Comparison Of Genomic Profiles Research Articles

Circulating Tumour DNA as a Biomarker Source in Metastatic Prostate Cancer

Tumour molecular features are increasingly linked to treatment response and patient prognosis in advanced prostate cancer. Plasma cell-free circulating tumour DNA (ctDNA) isolated from a minimally invasive blood draw offers a convenient source of tumour material to develop clinical biomarkers. Importantly, the burden of ctDNA in the blood has strong prognostic implications at different points during the natural history of metastatic progression. In prostate cancer, the identification of somatic profiles from ctDNA requires a broad next-generation sequencing approach because of the low mutation rate and frequent structural rearrangements. Nevertheless, comparison of genomic profiles between liquid and tissue biopsies has demonstrated that ctDNA is a surrogate for tumour tissue in the metastatic setting. Our understanding of resistance to androgen receptor (AR) directed therapies has been significantly augmented by the frequent detection of AR gene amplifications, mutations, and structural rearrangements via liquid biopsy. Furthermore, early studies suggest that distinct molecular subtypes derived from ctDNA profiling can help determine the optimal therapeutic regimen for an individual patient and enable real-time monitoring for therapy response and resistance. Indeed, in clinical trials targeting the DNA damage repair pathway in prostate cancer, ctDNA-based assessment of DNA repair status is already under evaluation as a predictive biomarker. Recent advances in the study of circulating DNA fragments now make it possible to interrogate aspects of the epigenome. In this review, we describe the various applications of plasma ctDNA in metastatic prostate cancer, including its potential role as a clinically informative liquid biomarker.

Characterization and comparison of genomic profiles between primary cancer cell lines and parent atypical meningioma tumors

BackgroundMeningiomas are the second most common primary tumors of the central nervous system. However, there is a paucity of data on meningioma biology due to the lack of suitable preclinical in vitro and in vivo models. In this study, we report the establishment and characterization of patient-derived, spontaneously immortalized cancer cell lines derived from World Health Organization (WHO) grade I and atypical WHO grade II meningiomas.MethodsWe evaluated high-resolution 3T MRI neuroimaging findings in meningioma patients which were followed by histological analysis. RT-qPCR and immunostaining analyses were performed to determine the expression levels of meningioma-related factors. Additionally, flow cytometry and sorting assays were conducted to investigate and isolate the CD133 and CD44 positive cells from primary atypical meningioma cells. Further, we compared the gene expression profiles of meningiomas and cell lines derived from them by performing whole-exome sequencing of the blood and tumor samples from the patients, and the primary cancer cell lines established from the meningioma tumor.ResultsOur results were consistent with earlier studies that reported mutations in NF2, SMO, and AKT1 genes in atypical meningiomas, and we also observed mutations in MYBL2, a gene that was recently discovered. Significantly, the genomic signature was consistent between the atypical meningioma cancer cell lines and the tumor and blood samples from the patient.ConclusionOur results lead us to conclude that established meningioma cell lines with a genomic signature identical to tumors might be a valuable tool for understanding meningioma tumor biology, and for screening therapeutic agents to treat recurrent meningiomas.

DONOR-FINDER: A Web Tool for the Automatic Comparison of Genomic Profiles in ART.

The use of genetic tests in assisted reproduction is growing fast. Among potential usages, the selection of the most suitable donor profile stands out. Being able to consider the genomic compatibility between donor and recipient is very important in order to prevent certain diseases. Nevertheless, taking this new factor into account can significantly increase the time needed for donor selection. This paper describes a web-tool designed to automatize the comparison of genomic and phenotypic profiles in assisted reproduction practices, which potentially reduces the chance of error and the time needed in donor-matching processes.

Whole exome sequencing reveals the different responsiveness to Enterovirus 71 vaccination in Chinese children

