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Related Concept Videos

Genomics02:02

Genomics

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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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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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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Genomic DNA in Prokaryotes00:46

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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Genomic DNA in Eukaryotes00:58

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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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Exploring X Chromosomal Aberrations in Ovarian Cells by Using Fluorescence In Situ Hybridization
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Consistent testing for recurrent genomic aberrations.

V Walter1, F A Wright2, A B Nobel3

  • 1Department of Biochemistry and Molecular Biology, Pennyslvania State University College of Medicine, Milton S. Hershey Medical Center, 500 University Drive, P.O. Box 850, Hershey, Pennsylvania 17033 U.S.A.

Biometrika
|February 26, 2019
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Summary
This summary is machine-generated.

This study introduces a cyclic shift method to detect recurrent deviations in genomic data, improving the identification of aberrant markers across multiple samples and variables.

Keywords:
ConsistencyDNA copy numberDNA methylationGenome-wide association studyHypothesis testing

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Area of Science:

  • Genomics
  • Statistical Genetics
  • Bioinformatics

Background:

  • Genomic data analysis often involves identifying deviations from normal patterns.
  • Detecting recurrent, localized departures across multiple samples is crucial for marker identification.

Purpose of the Study:

  • To develop a statistical method for detecting recurrent departures from stationarity in ordered genomic data.
  • To identify aberrant markers in DNA copy number, DNA methylation, and meta-analyses of GWAS.

Main Methods:

  • A cyclic shift-based procedure is proposed for testing recurrent departures from stationarity.
  • The method analyzes data with measurements at an ordered set of variables, focusing on single-variable or small-window departures across multiple samples.
  • Theoretical analysis establishes the consistency of the cyclic shift p-values under specific assumptions.

Main Results:

  • The proposed cyclic shift procedure is shown to be consistent for detecting recurrent departures.
  • The method is applicable to various genomic datasets, including DNA copy number, methylation, and GWAS meta-analyses.
  • Results hold for any test statistic meeting a simple invariance condition.

Conclusions:

  • The cyclic shift method provides a robust approach for identifying recurrent aberrant markers in genomic studies.
  • This statistical framework enhances the analysis of complex genomic datasets, aiding in the discovery of significant biological patterns.