Analysis Of Genomic Rearrangements Research Articles

Urinary extracellular vesicles miRNA-A new era of prostate cancer biomarkers.

Prostate cancer is the second most common male cancer worldwide showing the highest rates of incidence in Western Europe. Although the measurement of serum prostate-specific antigen levels is the current gold standard in PCa diagnosis, PSA-based screening is not considered a reliable diagnosis and prognosis tool due to its lower sensitivity and poor predictive score which lead to a 22%-43% overdiagnosis, unnecessary biopsies, and over-treatment. These major limitations along with the heterogeneous nature of the disease have made PCa a very unappreciative subject for diagnostics, resulting in poor patient management; thus, it urges to identify and validate new reliable PCa biomarkers that can provide accurate information in regard to disease diagnosis and prognosis. Researchers have explored the analysis of microRNAs (miRNAs), messenger RNAs (mRNAs), small proteins, genomic rearrangements, and gene expression in body fluids and non-solid tissues in search of lesser invasive yet efficient PCa biomarkers. Although the presence of miRNAs in body fluids like blood, urine, and saliva initially sparked great interest among the scientific community; their potential use as liquid biopsy biomarkers in PCa is still at a very nascent stage with respect to other well-established diagnostics and prognosis tools. Up to date, numerous studies have been conducted in search of PCa miRNA-based biomarkers in whole blood or blood serum; however, only a few studies have investigated their presence in urine samples of which less than two tens involve the detection of miRNAs in extracellular vesicles isolated from urine. In addition, there exists some discrepancy around the identification of miRNAs in PCa urine samples due to the diversity of the urine fractions that can be targeted for analysis such as urine circulating cells, cell-free fractions, and exosomes. In this review, we aim to discuss research output from the most recent studies involving the analysis of urinary EVs for the identification of miRNA-based PCa-specific biomarkers.

275 (PB055) - Large genome rearrangement of BRCA1/2 in BRCA mutation negative ovarian cancer patients

Background: We performed large genomic rearrangement (LGR) analysis of BRCA1/2 in ovarian cancer patients who were negative for BRCA1/2 as a result of the Next Generation Sequencing (NGS) analysis to determine the prevalence and the characteristics of the mutations.

Genome assembly using quantum and quantum-inspired annealing

Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for de novo genome assembly, which is used for the analysis of genomic rearrangements, chromosome phasing, and reconstructing genomes without a reference, require solving tasks of high computational complexity. Here we demonstrate a method for solving genome assembly tasks with the use of quantum and quantum-inspired optimization techniques. Within this method, we present experimental results on genome assembly using quantum annealers both for simulated data and the phi X 174 bacteriophage. Our results pave a way for an increase in the efficiency of solving bioinformatics problems with the use of quantum computing and, in particular, quantum annealing. We expect that the new generation of quantum annealing devices would outperform existing techniques for de novo genome assembly. To the best of our knowledge, this is the first experimental study of de novo genome assembly problems both for real and synthetic data on quantum annealing devices and quantum-inspired techniques.

Cytoplasmic MSH2 Related to Genomic Deletions in the MSH2/EPCAM Genes in Colorectal Cancer Patients With Suspected Lynch Syndrome.

BackgroundA large proportion of patients with Lynch syndrome (LS) have MSH2 abnormalities, but genotype-phenotype studies of MSH2 mutations in LS are still lacking. The aim of this study was to comprehensively analyze the clinicopathological characteristics and molecular basis of colorectal cancer (CRC) in patients with uncommon MSH2 cytoplasmic expression.MethodsWe retrospectively reviewed 4195 consecutive cases of CRC patients diagnosed between January 2015 and December 2017 at the Cancer Hospital Chinese Academy of Medical Sciences. Of the 4195 patients with CRC, 69 were indicated to have abnormal MSH2 expression through tumor immunohistochemical staining. Genetic tests, such as next-generation sequencing, large genomic rearrangement (LGR) analysis, microsatellite instability status analysis and genomic breakpoint analysis, were performed. Clinicopathological and molecular characteristics and clinical immunotherapy response were analyzed.ResultsForty-five of 69 patients were identified to have LS with pathogenic germline mutations in MSH2 and/or EPCAM. Of these LS patients, 26.7% were confirmed to harbor large genomic rearrangements (LGRs). Of note, three tumors from two unrelated family pedigrees exhibited a rare cytoplasmic MSH2 staining pattern that was found in LS patients with EPCAM/MSH2 deletions. RNA analysis showed that two novel mRNA fusions of EPCAM and MSH2 resulted in the predicted protein fusion with MSH2 cytoplasmic localization. Analyses of genomic breakpoints indicated that two novel deletions of EPCAM and MSH2 originated from Alu repeat-mediated recombination events. Our study also provides clinical evidence for the beneficial effect of the PD-1 inhibitor pembrolizumab for CRC patients that exhibit cytoplasmic MSH2 staining.ConclusionOur study demonstrates that the rare cytoplasmic MSH2 staining pattern should be fully recognized by pathologists and geneticists. Given the specific genotype-phenotype correlation in LS screening, we advocate that all CRC patients with cytoplasmic MSH2 staining in histology should be screened for LGRs of EPCAM and MSH2.