PurposeTo explore the molecular genetic mechanisms underlying different responsiveness to Enterovirus 71 (EV71) vaccine. MethodsWe recruited 10,245 healthy children into a phase 3 clinical trial to evaluate the efficacy of EV71 vaccine in 2012. Fifty subjects from the trial were divided into the potent immune response group (20 subjects) and the ineffective immune response group (30 subjects). Whole-exome sequencing was performed for these 50 samples and we conducted bioinformatics analyses based on online public database. ResultsA total of 222,180 germline variants were detected across 50 subjects. Single nucleotide variant (SNV)-based screening of the subjects with potent or ineffective immune response allowed the identification of a potentially detrimental heterozygous missense variant (c.3784C>T) in EEA1. We also retained TRIM59 and ABCA7 genes that contain different loss of function (LoF) variants shared in two cases and involved in the immune response process. Then, we conducted high-resolution typing of 9 classical HLA genes, HLA-DRB1*03:01, HLA-DQA1*05:01 and HLA-DQB1*02:01 alleles were frequently (recurrence ≥5) observed only in ineffective immune responders. ConclusionsOur study is a meaningful attempt on the comparison of genomic profiles between potent and ineffective immune responders induced by EV71 vaccine, and several candidate potentially detrimental genes were identified.

Karyotype of the blastocoel fluid demonstrates low concordance with both trophectoderm and inner cell mass

To compare the genomic profiles of blastocoel fluid (BF), inner cell mass (ICM), and trophectoderm (TE) cells derived from the same blastocyst. Prospective study. Academic and invitro fertilization units. Sixteen donated cryopreserved embryos at blastocyst stage. BF, TE, and ICM cells were retrieved from each blastocyst for chromosome analysis by means of next-generation sequencing (NGS). Aneuploidy screening and assessment of mosaicism in BF, TE and ICM samples with subsequent comparison of genomic profiles between the three blastocyst compartments. Out of 16 blastocysts, 10 BF samples and 14TE and ICM samples provided reliable NGS data for comprehensive chromosome analysis. Only 40.0% of BF-DNA karyotypes were fully concordant with TE or ICM, compared with 85.7% concordance between TE and ICM. In addition, BF-DNA was burdened with mosaic aneuploidies and the total number of affected chromosomes in BF was significantly higher compared with the TE and ICM. BF-DNA can be successfully amplified and subjected to NGS, but owing to increased discordance with ICM and TE, BF does not adequately represent the status of the rest of the embryo. To overcome biologic and technical challenges associated with BF sampling and processing, blastocentesis would require improvement in both laboratory protocols and aneuploidy calling algorithms. Therefore, TE biopsy remains the most effective way to predict embryonic karyotype, and the use of BF as a single source of DNA for preimplantation genetic screening is not yet advised.

Comparison of genomic profiles to reveal heterogenous patterns of tumor evolution in primary and recurrent diffuse gliomas.

e14060Background: Diffuse gliomas represent heterogeneous group of tumors with highly variable biological behavior. Despite of radical surgical resection and intensive therapy, recurrent lesions wi...

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature

Evaluating cell lines as tumour models by comparison of genomic profiles

Cancer cell lines are frequently used as in vitro tumour models. Recent molecular profiles of hundreds of cell lines from The Cancer Cell Line Encyclopedia and thousands of tumour samples from the Cancer Genome Atlas now allow a systematic genomic comparison of cell lines and tumours. Here we analyse a panel of 47 ovarian cancer cell lines and identify those that have the highest genetic similarity to ovarian tumours. Our comparison of copy-number changes, mutations and mRNA expression profiles reveals pronounced differences in molecular profiles between commonly used ovarian cancer cell lines and high-grade serous ovarian cancer tumour samples. We identify several rarely used cell lines that more closely resemble cognate tumour profiles than commonly used cell lines, and we propose these lines as the most suitable models of ovarian cancer. Our results indicate that the gap between cell lines and tumours can be bridged by genomically informed choices of cell line models for all tumour types.

Prevalence, antimicrobial susceptibility, and molecular characterization by PCR and pulsed field gel electrophoresis (PFGE) of Salmonella spp. isolated from foods of animal origin in San Luis, Argentina

This study was aimed to determine the prevalence of Salmonella spp. in foods of animal origin sold at retail stores over the period 2005–2011 in San Luis, Argentina. Characterization of isolates was performed by biochemical and serological tests, antimicrobial susceptibility assays, detection of invA invasion gene by PCR and comparison of genomic profiles by XbaI DNA restriction and PFGE. Twenty seven Salmonella strains were detected in 27 (6.32%) of 427 samples of foods analysed. Sixteen S. Enteritidis and one S. Montevideo strains from chicken meat (17 positive samples/115 total samples), six S. Anatum strains from pork sausages (6/90), two S. Typhimurium strains from liquid egg (2/60) and two S. Montevideo strains from chicken giblets (2/62) were isolated. No Salmonella strains were recovered from chicken carcasses (0/100). Salmonella strains were susceptible to antimicrobials commonly used for clinical treatment. All isolates carried the invA gene. DNA restriction and PFGE analysis revealed similar genomic profiles within each Salmonella serovar regardless of the food type, sampling year, or retail store where samples were purchased, suggesting the possibility of circulation and transmission of clones of limited diversity in our region.

