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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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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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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%...
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Sanger Sequencing01:57

Sanger Sequencing

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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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Single Nucleotide Polymorphisms-SNPs01:05

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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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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.
Genes exist in different versions called alleles,...
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Cancers Originate from Somatic Mutations in a Single Cell02:21

Cancers Originate from Somatic Mutations in a Single Cell

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Cancer arises from mutations in the critical genes that allow healthy cells to escape cell cycle regulation and acquire the ability to proliferate indefinitely. Though originating from a single mutation event in one of the originator cells, cancer progresses when the mutant cell lines continue to gain more and more mutations, and finally, become malignant. For example, chronic myelogenous leukemia (CML) develops initially as a non-lethal increase in white blood cells, which progressively...
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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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Somatic and Germline Variant Calling from Next-Generation Sequencing Data.

Ti-Cheng Chang1, Ke Xu2, Zhongshan Cheng2

  • 1Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA. ti-cheng.chang@stjude.org.

Advances in Experimental Medicine and Biology
|March 1, 2022
PubMed
Summary
This summary is machine-generated.

Next-generation sequencing (NGS) enables human genome re-sequencing for disease gene discovery. Accurate variant calling, despite challenges like artifacts and heterogeneity, is crucial for precision medicine applications.

Keywords:
ContaminationEnsemble variant callingGermline variantLow-frequency variantsMachine learningNext-generation sequencingSingle-cell sequencingSomatic variantThird-generation sequencingTumor-only variant callingVariant annotationVariant callingVariant prioritization

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Area of Science:

  • Genomics
  • Bioinformatics
  • Medical Genetics

Background:

  • Next-generation sequencing (NGS) is a powerful tool for human genome re-sequencing.
  • It facilitates the discovery of pathogenic genetic variants and disease-causing genes, particularly in cancers.
  • Advances in NGS have made whole-genome sequencing cost-effective and timely for patient studies.

Purpose of the Study:

  • To provide a comprehensive overview of variant calling algorithms and their associated challenges.
  • To review existing workflows for variant calling and annotation.
  • To explore strategies, strengths, and limitations of different variant callers.

Main Methods:

  • Introduction to the general scheme of variant calling algorithms.
  • Review of existing variant calling and annotation workflows.
  • Exploration of strategies, strengths, and caveats of various variant callers.

Main Results:

  • Variant calling accuracy is challenged by sequencing artifacts, read misalignments, and biological complexities (e.g., tumor heterogeneity).
  • Somatic variant detection faces additional complexities from chromosomal abnormalities, contamination, and low-frequency variants.
  • Ensemble approaches, harmonizing multiple algorithms, show promise for improving variant calling performance.

Conclusions:

  • Accurate variant calling and annotation are fundamental for identifying disease-associated variants using NGS.
  • Careful consideration of challenges and algorithm selection is essential for reliable variant detection.
  • NGS-based variant identification supports the selection of candidate variants for precision medicine.