Analyzing Genome Rearrangements in Saccharomyces cerevisiae.

Methods Mol Biol

Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0669, USA.

Published: June 2018


Category Ranking

98%

Total Visits

921

Avg Visit Duration

2 minutes

Citations

20

Article Abstract

Genome rearrangements underlie different human diseases including many cancers. Determining the rates at which genome rearrangements arise and isolating unique, independent genome rearrangements is critical to understanding the genes and pathways that prevent or promote genome rearrangements. Here, we describe quantitative S. cerevisiae genetic assays for measuring the rates of accumulating genome rearrangements including deletions, translocations, and broken chromosomes healed by de novo telomere addition that result in the deletion of two counter-selectable genes, CAN1 and URA3, placed in the nonessential regions of the S. cerevisiae genome. The assays also allow for the isolation of individual genome rearrangements for structural studies, and a method for analyzing genome rearrangements by next-generation DNA sequencing is provided.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5657460PMC
http://dx.doi.org/10.1007/978-1-4939-7306-4_5DOI Listing

Publication Analysis

Top Keywords

genome rearrangements
32
analyzing genome
8
rearrangements
8
genome
8
cerevisiae genome
8
rearrangements saccharomyces
4
saccharomyces cerevisiae
4
rearrangements underlie
4
underlie human
4
human diseases
4

Similar Publications

Introduction: Complex chromosomal rearrangements (CCRs) are frequently associated with infertility and have been described in the literature. Chromoanagenesis corresponds to a group of CCRs with a high number of chromosome breakpoints. These CCRs involving small structural variations can only be identified by using high-resolution genomic techniques.

View Article and Find Full Text PDF

The first complete mitochondrial genome of Spinturnix psi (Dermanyssoidea, Spinturnicidae): gene content, composition, rearrangement and phylogenetic implications.

Exp Appl Acarol

September 2025

Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, 22 Wanhua St, Dali, 671000, China.

The family Spinturnicidae belongs to the suborder Monogynapsida, superfamily Dermanyssoidea, and exclusively parasitizes the body surface of bats. In the present study, we determined the complete mitochondrial genome of Spinturnix psi, a species of bat mite, and subsequently conducted a comprehensive analysis of its genomic information. The mitochondrial genome of S.

View Article and Find Full Text PDF

Germline Findings From Tumor-Only Comprehensive Genomic Profiling in the RATIONAL Study: A Missed Opportunity?

JCO Precis Oncol

September 2025

Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy.

Purpose: Tumor comprehensive genomic profiling (CGP) may detect potential germline pathogenic/likely pathogenic (P/LP) alterations as secondary findings. We analyzed the frequency of potentially germline variants and large rearrangements (LRs) in the RATIONAL study, an Italian multicenter, observational clinical trial that collects next-generation sequencing-based tumor profiling data, and evaluated how these findings were managed by the enrolling centers.

Patients And Methods: Patients prospectively enrolled in the pathway-B of the RATIONAL study and undergoing CGP with the FoundationOne CDx assays were included in the analysis.

View Article and Find Full Text PDF

Background And Objective: Parental chromosomal structural variations (SVs) represent a primary genetic factor contributing to recurrent spontaneous abortion (RSA). Individuals carrying SVs with complex chromosomal rearrangements (CCRs) typically exhibit a normal phenotype but are at an increased risk of miscarriage. Current standard clinical detection methods are insufficient for the identification and interpretation of all SV types, particularly complex and occult SVs, thereby presenting a significant challenge for clinical genetic counseling.

View Article and Find Full Text PDF

IGL::CCND1 detected by optical genome mapping revises diagnosis of a B-cell lymphoma.

Am J Clin Pathol

September 2025

Laboratory for Clinical Genomics and Advanced Technology (CGAT)-Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, United States.

Objective: Differentiating between the repertoire of immunoglobulin rearrangements is important in guiding diagnoses and management of B-cell lymphoma processes. A subset of these disease entities, such as chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL), can show distinct genomic profiles with a shared cell of origin. In this report, we describe a rare case in which differentiating between the immunoglobulin family of rearrangements (IGH, IGK, IGL) with optical genome mapping (OGM) helped revise the clinical suspicion of CLL.

View Article and Find Full Text PDF