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Related Concept Videos

Sanger Sequencing01:57

Sanger Sequencing

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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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.
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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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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RNA-seq03:21

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Evolutionary Relationships through Genome Comparisons02:54

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Rare variant detection using family-based sequencing analysis.

Gang Peng1, Yu Fan, Timothy B Palculict

  • 1Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

Proceedings of the National Academy of Sciences of the United States of America
|February 22, 2013
PubMed
Summary
This summary is machine-generated.

Family-Based Sequencing Program (FamSeq) improves genomic analysis by integrating Mendelian transmission and raw sequencing data. This method significantly reduces false negative variants, enhancing the identification of disease-associated genes in family studies.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Statistical Genetics

Background:

  • Next-generation sequencing (NGS) is crucial for genomic analysis but suffers from high rates of missing true variants.
  • Accurate variant detection is essential for identifying genetic causes of diseases.

Purpose of the Study:

  • To develop a robust statistical method for identifying variants missed by standard analysis.
  • To enhance variant detection in family-based sequencing studies.

Main Methods:

  • Developed the Family-Based Sequencing Program (FamSeq), integrating Mendelian transmission information with raw sequencing reads.
  • Conducted sequence data simulations and analyzed whole-genome and targeted sequencing data from 28 families.
  • Evaluated FamSeq performance using HapMap samples, Sanger sequencing confirmation, and analysis of families with Wilms tumor and neurodevelopmental disorders.

Main Results:

  • FamSeq reduced false negative variants by 14-33% compared to standard methods.
  • 84% of variants uniquely identified by FamSeq in a Wilms tumor family were Sanger-confirmed.
  • FamSeq corrected de novo variant calls in disease candidate genes and increased variant detection with more family members.

Conclusions:

  • FamSeq is a robust method for improving variant detection in family-based sequencing.
  • The study provides insights into factors influencing family-based variant calling, guiding future study design and analysis.
  • FamSeq enhances the ability to identify novel disease-associated genes through more accurate genomic analysis.