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Mutations01:39

Mutations

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Mutations01:35

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Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
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Lesson: Translation
Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes the final step in the expression of genes. This process is carried out by ribosomes, complexes of protein and specialized RNA molecules. Ribosomes, transfer RNA (tRNA), and other proteins produce a chain of amino acids—the polypeptide—as the end product of translation.
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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.
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Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
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SeekPCMdb: knowledge on disease-associated protein-coding mutations.

Peng Yang1,2,3, Ziyang Wang1,2,4, Tuo Xiong1,2,4

  • 1China National Center for Bioinformation, Beijing100101, China.

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|November 22, 2025
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Summary
This summary is machine-generated.

SeekPCMdb is a new database cataloging human disease-related protein-coding mutations (PCMs) from scientific literature. It offers a unique, accessible resource for studying genotype-phenotype correlations and mutation impacts.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Medical Genetics

Background:

  • Protein-coding mutations (PCMs) are vital in human disease development and progression.
  • Next-generation sequencing has increased reported disease-associated PCMs, but they are fragmented in literature.
  • Systematic investigation of these mutations is hindered by their scattered accessibility.

Purpose of the Study:

  • To introduce SeekPCMdb, a literature-derived knowledge base for systematically cataloging human disease-related PCMs.
  • To provide a centralized and accessible resource for researchers studying genotype-phenotype correlations.
  • To facilitate the assessment of mutation pathogenicity and the identification of cross-disease mutational patterns.

Main Methods:

  • A semi-automated workflow combining manual curation and large language model (LLM)-assisted information extraction.
  • Extraction of gene-mutation-disease relationships from over 12,000 PubMed abstracts.
  • Development of a user-friendly web interface with interactive searching, visualization, and multi-dimensional filtering.

Main Results:

  • SeekPCMdb currently contains 11,395 curated entries, encompassing 3,516 genes, 4,505 diseases, and 23 mutation types.
  • 63.7% of PCMs in SeekPCMdb are not found in ClinVar, highlighting its novel contribution.
  • Entries are richly annotated, supporting detailed biological interpretation.

Conclusions:

  • SeekPCMdb bridges unstructured literature and structured mutation knowledge, offering a valuable resource.
  • The database enhances the systematic investigation of disease-associated PCMs.
  • It supports research into genotype-phenotype correlations, mutation pathogenicity, and mutational patterns across diseases.