cases. Our results show that the designed panel can be used for the molecular investigation of patients with ISS, and it may even detect CNVs in SHOX and its enhancers, which may be present in a significant fraction of patients.
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Affiliation(s)
- Mariana F A Funari
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Juliana S de Barros
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Lucas S Santana
- Unidade de Endocrinologia Genética/LIM25, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Antonio M Lerario
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.,Unidade de Endocrinologia Genética/LIM25, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.,Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan
| | - Bruna L Freire
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Thais K Homma
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.,Unidade de Endocrinologia Genética/LIM25, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Gabriela A Vasques
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.,Unidade de Endocrinologia Genética/LIM25, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Berenice B Mendonca
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Mirian Y Nishi
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Alexander A L Jorge
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.,Unidade de Endocrinologia Genética/LIM25, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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123
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Xiao R, An Y, Ye W, Derakhshan A, Cheng H, Yang X, Allen C, Chen Z, Schmitt NC, Van Waes C. Dual Antagonist of cIAP/XIAP ASTX660 Sensitizes HPV - and HPV + Head and Neck Cancers to TNFα, TRAIL, and Radiation Therapy. Clin Cancer Res 2019; 25:6463-6474. [PMID: 31266830 DOI: 10.1158/1078-0432.ccr-18-3802] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/24/2019] [Accepted: 06/28/2019] [Indexed: 12/13/2022]
Abstract
PURPOSE Human papillomavirus-negative (HPV-) head and neck squamous cell carcinomas (HNSCC) harbor frequent genomic amplification of Fas-associated death domain, with or without concurrent amplification of Baculovirus inhibitor of apoptosis repeat containing (BIRC2/3) genes encoding cellular inhibitor of apoptosis proteins 1/2 (cIAP1/2). Antagonists targeting cIAP1 have been reported to enhance sensitivity of HPV-, but not HPV+ tumors, to TNF family death ligands (TNF and TRAIL) and radiation.Experimental Design: We tested a novel dual cIAP/XIAP antagonist ASTX660 in HPV+ and HPV- cell lines in combination with death ligands TNFα and TRAIL, and in preclinical xenograft models with radiation, an inducer of death ligands. The dependence of activity on TNF was examined by antibody depletion. RESULTS ASTX660 sensitized subsets of HPV- and HPV+ HNSCC cell lines to TNFα and TRAIL. These antitumor effects of ASTX660 are the result of both apoptosis and/or necroptosis among HPV- cells, and primarily by apoptosis (caspase 3 and caspase 8 cleavage) in HPV+ cells. ASTX660 enhanced restoration of protein expression and inhibitory activity of proapoptotic tumor suppressor TP53 in HPV+ HNSCC. Furthermore, ASTX660 combined with radiotherapy, an inducer of death ligands, significantly delayed growth of both HPV- and HPV+ human tumor xenografts, an effect attenuated by anti-TNFα pretreatment blockade. CONCLUSIONS IAP1/XIAP antagonist, ASTX660, sensitizes HPV+ HNSCC to TNFα via a mechanism involving restoration of TP53. These findings serve to motivate further studies of dual cIAP/XIAP antagonists and future clinical trials combining these antagonists with radiotherapy to treat both HPV+ and HPV- HNSCC.
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Affiliation(s)
- Roy Xiao
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, Ohio.,Medical Research Scholars Program, NIH, Bethesda, Maryland.,Tumor Biology Section, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Yi An
- Tumor Biology Section, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Wenda Ye
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, Ohio.,Medical Research Scholars Program, NIH, Bethesda, Maryland.,Tumor Biology Section, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Adeeb Derakhshan
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, Ohio.,Medical Research Scholars Program, NIH, Bethesda, Maryland.,Tumor Biology Section, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Hui Cheng
- Tumor Biology Section, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Xinping Yang
- Tumor Biology Section, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Clint Allen
- Office of the Clinical Director, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland.,Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland
| | - Zhong Chen
- Tumor Biology Section, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Nicole C Schmitt
- Office of the Clinical Director, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland.,Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland
| | - Carter Van Waes
- Tumor Biology Section, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland.
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124
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Yang P, Huang X, Lai C, Li L, Li T, Huang P, Ouyang S, Yan J, Cheng S, Lei G, Wang Z, Yu L, Hong Z, Li R, Dong H, Wang C, Yu Y, Wang X, Li X, Wang L, Lv F, Yin Y, Yang H, Song J, Gao Q, Wang X, Zhang S. SET domain containing 1B gene is mutated in primary hepatic neuroendocrine tumors. Int J Cancer 2019; 145:2986-2995. [PMID: 30977120 DOI: 10.1002/ijc.32334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/27/2019] [Indexed: 11/09/2022]
Abstract
Primary hepatic neuroendocrine tumors (PHNETs) are extremely rare NETs originating from the liver. These tumors are associated with heterogeneous prognosis, and few treatment targets for PHNETs have been identified. Because the major genetic alterations in PHNET are still largely unknown, we performed whole-exome sequencing of 22 paired tissues from PHNET patients and identified 22 recurring mutations of somatic genes involved in the following activities: epigenetic modification (BPTF, MECP2 and WDR5), cell cycle (TP53, ATM, MED12, DIDO1 and ATAD5) and neural development (UBR4, MEN1, GLUL and GIGYF2). Here, we show that TP53 and the SET domain containing the 1B gene (SETD1B) are the most frequently mutated genes in this set of samples (3/22 subjects, 13.6%). A biological analysis suggests that one of the three SETD1B mutants, A1054del, promotes cell proliferation, migration and invasion compared to wild-type SETD1B. Our work unveils that SETD1B A1054del mutant is functional in PHNET and implicates genes including TP53 in the disease. Our findings thus characterize the mutational landscapes of PHNET and implicate novel gene mutations linked to PHNET pathogenesis and potential therapeutic targets.
