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  • American Association for Cancer Research (AACR)  (14)
  • 1
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 13_Supplement ( 2017-07-01), p. LB-278-LB-278
    Abstract: Although most human cancers display a single histology, there are unusual cases where two or more distinct tissue types present within a primary tumor. One such example is metaplastic breast carcinoma. Metaplastic breast carcinoma is a rare but aggressive cancer with a heterogenous histology, including squamous, chondroid, and spindle cells. Metaplastic carcinomas often contain an admixed conventional ductal invasive or in situ mammary carcinoma component, and are typically triple-negative for estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 (HER-2) amplification/overexpression. An unanswered question is the origin of metaplastic breast cancers. While they may arise independently from their ductal components, their close juxtaposition favors a model that postulates a shared origin, either as two derivatives from the same primary cancer, or one histology as a clonal outgrowth of the other. Understanding the mechanism of development of these tumors may inform clinical decisions. We performed exome sequencing for paired metaplastic and adjacent conventional invasive ductal carcinomas in eight patients and created a pipeline to identify somatic variants and predict their functional impact in these samples, without having matched normal tissue. We then determined the genetic relationships between the histologically distinct compartments. In each case, the tumor components have nearly identical landscapes of somatic variation, implying that the differing histologies do not derive from genetic clonal divergence, suggesting that epigenetic or noncoding changes mediate the metaplastic phenotype. This indicates that alternative therapeutic approaches, including epigenetic therapies, may render metaplastic breast cancers susceptible to current and future therapies. Citation Format: Bracha E. Avigdor, Katie Beierl, Christopher D. Gocke, Daniel J. Zabransky, Karen Cravero, Kelly Kyker-Snowmana, Berry Button, David Chu, Sarah Croessmann, Rory L. Cochran, Roisin M. Connolly, Ben H. Park, Ashley Cimino-Mathews, Sarah J. Wheelan. Whole exome sequencing of metaplastic breast carcinoma indicates monoclonality with associated ductal carcinoma component [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-278. doi:10.1158/1538-7445.AM2017-LB-278
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 2
    In: Clinical Cancer Research, American Association for Cancer Research (AACR), Vol. 23, No. 16 ( 2017-08-15), p. 4875-4884
    Abstract: Purpose: Although most human cancers display a single histology, there are unusual cases where two or more distinct tissue types present within a primary tumor. One such example is metaplastic breast carcinoma, a rare but aggressive cancer with a heterogeneous histology, including squamous, chondroid, and spindle cells. Metaplastic carcinomas often contain an admixed conventional ductal invasive or in situ mammary carcinoma component, and are typically triple-negative for estrogen receptor, progesterone receptor, and HER-2 amplification/overexpression. An unanswered question is the origin of metaplastic breast cancers. While they may arise independently from their ductal components, their close juxtaposition favors a model that postulates a shared origin, either as two derivatives from the same primary cancer or one histology as an outgrowth of the other. Understanding the mechanism of development of these tumors may inform clinical decisions. Experimental Design: We performed exome sequencing for paired metaplastic and adjacent conventional invasive ductal carcinomas in 8 patients and created a pipeline to identify somatic variants and predict their functional impact, without having normal tissue. We then determined the genetic relationships between the histologically distinct compartments. Results: In each case, the tumor components have nearly identical landscapes of somatic mutation, implying that the differing histologies do not derive from genetic clonal divergence. Conclusions: A shared origin for tumors with differing histologies suggests that epigenetic or noncoding changes may mediate the metaplastic phenotype and that alternative therapeutic approaches, including epigenetic therapies, may be required for metaplastic breast cancers. Clin Cancer Res; 23(16); 4875–84. ©2017 AACR.
