scholarly journals Contribution of Large Genomic Rearrangements in Italian Lynch Syndrome Patients: Characterization of a Novel Alu-Mediated Deletion

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Francesca Duraturo ◽  
Angela Cavallo ◽  
Raffaella Liccardo ◽  
Bianca Cudia ◽  
Marina De Rosa ◽  
...  
Keyword(s):  
Lynch Syndrome ◽  
Germ Line ◽  
Point Mutations ◽  
Low Frequency ◽  
Genomic Rearrangements ◽  
Dna Mismatch ◽  
Mmr Genes ◽  
Large Genomic Rearrangements ◽  
Large Deletions ◽  
Long Range Pcr

Lynch syndrome is associated with germ-line mutations in the DNA mismatch repair (MMR) genes, mainlyMLH1andMSH2. Most of the mutations reported in these genes to date are point mutations, small deletions, and insertions. Large genomic rearrangements in the MMR genes predisposing to Lynch syndrome also occur, but the frequency varies depending on the population studied on average from 5 to 20%. The aim of this study was to examine the contribution of large rearrangements in theMLH1andMSH2genes in a well-characterised series of 63 unrelated Southern Italian Lynch syndrome patients who were negative for pathogenic point mutations in theMLH1,MSH2, andMSH6genes. We identified a large novel deletion in theMSH2gene, including exon 6 in one of the patients analysed (1.6% frequency). This deletion was confirmed and localised by long-range PCR. The breakpoints of this rearrangement were characterised by sequencing. Further analysis of the breakpoints revealed that this rearrangement was a product of Alu-mediated recombination. Our findings identified a novel Alu-mediated rearrangement withinMSH2gene and showed that large deletions or duplications inMLH1andMSH2genes are low-frequency mutational events in Southern Italian patients with an inherited predisposition to colon cancer.

scholarly journals Insertion of an SVA Element in MSH2 as a Novel Cause of Lynch Syndrome

2020 ◽  
Author(s):  
Ciyu Yang ◽  
Yirong Li ◽  
Magan Trottier ◽  
Michael Farrell ◽  
Vikas Rai ◽  
...  
Keyword(s):  
Lynch Syndrome ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Dna Mismatch ◽  
Mmr Genes ◽  
Antisense Orientation ◽  
The Family ◽  
Long Range Pcr ◽  
Early Onset Colorectal Cancer ◽  
Generation Sequencing

Germline mutations in the DNA mismatch repair (MMR) genes cause Lynch syndrome (LS). Insertions of retrotransposons in MMR genes have been reported as a rare cause of LS. Here, we present a novel SINE-VNTR-Alu (SVA) insertion in exon 12 of MSH2 in an individual with early-onset colorectal cancer and strong LS family history. RT-PCR analysis indicated a larger aberrant MSH2 transcript in one of the family members. MSK-IMPACT next-generation sequencing testing and long-range PCR revealed an insertion in MSH2 exon 12 at the c.1972 position in an antisense orientation. The insertion was further characterized as an SVA element approximately 3 kb in length, belonging to the SVA_F1 family of retrotransposons.

scholarly journals Large genomic rearrangements and germline epimutations in Lynch syndrome

2009 ◽  
Vol 124 (10) ◽  
pp. 2333-2340 ◽  
Author(s):  
Annette Gylling ◽  
Maaret Ridanpää ◽  
Outi Vierimaa ◽  
Kristiina Aittomäki ◽  
Kristiina Avela ◽  
...  
Keyword(s):  
Lynch Syndrome ◽  
Genomic Rearrangements ◽  
Large Genomic Rearrangements

scholarly journals Recapitulation of human germline coding variation in an ultra-mutated infant leukemia

2018 ◽  
Author(s):  
Alexander M Gout ◽  
Rishi S Kotecha ◽  
Parwinder Kaur ◽  
Ana Abad ◽  
Bree Foley ◽  
...  
Keyword(s):  
Mismatch Repair ◽  
Lymphoblastic Leukemia ◽  
Rapid Evolution ◽  
Point Mutations ◽  
Low Frequency ◽  
Mismatch Repair Gene ◽  
Repair Gene ◽  
Dna Mismatch ◽  
Proof Reading ◽  
Highly Correlated