Unraveling Genome Evolution Throughout Visual Analysis: The XCout Portal.

Due to major breakthroughs in sequencing technologies throughout the last decades, the time and cost per sequencing experiment have reduced drastically, overcoming the data generation barrier during the early genomic era. Such a shift has encouraged the scientific community to develop new computational methods that are able to compare large genomic sequences, thus enabling large-scale studies of genome evolution. The field of comparative genomics has proven itself invaluable for studying the evolutionary mechanisms and the forces driving genome evolution. In this line, a full genome comparison study between 2 species requires a quadratic number of comparisons in terms of the number of sequences (around 400 chromosome comparisons in the case of mammalian genomes); however, when studying conserved syntenies or evolutionary rearrangements, many sequence comparisons can be skipped for not all will contain significant signals. Subsequently, the scientific community has developed fast heuristics to perform multiple pairwise comparisons between large sequences to determine whether significant sets of conserved similarities exist. The data generation problem is no longer an issue, yet the limitations have shifted toward the analysis of such massive data. Therefore, we present XCout, a Web-based visual analytics application for multiple genome comparisons designed to improve the analysis of large-scale evolutionary studies using novel techniques in Web visualization. XCout enables to work on hundreds of comparisons at once, thus reducing the time of the analysis by identifying significant signals between chromosomes across multiple species. Among others, XCout introduces several techniques to aid in the analysis of large-scale genome rearrangements, particularly (1) an interactive heatmap interface to display comparisons using automatic color scales based on similarity thresholds to ease detection at first sight, (2) an overlay system to detect individual signal contributions between chromosomes, (3) a tracking tool to trace conserved blocks across different species to perform evolutionary studies, and (4) a search engine to search annotations throughout different species.

Achieving large and distant ancestral genome inference by using an improved discrete quantum-behaved particle swarm optimization algorithm

BackgroundReconstructing ancestral genomes is one of the central problems presented in genome rearrangement analysis since finding the most likely true ancestor is of significant importance in phylogenetic reconstruction. Large scale genome rearrangements can provide essential insights into evolutionary processes. However, when the genomes are large and distant, classical median solvers have failed to adequately address these challenges due to the exponential increase of the search space. Consequently, solving ancestral genome inference problems constitutes a task of paramount importance that continues to challenge the current methods used in this area, whose difficulty is further increased by the ongoing rapid accumulation of whole-genome data.ResultsIn response to these challenges, we provide two contributions for ancestral genome inference. First, an improved discrete quantum-behaved particle swarm optimization algorithm (IDQPSO) by averaging two of the fitness values is proposed to address the discrete search space. Second, we incorporate DCJ sorting into the IDQPSO (IDQPSO-Median). In comparison with the other methods, when the genomes are large and distant, IDQPSO-Median has the lowest median score, the highest adjacency accuracy, and the closest distance to the true ancestor. In addition, we have integrated our IDQPSO-Median approach with the GRAPPA framework. Our experiments show that this new phylogenetic method is very accurate and effective by using IDQPSO-Median.ConclusionsOur experimental results demonstrate the advantages of IDQPSO-Median approach over the other methods when the genomes are large and distant. When our experimental results are evaluated in a comprehensive manner, it is clear that the IDQPSO-Median approach we propose achieves better scalability compared to existing algorithms. Moreover, our experimental results by using simulated and real datasets confirm that the IDQPSO-Median, when integrated with the GRAPPA framework, outperforms other heuristics in terms of accuracy, while also continuing to infer phylogenies that were equivalent or close to the true trees within 5 days of computation, which is far beyond the difficulty level that can be handled by GRAPPA.