    Type of Medium: Online Resource
    ISSN: 1078-0432 , 1557-3265
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 3
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    American Association for Cancer Research (AACR) ; 2018
    In:  Cancer Research Vol. 78, No. 13_Supplement ( 2018-07-01), p. 129-129
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 13_Supplement ( 2018-07-01), p. 129-129
    Abstract: The human microbiome may play a role in prostate health and disease as both direct and indirect interactions. Direct interactions between microbiota and prostate cancer include prostate infections, inflammation, prostatitis, and potentially interactions with the urinary microbiome. Indirectly, the gastrointestinal (GI) microbiota may influence prostate cancer via xenobiotic metabolism, augmentation of treatment response, and contributions to systemic inflammation and cytokines. In the present study, we are seeking to understand how different prostate cancer treatments may be affected by the microbial composition of the GI tract. We are currently developing a biorepository of fecal specimens from prostate cancer patients in different clinical states of disease. A key question during the planning phase of this biorepository was if samples can be collected and banked in the form of a rectal swab, instead of the more traditional method of a stool sample. Rectal swabs provide an advantage over collection of stool specimens in that they are easily collected (the patient can self-collect) in a standardized, “on demand” fashion during routine patient visits. Therefore, a pilot study was undertaken to compare the microbial profile of samples collected via both methods from the same individual. We concomitantly collected both stool samples and rectal swabs from 6 patients undergoing active surveillance for prostate cancer at the Johns Hopkins Hospital. All samples were stored at -80°C until we were ready to isolate bacterial DNA. DNA was extracted with a phenol:chloroform based protocol that we have optimized for microbiome studies that includes multiple enzyme digest and bead beating. We conducted Illumina amplicon sequencing of PCR products amplified with universal primers designed against the V6 hypervariable region of the bacterial 16S rRNA gene. We tested our sequencing strategy against Microbiome Reference Standards obtained from American Type Culture Collection (ATCC). The results of our analysis from prostate cancer patients indicated high similarity of bacterial profiles obtained for matched stool and swabs in 4 of the 6 patients. In both of the cases that were dissimilar, there was a greater representation of Enterobacteriaceae in the stool sample versus the swab. We conclude that collection of rectal swabs is a more feasible and convenient means of sampling the GI microbiota in prostate cancer patients, especially when aiming to conduct longitudinal studies with multiple sample collections to correlate microbiota profiles to treatments and/or treatment response. Due to the differences that were identified, we recommend deciding on the sample collection method at the onset of biobanking, and keeping the sampling method consistent throughout. Citation Format: Sarah E. Ernst, Mark C. Markowski, Anuj Gupta, Sarah J. Wheelan, H. Ballentine Carter, Alan W. Partin, Cynthia L. Sears, Karen S. Sfanos. Biobanking and feasibility considerations for prostate cancer gastrointestinal microbiome studies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 129.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
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  • 4
    In: Cancer Immunology Research, American Association for Cancer Research (AACR), Vol. 10, No. 5 ( 2022-05-03), p. 656-669
    Abstract: Therapeutic combinations to alter immunosuppressive, solid tumor microenvironments (TME), such as in breast cancer, are essential to improve responses to immune checkpoint inhibitors (ICI). Entinostat, an oral histone deacetylase inhibitor, has been shown to improve responses to ICIs in various tumor models with immunosuppressive TMEs. The precise and comprehensive alterations to the TME induced by entinostat remain unknown. Here, we employed single-cell RNA sequencing on HER2-overexpressing breast tumors from mice treated with entinostat and ICIs to fully characterize changes across multiple cell types within the TME. This analysis demonstrates that treatment with entinostat induced a shift from a protumor to an antitumor TME signature, characterized predominantly by changes in myeloid cells. We confirmed myeloid-derived suppressor cells (MDSC) within entinostat-treated tumors associated with a less suppressive granulocytic (G)-MDSC phenotype and exhibited altered suppressive signaling that involved the NFκB and STAT3 pathways. In addition to MDSCs, tumor-associated macrophages were epigenetically reprogrammed from a protumor M2-like phenotype toward an antitumor M1-like phenotype, which may be contributing to a more sensitized TME. Overall, our in-depth analysis suggests that entinostat-induced changes on multiple myeloid cell types reduce immunosuppression and increase antitumor responses, which, in turn, improve sensitivity to ICIs. Sensitization of the TME by entinostat could ultimately broaden the population of patients with breast cancer who could benefit from ICIs.