AbstractBackgroundMixed lineage leukemia/Histone-lysine N-methyltransferase 2Agene rearrangements occur in 80% of infant acute lymphoblastic leukemia, but the role of cooperating events is unknown. While infant leukemias typically carry few somatic lesions, we identified a case with over 100 somatic point mutations per megabase and here report unique genomic-features of this case.ResultsThe patient presented at 82 days of age, one of the earliest manifestations of cancer hypermutation recorded. The transcriptional profile showed global similarities to canonical cases. Coding lesions were predominantly clonal and almost entirely targeting alleles reported in human genetic variation databases with a notable exception in the mismatch repair gene,MSH2. There were no rare germline alleles or somatic mutations affecting proof-reading polymerase genesPOLEorPOLD1, however there was a predicted damaging mutation in the error prone replicative polymerase,POLK. The patient’s diagnostic leukemia transcriptome was depleted of rare and low-frequency germline alleles due to loss-of-heterozygosity, while somatic point mutations targeted low-frequency and common human alleles in proportions that offset this discrepancy. Somatic signatures of ultra-mutations were highly correlated with germline single nucleotide polymorphic sites indicating a common role for 5-methylcytosine deamination, DNA mismatch repair and DNA adducts.ConclusionsThese data suggest similar molecular processes shaping population-scale human genome variation also underlies the rapid evolution of an infant ultra-mutated leukemia.

scholarly journals The cause of on-target point mutations generated by CRISPR-Cas9 treatment in the yeast Xanthophyllomyces dendrorhous

2021 ◽  
Author(s):  
Jixuan Hong ◽  
Ziyue Meng ◽  
Zixi Zhang ◽  
Hang Su ◽  
Yuxuan Fan ◽  
...  
Keyword(s):  
Dna Repair ◽  
Dna Polymerases ◽  
Point Mutations ◽  
Low Frequency ◽  
Genomic Rearrangements ◽  
Target Point ◽  
Xanthophyllomyces Dendrorhous ◽  
Nucleotide Substitutions ◽  
Sequence Dependence ◽  
Substitution Mutations

ABSTRACTRecognizing outcomes of DNA repair induced by CRISPR-Cas9 cutting is vital for precise genome editing. Reported DNA repair outcomes after Cas9 cutting include deletions/insertions and low frequency of genomic rearrangements and nucleotide substitutions. Thus far, substitution mutations caused by CRISPR-Cas9 has not attracted much attention. Here, we identified on-target point mutations induced by CRISPR-Cas9 treatment in the yeast Xanthophyllomyces dendrorhous by Sanger and Illumina sequencing. Different from previous studies, our findings suggested that the on-target mutations are not random and they cannot render the gRNA effective. Moreover, these point mutations showed strong sequence dependence that is not consistent with the observations in Hela cells, in which CRISPR-mediated substitutions were considered lacking sequence dependence and conversion preferences. Furthermore, this study demonstrated that the NHEJ components Ku70, Ku80, Mre11, or RAD50, and the overlapping roles of non-essential DNA polymerases were necessary for the emergence of point mutations, increasing the knowledge on CRISPR-Cas9 mediated DNA repair.

scholarly journals Novel Implications in Molecular Diagnosis of Lynch Syndrome

2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Raffaella Liccardo ◽  
Marina De Rosa ◽  
Paola Izzo ◽  
Francesca Duraturo
Keyword(s):  
Lynch Syndrome ◽  
Clinical Manifestations ◽  
Mendelian Inheritance ◽  
Dna Mismatch ◽  
Variants Of Unknown Significance ◽  
Mmr Genes ◽  
Risk Alleles ◽  
Detection Analysis ◽  
Unknown Significance ◽  
Analytical Strategies

