Can Whole Genome Sequencing detect copy number variants?
Can Whole Genome Sequencing detect copy number variants?
Whole genome sequencing (WGS) has the potential to outperform clinical microarrays for the detection of structural variants (SV) including copy number variants (CNVs), but has been challenged by high false positive rates.
How are copy number variants detected?
CNV regions are detected by comparing the assembled contigs to the reference genome. In this methods short reads are not aligned to the reference genome first. Since in WES targeted regions are exonic regions, they are very short and discontinuous across the genome.
Can NGS detect copy number variation?
By providing a base-by-base view of the genome, NGS detects small or novel copy number variants that arrays often miss. NGS can also map the exact location of a CNV. The high resolution of sequencing complements the high throughput of arrays, enabling a comprehensive view of the genome.
What is copy number variation analysis?
Introduction. The copy number variation (CNV) pipeline uses either NGS or Affymetrix SNP 6.0 (SNP6) array data to identify genomic regions that are repeated and infer the copy number of these repeats. Three sets of pipelines have been used for CNV inferences.
How do you assess CNV?
CNV calls were assessed for array-based confirmation by comparing the median probe depth in the candidate region against a size-matched background on chromosome 1 and an empirical P value was calculated.
How is gene copy number determined?
To determine copy number, a relative quantitation analysis is performed between the unknown sample and a calibrator sample (one in which the copy number of the target gene is known). The sample is combined with both assays, master mix, and then run in quadruplicate in the real-time PCR instrument.
Why is copy number variation important?
Copy number variation provides the raw material for gene family expansion and diversification, which is an important evolutionary force. Moreover, copy number variants (CNVs) can influence gene transcriptional and translational levels and have been associated with complex disease susceptibility.
How do you measure CNV?
The CNV is simply given by the ratio of the estimated concentration of the target gene to the estimated concentration of the reference gene. Both of these concentrations are estimated by applying the Poisson law as explained in the item Poisson Law Computation.
Can NGS detect LOH?
Both LOH and copy number variation detected by NGS data correlated with microarray data, demonstrating the somatic LOH second hit can be detected directly from the NGS data.
What Causes copy number variation?
CNVs can result from structural variations within the genome including deletions, duplications, insertions or unbalanced translocations and inversions, which can lead to either a loss or gain of genomic segments.
What is a copy number in genetics?
(KAH-pee NUM-ber VAYR-ee-unt) Refers to the genetic trait involving the number of copies of a particular gene present in the genome of an individual. Genetic variants, including insertions, deletions, and duplications of segments of DNA, are also collectively referred to as copy number variants.