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Clinical application of CNV-seq for diagnosing abnormal brain development in children

Shaohua Zhu1,2, Shibing Cheng2, Chunyang Jia1

  • 1Medical Genetic Centre, Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China.

Scientific Reports
|September 29, 2025
PubMed

Insights

Copy number variation sequencing (CNV-Seq) effectively diagnoses genetic causes of abnormal brain development (ABD) in children. The study found a higher detection rate of pathogenic copy number variations in syndromic cases, highlighting the need for increased attention to non-syndromic cases.

Area of Science:

  • Medical Genetics
  • Pediatric Neurology
  • Genomic Medicine

Background:

  • Abnormal brain development (ABD) presents a significant diagnostic challenge in pediatric patients.
  • Identifying the genetic etiology is crucial for accurate diagnosis, prognosis, and management.
  • Copy number variation sequencing (CNV-Seq) is an emerging tool for detecting genetic abnormalities.

Purpose of the Study:

  • To evaluate the diagnostic utility of CNV-Seq in pediatric patients with ABD.
  • To compare the detection rates of genetic abnormalities between syndromic (S-ABD) and non-syndromic (NS-ABD) groups.
  • To assess the clinical implications of CNV-Seq findings for patient management.

Main Methods:

  • Retrospective analysis of 130 pediatric patients diagnosed with ABD.
  • Categorization into syndromic (S-ABD) and non-syndromic (NS-ABD) groups.
  • Application of CNV-Seq to identify chromosomal aneuploidies and copy number variations (CNVs).

Main Results:

  • Overall, 32.3% of patients had detectable genetic abnormalities, including aneuploidies and CNVs.
  • Pathogenic CNV (pCNV) detection was significantly higher in the S-ABD group (70.4%) compared to the NS-ABD group (26.7%).
  • Non-syndromic ABD cases showed a higher proportion of variants of uncertain significance (VUS) and a lower positive detection rate, posing a risk of underdiagnosis.

Conclusions:

  • CNV-Seq is a valuable diagnostic tool for pediatric ABD, with a high yield in syndromic cases.
  • The lower detection rate in NS-ABD patients underscores the need for careful clinical evaluation and potentially advanced genetic testing.
  • Improved genetic counseling and timely prenatal diagnosis are essential for better clinical outcomes in ABD patients.

Keywords:
Abnormal brain development (ABD)AneuploidyCNV-seqCopy number variation (CNV)

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Comparing Copy Number Variations and SNPs02:26

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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%...