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Related Concept Videos

Genomics02:02

Genomics

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...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
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Transcriptome and genome sequencing uncovers functional variation in humans.

Tuuli Lappalainen1, Michael Sammeth, Marc R Friedländer

  • 1Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland. tuuli.e.lappalainen@gmail.com

Nature
|September 17, 2013
PubMed
Summary

Genetic variants widely impact gene regulation and expression, revealing mechanisms behind human traits and diseases. This study analyzes RNA sequencing data to map functional genetic variations across human populations.

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Area of Science:

  • Genomics
  • Transcriptomics
  • Human Genetics

Background:

  • Millions of genetic variants are discovered through genome sequencing.
  • Interpreting functional effects of these variants is crucial for understanding human trait variation.
  • High-throughput RNA sequencing provides insights into gene expression and regulation.

Purpose of the Study:

  • To analyze messenger RNA (mRNA) and microRNA (miRNA) from lymphoblastoid cell lines of 462 individuals.
  • To characterize widespread genetic variation affecting gene regulation and expression.
  • To infer causal variants for disease-associated loci.

Main Methods:

  • Sequencing and deep analysis of mRNA and miRNA.
  • Utilizing uniformly processed, high-throughput RNA-sequencing data from the 1000 Genomes Project.
  • Integrating RNA-sequencing data with high-quality human genome sequences.

Main Results:

  • Discovery of extremely widespread genetic variation impacting the regulation of most genes.
  • Identification of common yet genetically independent variation in transcript structure and expression levels.
  • Characterization of causal regulatory variation, illuminating cellular mechanisms.
  • Inference of putative causal variants for numerous disease-associated loci.

Conclusions:

  • Genetic variation significantly affects transcriptome regulation and expression across human populations.
  • The study enhances understanding of cellular mechanisms underlying regulatory and loss-of-function variations.
  • Provides a comprehensive landscape of functional variants in the human genome.