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Affiliation(s)
- Penghui Yang
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China.,State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | | | - Chengcai Lai
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- BGI-Shenzhen, Shenzhen, China.,Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Tieling Li
- Chinese PLA General Hospital, Beijing, China
| | - Peide Huang
- BGI-Shenzhen, Shenzhen, China.,Section of Molecular Disease Biology, Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jin Yan
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Sijie Cheng
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Guanglin Lei
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Zhaohai Wang
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Linxiang Yu
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Zhixian Hong
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Ruisheng Li
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
| | - Hui Dong
- Eastern Hepatobiliary Surgery Institute/Hospital, Shanghai, China
| | - Cheng Wang
- Chinese PLA General Hospital, Beijing, China.,Beijing 307 Hospital Affiliated with the Academy of Medical Sciences, Beijing, China
| | - Yinghao Yu
- Fuzhou General Hospital of Nanjing Military Command of Chinese PLA, Fuzhou, China
| | - Xuan Wang
- The 81st Hospital of PLA, Nanjing, China
| | - Xianghong Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Liming Wang
- Cancer Hospital Chinese Academy of Medical Science, Beijing, China
| | - Fudong Lv
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Ye Yin
- BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jianxun Song
- Microbial pathogenesis and Immunology, Texas A&M University College of Medicine, Bryan, TX
| | | | - Xiliang Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shaogeng Zhang
- Beijing 302 Hospital/5th Medical Center of Chinese PLA General of Hospital, Beijing, China
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125
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Chiang T, Liu X, Wu TJ, Hu J, Sedlazeck FJ, White S, Schaid D, Andrade MD, Jarvik GP, Crosslin D, Stanaway I, Carrell DS, Connolly JJ, Hakonarson H, Groopman EE, Gharavi AG, Fedotov A, Bi W, Leduc MS, Murdock DR, Jiang Y, Meng L, Eng CM, Wen S, Yang Y, Muzny DM, Boerwinkle E, Salerno W, Venner E, Gibbs RA. Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel. Genet Med 2019; 21:2135-2144. [PMID: 30890783 PMCID: PMC6752313 DOI: 10.1038/s41436-019-0475-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/25/2019] [Indexed: 12/24/2022] Open
Abstract
PURPOSE To provide a validated method to confidently identify exon-containing copy-number variants (CNVs), with a low false discovery rate (FDR), in targeted sequencing data from a clinical laboratory with particular focus on single-exon CNVs. METHODS DNA sequence coverage data are normalized within each sample and subsequently exonic CNVs are identified in a batch of samples, when the target log2 ratio of the sample to the batch median exceeds defined thresholds. The quality of exonic CNV calls is assessed by C-scores (Z-like scores) using thresholds derived from gold standard samples and simulation studies. We integrate an ExonQC threshold to lower FDR and compare performance with alternate software (VisCap). RESULTS Thirteen CNVs were used as a truth set to validate Atlas-CNV and compared with VisCap. We demonstrated FDR reduction in validation, simulation, and 10,926 eMERGESeq samples without sensitivity loss. Sixty-four multiexon and 29 single-exon CNVs with high C-scores were assessed by Multiplex Ligation-dependent Probe Amplification (MLPA). CONCLUSION Atlas-CNV is validated as a method to identify exonic CNVs in targeted sequencing data generated in the clinical laboratory. The ExonQC and C-score assignment can reduce FDR (identification of targets with high variance) and improve calling accuracy of single-exon CNVs respectively. We propose guidelines and criteria to identify high confidence single-exon CNVs.
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Affiliation(s)
- Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - Xiuping Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Tsung-Jung Wu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Daniel Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Gail P Jarvik
- University of Washington Medical Center, Seattle, WA, USA
| | - David Crosslin
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Ian Stanaway
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | | | | | - Emily E Groopman
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY, USA
| | - Alexander Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | | | - David R Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yunyun Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Shu Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,UTHealth School of Public Health, Houston, TX, USA
| | - William Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Abstract
Scoliosis is a common manifestation of neurofibromatosis type 1, causing significant morbidity. The etiology of dystrophic scoliosis in neurofibromatosis type 1 is not fully understood and therapies are lacking. Somatic mutations in NF1 have been shown in tibial pseudarthrosis providing rationale for similar processes in neurofibromatosis type 1-associated dystrophic scoliosis. Spinal samples from surgical procedures with matched peripheral blood of two individuals with neurofibromatosis type 1 and dystrophic scoliosis were obtained and DNA extracted. Next generation sequencing of various spinal sections as well as the germline/blood sample were performed using a RASopathy gene panel (includes the NF1 gene). Variants were compared between the spinal tissue samples and the germline data. In addition, the next generation sequencing allele frequency data were used to detect somatic loss of heterozygosity. All samples had a detected potentially inactivating NF1 germline mutation. Both individuals demonstrated an allelic imbalance inclusive of NF1 in the next generation sequencing data. In addition, for the same two individuals, there was an increase in the % variant reads for the germline mutation in some of the surgical spinal samples corresponding to the allelic imbalance. Contra analysis did not show any deletion in Chromosome 17 next generation sequencing data. Microarray analysis verified somatic copy neutral loss of heterozygosity for these two individuals for the majority of the chromosome 17 q-arm, inclusive of the NF1 gene. These results suggest that the cause of dystrophic scoliosis is multifactorial and that a somatic NF1 mutation contributes to the etiology.
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127
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Fu JM, Leslie EJ, Scott AF, Murray JC, Marazita ML, Beaty TH, Scharpf RB, Ruczinski I. Detection of de novo copy number deletions from targeted sequencing of trios. Bioinformatics 2019; 35:571-578. [PMID: 30084993 PMCID: PMC6378941 DOI: 10.1093/bioinformatics/bty677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/25/2018] [Accepted: 08/01/2018] [Indexed: 11/25/2022] Open
Abstract
MOTIVATION De novo copy number deletions have been implicated in many diseases, but there is no formal method to date that identifies de novo deletions in parent-offspring trios from capture-based sequencing platforms. RESULTS We developed Minimum Distance for Targeted Sequencing (MDTS) to fill this void. MDTS has similar sensitivity (recall), but a much lower false positive rate compared to less specific CNV callers, resulting in a much higher positive predictive value (precision). MDTS also exhibited much better scalability. AVAILABILITY AND IMPLEMENTATION MDTS is freely available as open source software from the Bioconductor repository. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jack M Fu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Alan F Scott
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jeffrey C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Mary L Marazita
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Robert B Scharpf
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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128
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Davidson G, Coassolo S, Kieny A, Ennen M, Pencreach E, Malouf GG, Lipsker D, Davidson I. Dynamic Evolution of Clonal Composition and Neoantigen Landscape in Recurrent Metastatic Melanoma with a Rare Combination of Driver Mutations. J Invest Dermatol 2019; 139:1769-1778.e2. [PMID: 30776432 DOI: 10.1016/j.jid.2019.01.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 12/14/2022]
Abstract
In melanoma, initiating oncogenic mutations in BRAF or NRAS are detected in premalignant lesions that accumulate additional mutations and genomic instability as the tumor evolves to the metastatic state. Here we investigate evolution of clonal composition and neoantigen landscape in an atypical melanoma displaying recurrent cutaneous lesions over a 6-year period without development of extracutaneous metastases. Whole exome sequencing of four cutaneous lesions taken during the 6-year period identified a collection of single nucleotide variants and small insertions and deletions shared among all tumors, along with progressive selection of subclones displaying fewer single nucleotide variants. Later tumors also displayed lower neoantigen burden compared to early tumors, suggesting that clonal evolution was driven, at least in part, by counter selection of subclones with high neoantigen burdens. Among the selected mutations are a missense mutation in MAP2K1 (F53Y) and an inversion on chromosome 7 generating a AKAP9-BRAF fusion. The mutant proteins cooperatively activate the MAPK signaling pathway confirming they are potential driver mutations of this tumor. We therefore describe the long-term genetic evolution of cutaneous metastatic melanoma characterized by an unexpected phenotypic stability and neoantigen-driven clonal selection.
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Affiliation(s)
- Guillaume Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Unité Mixte de Recherche 7104, Le Centre National de la Recherche Scientifique, U1258 Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Illkirch Cédex, France
| | - Sébastien Coassolo
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Unité Mixte de Recherche 7104, Le Centre National de la Recherche Scientifique, U1258 Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Illkirch Cédex, France
| | - Alice Kieny
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Unité Mixte de Recherche 7104, Le Centre National de la Recherche Scientifique, U1258 Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Illkirch Cédex, France; Faculté de Médecine and Service de Dermatologie, Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Marie Ennen
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Unité Mixte de Recherche 7104, Le Centre National de la Recherche Scientifique, U1258 Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Illkirch Cédex, France
| | - Erwan Pencreach
- Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Gabriel G Malouf
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Unité Mixte de Recherche 7104, Le Centre National de la Recherche Scientifique, U1258 Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Illkirch Cédex, France
| | - Dan Lipsker
- Faculté de Médecine and Service de Dermatologie, Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Unité Mixte de Recherche 7104, Le Centre National de la Recherche Scientifique, U1258 Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Illkirch Cédex, France.
