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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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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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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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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.
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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
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Federated learning and Indigenous genomic data sovereignty.

Nima Boscarino1, Reed A Cartwright2,3, Keolu Fox4

  • 1Hugging Face, Brooklyn, New York, NY, USA.

Nature Machine Intelligence
|December 12, 2022
PubMed
Summary
This summary is machine-generated.

Indigenous peoples need better representation in genomic data for accurate precision health. Federated learning offers a secure way to share data with community consent, respecting Indigenous data sovereignty.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Health Equity

Background:

  • Indigenous peoples are significantly under-represented in current genomic datasets.
  • This under-representation limits the accuracy and applicability of precision health initiatives for these communities.
  • Existing data sharing models can conflict with Indigenous rights to data governance.

Purpose of the Study:

  • To highlight the challenges posed by under-representation of Indigenous peoples in genomic data.
  • To explore federated learning as a potential solution for secure and consented data sharing.
  • To promote equitable advancements in precision health for Indigenous populations.

Main Methods:

  • Review of current genomic data sharing practices and their impact on Indigenous communities.
  • Analysis of federated learning principles and their applicability to genomic data.
  • Examination of ethical considerations for community-consented data use.

Main Results:

  • Under-representation in genomic datasets leads to biased machine learning models in precision health.
  • Federated learning enables model training on decentralized data without direct data sharing.
  • This approach can uphold Indigenous data sovereignty and facilitate collaborative research.

Conclusions:

  • Addressing the under-representation of Indigenous peoples in genomic data is crucial for equitable precision health.
  • Federated learning presents a promising, privacy-preserving method for Indigenous genomic data sharing.
  • Implementing federated learning requires strong community engagement and adherence to Indigenous data governance principles.