    Type of Medium: Online Resource
    ISSN: 2326-6066 , 2326-6074
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 19 ( 2017-10-01), p. 5248-5258
    Abstract: The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased more than 200% in the past 20 years. Recent genetic sequencing efforts have elucidated relevant genes in head and neck cancer, but HPV-related tumors have consistently shown few DNA mutations. In this study, we sought to analyze alternative splicing events (ASE) that could alter gene function independent of mutations. To identify ASE unique to HPV-related tumors, RNA sequencing was performed on 46 HPV-positive OPSCC and 25 normal tissue samples. A novel algorithm using outlier statistics on RNA-sequencing junction expression identified 109 splicing events, which were confirmed in a validation set from The Cancer Genome Atlas. Because the most common type of splicing event identified was an alternative start site (39%), MBD-seq genome-wide CpG methylation data were analyzed for methylation alterations at promoter regions. ASE in six genes showed significant negative correlation between promoter methylation and expression of an alternative transcriptional start site, including AKT3. The novel AKT3 transcriptional variant and methylation changes were confirmed using qRT-PCR and qMSP methods. In vitro silencing of the novel AKT3 variant resulted in significant growth inhibition of multiple head and neck cell lines, an effect not observed with wild-type AKT3 knockdown. Analysis of ASE in HPV-related OPSCC identified multiple alterations likely involved in carcinogenesis, including a novel, functionally active transcriptional variant of AKT3. Our data indicate that ASEs represent a significant mechanism of oncogenesis with untapped potential for understanding complex genetic changes that result in the development of cancer. Cancer Res; 77(19); 5248–58. ©2017 AACR.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 6
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 23 ( 2017-12-01), p. 6538-6550
    Abstract: Chromatin alterations mediate mutations and gene expression changes in cancer. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has been utilized to study genome-wide chromatin structure in human cancer cell lines, yet numerous technical challenges limit comparable analyses in primary tumors. Here we have developed a new whole-genome analytic pipeline to optimize ChIP-Seq protocols on patient-derived xenografts from human papillomavirus–related (HPV+) head and neck squamous cell carcinoma (HNSCC) samples. We further associated chromatin aberrations with gene expression changes from a larger cohort of the tumor and normal samples with RNA-Seq data. We detect differential histone enrichment associated with tumor-specific gene expression variation, sites of HPV integration in the human genome, and HPV-associated histone enrichment sites upstream of cancer driver genes, which play central roles in cancer-associated pathways. These comprehensive analyses enable unprecedented characterization of the complex network of molecular changes resulting from chromatin alterations that drive HPV-related tumorigenesis. Cancer Res; 77(23); 6538–50. ©2017 AACR.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 7
    In: Cancer Prevention Research, American Association for Cancer Research (AACR), Vol. 9, No. 4 ( 2016-04-01), p. 265-274
    Abstract: Adenoid cystic carcinomas (ACC) of the salivary glands are challenging to understand, treat, and cure. To better understand the genetic alterations underlying the pathogenesis of these tumors, we performed comprehensive genome analyses of 25 fresh-frozen tumors, including whole-genome sequencing and expression and pathway analyses. In addition to the well-described MYB–NFIB fusion that was found in 11 tumors (44%), we observed five different rearrangements involving the NFIB transcription factor gene in seven tumors (28%). Taken together, NFIB translocations occurred in 15 of 25 samples (60%, 95% CI, 41%–77%). In addition, mRNA expression analysis of 17 tumors revealed overexpression of NFIB in ACC tumors compared with normal tissues (P = 0.002). There was no difference in NFIB mRNA expression in tumors with NFIB fusions compared with those without. We also report somatic mutations of genes involved in the axonal guidance and Rho family signaling pathways. Finally, we confirm previously described alterations in genes related to chromatin regulation and Notch signaling. Our findings suggest a separate role for NFIB in ACC oncogenesis and highlight important signaling pathways for future functional characterization and potential therapeutic targeting. Cancer Prev Res; 9(4); 265–74. ©2016 AACR.