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129
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Rosa-Rosa JM, Caniego-Casas T, Leskela S, Cristobal E, González-Martínez S, Moreno-Moreno E, López-Miranda E, Holgado E, Pérez-Mies B, Garrido P, Palacios J. High Frequency of ERBB2 Activating Mutations in Invasive Lobular Breast Carcinoma with Pleomorphic Features. Cancers (Basel) 2019; 11:cancers11010074. [PMID: 30641862 PMCID: PMC6356653 DOI: 10.3390/cancers11010074] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/30/2018] [Accepted: 01/07/2019] [Indexed: 12/11/2022] Open
Abstract
Background: Characterisation of molecular alterations of pleomorphic lobular carcinoma (PLC), an aggressive subtype of invasive lobular carcinoma (ILC), have not been yet completely accomplished. Methods: To investigate the molecular alterations of invasive lobular carcinoma with pleomorphic features, a total of 39 tumour samples (in situ and invasive lesions and lymph node metastases) from 27 patients with nuclear grade 3 invasive lobular carcinomas were subjected to morphological, immunohistochemical and massive parallel sequencing analyses. Results: Our observations indicated that invasive lobular carcinomas with pleomorphic features were morphologically and molecularly heterogeneous. All cases showed absence or aberrant expression of E-cadherin and abnormal expression of β-catenin and p120. CDH1 (89%), PIK3CA (33%) and ERRB2 (26%) were the most common mutated genes. ERBB2 mutations preferentially affected the tyrosine-kinase activity domain, being the most frequent the targetable mutation p.L755S (57%). We also observed higher frequency of mutations in ARID1B, KMT2C, MAP3K1, TP53 and ARID1A in PLC than previously reported in classic ILC. Alterations related to progression from in situ to invasive carcinoma and/or to lymph node metastases included TP53 mutation, amplification of PIK3CA and CCND1 and loss of ARID1A expression. Conclusions: The high frequency of ERBB2 mutations observed suggests that ERBB2 mutation testing should be considered in all invasive lobular carcinomas with nuclear grade 3.
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Affiliation(s)
| | | | - Susanna Leskela
- CIBER-ONC, Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain.
| | - Eva Cristobal
- Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain.
| | | | | | - Elena López-Miranda
- Department of Medical Oncology, Hospital Ramón y Cajal, 28034 Madrid, Spain.
| | - Esther Holgado
- Department of Medical Oncology, Hospital Ramón y Cajal, 28034 Madrid, Spain.
| | - Belén Pérez-Mies
- Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain.
- Department of Pathology, Hospital Ramón y Cajal, 28034 Madrid, Spain.
- Facultad de Medicina, Universidad de Alcalá de Henares, 28029 Madrid, Spain.
| | - Pilar Garrido
- CIBER-ONC, Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain.
- Department of Medical Oncology, Hospital Ramón y Cajal, 28034 Madrid, Spain.
- Facultad de Medicina, Universidad de Alcalá de Henares, 28029 Madrid, Spain.
| | - José Palacios
- CIBER-ONC, Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain.
- Department of Pathology, Hospital Ramón y Cajal, 28034 Madrid, Spain.
- Facultad de Medicina, Universidad de Alcalá de Henares, 28029 Madrid, Spain.
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130
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Roca I, González-Castro L, Fernández H, Couce ML, Fernández-Marmiesse A. Free-access copy-number variant detection tools for targeted next-generation sequencing data. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 779:114-125. [DOI: 10.1016/j.mrrev.2019.02.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 12/25/2018] [Accepted: 02/22/2019] [Indexed: 01/23/2023]
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131
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Jiménez-Otero N, de Uña-Álvarez J, Pardo-Fernández JC. Goodness-of-fit tests for disorder detection in NGS experiments. Biom J 2018; 61:424-441. [PMID: 30589104 DOI: 10.1002/bimj.201700284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 09/28/2018] [Accepted: 10/07/2018] [Indexed: 11/11/2022]
Abstract
Next-generation sequencing (NGS) experiments are often performed in biomedical research nowadays, leading to methodological challenges related to the high-dimensional and complex nature of the recorded data. In this work we review some of the issues that arise in disorder detection from NGS experiments, that is, when the focus is the detection of deletion and duplication disorders for homozygosity and heterozygosity in DNA sequencing. A statistical model to cope with guanine/cytosine bias and phasing and prephasing phenomena at base level is proposed, and a goodness-of-fit procedure for disorder detection is derived. The method combines the proper evaluation of local p-values (one for each DNA base) with suitable corrections for multiple comparisons and the discrete nature of the p-values. A global test for the detection of disorders in the whole DNA region is proposed too. The performance of the introduced procedures is investigated through simulations. A real data illustration is provided.
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Affiliation(s)
| | - Jacobo de Uña-Álvarez
- Department of Statistics and Operations Research, SiDOR Research Group & CINBIO, University of Vigo, Vigo, Pontevedra, Spain
| | - Juan Carlos Pardo-Fernández
- Department of Statistics and Operations Research, SiDOR Research Group & CINBIO, University of Vigo, Vigo, Pontevedra, Spain
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132
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High-resolution deconstruction of evolution induced by chemotherapy treatments in breast cancer xenografts. Sci Rep 2018; 8:17937. [PMID: 30560892 PMCID: PMC6298990 DOI: 10.1038/s41598-018-36184-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/14/2018] [Indexed: 12/30/2022] Open
Abstract
The processes by which tumors evolve are essential to the efficacy of treatment, but quantitative understanding of intratumoral dynamics has been limited. Although intratumoral heterogeneity is common, quantification of evolution is difficult from clinical samples because treatment replicates cannot be performed and because matched serial samples are infrequently available. To circumvent these problems we derived and assayed large sets of human triple-negative breast cancer xenografts and cell cultures from two patients, including 86 xenografts from cyclophosphamide, doxorubicin, cisplatin, docetaxel, or vehicle treatment cohorts as well as 45 related cell cultures. We assayed these samples via exome-seq and/or high-resolution droplet digital PCR, allowing us to distinguish complex therapy-induced selection and drift processes among endogenous cancer subclones with cellularity uncertainty <3%. For one patient, we discovered two predominant subclones that were granularly intermixed in all 48 co-derived xenograft samples. These two subclones exhibited differential chemotherapy sensitivity–when xenografts were treated with cisplatin for 3 weeks, the post-treatment volume change was proportional to the post-treatment ratio of subclones on a xenograft-to-xenograft basis. A subsequent cohort in which xenografts were treated with cisplatin, allowed a drug holiday, then treated a second time continued to exhibit this proportionality. In contrast, xenografts from other treatment cohorts, spatially dissected xenograft fragments, and cell cultures evolved in diverse ways but with substantial population bottlenecks. These results show that ecosystems susceptible to successive retreatment can arise spontaneously in breast cancer in spite of a background of irregular subclonal bottlenecks, and our work provides to our knowledge the first quantification of the population genetics of such a system. Intriguingly, in such an ecosystem the ratio of common subclones is predictive of the state of treatment susceptibility, showing how measurements of subclonal heterogeneity could guide treatment for some patients.