Isolation and genomic analysis of circulating tumor cells from castration resistant metastatic prostate cancer

BackgroundThe number of circulating tumor cells (CTCs) in metastatic prostate cancer patients provides prognostic and predictive information. However, it is the molecular characterization of CTCs that offers insight into the biology of these tumor cells in the context of personalized treatment.MethodsWe developed a novel approach to isolate CTCs away from hematopoietic cells with high purity, enabling genomic analysis of these cells. The isolation protocol involves immunomagnetic enrichment followed by fluorescence activated cell sorting (IE/FACS). To evaluate the feasibility of isolation of CTCs by IE/FACS and downstream genomic profiling, we conducted a pilot study in patients with metastatic castration resistant prostate cancer (CRPC). Twenty (20) sequential CRPC patients were assayed using CellSearch™. Twelve (12) patients positive for CTCs were subjected to immunomagnetic enrichment and fluorescence activated cell sorting (IE/FACS) to isolate CTCs. Genomic DNA of CTCs was subjected to whole genome amplification (WGA) followed by gene copy number analysis via array comparative genomic hybridization (aCGH).ResultsCTCs from nine (9) patients successfully profiled were observed to have multiple copy number aberrations including those previously reported in primary prostate tumors such as gains in 8q and losses in 8p. High-level copy number gains at the androgen receptor (AR) locus were observed in 7 (78%) cases. Comparison of genomic profiles between CTCs and archival primary tumors from the same patients revealed common lineage. However, high-level copy number gains in the AR locus were observed in CTCs, but not in the matched archival primary tumors.ConclusionsWe developed a new approach to isolate prostate CTCs without significant leukocyte admixture, and to subject them to genome-wide copy number analysis. Our assay may be utilized to explore genomic events involved in cancer progression, e.g. development of castration resistance and to monitor therapeutic efficacy of targeted therapies in clinical trials in a relatively non-invasive manner.

Comparison of genomic profiles in human neuroblastic SH-SY5Y and substrate-adherent SH-EP cells using array comparative genomic hybridization

Human neuroblastoma is the most commonly diagnosed solid tumor in children. The existence and development of S-type cells is important for the prognosis and malignant properties in neuroblastoma patients. However, their origin is controversial and the relationship between S- and N-type cells in neuroblastoma has not yet been clarified. To investigate the feasibility of inter-conversion and characteristic features between S-type cells lacking malignant potential and N-type cells having metastatic potential, the genomic profiles of neuroblastoma SH-EP (S-type) and SH-SY5Y (N-type) cells were compared at high resolution. Common gain segments (>10 Mb) between SH-EP and SH-SY5Y cells were observed at 1q21.1–q44 and 17q21.32–q25.3. The results of the fluorescent in situ hybridization (FISH) analysis showed good agreement with the array-CGH data. Genome-wide inspection of SH-EP and SH-SY5Y cells successfully identified not only common chromosomal aberrations but also genomic variations, suggesting that interconversion could not take place between S- and Ntype cells. The identified differences between less aggressive S-type cells (SH-EP) and highly aggressive neuroblastic N-type cells (SH-SY5Y) might be useful for understanding tumorigenicity and discovery of potential new markers in neuroblastoma. This is the first effort to compare genomic profiles between less aggressive S-type cells (SH-EP) and highly aggressive neuroblastic N-type cells (SH-SY5Y) at high resolution.

Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia

High-resolution genomic microarrays enable simultaneous detection of copy-number aberrations such as the known recurrent aberrations in chronic lymphocytic leukemia [del(11q), del(13q), del(17p) and trisomy 12], and copy-number neutral loss of heterozygosity. Moreover, comparison of genomic profiles from sequential patients' samples allows detection of clonal evolution. We screened samples from 369 patients with newly diagnosed chronic lymphocytic leukemia from a population-based cohort using 250K single nucleotide polymorphism-arrays. Clonal evolution was evaluated in 59 follow-up samples obtained after 5-9 years. At diagnosis, copy-number aberrations were identified in 90% of patients; 70% carried known recurrent alterations, including del(13q) (55%), trisomy 12 (10.5%), del(11q) (10%), and del(17p) (4%). Additional recurrent aberrations were detected on chromosomes 2 (1.9%), 4 (1.4%), 8 (1.6%) and 14 (1.6%). Thirteen patients (3.5%) displayed recurrent copy-number neutral loss of heterozygosity on 13q, of whom 11 had concurrent homozygous del(13q). Genomic complexity and large 13q deletions correlated with inferior outcome, while the former was linked to poor-prognostic aberrations. In the follow-up study, clonal evolution developed in 8/24 (33%) patients with unmutated IGHV, and in 4/25 (16%) IGHV-mutated and treated patients. In contrast, untreated patients with mutated IGHV (n=10) did not acquire additional aberrations. The most common secondary event, del(13q), was detected in 6/12 (50%) of all patients with acquired alterations. Interestingly, aberrations on, for example, chromosome 6q, 8p, 9p and 10q developed exclusively in patients with unmutated IGHV. Whole-genome screening revealed a high frequency of genomic aberrations in newly diagnosed chronic lymphocytic leukemia. Clonal evolution was associated with other markers of aggressive disease and commonly included the known recurrent aberrations.

Abstract 1603: Primary breast cancer xenografts maintain the molecular profiles of corresponding patients’ tumors and recapitulate a part of stroma microenvironment

Abstract Identifying new therapeutic agents for breast cancer (BC) treatment requires preclinical models that recapitulate the molecular characteristics of their respective clinical tumors. In this work, we analyzed the genomic and expression profiles of human BC xenografts and their corresponding patient's tumors. Eighteen BC xenografts were obtained by grafting tumor fragments from patients into Swiss nude mice. The molecular characterization of patient's and xenograft's tumors (early and late in vivo passages) was performed by DNA copy number analysis (aCGH) and gene expression analysis using Affymetrix Microarrays. Comparison of genomic profiles of BC xenografts with those of respective patient's tumors, showed a correlation coefficient higher than 0.50 in 14/18 paired tumors. Unsupervised hierarchical clustering analysis showed that 16/18 pairs segregated together further indicating the striking similarity between pairs. At the level of gene expression profile few variations were found between patient's tumor and their respective xenografts, i.e. 371 genes that were differentially expressed in more than 84% of paired tumors and that largely represent human stromal compartment related genes. Furthermore, analysis of gene expression by murine stroma revealed a partial but significant recapitulation of the primitive human stroma. Finally, we found that sequential mouse to mouse tumor passages did not affect neither genomic rearrangements nor gene expression profiles, suggesting a striking genetic stability of these models across the time. In conclusions, this panel of human BC xenografts accurately maintains the genomic and the expression profiles of their corresponding patient's tumors and are stable across sequential in vivo passages. Consequently, these xenografts represent a validated model for preclinical investigation of new therapeutic agents. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1603. doi:10.1158/1538-7445.AM2011-1603

A genomic and transcriptomic approach for a differential diagnosis between primary and secondary ovarian carcinomas in patients with a previous history of breast cancer

BackgroundThe distinction between primary and secondary ovarian tumors may be challenging for pathologists. The purpose of the present work was to develop genomic and transcriptomic tools to further refine the pathological diagnosis of ovarian tumors after a previous history of breast cancer.MethodsSixteen paired breast-ovary tumors from patients with a former diagnosis of breast cancer were collected. The genomic profiles of paired tumors were analyzed using the Affymetrix GeneChip® Mapping 50 K Xba Array or Genome-Wide Human SNP Array 6.0 (for one pair), and the data were normalized with ITALICS (ITerative and Alternative normaLIzation and Copy number calling for affymetrix Snp arrays) algorithm or Partek Genomic Suite, respectively. The transcriptome of paired samples was analyzed using Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays, and the data were normalized with gc-Robust Multi-array Average (gcRMA) algorithm. A hierarchical clustering of these samples was performed, combined with a dataset of well-identified primary and secondary ovarian tumors.ResultsIn 12 of the 16 paired tumors analyzed, the comparison of genomic profiles confirmed the pathological diagnosis of primary ovarian tumor (n = 5) or metastasis of breast cancer (n = 7). Among four cases with uncertain pathological diagnosis, genomic profiles were clearly distinct between the ovarian and breast tumors in two pairs, thus indicating primary ovarian carcinomas, and showed common patterns in the two others, indicating metastases from breast cancer. In all pairs, the result of the transcriptomic analysis was concordant with that of the genomic analysis.ConclusionsIn patients with ovarian carcinoma and a previous history of breast cancer, SNP array analysis can be used to distinguish primary and secondary ovarian tumors. Transcriptomic analysis may be used when primary breast tissue specimen is not available.