Novel germline STK11 variants and breast cancer phenotype identified in an Indian cohort of Peutz-Jeghers syndrome.

Peutz-Jeghers syndrome (PJS) caused by germline STK11 variants is a rare autosomal dominant cancer predisposition syndrome characterized by multiple gastrointestinal (GI) hamartomatous polyps, mucocutaneous pigmentation and a high inherited risk of developing GI, breast and other cancers. Despite GI and breast being the two most common PJS-associated cancer sites, the immunohistochemical (IHC) and molecular features of these tumors in carriers of STK11 variant is not known. Detailed phenotyping including tumor IHC and its correlation with comprehensive STK11 genotyping by full gene sequencing followed by large genomic rearrangement analysis was performed in an Indian PJS cohort. A total of 4 distinct STK11 pathogenic or likely pathogenic variants were identified in 10 PJS cases from 7 of the 19 families tested-in 4/5 classical PJS families and 3/14 suspected PJS families. The pathogenic STK11 variant identified was novel in 3/7 families. In addition, four distinct, likely benign variants identified in seven families were also novel. All of the four breast cancer cases in families with STK11 pathogenic variant were estrogen receptor (ER)-positive and Her2-negative. Several novel STK11 variants identified in this Indian PJS cohort highlight the need to study PJS in different populations across the world. This is the first report showing ER positivity in breast cancer in carriers of STK11 variants and needs confirmation in a larger pooled cohort of PJS associated breast cancers. This could help establish the role of chemoprevention or prophylactic oophorectomy in female carriers of STK11 pathogenic variants.

Analysis of Fission Yeast Single DNA Molecules on the Megabase Scale Using DNA Combing.

DNA combing enables the quantitative analysis of DNA replication, DNA recombination, DNA-protein interaction, and DNA methylation along genomic single DNA molecules at 1kb resolution. However, DNA combing has been restricted to short 200-500kb long DNA fragments, which introduces significant bias in data analysis. An improved DNA combing methodology that allows to routinely image Mb-scale single DNA molecules and occasionally up to full-length fission yeast chromosomes is presented in this chapter. DNA combing of Mb-scale single DNA molecules can be applied to accurately measure the dynamic properties of DNA replication such as the rate of origin firing, replication fork velocity, fork directionality and the frequency of fork blockage. In addition, Mb-scale single DNA molecules enable the quantitative analysis of complex genomic rearrangements including gross chromosomal translocations, repetitive DNA sequences, large deletions, and duplications, which are difficult to investigate with deep sequencing strategies.

BRCA1/2 mutations, including large genomic rearrangements, among unselected ovarian cancer patients in Korea.

ObjectiveWe performed small-scale mutation and large genomic rearrangement (LGR) analysis of BRCA1/2 in ovarian cancer patients to determine the prevalence and the characteristics of the mutations.MethodsAll ovarian cancer patients who visited a single institution between September 2015 and April 2017 were included. Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), and long-range polymerase chain reaction (PCR) were performed to comprehensively study BRCA1/2. The genetic risk models BRCAPRO, Myriad, and BOADICEA were used to evaluate the mutation analysis.ResultsIn total, 131 patients were enrolled. Of the 131 patients, Sanger sequencing identified 16 different BRCA1/2 small-scale mutations in 20 patients (15.3%). Two novel nonsense mutations were detected in 2 patients with a serous borderline tumor and a large-cell neuroendocrine carcinoma. MLPA analysis of BRCA1/2 in Sanger-negative patients revealed 2 LGRs. The LGRs accounted for 14.3% of all identified BRCA1 mutations, and the prevalence of LGRs identified in this study was 1.8% in 111 Sanger-negative patients. The genetic risk models showed statistically significant differences between mutation carriers and non-carriers. The 2 patients with LGRs had at least one blood relative with breast or ovarian cancer.ConclusionTwenty-two (16.8%) of the unselected ovarian cancer patients had BRCA1/2 mutations that were detected through comprehensive BRCA1/2 genetic testing. Ovarian cancer patients with Sanger-negative results should be considered for LGR detection if they have one blood relative with breast or ovarian cancer. The detection of more BRCA1/2 mutations in patients is important for efforts to provide targeted therapy to ovarian cancer patients.

Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches.