About 10% of total colorectal cancers are associated with known Mendelian inheritance, as Familial Adenomatous Polyposis (FAP) and Lynch syndrome (LS). In these cancer types the clinical manifestations of disease are due to mutations in high-risk alleles, with a penetrance at least of 70%. The LS is associated with germline mutations in the DNA mismatch repair (MMR) genes. However, the mutation detection analysis of these genes does not always provide informative results for genetic counseling of LS patients. Very often, the molecular analysis reveals the presence of variants of unknown significance (VUSs) whose interpretation is not easy and requires the combination of different analytical strategies to get a proper assessment of their pathogenicity. In some cases, these VUSs may make a more substantial overall contribution to cancer risk than the well-assessed severe Mendelian variants. Moreover, it could also be possible that the simultaneous presence of these genetic variants in several MMR genes that behave as low risk alleles might contribute in a cooperative manner to increase the risk of hereditary cancer. In this paper, through a review of the recent literature, we have speculated a novel inheritance model in the Lynch syndrome; this could pave the way toward new diagnostic perspectives.

scholarly journals Sanger sequencing of MMR genes in a one-plate system

2018 ◽  
Vol 26 (2) ◽  
pp. 153-163
Author(s):  
Lucian Negura ◽  
Anca Negura
Keyword(s):  
Colorectal Cancer ◽  
Lynch Syndrome ◽  
Sanger Sequencing ◽  
Germ Line ◽  
Cost Effective ◽  
Complete Analysis ◽  
Continuous Increase ◽  
Technical Problems ◽  
Mmr Genes ◽  
Incidence And Mortality

Abstract Both incidence and mortality of colorectal cancer (CRC) in Romania have shown a continuous increase during the last decades. Hereditary Non-Polyposic Colorectal Cancer (HNPCC), also known as Lynch syndrome, is mainly attributable to mismatch repair (MMR) genes MSH2, MSH6, and MLH1. Individuals carrying germ-line mutations of these genes present high lifetime risk of colorectal and other cancers, compared to non-carriers. Oncogenetics is developed worldwide nowadays, for identifying hereditary predisposition to cancer and offering appropriate clinical follow-up to patients and mutation carriers in Lynch families. Molecular oncogenetic diagnosis in Lynch syndrome is based on complete Sanger sequencing of entire MMR genes, which is time and resources consuming, therefore needing an appropriate and adapted optimization. Conventional sequencing requires a sufficient number of available samples to be processed simultaneously, which increases the waiting time for diagnostic results. Complete analysis for only one patient meets difficult technical problems due to the complex co-amplification of all gene regions of interest within the same conditions, therefore increasing the costs and reducing the cost-effectiveness of the test. Here we present an original and robust technical protocol for sequencing the entire MSH2, MSH6, and MLH1 coding sequence for one patient in a single PCR plate. Our optimized and verified system overcomes all technical problems and offers a quick, robust, and cost-effective possibility to personalize molecular oncogenetic diagnosis in Lynch syndrome.

scholarly journals Clinical and genetic aspects of differential diagnostics of hereditary non-polyposis colorectal cancer

2019 ◽  
Vol 6 (2) ◽  
pp. 21-27
Author(s):  
A. V. Semyanikhina ◽  
A. O. Rasulov ◽  
L. N. Lyubchenko
Keyword(s):  
Colorectal Cancer ◽  
Colon Cancer ◽  
Lynch Syndrome ◽  
Mismatch Repair ◽  
Heterogeneous Group ◽  
Differential Diagnostics ◽  
Genetic Characteristics ◽  
Dna Mismatch ◽  
Mmr Genes ◽  
Long Time

Lynch syndrome was synonymous with hereditary non-polyposis colorectal cancer for a long time, however, mapping of the DNA mismatch repair (MMR) genes has led to distinguish Lynch syndrome as an independent syndromic unit from a number of Lynch-like syndromes that phenotypically mimic with the most frequent hereditary variant of colon cancer but genetically representing quite a heterogeneous group. This article presents up to date clinical and genetic characteristics of Lynch syndrome and Lynch-like conditions.