Patterns of Gene Expression and Copy-Number Alterations in von-Hippel Lindau Disease-Associated and Sporadic Clear Cell Carcinoma of the Kidney

Recent insights into the role of the von-Hippel Lindau (VHL) tumor suppressor gene in hereditary and sporadic clear-cell renal cell carcinoma (ccRCC) have led to new treatments for patients with metastatic ccRCC, although virtually all patients eventually succumb to the disease. We performed an integrated, genome-wide analysis of copy-number changes and gene expression profiles in 90 tumors, including both sporadic and VHL disease-associated tumors, in hopes of identifying new therapeutic targets in ccRCC. We identified 14 regions of nonrandom copy-number change, including 7 regions of amplification (1q, 2q, 5q, 7q, 8q, 12p, and 20q) and 7 regions of deletion (1p, 3p, 4q, 6q, 8p, 9p, and 14q). An analysis aimed at identifying the relevant genes revealed VHL as one of three genes in the 3p deletion peak, CDKN2A and CDKN2B as the only genes in the 9p deletion peak, and MYC as the only gene in the 8q amplification peak. An integrated analysis to identify genes in amplification peaks that are consistently overexpressed among amplified samples confirmed MYC as a potential target of 8q amplification and identified candidate oncogenes in the other regions. A comparison of genomic profiles revealed that VHL disease-associated tumors are similar to a subgroup of sporadic tumors and thus more homogeneous overall. Sporadic tumors without evidence of biallelic VHL inactivation fell into two groups: one group with genomic profiles highly dissimilar to the majority of ccRCC and a second group with genomic profiles that are much more similar to tumors with biallelic inactivation of VHL.

A genomic and transcriptomic approach to distinguish primary and metastatic ovary tumors

e22150 Background: Distinction of primary ovarian tumors from metastatic tumors involving the ovary is in some cases challenging for final pathologic diagnosis and for treatment with efficient chemotherapy Methods: We gathered from our biobank 16 pairs of breast/ovarian tumors for some of which the diagnosis was uncertain. We investigated the possibility to improve diagnosis using genomic and transcriptomic tools. The pangenomic profiles of 16 pairs of primary breast carcinoma and ovary tumors (primary tumors or metastases from breast carcinoma) from the same patients were analyzed using the Affymetrix GeneChip Mapping 50K (XbaI) SNP arrays. The data were normalized with ITALICS algorithm. We analyzed the transcriptome of the paired samples using Affymetrix U133plus2 arrays. The data were normalized with GCRMA algorithm and a hierarchical clustering of these samples was performed, together with a dataset of primary and secondary ovary tumors. Results: Primary infiltrating lobular carcinoma (ILC) was observed in 6 patients, infiltrating ductal carcinoma (IDC) in 7 patients, 1 patient had one ILC and one IDC, 1 patient had a mixed IDC+ILC and 1 patient an undifferentiated cancer. All patients received adequate loco-regional and systemic therapies. Median time to diagnosis of ovarian tumor was 54 months. Ovarian tumors were considered as primary in 7 patients, and metastatic in 9 patients, and diagnosis was ambiguous in 4 of them. Four patients developed extra-abdominal metastases. Median survival from breast cancer diagnosis was 78 months, and from ovarian tumor diagnosis was 29 months. CGH array: In 12 pairs, the comparison of genomic profiles one with each other, confirmed the pathological characteristics of the tumors. In 4 cases, the genomic profiles established clearly the status of the ovary tumor whereas the pathological analysis did not. Transcriptome: The status established by the transcriptomic analysis was for each sample in total agreement with the status established by the genomic analysis. Conclusions: We clearly established in this training series that CGH array analysis could help to discriminate between primary and secondary ovarian tumors from breast cancer. Transcriptomic data confirmed these results. Further validation data are warranted. No significant financial relationships to disclose.