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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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Updated: May 25, 2026

Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients

Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients

Published on: June 16, 2017

Clonal diversity analysis using SNP microarray: a new prognostic tool for chronic lymphocytic leukemia.

Linsheng Zhang¹, Iya Znoyko, Luciano J Costa

¹Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, USA.

Cancer Genetics

|January 31, 2012

Summary

This summary is machine-generated.

Whole genome SNP microarrays reveal clonal diversity in chronic lymphocytic leukemia (CLL), offering a new prognostic tool. This method improves disease monitoring and predicts progression better than current techniques.

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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

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Published on: December 28, 2015

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Last Updated: May 25, 2026

Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients

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HPLC-based Assay to Monitor Extracellular Nucleotide/Nucleoside Metabolism in Human Chronic Lymphocytic Leukemia Cells

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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Published on: December 28, 2015

Area of Science:

Oncology
Genetics
Genomics

Background:

Chronic lymphocytic leukemia (CLL) is a heterogeneous disease with limited current monitoring methods for predicting progression and treatment response.
Existing cytogenetic and FISH studies have limitations in detecting genomic abnormalities and clonal evolution, hindering prognostic accuracy.

Purpose of the Study:

To investigate the prognostic value of assessing clonal diversity in CLL patients using whole genome analysis.
To explore the utility of high-resolution single nucleotide polymorphism (SNP) microarrays for detecting genetic variation and inferring clonal evolution.

Main Methods:

Analysis of genetic variation and percent mosaicism in 25 CLL patients using the Infinium Omni1 BeadChip SNP microarray.
Calculation of mosaicism percentages using a mathematical algorithm and the Simulated DNA Copy Number (SiDCoN) tool.
Comparison of SNP array data with fluorescence in situ hybridization (FISH) results for concordance.

Main Results:

SNP microarray data showed 98% concordance with FISH results.
Clonal diversity, defined by multiple genetic abnormalities with varying mosaicism, was identified in 48% of patients.
Clonal diversity correlated with advanced disease stages (Rai III-IV) and prior treatment, while its absence was linked to asymptomatic or stable disease.

Conclusions:

SNP microarray analysis enables comprehensive assessment of genomic alterations and clonal diversity, serving as a reliable indicator of clonal evolution in CLL.
Whole genome SNP microarray analysis offers a novel and robust prognostic tool for CLL patients by evaluating clonal diversity and evolution.
This approach enhances the ability to predict disease progression and guide treatment decisions in chronic lymphocytic leukemia.