Genome rearrangements are mutations that change the gene content of a genome or the arrangement of the genes on a genome. Several years of research on genome rearrangements have established different algorithmic approaches for solving some fundamental problems in comparative genomics based on gene order information. This review summarizes the literature on genome rearrangement analysis along two lines of research. The first line considers rearrangement models that are particularly well suited for a theoretical analysis. These models use rearrangement operations that cut chromosomes into fragments and then join the fragments into new chromosomes. The second line works with rearrangement models that reflect several biologically motivated constraints, e.g., the constraint that gene clusters have to be preserved. In this chapter, the border between algorithmically "easy" and "hard" rearrangement problems is sketched and a brief review is given on the available software tools for genome rearrangement analysis.

Analysis of genomic rearrangements in macrophages dissected from human atherosclerotic plaques

Analysis of genomic rearrangements in macrophages dissected from human atherosclerotic plaques

A Comparative Study of Pygmy Hippopotamus (Choeropsis liberiensis) Karyotype by Cross-Species Chromosome Painting

The family Hippopotamidae is comprised of two genera with two living species, the common hippo (Hippopotamus amphibius) and the pygmy hippo (Choeropsis liberiensis). Unlike the common hippo, the karyotype of C. liberiensis has not yet been investigated via cross-species chromosome painting methods. We established chromosomal homologies between the pygmy hippo, pig, and cattle by fluorescence in situ hybridization using whole chromosome, arm-specific, region specific, and bacterial artificial chromosome (BAC) probes. Probes from the 18 pig autosomes painted 45 conserved chromosomal segments in the pygmy hippo genome. The pygmy hippo and cattle homology map was deduced from our hybridization results of painting probes to pygmy hippo chromosomes with a combination of previously published dromedary hybridization data. On the pygmy hippo and cattle homology map, 29 cattle autosomes revealed 39 conservative segments on pygmy hippo chromosomes. For a more detailed structural analysis of genome rearrangements and X chromosome structure, we used cattle region specific and BAC probes. Our report demonstrates that cattle probes are useful not only in comparative studies within Ruminantia, but also in more phylogenetically distant Artiodactyla species.

Analysis of genome structure and rearrangements using single cell sequencing approaches

Analysis of genome structure and rearrangements using single cell sequencing approaches

Abstract 780: Multi-omic profiling of gliomas reveals distinct DNA methylation changes at tumor recurrence

Abstract Varying possibilities of tumor relapse for lower grade glioma (LGG, WHO grade II and III) and glioblastoma (GBM, WHO grade IV) have led to heterogenous clinical outcomes for patients. Our current study aims to establish a molecular profile of recurrence of matched primary and recurrent LGG (n = 28) and recurrent GBM (n = 24) tumor samples. The Cancer Genome Atlas (TCGA) has comprehensively profiled these matched primary/recurrent tumor sets; whole genomes, coding exomes, methylomes, and transcriptomes have been sequenced, and the samples have undergone targeted profiling of the proteome. While unsupervised analysis techniques have not led to a clear recurrence signature, supervised analysis methods have revealed interesting patterns. Protein profiling has shown that recurrent gliomas retain the overall molecular signature of their primary counterpart, but the DNA damage response, apoptosis and RTK pathways are downregulated in the recurrent gliomas, in contrast to RAS/MAPK, PI3K/AKT, and EMT pathways, which are upregulated. Whole genome sequencing and rearrangement analysis have revealed increased genomic complexity among most recurrent gliomas as well as new fusions of interest in recurrent LGG samples (PTPRZ1-MET and involving ATRX). Using genome-wide Illumina HumanMethylation 450K data we observed that 78.6% of LGGs showed depletion of DNA methylation at recurrence and 50% of GBM tumors showed an enrichment of DNA methylation at recurrence. Patient centric enrichment analysis allowed us to discover a candidate biological subgroup characterized by a subset of LGG recurrences (50%) exhibiting an aberrant CpG methylation loss at inintergenic opensea regions when compared with canonical CpG islands and shores (fold > 1.3 and confidence intervals of 99%). Importantly, inspection of CpG sites significantly hypomethylated at openseas showed that this pronounced epigenetic signature maps to candidate TSS distal and hypomethylated enhancers. The gene-targets of these hypomethylated CpG sites show a corresponding up-regulation of expression. Pathway analysis has demonstrated that these upregulated genes are involved in cellular growth and proliferation, cellular function and maintenance, and cell cycle regulation. Our results provide evidence that DNA methylation may represent a stable signature of glioma recurrence and that the crosstalk between DNA hypomethylation at openseas and chromosomal instability may be involved in glioma recurrence. We plan to further integrate our findings between data types and correlate with treatment and patient clinical outcome. Citation Format: Lindsay C. Stetson, Camila Ferreira de Souza, Tathiane Maistro Malta, Thais Sarraf Sabedot, Quinn Ostrom, Peter Liao, Daniela Pretti da Cunha Tirapelli, Luciano Neder, Carlos Gilberto Carlotti, Rehan Akbani, Sofie Salama, Laila Poisson, Daniel Brat, The Cancer Genome Atlas Network, Houtan Noushmehr, Jill Barnholtz-Sloan. Multi-omic profiling of gliomas reveals distinct DNA methylation changes at tumor recurrence. [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 780.

