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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%...

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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,...

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer

Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer

Published on: November 2, 2013

Replication linkage study for prostate cancer susceptibility genes.

B K Suarez¹, J Lin, J S Witte

¹Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA.

|October 12, 2000

Summary

This study found no evidence for prostate cancer (CaP) susceptibility loci HPC1 or PCaP on chromosome 1. However, strong evidence for a CaP locus on chromosome 16p was observed, while evidence for 16q was weakened.

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Area of Science:

Genetics
Oncology
Human Genetics

Background:

Over a dozen linkage studies for prostate cancer (CaP) susceptibility loci have been published.
Previous research identified potential loci HPC1 (1q24-25) and PCaP (1q42.2-43) on chromosome 1, and loci on chromosome 16.

Purpose of the Study:

To perform a replication linkage study for prostate cancer susceptibility loci on chromosomes 1 and 16.
To validate findings from previous genome screens in new and expanded multiplex CaP families.

Main Methods:

Utilized linkage analysis in 45 new and 4 expanded multiplex prostate cancer families.
Analyzed 30 short-sequence tandem repeat markers on chromosome 1 and 22 markers on chromosome 16.
Calculated multipoint Z-scores to assess linkage evidence.

Main Results:

No evidence for a prostate cancer susceptibility locus was found in the 1q24-25 region (HPC1).
Equivocal evidence for a locus at 1q42.2-43 (PCaP) was observed.
Strong evidence for a susceptibility locus on chromosome 16p was detected, with weakened evidence for 16q.

Conclusions:

The replication study does not support the existence of the HPC1 locus.
Evidence for the PCaP locus on chromosome 1 remains equivocal.
A prostate cancer susceptibility locus on 16p is strongly supported, but evidence for 16q is diminished.