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133
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Nieboer MM, Dorssers LCJ, Straver R, Looijenga LHJ, de Ridder J. TargetClone: A multi-sample approach for reconstructing subclonal evolution of tumors. PLoS One 2018; 13:e0208002. [PMID: 30496231 PMCID: PMC6264523 DOI: 10.1371/journal.pone.0208002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 11/11/2018] [Indexed: 11/18/2022] Open
Abstract
Most tumors are composed of a heterogeneous population of subclones. A more detailed insight into the subclonal evolution of these tumors can be helpful to study progression and treatment response. Problematically, tumor samples are typically very heterogeneous, making deconvolving individual tumor subclones a major challenge. To overcome this limitation, reducing heterogeneity, such as by means of microdissections, coupled with targeted sequencing, is a viable approach. However, computational methods that enable reconstruction of the evolutionary relationships require unbiased read depth measurements, which are commonly challenging to obtain in this setting. We introduce TargetClone, a novel method to reconstruct the subclonal evolution tree of tumors from single-nucleotide polymorphism allele frequency and somatic single-nucleotide variant measurements. Furthermore, our method infers copy numbers, alleles and the fraction of the tumor component in each sample. TargetClone was specifically designed for targeted sequencing data obtained from microdissected samples. We demonstrate that our method obtains low error rates on simulated data. Additionally, we show that our method is able to reconstruct expected trees in a testicular germ cell cancer and ovarian cancer dataset. The TargetClone package including tree visualization is written in Python and is publicly available at https://github.com/UMCUGenetics/targetclone.
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Affiliation(s)
- Marleen M. Nieboer
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lambert C. J. Dorssers
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Roy Straver
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leendert H. J. Looijenga
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jeroen de Ridder
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
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134
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Kechin A, Khrapov E, Boyarskikh U, Kel A, Filipenko M. BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes. Comput Biol Chem 2018; 77:297-306. [PMID: 30408727 DOI: 10.1016/j.compbiolchem.2018.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 09/14/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022]
Abstract
The use of targeted next-generation sequencing (NGS) provides great new opportunities for molecular and medical genetics. However, in order to take advantage of these opportunities, we need to have reliable tools for extracting the necessary information from the huge amount of data generated by NGS. Here we present our automatic multithreaded workflow for processing NGS data of BRCA1 and BRCA2 genes obtained with NGS technology named BRCA-analyzer. Optimizing it on the sequencing data of 899 samples from 693 patients, we were able to find the most reliable tools and adjust their parameters in such a way that all pathogenic variants found were confirmed by Sanger's sequencing. For 82 and 24 DNA samples from blood and formalin-fixed paraffin-embedded blocks, NGS libraries were prepared with GeneRead BRCA panel v2 (Qiagen). The reads obtained were processed with BRCA-analyzer and Qiagen GeneRead Data analysis workflow. In total 27 pathogenic variants were found and confirmed by Sanger's sequencing, with all of them determined with BRCA-analyzer. Qiagen GeneRead Data analysis discarded 5 true pathogenic variants due to their location in homopolymeric sequence stretches. For other 793 samples, libraries were prepared by the in-house method, and NGS data were analyzed by BRCA-analyzer in comparison to another free automatic amplicon NGS workflow Canary. From total 137 pathogenic variations, BRCA-analyzer found 135 and Canary 123. Mutations were missed by BRCA-analyzer due to the trimming primer sequences from reads before mapping to be fixed in the next version. On the freely available NGS data, we showed that BRCA-analyzer could also be used for hybrid capture gene panels, although it needs more extensive testing on such library preparation methods. Thus, BRCA-analyzer is an automatic workflow for processing NGS data of BRCA1/2 genes with variant filters adapted to amplicon-based targeted NGS data. BRCA-analyzer can be used to identify germline as well as somatic mutations. BRCA-analyzer is freely available at https://github.com/aakechin/BRCA-analyzer.
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Affiliation(s)
- Andrey Kechin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Evgeniy Khrapov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Uljana Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Alexander Kel
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; geneXplain GmbH, Wolfenbüttel, 38302, Germany; biosoft.ru, Novosibirsk, 630058, Russia
| | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
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135
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Cheng H, Yang X, Si H, Saleh AD, Xiao W, Coupar J, Gollin SM, Ferris RL, Issaeva N, Yarbrough WG, Prince ME, Carey TE, Van Waes C, Chen Z. Genomic and Transcriptomic Characterization Links Cell Lines with Aggressive Head and Neck Cancers. Cell Rep 2018; 25:1332-1345.e5. [PMID: 30380422 PMCID: PMC6280671 DOI: 10.1016/j.celrep.2018.10.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 08/28/2018] [Accepted: 09/28/2018] [Indexed: 12/12/2022] Open
Abstract
Cell lines are important tools for biological and preclinical investigation, and establishing their relationship to genomic alterations in tumors could accelerate functional and therapeutic discoveries. We conducted integrated analyses of genomic and transcriptomic profiles of 15 human papillomavirus (HPV)-negative and 11 HPV-positive head and neck squamous cell carcinoma (HNSCC) lines to compare with 279 tumors from The Cancer Genome Atlas (TCGA). We identified recurrent amplifications on chromosomes 3q22-29, 5p15, 11q13/22, and 8p11 that drive increased expression of more than 100 genes in cell lines and tumors. These alterations, together with loss or mutations of tumor suppressor genes, converge on important signaling pathways, recapitulating the genomic landscape of aggressive HNSCCs. Among these, concurrent 3q26.3 amplification and TP53 mutation in most HPV(-) cell lines reflect tumors with worse survival. Our findings elucidate and validate genomic alterations underpinning numerous discoveries made with HNSCC lines and provide valuable models for future studies.
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Affiliation(s)
- Hui Cheng
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Xinping Yang
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Han Si
- Translational Bioinformatics, MedImmune, Gaithersburg, MD 20878, USA
| | - Anthony D Saleh
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Wenming Xiao
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Jamie Coupar
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Susanne M Gollin
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Robert L Ferris
- Division of Head and Neck Surgery, Departments of Otolaryngology, Radiation Oncology, and Immunology, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232, USA
| | - Natalia Issaeva
- Department of Surgery, Division of Otolaryngology, Molecular Virology Research Program, Smilow Cancer Hospital, Yale Cancer Center, Yale University Medical School, New Haven, CT 06520, USA
| | - Wendell G Yarbrough
- Department of Surgery, Division of Otolaryngology, Molecular Virology Research Program, Smilow Cancer Hospital, Yale Cancer Center, Yale University Medical School, New Haven, CT 06520, USA
| | - Mark E Prince
- Cancer Biology Program, Program in the Biomedical Sciences, Rackham Graduate School, and the Department of Otolaryngology-Head and Neck Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas E Carey
- Cancer Biology Program, Program in the Biomedical Sciences, Rackham Graduate School, and the Department of Otolaryngology-Head and Neck Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carter Van Waes
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA.
| | - Zhong Chen
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA.
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136
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Kang Y, Nam SH, Park KS, Kim Y, Kim JW, Lee E, Ko JM, Lee KA, Park I. DeviCNV: detection and visualization of exon-level copy number variants in targeted next-generation sequencing data. BMC Bioinformatics 2018; 19:381. [PMID: 30326846 PMCID: PMC6192323 DOI: 10.1186/s12859-018-2409-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/04/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Targeted next-generation sequencing (NGS) is increasingly being adopted in clinical laboratories for genomic diagnostic tests. RESULTS We developed a new computational method, DeviCNV, intended for the detection of exon-level copy number variants (CNVs) in targeted NGS data. DeviCNV builds linear regression models with bootstrapping for every probe to capture the relationship between read depth of an individual probe and the median of read depth values of all probes in the sample. From the regression models, it estimates the read depth ratio of the observed and predicted read depth with confidence interval for each probe which is applied to a circular binary segmentation (CBS) algorithm to obtain CNV candidates. Then, it assigns confidence scores to those candidates based on the reliability and strength of the CNV signals inferred from the read depth ratios of the probes within them. Finally, it also provides gene-centric plots with confidence levels of CNV candidates for visual inspection. We applied DeviCNV to targeted NGS data generated for newborn screening and demonstrated its ability to detect novel pathogenic CNVs from clinical samples. CONCLUSIONS We propose a new pragmatic method for detecting CNVs in targeted NGS data with an intuitive visualization and a systematic method to assign confidence scores for candidate CNVs. Since DeviCNV was developed for use in clinical diagnosis, sensitivity is increased by the detection of exon-level CNVs.