Analysis of genomic rearrangements by using the Burrows-Wheeler transform of short-read data.

BackgroundThe potential utility of the Burrows-Wheeler transform (BWT) of a large amount of short-read data ("reads") has not been fully studied. The BWT basically serves as a lossless dictionary of reads, unlike the heuristic and lossy reads-to-genome mapping results conventionally obtained in the first step of sequence analysis. Thus, it is naturally expected to lead to development of sensitive methods for analysis of short-read data. Recently, one of the most active areas of research in sequence analysis is sensitive detection of rare genomic rearrangements from whole-genome sequencing (WGS) data of heterogeneous cancer samples. The application the BWT of reads to the analysis of genomic rearrangements is addressed in this study.ResultsA new method for sensitive detection of genomic rearrangements by using the BWT of reads in the following three steps is proposed: first, breakpoint regions, which contain breakpoints and are joined together by rearrangement, are predicted from the distribution of so-called discordant pairs by using a kind of the conjugate gradient method; second, reads partially matching the breakpoint regions are collected from the BWT of reads; and third, breakpoints are detected as branching points among the collected reads, and their precise positions are determined. The method was experimentally implemented, and its performance (i.e., sensitivity and specificity) was evaluated by using simulated data with known artificial rearrangements. It was applied to publicly available real biological WGS data of cancer patients, and the detection results were compared with published results.ConclusionsServing as a lossless dictionary of reads, the BWT of short reads enables sensitive analysis of genomic rearrangements in heterogeneous cancer-genome samples when used in conjunction with breakpoint-region predictions based on a conjugate gradient method.

Scaffold assembly based on genome rearrangement analysis

Advances in DNA sequencing technology over the past decade have increased the volume of raw sequenced genomic data available for further assembly and analysis. While there exist many algorithms for assembly of sequenced genomic material, they often experience difficulties in constructing complete genomic sequences. Instead, they produce long genomic subsequences (scaffolds), which then become a subject to scaffold assembly aimed at reconstruction of their order along genome chromosomes. The balance between reliability and cost for scaffold assembly is not there just yet, which inspires one to seek for new approaches to address this problem. We present a new method for scaffold assembly based on the analysis of gene orders and genome rearrangements in multiple related genomes (some or even all of which may be fragmented). Evaluation of the proposed method on artificially fragmented mammalian genomes demonstrates its high reliability. We also apply our method for incomplete anophelinae genomes, which expose high fragmentation, and further validate the assembly results with referenced-based scaffolding. While the two methods demonstrate consistent results, the proposed method is able to identify more assembly points than the reference-based scaffolding.

Analysis of BRCA1and BRCA2 large genomic rearrangements in Sri Lankan familial breast cancer patients and at risk individuals.

BackgroundMajority of mutations found to date in the BRCA1/BRCA2 genes in breast and/or ovarian cancer families are point mutations or small insertions and deletions scattered over the coding sequence and splice junctions. Such mutations and sequence variants of BRCA1 and BRCA2 genes were previously identified in a group of Sri Lankan breast cancer patients. Large genomic rearrangements have been characterized in BRCA1 and BRCA2 genes in several populations but these have not been characterized in Sri Lankan breast cancer patients.FindingsA cohort of familial breast cancer patients (N = 57), at risk individuals (N = 25) and healthy controls (N = 23) were analyzed using multiplex ligation-dependent probe amplification method to detect BRCA1 and BRCA2 large genomic rearrangements. One familial breast cancer patient showed an ambiguous deletion in exon 6 of BRCA1 gene. Full sequencing of the ambiguous region was used to confirm MLPA results. Ambiguous deletion detected by MLPA was found to be a false positive result confirming that BRCA1 large genomic rearrangements were absent in the subjects studied. No BRCA2 rearrangement was also identified in the cohort.ConclusionThus this study demonstrates that BRCA1 and BRCA2 large genomic rearrangements are unlikely to make a significant contribution to aetiology of breast cancer in Sri Lanka.

