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Loss of Tumor Suppressor Gene Functions

Loss of Tumor Suppressor Gene Functions

Tumor suppressor genes are normal genes that can slow down cell division, repair DNA mistakes, or program the cells for apoptosis in case of irreparable damage. Hence, they play an essential role in preventing the proliferation of damaged cells.
When the tumor suppressor genes develop mutations or are lost, cells start growing out of control, leading to cancer. However, a single functional copy of the tumor suppressor gene is enough for the cells to maintain their normal functions and cell...

Loss of Tumor Suppressor Gene Functions

Loss of Tumor Suppressor Gene Functions

Tumor suppressor genes are normal genes that can slow down cell division, repair DNA mistakes, or program the cells for apoptosis in case of irreparable damage. Hence, they play an essential role in preventing the proliferation of damaged cells.
When the tumor suppressor genes develop mutations or are lost, cells start growing out of control, leading to cancer. However, a single functional copy of the tumor suppressor gene is enough for the cells to maintain their normal functions and cell...

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

Hardy-Weinberg Principle

Hardy-Weinberg Principle

Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.In the early 20th century,...

Homologous Recombination

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

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HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

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Published on: March 31, 2019

LOHAS: loss-of-heterozygosity analysis suite.

Hsin-Chou Yang¹, Lun-Ching Chang, Richard M Huggins

¹Institute of Statistical Science, Academia Sinica, Nankang, Taipei, Taiwan. hsinchou@stat.sinica.edu.tw

Genetic Epidemiology

|February 12, 2011

Summary

This summary is machine-generated.

Computational methods were developed to detect loss of heterozygosity (LOH) and long contiguous stretches of homozygosity (LCSH) using SNP array data. These methods aid in cancer research and population genetics by identifying genetic alterations and patterns.

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Comparative Lesions Analysis Through a Targeted Sequencing Approach

Comparative Lesions Analysis Through a Targeted Sequencing Approach

Published on: November 5, 2019

Area of Science:

Genetics
Genomics
Computational Biology

Background:

Loss of heterozygosity (LOH) detection is crucial for genetic, genomic, and cancer research.
Long contiguous stretches of homozygosity (LCSH) analysis is important for population genetics, identifying nonrandom mating, and mapping genomic regions.

Purpose of the Study:

To develop and apply computational methods for detecting LOH and LCSH.
To analyze SNP array data for cancer genetics and population studies.
To identify genomic segments associated with LOH and LCSH.

Main Methods:

Development of computational algorithms for LOH and LCSH analysis.
Utilizing genome-wide and customized SNP array data.
Application of unsupervised analysis for sample clustering and pattern identification.
Conducting simulation studies to evaluate LOH association test performance.

Main Results:

Identified common gene regions for LOH (e.g., ETV6, CDKN1B) and frequent LCSH regions (e.g., chromosome 16 centromeric gene desert).
Unsupervised analysis successfully separated cancer subtypes and ethnic subpopulations based on LOH/LCSH patterns.
Developed LOH association test demonstrates good power and type 1 error control.

Conclusions:

The developed computational methods effectively detect LOH and LCSH from SNP array data.
These methods are applicable to both cancer research and general population studies.
The LOHAS package in R provides a valuable tool for genetic and genomic analyses.