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Affiliation(s)
- Yeeok Kang
- SD Genomics Co., Ltd., 11F, Seoul Gangnam Post Office, 619 Gaepo-ro, Gangnam-gu, Seoul, 06336, Republic of Korea.,Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Seong-Hyeuk Nam
- SD Genomics Co., Ltd., 11F, Seoul Gangnam Post Office, 619 Gaepo-ro, Gangnam-gu, Seoul, 06336, Republic of Korea
| | - Kyung Sun Park
- SD Genomics Co., Ltd., 11F, Seoul Gangnam Post Office, 619 Gaepo-ro, Gangnam-gu, Seoul, 06336, Republic of Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, 211 Eonjuro, Gangnam-gu, Seoul, 06273, Republic of Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eunjung Lee
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, USA
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, 211 Eonjuro, Gangnam-gu, Seoul, 06273, Republic of Korea.
| | - Inho Park
- SD Genomics Co., Ltd., 11F, Seoul Gangnam Post Office, 619 Gaepo-ro, Gangnam-gu, Seoul, 06336, Republic of Korea.
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137
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Pan X, Ji X, Zhang R, Zhou Z, Zhong Y, Peng W, Sun N, Xu X, Xia L, Li P, Lu J, Tu J. Landscape of somatic mutations in gastric cancer assessed using next-generation sequencing analysis. Oncol Lett 2018; 16:4863-4870. [PMID: 30250552 PMCID: PMC6144630 DOI: 10.3892/ol.2018.9314] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/07/2018] [Indexed: 12/15/2022] Open
Abstract
Gastric cancer is a highly heterogeneous disease and the second leading cause of cancer-associated mortality. However, the genomic basis of gastric cancer is not completely understood and the underlying genetic heterogeneity has not been well studied. In the present study, 1,021 genes were sequenced and the somatic mutations of 45 formalin-fixed, paraffin-embedded gastric adenocarcinoma samples were assessed using next-generation sequencing technologies. In the present study, a median sequencing coverage depth of 708-fold was achieved. Somatic genomic alterations were detected in 37/45 patients (82.4%) and the most frequent genetic alterations identified were tumor protein P53 (TP53) gene mutations. Mutations in MLL4, ERBB3, FBXW7, MLL3, MTOR, NOTCH1, PIK3CA, KRAS, ERBB4 and EGFR were also detected. Patients with TP53 mutations had a higher number of somatic mutations, and the total number of somatic mutations was weakly correlated with patient age. These results provided data on the intratumoral heterogeneity of gastric cancer and may be used in order to develop personalized cancer therapy.
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Affiliation(s)
- Xuan Pan
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210009, P.R. China
| | - Xiaozhi Ji
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210009, P.R. China.,Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Renmin Zhang
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210009, P.R. China.,Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Zhaofei Zhou
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210009, P.R. China
| | - Yuejiao Zhong
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210009, P.R. China
| | - Wei Peng
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210009, P.R. China
| | - Ning Sun
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210009, P.R. China
| | - Xinyu Xu
- Department of Pathology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210009, P.R. China
| | - Lei Xia
- Department of Pathology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210009, P.R. China
| | - Pansong Li
- Department of Research and Development, Geneplus-Beijing Institute, Beijing 102206, P.R. China
| | - Jianwei Lu
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210009, P.R. China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, P.R. China
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138
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Circulating tumor DNA analysis depicts subclonal architecture and genomic evolution of small cell lung cancer. Nat Commun 2018; 9:3114. [PMID: 30082701 PMCID: PMC6079068 DOI: 10.1038/s41467-018-05327-w] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/29/2018] [Indexed: 11/10/2022] Open
Abstract
Subclonal architecture and genomic evolution of small-cell lung cancer (SCLC) under treatment has not been well studied primarily due to lack of tumor specimens, particularly longitudinal samples acquired during treatment. SCLC is characterized by early hematogenous spread, which makes circulating cell-free tumor DNA (ctDNA) sequencing a promising modality for genomic profiling. Here, we perform targeted deep sequencing of 430 cancer genes on pre-treatment tumor biopsies, as well as on plasma samples collected prior to and during treatment from 22 SCLC patients. Similar subclonal architecture is observed between pre-treatment ctDNA and paired tumor DNA. Mean variant allele frequency of clonal mutations from pre-treatment ctDNA is associated with progression-free survival and overall survival. Pre- and post-treatment ctDNA mutational analysis demonstrate that mutations of DNA repair and NOTCH signaling pathways are enriched in post-treatment samples. These data suggest that ctDNA sequencing is promising to delineate genomic landscape, subclonal architecture, and genomic evolution of SCLC. Small cell lung cancer (SCLC) may evolve under treatment. But tumor tissues are often not available to study evolution of SCLC. Here, the authors utilize circulating tumor DNA to investigate the genomic evolution and subclonal architecture of SCLC during therapy.
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139
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A kidney-disease gene panel allows a comprehensive genetic diagnosis of cystic and glomerular inherited kidney diseases. Kidney Int 2018; 94:363-371. [DOI: 10.1016/j.kint.2018.02.027] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 02/09/2018] [Accepted: 02/15/2018] [Indexed: 12/14/2022]
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140
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Pan CC, Tsuzuki T, Morii E, Fushimi H, Chen PCH, Epstein JI. Whole-exome sequencing demonstrates recurrent somatic copy number alterations and sporadic mutations in specialized stromal tumors of the prostate. Hum Pathol 2018; 76:9-16. [DOI: 10.1016/j.humpath.2017.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/23/2017] [Accepted: 12/07/2017] [Indexed: 12/30/2022]
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141
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Herman DS, Smith C, Liu C, Vaughn CP, Palaniappan S, Pritchard CC, Shirts BH. Efficient Detection of Copy Number Mutations in PMS2 Exons with a Close Homolog. J Mol Diagn 2018; 20:512-521. [PMID: 29792936 DOI: 10.1016/j.jmoldx.2018.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 03/23/2018] [Indexed: 01/25/2023] Open
Abstract
Detection of 3' PMS2 copy-number mutations that cause Lynch syndrome is difficult because of highly homologous pseudogenes. To improve the accuracy and efficiency of clinical screening for these mutations, we developed a new method to analyze standard capture-based, next-generation sequencing data to identify deletions and duplications in PMS2 exons 9 to 15. The approach captures sequences using PMS2 targets, maps sequences randomly among regions with equal mapping quality, counts reads aligned to homologous exons and introns, and flags read count ratios outside of empirically derived reference ranges. The method was trained on 1352 samples, including 8 known positives, and tested on 719 samples, including 17 known positives. Clinical implementation of the first version of this method detected new mutations in the training (N = 7) and test (N = 2) sets that had not been identified by our initial clinical testing pipeline. The described final method showed complete sensitivity in both sample sets and false-positive rates of 5% (training) and 7% (test), dramatically decreasing the number of cases needing additional mutation evaluation. This approach leveraged the differences between gene and pseudogene to distinguish between PMS2 and PMS2CL copy-number mutations. These methods enable efficient and sensitive Lynch syndrome screening for 3' PMS2 copy-number mutations and may be applied similarly to other genomic regions with highly homologous pseudogenes.
