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Related Concept Videos

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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Genome-wide Association Studies-GWAS01:11

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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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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
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Natural selection—probably the most well-known evolutionary mechanism—increases the prevalence of traits that enhance survival and reproduction. However, evolution does not merely propagate favorable traits, nor does it always benefit populations.
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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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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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BAMboozle removes genetic variation from human sequence data for open data sharing.

Christoph Ziegenhain1, Rickard Sandberg2

  • 1Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden.

Nature Communications
|October 29, 2021
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Summary
This summary is machine-generated.

BAMboozle is a new tool that removes sensitive genetic variants from human sequence data, enabling broader data sharing. This method protects privacy without compromising crucial biological information in genomics research.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Data Privacy

Background:

  • Re-identification risks in human genetic data hinder open data sharing in life sciences.
  • Sensitive genetic variant information can limit data accessibility even when not the primary research focus.

Purpose of the Study:

  • To develop a versatile tool, BAMboozle, for eliminating sensitive genetic information from human sequence data.
  • To facilitate open data sharing in genomics by mitigating re-identification risks.

Main Methods:

  • BAMboozle reverts aligned sequencing reads to the human genome reference sequence.
  • The tool was applied to functional genomics datasets, including single-cell RNA sequencing (scRNA-seq) and scATAC-seq.

Main Results:

  • BAMboozle successfully removed donor-related single nucleotide polymorphisms (SNPs) and indels without revealing altered positions.
  • Functional genomics data processed with BAMboozle retained essential biological information, such as gene expression signatures and splice kinetics.
  • BAMboozled data remains suitable for methods benchmarking.

Conclusions:

  • BAMboozle effectively removes genetic variation from aligned sequence data, enhancing privacy.
  • This advancement supports increased open data sharing in genomics research where genetic variants are not the primary interest.