Analysis of genomic rearrangements, horizontal gene transfer and role of plasmids in the evolution of industrial important Thermus species.

BackgroundBacteria of genus Thermus inhabit both man-made and natural thermal environments. Several Thermus species have shown biotechnological potential such as reduction of heavy metals which is essential for eradication of heavy metal pollution; removing of organic contaminants in water; opening clogged pipes, controlling global warming among many others. Enzymes from thermophilic bacteria have exhibited higher activity and stability than synthetic or enzymes from mesophilic organisms.ResultsUsing Meiothermus silvanus DSM 9946 as a reference genome, high level of coordinated rearrangements has been observed in extremely thermophilic Thermus that may imply existence of yet unknown evolutionary forces controlling adaptive re-organization of whole genomes of thermo-extremophiles. However, no remarkable differences were observed across species on distribution of functionally related genes on the chromosome suggesting constraints imposed by metabolic networks. The metabolic network exhibit evolutionary pressures similar to levels of rearrangements as measured by the cross-clustering index. Using stratigraphic analysis of donor-recipient, intensive gene exchanges were observed from Meiothermus species and some unknown sources to Thermus species confirming a well established DNA uptake mechanism as previously proposed.ConclusionGlobal genome rearrangements were found to play an important role in the evolution of Thermus bacteria at both genomic and metabolic network levels. Relatively higher level of rearrangements was observed in extremely thermophilic Thermus strains in comparison to the thermo-tolerant Thermus scotoductus. Rearrangements did not significantly disrupt operons and functionally related genes. Thermus species appeared to have a developed capability for acquiring DNA through horizontal gene transfer as shown by the donor-recipient stratigraphic analysis.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-813) contains supplementary material, which is available to authorized users.

The evolution of the random reversal graph

Genomes are typically represented as signed permutations, where each integer corresponds to a single gene and its sign indicates the orientation of the gene. In this paper we study genome rearrangements via reversals (Sankoff and Blanchette, 1999) [20], flipping entire segments of genes and changing their orientations. This abstraction leads to the notion of the reversal graph in which two signed permutations are neighbors if they differ by one reversal. We identify the evolution of multiple genomes within the random reversal graph, i.e.the probability space consisting of subgraphs over signed permutations, obtained by selecting edges (reversals) with independent probability λn, which is an important framework for the analysis of genome rearrangements in the sense of relating the reversal rate λn with the global evolution of genomes. Our main result shows that the structure of the random reversal graph changes dramatically at λn=1/n+12. For λn=(1-∊)n+12, the random graph consists of components of size at most O(nlnn) a.s.and for (1+∊)n+12, there emerges a unique largest component of size ∼℘(∊)·2n·n! a.s., where ℘(∊) is the survival probability of a certain branching process. This “giant” component is furthermore dense in the reversal graph.

EPCAM germline and somatic rearrangements in lynch syndrome: identification of a novel 3′EPCAM deletion

3'EPCAM (Epithelial Cell Adhesion Molecule) genomic rearrangements can be a cause of mismatch repair deficiency in rare Lynch syndrome families. 3'EPCAM deletions include the polyadenylation signal and might result in promoter hypermethylation of the centromeric MSH2 gene in cis. A somatic rearrangement in trans affecting MSH2 is responsible for the final mismatch repair deficiency in the corresponding tumors but the mechanisms are not well documented. In this report two germline 3'EPCAM deletions are described together with the corresponding somatic mutations in the patient's colorectal tumors. Mutation and breakpoint analysis resulted in the identification of one novel (c.556-531_*872del) and one known EPCAM deletion (c.859-689_*14697del). Both deletions resulted from Alu mediated homologous recombination causing aberrant EPCAM-MSH2 fusion transcripts. The colorectal tumors of the deletion carriers were MSI-high. Strong hypermethylation of the MSH2 promoter was measured. Analysis of somatic genomic rearrangements showed a 4 Mb deletion including the EPCAM, MSH2 and MSH6 genes in one tumor and copy neutral loss of heterozygosity in the EPCAM-MSH2 region in the other tumor. This indicates that hemi- and homozygous hypermethylation of the MSH2 promoter and hence complete silencing of MSH2 expression was responsible for the mismatch repair deficiency in both colorectal tumors.