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Affiliation(s)
- Daniel S Herman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Laboratory Medicine, University of Washington, Seattle, Washington.
| | - Christina Smith
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Chang Liu
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | | | - Selvi Palaniappan
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
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142
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Knaus BJ, Grünwald NJ. Inferring Variation in Copy Number Using High Throughput Sequencing Data in R. Front Genet 2018; 9:123. [PMID: 29706990 PMCID: PMC5909048 DOI: 10.3389/fgene.2018.00123] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/26/2018] [Indexed: 12/30/2022] Open
Abstract
Inference of copy number variation presents a technical challenge because variant callers typically require the copy number of a genome or genomic region to be known a priori. Here we present a method to infer copy number that uses variant call format (VCF) data as input and is implemented in the R package vcfR. This method is based on the relative frequency of each allele (in both genic and non-genic regions) sequenced at heterozygous positions throughout a genome. These heterozygous positions are summarized by using arbitrarily sized windows of heterozygous positions, binning the allele frequencies, and selecting the bin with the greatest abundance of positions. This provides a non-parametric summary of the frequency that alleles were sequenced at. The method is applicable to organisms that have reference genomes that consist of full chromosomes or sub-chromosomal contigs. In contrast to other software designed to detect copy number variation, our method does not rely on an assumption of base ploidy, but instead infers it. We validated these approaches with the model system of Saccharomyces cerevisiae and applied it to the oomycete Phytophthora infestans, both known to vary in copy number. This functionality has been incorporated into the current release of the R package vcfR to provide modular and flexible methods to investigate copy number variation in genomic projects.
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Affiliation(s)
- Brian J Knaus
- Horticultural Crops Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR, United States
| | - Niklaus J Grünwald
- Horticultural Crops Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR, United States
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143
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Fujimaru T, Mori T, Sekine A, Mandai S, Chiga M, Kikuchi H, Ando F, Mori Y, Nomura N, Iimori S, Naito S, Okado T, Rai T, Hoshino J, Ubara Y, Uchida S, Sohara E. Kidney enlargement and multiple liver cyst formation implicate mutations in PKD1/2 in adult sporadic polycystic kidney disease. Clin Genet 2018. [PMID: 29520754 DOI: 10.1111/cge.13249] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Distinguishing autosomal-dominant polycystic kidney disease (ADPKD) from other inherited renal cystic diseases in patients with adult polycystic kidney disease and no family history is critical for correct treatment and appropriate genetic counseling. However, for patients with no family history, there are no definitive imaging findings that provide an unequivocal ADPKD diagnosis. We analyzed 53 adult polycystic kidney disease patients with no family history. Comprehensive genetic testing was performed using capture-based next-generation sequencing for 69 genes currently known to cause hereditary renal cystic diseases including ADPKD. Through our analysis, 32 patients had PKD1 or PKD2 mutations. Additionally, 3 patients with disease-causing mutations in NPHP4, PKHD1, and OFD1 were diagnosed with an inherited renal cystic disease other than ADPKD. In patients with PKD1 or PKD2 mutations, the prevalence of polycystic liver disease, defined as more than 20 liver cysts, was significantly higher (71.9% vs 33.3%, P = .006), total kidney volume was significantly increased (median, 1580.7 mL vs 791.0 mL, P = .027) and mean arterial pressure was significantly higher (median, 98 mm Hg vs 91 mm Hg, P = .012). The genetic screening approach and clinical features described here are potentially beneficial for optimal management of adult sporadic polycystic kidney disease patients.
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Affiliation(s)
- T Fujimaru
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - T Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - A Sekine
- Nephrology Center, Toranomon Hospital, Tokyo, Japan
| | - S Mandai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - M Chiga
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - H Kikuchi
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - F Ando
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Y Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - N Nomura
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - S Iimori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - S Naito
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - T Okado
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - T Rai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - J Hoshino
- Nephrology Center, Toranomon Hospital, Tokyo, Japan.,Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - Y Ubara
- Nephrology Center, Toranomon Hospital, Tokyo, Japan.,Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - S Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - E Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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144
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Role of copy number variants in sudden cardiac death and related diseases: genetic analysis and translation into clinical practice. Eur J Hum Genet 2018; 26:1014-1025. [PMID: 29511324 DOI: 10.1038/s41431-018-0119-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 12/22/2022] Open
Abstract
Several studies have identified copy number variants (CNVs) as responsible for cardiac diseases associated with sudden cardiac death (SCD), but very few exhaustive analyses in large cohorts of patients have been performed, and they have been generally focused on a specific SCD-related disease. The aim of the present study was to screen for CNVs the most prevalent genes associated with SCD in a large cohort of patients who suffered sudden unexplained death or had an inherited cardiac disease (cardiomyopathy or channelopathy). A total of 1765 European patients were analyzed with a homemade algorithm for the assessment of CNVs using high-throughput sequencing data. Thirty-six CNVs were identified (2%), and most of them appeared to have a pathogenic role. The frequency of CNVs among cases of sudden unexplained death, patients with a cardiomyopathy or a channelopathy was 1.4% (8/587), 2.3% (20/874), and 2.6% (8/304), respectively. Detection rates were particularly high for arrhythmogenic cardiomyopathy (5.1%), long QT syndrome (4.7%), and dilated cardiomyopathy (4.4%). As such large genomic rearrangements underlie a non-neglectable portion of cases, we consider that their analysis should be performed as part of the routine genetic testing of sudden unexpected death cases and patients with SCD-related diseases.
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145
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Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes. Oncotarget 2018; 8:27997-28007. [PMID: 28427202 PMCID: PMC5438625 DOI: 10.18632/oncotarget.15881] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/20/2017] [Indexed: 12/23/2022] Open
Abstract
Breast cancer (BC) has been genetically profiled through large-scale genome analyses. However, the role and clinical implications of genetic alterations in metastatic BC (MBC) have not been evaluated. Therefore, we conducted whole-exome sequencing (WES) and RNA-Seq of 37 MBC samples and targeted deep sequencing of another 29 MBCs. We evaluated somatic mutations from WES and targeted sequencing and assessed gene expression and performed pathway analysis from RNA-Seq. In this analysis, PIK3CA was the most commonly mutated gene in estrogen receptor (ER)-positive BC, while in ER-negative BC, TP53 was the most commonly mutated gene (p = 0.018 and p < 0.001, respectively). TP53 stopgain/loss and frameshift mutation was related to low expression of TP53 in contrast nonsynonymous mutation was related to high expression. The impact of TP53 mutation on clinical outcome varied with regard to ER status. In ER-positive BCs, wild type TP53 had a better prognosis than mutated TP53 (median overall survival (OS) (wild type vs. mutated): 88.5 ± 54.4 vs. 32.6 ± 10.7 (months), p = 0.002). In contrast, mutated TP53 had a protective effect in ER-negative BCs (median OS: 0.10 vs. 32.6 ± 8.2, p = 0.026). However, PIK3CA mutation did not affect patient survival. In gene expression analysis, CALM1, a potential regulator of AKT, was highly expressed in PIK3CA-mutated BCs. In conclusion, mutation of TP53 was associated with expression status and affect clinical outcome according to ER status in MBC. Although mutation of PIK3CA was not related to survival in this study, mutation of PIK3CA altered the expression of other genes and pathways including CALM1 and may be a potential predictive marker of PI3K inhibitor effectiveness.