    Type of Medium: Online Resource
    ISSN: 1940-6207 , 1940-6215
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2016
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  • 8
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 76, No. 14_Supplement ( 2016-07-15), p. LB-160-LB-160
    Abstract: Introduction: Telomerase activity (TA) is increased in most human cancers (80 - 90%) as a mechanism to maintain telomere function, yet the complex regulatory mechanisms driving TA in different cancer types remain obscure. Telomerase consists of at least two essential elements, a catalytic component (TERT) and an RNA subunit (hTR or TERC). Early data showed that TERC was constitutively expressed at similar levels in different tissues and cancer and that TERT mRNA levels best correlated with enzymatic activity across normal tissues and cancer cells. However, accumulating evidence suggests a more important role for the regulation of TERC in telomere maintenance, as well as possible telomerase activity-independent functions. MYC (c-Myc) is overexpressed in most prostate cancers and is known to regulate TERT mRNA levels in a number of cell types and hence to drive TA. However, there are no prior studies of MYC regulation of TERC. We performed a comprehensive study of TERC expression in cancer cell lines and prostatic tissue, across normal, high grade prostatic intraepithelial neoplasia (PIN), primary carcinomas (PCa), and castrate resistant metastatic disease. We further explored MYC regulation of TERC in Pca and examined cell proliferation in TERC-depleted Pca cell lines. Experiments and results: Using a novel chromogenic In Situ Hybridization (CISH) RNA assay in FFPE tissues, validated in cell lines by RT-PCR, we found consistent TERC overexpression in nuclei of PIN (p & lt;0.001, N = 26 patients) and Pca cells (p & lt;0.001, N = 66 patients), that was confirmed by qRT-PCR (n = 25) and RNAseq (n = 12) in tumor/benign frozen tissue pairs. There was no association with Gleason score or pathologic stage, and a weak correlation between TERC and TERT levels by RT-PCR. There was a correlation between TERC CISH and MYC protein expression in prostate tissue (Spearman 0.4540, p & lt;0.0001). Further, we show: i) that forced reductions of MYC resulted in decreased TERC levels in 8 cancer cell lines (prostate, lung, breast, and colorectal); ii) MYC occupies the TERC locus by chromatin immunoprecipitation (ChIP); iii) there is a decrease in human TERC promoter activity with MYC silencing; iv) increased Terc levels in PIN and carcinoma in 2 different mouse models of prostate-restricted overexpression of MYC; and v) knockdown of TERC by siRNA resulted in reduced growth and decreased Ki-67 in TERC depleted human prostate cancer cells. Conclusions: We report consistent overexpression of TERC in PIN and PCa and show the first evidence of MYC regulation of TERC. These studies suggest an important role for MYC-regulated TERC overexpression in human prostate cancer development and progression. Further studies are required to better understand the functional roles of TERC (e.g. TA mediated vs. other activity) in carcinogenesis of the prostate and other organ sites and its regulation by MYC. Citation Format: Javier A. Baena Del Valle, Qizhi Zheng, Michael Rubenstein, Alan K. Meeker, Christopher M. Heaphy, Gretchen Hubbard, Charles J. Bieberich, Srinivasan Yegnasubramanian, David Esopi, Sarah J. Wheelan, Angelo M. De Marzo. Human telomerase RNA component (hTR/TERC) is consistently overexpressed in prostate cancer, required for cell proliferation and is positively regulated by MYC. [abstract] . In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-160.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2016
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  • 9
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 75, No. 15_Supplement ( 2015-08-01), p. 4270-4270
    Abstract: Introduction: Fields of forensics, paternity, and hematopoietic stem cell transplantation (HSCT) require human identity testing. The polymorphic nature of short tandem repeats (STRs) makes them most frequently used but they are relatively insensitive. In 2000, we demonstrated proof-of-principle for the use of SNPs for bone marrow engraftment testing; however, due to the high error rate of NGS platforms, use of a single SNP for this purpose is not possible. Here, we hypothesized that using multiple SNPs on a short amplicon (microhaplotype) could overcome the inherently high error rate of NGS, and use it for ultrasensitive detection of human DNA mixes. Methods: As proof-of-principle, we identified a 119 bp region on HLA-A Exon 3 that contains a cluster of 18 SNPs. Using cell lines with known HLA-A haplotypes, we made serial dilutions from 1% to 0.001%. By sequencing each dilution at least twice we were able to determine accuracy and limit of detection. Samples collected from