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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

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%...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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.
GWAS does not require the identification of the target gene involved in...
Single Nucleotide Polymorphisms-SNPs01:05

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,...

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Related Experiment Video

Updated: Jun 13, 2026

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
09:16

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

SNP-Based Chromosomal Microarray Analysis in the Era of Optical Genome Mapping: An Enriched Case-Series Evaluating

Alexander R Marr1, Patrick R Gonzales1, Shivani Golem1

  • 1Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA.

Cancers
|June 12, 2026
PubMed
Summary

Chromosomal microarray analysis (CMA) is crucial for detecting small copy-neutral loss of heterozygosity (CN-LOH) events, even those under 25 Mb. Optical genome mapping (OGM) is improving, but CMA remains essential for comprehensive cancer genomic assessment.

Keywords:
chromosomal microarraycopy-neutral loss of heterozygositycytogeneticsgenomicskaryotypeoptical genome mapping

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Area of Science:

  • Genomic Medicine
  • Cytogenetics
  • Cancer Genomics

Background:

  • Chromosomal microarray analysis (CMA) is a cornerstone in cytogenetics for identifying copy number alterations and copy-neutral loss of heterozygosity (CN-LOH).
  • Optical genome mapping (OGM) is emerging as a novel technology with the potential to supplant traditional cytogenetic methods.
  • The continued necessity of CMA in routine diagnostic workflows alongside OGM requires further investigation.

Purpose of the Study:

  • To evaluate the diagnostic utility of CMA in detecting CN-LOH events in hematologic malignancies.
  • To compare the detection capabilities of CMA with the current benchmarks of OGM for CN-LOH.
  • To assess the clinical relevance of CN-LOH events identified by CMA.

Main Methods:

  • Retrospective analysis of 53 primary neoplastic cases with CMA-detected CN-LOH events from a larger cohort of 327 hematologic malignancy specimens.
  • Assessment of CN-LOH event size, genomic content, and correlation with next-generation sequencing (NGS) findings.
  • Evaluation of CN-LOH frequency in a separate cohort of newly diagnosed B-cell acute lymphoblastic leukemia (B-ALL).

Main Results:

  • Nearly half of CMA-detected CN-LOH events were smaller than 25 Mb, falling below OGM's current detection threshold.
  • Clinically significant genes (e.g., FLT3, JAK2, TP53) were frequently located within these CN-LOH regions.
  • NGS identified pathogenic variants in two-thirds of CN-LOH regions, highlighting the clinical importance of detecting these events.
  • In B-ALL, CN-LOH was infrequent, and OGM could detect most CMA-identified alterations; however, OGM also resolved complex rearrangements in a single assay.

Conclusions:

  • CMA remains indispensable for detecting CN-LOH events, particularly those smaller than 25 Mb, which are currently below OGM's sensitivity.
  • OGM demonstrates superior capability in resolving complex structural variants.
  • An integrated diagnostic approach combining conventional cytogenetics, CMA, NGS, and OGM offers the most comprehensive genomic assessment for cancer patients until OGM sensitivity for CN-LOH improves.