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146
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Raaijmakers MIG, Widmer DS, Narechania A, Eichhoff O, Freiberger SN, Wenzina J, Cheng PF, Mihic-Probst D, Desalle R, Dummer R, Levesque MP. Co-existence of BRAF and NRAS driver mutations in the same melanoma cells results in heterogeneity of targeted therapy resistance. Oncotarget 2018; 7:77163-77174. [PMID: 27791198 PMCID: PMC5363577 DOI: 10.18632/oncotarget.12848] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/13/2016] [Indexed: 12/30/2022] Open
Abstract
Acquired chemotherapeutic resistance of cancer cells can result from a Darwinistic evolution process in which heterogeneity plays an important role. In order to understand the impact of genetic heterogeneity on acquired resistance and second line therapy selection in metastatic melanoma, we sequenced the exomes of 27 lesions which were collected from 3 metastatic melanoma patients treated with targeted or non-targeted inhibitors. Furthermore, we tested the impact of a second NRAS mutation in 7 BRAF inhibitor resistant early passage cell cultures on the selection of second line therapies.We observed a rapid monophyletic evolution of melanoma subpopulations in response to targeted therapy that was not observed in non-targeted therapy. We observed the acquisition of NRAS mutations in the BRAF mutated patient treated with a BRAF inhibitor in 1 of 5 of his post-resistant samples. In an additional cohort of 5 BRAF-inhibitor treated patients we detected 7 NRAS mutations in 18 post-resistant samples. No NRAS mutations were detected in pre-resistant samples. By sequencing 65 single cell clones we prove that NRAS mutations co-occur with BRAF mutations in single cells. The double mutated cells revealed a heterogeneous response to MEK, ERK, PI3K, AKT and multi RTK - inhibitors.We conclude that BRAF and NRAS co-mutations are not mutually exclusive. However, the sole finding of double mutated cells in a resistant tumor is not sufficient to determine follow-up therapy. In order to target the large pool of heterogeneous cells in a patient, we think combinational therapy targeting different pathways will be necessary.
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Affiliation(s)
| | - Daniel S Widmer
- Department of Dermatology, University of Zurich, University Hospital Zürich, Switzerland
| | | | - Ossia Eichhoff
- Department of Dermatology, University of Zurich, University Hospital Zürich, Switzerland
| | - Sandra N Freiberger
- Department of Dermatology, University of Zurich, University Hospital Zürich, Switzerland.,Department of Dermatology, Skin and Endothelium Research Division, Medical University of Vienna, Austria
| | - Judith Wenzina
- Department of Dermatology, University of Zurich, University Hospital Zürich, Switzerland.,Department of Dermatology, Skin and Endothelium Research Division, Medical University of Vienna, Austria
| | - Phil F Cheng
- Department of Dermatology, University of Zurich, University Hospital Zürich, Switzerland
| | - Daniela Mihic-Probst
- Department of Pathology, University of Zurich, University Hospital Zürich, Switzerland
| | - Rob Desalle
- American Museum of Natural History, New York, New York, USA
| | - Reinhard Dummer
- Department of Dermatology, University of Zurich, University Hospital Zürich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University of Zurich, University Hospital Zürich, Switzerland
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147
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Jiang W, Ding Y, Shen Y, Fan L, Zhou L, Li Z, Zheng Y, Zhao P, Liu L, Tong Z, Fang W, Wang W. Identifying the clonal origin of synchronous multifocal tumors in the hepatobiliary and pancreatic system using multi-omic platforms. Oncotarget 2018; 8:5016-5025. [PMID: 28008139 PMCID: PMC5354888 DOI: 10.18632/oncotarget.14018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/07/2016] [Indexed: 01/06/2023] Open
Abstract
Synchronous multifocal tumors often pose a diagnostic challenge for oncologists. The purpose of this study was to determine the clonal origin and metastatic relationship of synchronous multifocal tumors in the hepatobiliary and pancreatic system using multi-omic platforms. DNA samples were extracted from three masses harvested from a 50-year-old Han Chinese male patient who suffered from synchronous multifocal tumors in the pancreatic tail, upper biliary duct, and omentum at the time of diagnosis. The clonal origin of these samples was tested using two platforms: next-generation sequencing (NGS) of 390 key genes harboring cancer-relevant actionable mutations and whole-genome copy number variation (CNV) chip analysis. The NGS approach revealed high mutational concordance, and the gene CNV profiles were similar between lesions. Whole-genome CNVs for the three samples were further investigated using an Affymetrix chip. Using matched CNV chip data from The Cancer Genome Atlas (TCGA), we developed a computational model that generated tissue-specific CNV signatures for hepatocellular carcinoma, pancreatic carcinoma, and cholangiocarcinoma to accurately identify the origin of the tumor samples. After adding the patient's CNV chip data to the model, all three samples were clustered into the pancreatic cancer branch. Both our NGS and CNV chip analyses suggested that clinically diagnosed synchronous pancreatic cancer and cholangiocarcinoma originated from the same cell population in the pancreas in our patient. This study highlights the use of genomic tools to infer the origin of synchronous multifocal tumors, which could help to improve the accuracy of cancer diagnosis.
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Affiliation(s)
- Weiqin Jiang
- Cancer Biotherapy Center, First Affiliated Hospital, Zhejiang University, China
| | - Yongfeng Ding
- Department of Surgical Oncology, First Affiliated Hospital, Zhejiang University, China
| | - Yifei Shen
- Institute of Bioinformatics & Research Center for Air Pollution and Health, Zhejiang University, China
| | - Longjiang Fan
- Institute of Bioinformatics & Research Center for Air Pollution and Health, Zhejiang University, China
| | - Linfu Zhou
- Medical Biotechnology Laboratory, Zhejiang University, China
| | - Zhi Li
- Department of Radiology, First Affiliated Hospital, Zhejiang University, China
| | - Yi Zheng
- Cancer Biotherapy Center, First Affiliated Hospital, Zhejiang University, China
| | - Peng Zhao
- Cancer Biotherapy Center, First Affiliated Hospital, Zhejiang University, China
| | - Lulu Liu
- Cancer Biotherapy Center, First Affiliated Hospital, Zhejiang University, China
| | - Zhou Tong
- Cancer Biotherapy Center, First Affiliated Hospital, Zhejiang University, China
| | - Weijia Fang
- Cancer Biotherapy Center, First Affiliated Hospital, Zhejiang University, China
| | - Weilin Wang
- Key Laboratory of Precision Diagnosis & Treatment for Hepatobiliary & Pancreatic Tumor, First Affiliated Hospital, Zhejiang University, China.,Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, Zhejiang University, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, China
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148
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Wang Y, Li L, Han R, Jiao L, Zheng J, He Y. Clinical analysis by next-generation sequencing for NSCLC patients with MET amplification resistant to osimertinib. Lung Cancer 2018; 118:105-110. [PMID: 29571987 DOI: 10.1016/j.lungcan.2018.02.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/08/2018] [Accepted: 02/09/2018] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The efficacy of osimertinib was compromised by the development of resistance mechanisms, such as MET amplification. However, cohort studies of osimertinib resistance mechanism, and the correlation of MET and progression-free survival (PFS) after osimertinib resistance have been poorly investigated. OBJECTIVES This study was carried out to study the acquired MET amplification after osimertinib resistance in advanced lung adenocarcinoma patients, and interrogate the correlation of clinical prognosis and MET amplification. METHODS We performed capture-based sequencing on longitudinal plasma and tissue samples obtained before osimertinib treatment and after resistance development from lung adenocarcinoma patients to investigate the underlying resistance mechanism. We also investigated the correlation of MET amplification and patient prognosis after osimertinib resistance using Kaplan-Meier analysis. RESULTS Paired biopsies before osimertinib treatment and after the resistance development revealed underlying resistance mechanisms. In addition, a cohort of 13 patients who developed disease progression after osimertinib resistance was investigated. Patients with MET amplification after osimertinib resistance commonly had inferior median progression-free survival (mPFS) than patients without MET amplification appearance or increase (3.5 months vs. 9.9 months, p = .117). Patients in MET amplification group also displayed poor median overall survival (mOS) compared to MET amplification negative group (15.6 months vs. 30.7 months, p = .885). Furthermore, combinatorial treatment of first/third-generation EGFR-TKI and crizotinib was efficaciously administrated into two patients with newly acquired MET amplification after osimertinib resistance. Partial responses were achieved by them, both clinically and radiographically. CONCLUSIONS We investigated the osimertinib resistance mechanism in a small cohort of lung adenocarcinoma patients, and demonstrated MET amplification was correlated with inferior PFS/OS after osimertinib treatment. Moreover, we reported the first clinical evidence of efficacy generated by combination of first-generation EGFR-TKI icotinib and crizotinib after the resistance to osimertinib.