scholarly journals Same MSH2 Gene Mutation But Variable Phenotypes in 2 Families With Lynch Syndrome: Two Case Reports and Review of Genotype-Phenotype Correlation

2018 ◽  
Vol 11 ◽  
pp. 117954761775394 ◽  
Author(s):  
Raffaella Liccardo ◽  
Marina De Rosa ◽  
Francesca Duraturo
Keyword(s):  
Lynch Syndrome ◽  
Autosomal Dominant ◽  
Colonic Cancer ◽  
Case Reports ◽  
Phenotypic Expression ◽  
Point Mutations ◽  
Phenotype Correlation ◽  
Dna Mismatch ◽  
Large Rearrangements ◽  
Extracolonic Cancers

Lynch syndrome is an autosomal dominant syndrome that can be subdivided into Lynch syndrome I, or site-specific colonic cancer, and Lynch syndrome II, or extracolonic cancers, particularly carcinomas of the stomach, endometrium, biliary and pancreatic systems, and urinary tract. Lynch syndrome is associated with point mutations and large rearrangements in DNA MisMatch Repair ( MMR) genes. This syndrome shows a variable phenotypic expression in people who carry pathogenetic mutations. So far, a correlation in genotype-phenotype has not been definitely established. In this study, we describe 2 Lynch syndrome cases presenting with the same genotype but different phenotypes and discuss possible reasons for this.

Low frequency of large genomic rearrangements of BRCA1 and BRCA2 in western Denmark

2006 ◽  
Vol 168 (2) ◽  
pp. 168-171 ◽  
Author(s):  
Mads Thomassen ◽  
Anne-Marie Gerdes ◽  
Dorthe Cruger ◽  
Peter K.A. Jensen ◽  
Torben A. Kruse
Keyword(s):  
Low Frequency ◽  
Genomic Rearrangements ◽  
Brca1 And Brca2 ◽  
Large Genomic Rearrangements

scholarly journals Oligonucleotide-directed mutagenesis screen to identify pathogenic Lynch syndrome-associated MSH2 DNA mismatch repair gene variants

2016 ◽  
Vol 113 (15) ◽  
pp. 4128-4133 ◽  
Author(s):  
Hellen Houlleberghs ◽  
Marleen Dekker ◽  
Hildo Lantermans ◽  
Roos Kleinendorst ◽  
Hendrikus Jan Dubbink ◽  
...  
Keyword(s):  
Lynch Syndrome ◽  
Mismatch Repair ◽  
Dna Mismatch Repair ◽  
Embryonic Stem ◽  
Mismatch Repair Gene ◽  
Missense Mutations ◽  
Repair Gene ◽  
Dna Mismatch ◽  
Mmr Genes ◽  
Pathogenic Variants

Single-stranded DNA oligonucleotides can achieve targeted base-pair substitution with modest efficiency but high precision. We show that “oligo targeting” can be used effectively to study missense mutations in DNA mismatch repair (MMR) genes. Inherited inactivating mutations in DNA MMR genes are causative for the cancer predisposition Lynch syndrome (LS). Although overtly deleterious mutations in MMR genes can clearly be ascribed as the cause of LS, the functional implications of missense mutations are often unclear. We developed a genetic screen to determine the pathogenicity of these variants of uncertain significance (VUS), focusing on mutator S homolog 2 (MSH2). VUS were introduced into the endogenous Msh2 gene of mouse embryonic stem cells by oligo targeting. Subsequent selection for MMR-deficient cells using the guanine analog 6-thioguanine allowed the detection of MMR-abrogating VUS. The screen was able to distinguish weak and strong pathogenic variants from polymorphisms and was used to investigate 59 Msh2 VUS. Nineteen of the 59 VUS were identified as pathogenic. Functional assays revealed that 14 of the 19 detected variants fully abrogated MMR activity and that five of the detected variants attenuated MMR activity. Implementation of the screen in clinical practice allows proper counseling of mutation carriers and treatment of their tumors.

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