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Related Concept Videos

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
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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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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Genetic Screens02:46

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
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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.
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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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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
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pandasGWAS: a Python package for easy retrieval of GWAS catalog data.

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  • 1School of Mathematics, Hangzhou Normal University, Hangzhou, 311121, China.

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|May 4, 2023
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Summary

pandasGWAS offers a new Python package for accessing the NHGRI-EBI Catalog of human genome-wide association studies (GWAS). It provides programmatic access, simplifying data integration into Python analysis pipelines.

Keywords:
DatabaseGWASPandasPythonRESTfulRepository

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Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization
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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • The National Human Genome Research Institute (NHGRI)-European Bioinformatics Institute (EBI) Catalog of human genome-wide association studies (GWAS) has seen rapidly growing data and researcher interest since its 2008 establishment.
  • There is a high demand for accessible, open-source Python programs for analyzing GWAS data within current data analysis pipelines.

Purpose of the Study:

  • To introduce pandasGWAS, a novel Python package enabling programmatic access to the NHGRI-EBI GWAS Catalog.
  • To facilitate seamless integration of GWAS data into existing Python-based data analysis workflows.

Main Methods:

  • Developed pandasGWAS as an open-source Python package.
  • Implemented direct querying of the GWAS Catalog REST API, avoiding large local data downloads.
  • Designed the package to handle paginated data and transform it into pandas.DataFrame objects, preserving hierarchical data structures.

Main Results:

  • pandasGWAS provides the first Python client interface for the GWAS Catalog REST API.
  • The package efficiently queries and retrieves GWAS data based on user-defined criteria.
  • Transformed data is organized into pandas.DataFrame objects, simplifying downstream analysis.

Conclusions:

  • pandasGWAS offers a user-friendly, open-source Python solution for accessing the NHGRI-EBI GWAS Catalog.
  • Its data structure aligns closely with the GWAS Catalog REST API specifications.
  • The package enhances usability with intuitive mathematical symbol operations for data manipulation.