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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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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%...
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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Next-generation Sequencing03:00

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Genomics02:02

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genetic Variation01:25

Genetic Variation

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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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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Related Experiment Video

Updated: Dec 23, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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dv-trio: a family-based variant calling pipeline using DeepVariant.

Eddie K K Ip1,2, Clinton Hadinata1, Joshua W K Ho1,2,3

  • 1Victor Chang Cardiac Research Institute, Sydney, Australia.

Bioinformatics (Oxford, England)
|April 22, 2020
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Summary

We developed dv-trio, a family-based variant calling pipeline that enhances DeepVariant accuracy for disease mutation discovery in trios. This method leverages Mendelian genetics for improved next-generation sequencing analysis.

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Last Updated: Dec 23, 2025

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • DeepVariant, a deep neural network-based variant caller, excels at identifying single-nucleotide variants and small insertions/deletions from next-generation sequencing data.
  • While effective for single samples, DeepVariant's utility is limited in family-based sequencing studies where analyzing trios (parent-offspring) enhances mutation discovery power.

Purpose of the Study:

  • To improve variant calling accuracy in family-based sequencing studies.
  • To develop a novel pipeline that integrates trio information with DeepVariant for enhanced disease mutation discovery.

Main Methods:

  • Developed dv-trio, a family-based variant calling pipeline.
  • Incorporated Mendelian genetic models into DeepVariant's variant calling process.
  • Utilized trio data (father, mother, affected child) for analysis.

Main Results:

  • The dv-trio pipeline enhances DeepVariant's accuracy for variant calling in family trios.
  • This approach improves the power for discovering disease-causing mutations.

Conclusions:

  • dv-trio offers a significant advancement for variant calling in family-based genomic studies.
  • The pipeline provides a powerful tool for disease mutation discovery by leveraging trio data and Mendelian genetics.