Genomic Alterations
Genomic Alterations - Related Videos
11:52
Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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Cited by 15 •
2016
We describe a targeted RNA sequencing-based method that includes preparation of indexed cDNA libraries, hybridization and capture with custom probes and data analysis to interrogate selected transcripts for gene expression, mutations, and gene fusions. Targeted RNAseq permits cost-effective, rapid evaluation of selected transcripts on a desktop sequencer.
08:31
Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
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Cited by 2 •
2013
Single Virus Genomics (SVG) is a method to isolate and amplify the genomes of single virons. Viral suspensions of a mixed assemblage are sorted using flow cytometry onto a microscope slide with discrete wells containing agarose, thereby capturing the virion and reducing genome shearing during downstream processing. Whole genome amplification is achieved using multiple displacement amplification (MDA) resulting in genomic material that is suitable for sequencing.
09:45
Detection of Copy Number Alterations Using Single Cell Sequencing
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Cited by 9 •
2017
Single cell sequencing is an increasingly popular and accessible tool for addressing genomic changes at high resolution. We provide a protocol that uses single cell sequencing to identify copy number alterations in single cells.
08:31
Genome Editing
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2023
A well-established technique for modifying specific sequences in the genome is gene targeting by homologous recombination, but this method can be laborious and only works in certain organisms. Recent advances have led to the development of “genome editing”, which works by inducing double-strand breaks in DNA using engineered nuclease enzymes guided to target genomic sites by either proteins or RNAs that recognize specific sequences. When a cell attempts to repair this damage, mutations can be...
02:02
Genomics
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2020
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
FAQs
Genomic alterations can influence cancer by changing the balance between growth-promoting and growth-restraining genes. An alteration that activates an oncogene may support abnormal tumor development, whereas one that disables a tumor suppressor gene can remove an important barrier to disease progression. Interpreting these opposing functional effects helps researchers connect a DNA change with cancer behavior and treatment response.
Different alteration classes provide different forms of genomic evidence. Mutations affect the DNA sequence, while deletions and amplifications change the amount of genetic material; rearrangements, including translocations, change genomic structure. Examining these categories together can reveal whether cancer-associated changes primarily involve altered sequence, abnormal copy number, disrupted structure, or a combination of these patterns.
Replication errors, impaired DNA repair, environmental damage, and chromosome missegregation represent distinct routes to genomic change. These processes can produce the range of mutations, copy-number changes, and structural rearrangements observed in tumors. Linking an alteration to a possible originating process helps cancer researchers investigate how genome maintenance failures contribute to tumor development and progression.
Tumors can carry different alteration patterns, and those differences may help explain variation in development, progression, and treatment response. Studying alterations across patients supports cancer classification and biomarker discovery, while examining changes within tumors provides context for tumor evolution. This comparative perspective helps researchers account for the genetic diversity underlying cancer behavior rather than treating every tumor as identical.
Genomic profiling provides a systematic way to detect and characterize alterations in a tumor’s genome. The resulting profile can be examined for mutations, deletions, amplifications, and rearrangements, then related to disease features such as classification, progression, or treatment response. Its value comes from connecting a tumor’s genomic pattern with clinically and biologically meaningful cancer traits.
Researchers can use alteration patterns as biomarkers, meaning measurable features that help distinguish or interpret disease states. In cancer research, these patterns may contribute to classifying tumors, identifying treatment-relevant features, and selecting targeted therapies. Genomic information therefore helps researchers determine which molecular characteristics to investigate and which treatment options may be appropriate for a particular tumor.
Changes detected during treatment monitoring can indicate that a tumor’s genomic profile is no longer the same as it was at the start of therapy. Researchers can use this information to study treatment resistance and relate resistant disease to specific genomic alterations. This application extends profiling beyond initial diagnosis, helping track how tumor biology changes in response to treatment.
Patterns of genomic alterations provide a molecular record for examining how tumors develop and change over time. Comparing alterations within and among patients can clarify relationships between tumor progression, disease classification, and treatment response. This evolutionary context helps researchers interpret why tumors may show different behaviors and why genomic profiling remains useful from initial characterization through resistance monitoring.