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Affiliation(s)
- Yubo Wang
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing, PR China
| | - Li Li
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing, PR China
| | - Rui Han
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing, PR China
| | - Lin Jiao
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing, PR China
| | - Jie Zheng
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing, PR China
| | - Yong He
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing, PR China.
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149
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Hou H, Liu D, Zhang C, Jiang Y, Lu G, Zhou N, Yang X, Zhang X, Li Z, Zhu H, Qian Z, Zhang X. Targeted next generation sequencing in Chinese colorectal cancer patients guided anti-EGFR treatment and facilitated precision cancer medicine. Oncotarget 2017; 8:105072-105080. [PMID: 29285234 PMCID: PMC5739621 DOI: 10.18632/oncotarget.21349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 08/28/2017] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Colorectal cancer (CRC) patients with both RAS and BRAF wild-type tumors determined by non-next generation sequencing (NGS) testing may still not respond due to the presence of additional mutated genes such as PIK3CA or PTEN. In this study, a broad, hybrid capture-based NGS assay was used to identify RAS, BRAF and additional targetable genetic alterations from Chinese CRC tissues. METHODS Fifty-seven cases of CRC were enrolled, and all the patients signed the informed consent. In total, 7708 exons of 508 tumor-related genes and 78 introns of 19 frequently rearranged genes were assessed for base substitutions, INDELs, copy number alterations, and gene fusions. RESULTS The study found that 50.9% (29/57) of the tumors harbored KRAS mutations, 3.5% (2/57) harbored NRAS mutations and 3.5% (2/57) harbored BRAF mutations. More specifically, 89.7% (26/29) of RAS mutations were located in codon 12. Except for RAS and RAF, anti-EGFR therapy response genetic mutations in PTEN (n=2) and PIK3CA (n=1) were found in 4.7% (3/64) of the samples. Actionable alterations were found in HER2 (n = 7), CCND2 (n = 2), NF1 (n = 1), and BRCA1 (n = 1). CONCLUSIONS Our results illustrated that 82.5% (47/57) of the samples harbored at least one actionable genetic alteration identified by NGS. HER2 amplifications or mutations, which were identified in 12.3% of the tissues, defined a unique molecular subtype of CRC. The study suggests that high-throughput NGS testing in CRC tissues is a comprehensive and efficient genomic profiling assay to guide personalized therapy.
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Affiliation(s)
- Helei Hou
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Dong Liu
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Chuantao Zhang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Yanxia Jiang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Guifang Lu
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Na Zhou
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Xiaonan Yang
- BGI-Qingdao Institute, Qingdao SINO-GERMAN Ecopark, Qingdao, 266555, China
| | - Xiaoping Zhang
- Department of Clinical Laboratory, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhuokun Li
- BGI-Qingdao Institute, Qingdao SINO-GERMAN Ecopark, Qingdao, 266555, China
| | - Hongmei Zhu
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Zhaoyang Qian
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Xiaochun Zhang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
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150
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Sen ES, Dean P, Yarram-Smith L, Bierzynska A, Woodward G, Buxton C, Dennis G, Welsh GI, Williams M, Saleem MA. Clinical genetic testing using a custom-designed steroid-resistant nephrotic syndrome gene panel: analysis and recommendations. J Med Genet 2017; 54:795-804. [PMID: 28780565 PMCID: PMC5740557 DOI: 10.1136/jmedgenet-2017-104811] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 01/16/2023]
Abstract
BACKGROUND There are many single-gene causes of steroid-resistant nephrotic syndrome (SRNS) and the list continues to grow rapidly. Prompt comprehensive diagnostic testing is key to realising the clinical benefits of a genetic diagnosis. This report describes a bespoke-designed, targeted next-generation sequencing (NGS) diagnostic gene panel assay to detect variants in 37 genes including the ability to identify copy number variants (CNVs). METHODS This study reports results of 302 patients referred for SRNS diagnostic gene panel analysis. Phenotype and clinical impact data were collected using a standard proforma. Candidate variants detected by NGS were confirmed by Sanger sequencing/Multiplex Ligation-dependent Probe Amplification with subsequent family segregation analysis where possible. RESULTS Clinical presentation was nephrotic syndrome in 267 patients and suspected Alport syndrome (AS) in 35. NGS panel testing determined a likely genetic cause of disease in 44/220 (20.0%) paediatric and 10/47 (21.3%) adult nephrotic cases, and 17/35 (48.6%) of haematuria/AS patients. Of 71 patients with genetic disease, 32 had novel pathogenic variants without a previous disease association including two with deletions of one or more exons of NPHS1 or NPHS2. CONCLUSION Gene panel testing provides a genetic diagnosis in a significant number of patients presenting with SRNS or suspected AS. It should be undertaken at an early stage of the care pathway and include the ability to detect CNVs as an emerging mechanism for genes associated with this condition. Use of clinical genetic testing after diagnosis of SRNS has the potential to stratify patients and assist decision-making regarding management.
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Affiliation(s)
- Ethan S Sen
- Bristol Renal, School of Clinical Sciences, University of Bristol, Bristol, UK
- Bristol Royal Hospital for Children, Bristol, UK
| | - Philip Dean
- Bristol Genetics Laboratory, Southmead Hospital, Bristol, UK
| | | | | | - Geoff Woodward
- Bristol Genetics Laboratory, Southmead Hospital, Bristol, UK
| | - Chris Buxton
- Bristol Genetics Laboratory, Southmead Hospital, Bristol, UK
| | - Gemma Dennis
- Bristol Genetics Laboratory, Southmead Hospital, Bristol, UK
| | - Gavin I Welsh
- Bristol Renal, School of Clinical Sciences, University of Bristol, Bristol, UK
| | - Maggie Williams
- Bristol Genetics Laboratory, Southmead Hospital, Bristol, UK
| | - Moin A Saleem
- Bristol Renal, School of Clinical Sciences, University of Bristol, Bristol, UK
- Bristol Royal Hospital for Children, Bristol, UK
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