patients after BMT that tested as all donor were analyzed using this approach. Sample preparation and sequencing was done per manufacturer's protocol using the Ion Torrent Personal Genome Machine and 200 base chemistry. Additionally, we analyzed the 1000 Genomes database, using 300 bp windows, and identified many other loci that contained clusters of at least 9 SNPs. Results: Alignment and analysis of common European HLA-A haplotypes of this region show mean number of differences of ∼6 SNPs. Homozygous samples with known HLA-A genotypes that varied by multiple SNPs were analyzed and demonstrated no cross-talk between them. Analyzing serially diluted samples we were able to easily achieve a limit of detection of 1 in 10,000 molecules (0.01%). In BMT samples that tested as all donor by STR analysis, we were able to detect patient DNA of up to 1.5%. From 1000 Genomes data, we identified 4,349 loci that contained at least 9 SNPs within a 300 bp window. Informativity of identified loci was determined for 3 major ethnic groups using 1000 Genomes phased haplotype data. Conclusions: Ultrasensitive detection of human DNA mixes can be achieved using multiple SNPs within a short amplicon despite the high error rates associated with NGS. This assay may be useful to detect early relapse following bone marrow transplantation and other clinical applications. Citation Format: Marija Debeljak, Donald N. Freed, Jane A. Welch, Lisa Haley, Katie Beierl, Brian S. Iglehart, Aparna Pallavajjala, Christopher D. Gocke, Mary S. Leffell, Ming-Tseh Lin, Laura D. Wood, Jonathan Pevsner, Sarah J. Wheelan, James R. Eshleman. NGS based microhaplotype counting for ultrasensitive human DNA detection. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4270. doi:10.1158/1538-7445.AM2015-4270
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
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  • 10
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 81, No. 13_Supplement ( 2021-07-01), p. 2198-2198
    Abstract: Prostate cancer research has relied on a limited number of prostate cancer cell lines despite decades of effort in establishing them from human prostate cancers. These cell lines thus represent precious resources for in vitro and in vivo preclinical studies of prostate cancer and have fueled many advances in the field. While there has been tremendous effort in characterizing their molecular profiles and genomic features, comprehensive whole genome sequencing with allelic phasing of genomic alterations has not been undertaken to date. Here, we utilized powerful whole genome linked-read sequencing of high molecular weight DNA ( & gt;60Kbp) from eight common prostate cancer cell lines as well as four castrate resistant (CR) subclones derived from three of those cell lines. Long range information enabled assembly of mutations (single nucleotide variants-SNVs and small indels) and structural variants (SVs) across the genome into large phased blocks. This allowed accounting of multiple mutations within a given gene to assess whether they were present on a single allele, or on opposite alleles, to assess the “allelic status” of phased mutations. Using this phased mutational analysis, we found that in cell lines with microsatellite instability (MSI; LNCaP, LAPC4, DU145, CWR22Rv1), 10-20% of a priori defined driver genes are inactivated by at least two heterozygous mutations on opposite alleles. Overall, MSI cell lines had higher levels of mutations and fewer SVs than those that were microsatellite stable (MSS; PC3, VCaP). The phased SV analysis allowed identification of complex rearrangement chains consistent with chromothripsis (PC3, DU145) and chromoplexy (VCAP, LnCAP-C42b), including reconstruction of the complex chained TMPRSS2-ERG rearrangement in VCaP. Additionally, comparison of parental and CR subclones revealed previously known as well as several novel genomic alterations that were associated with the CR subclones, including chromosome 8 amplification (in LNCaP-Abl and LAPC4-CR), further androgen receptor amplification amongst a host of increased complex SVs (in VCAP-CR), SWI/SNF mutations and increased complex SVs (in LNCAP-C42b), CDK12 biallelic loss and numerous tandem duplications (in LAPC4-CR). This study therefore comprehensively characterizes allelically phased genomic alterations in the commonly used prostate cancer cell lines and provides a useful resource for future cancer research. Citation Format: Minh-Tam Pham, Harshath Gupta, Anuj Gupta, Ajay Vaghasia, Alyza M. Skaist, McKinzie A. Garrison, Roshan Chikamarne, Sarah J. Wheelan, William G. Nelson, Srinivasan Yegnasubramanian. Allelic phasing of genomic alterations through linked read whole genome sequencing in human prostate cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2198.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2021
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