Name: genome variation in cnvs and snps
Uploaded: 2021-04-07T12:11:59.000Z
Duration: 2 min 26 s
Channel: JoVE

K12 Standards

Louisiana Student Standards for Science

High School

Life Sciences

Biological Evolution: Unity And Diversity

HS-LS4-1

comparing-copy-number-variations-and-snps

Comparing Copy Number Variations and SNPs

Геномные вариации, такие как добавление или делеция сегментов ДНК, обычно наблюдаются в популяции. Геномные вариации в популяции могут возникать из-за однонуклеотидных изменений в ДНК или структурных изменений хромосом.
Вариация числа копий или CNV — это общий термин, определяющий структурные вариации, включающие сегменты ДНК длиной более 1 кг пары оснований.
Если вовлеченный хромосомный сегмент содержит ген, CNV могут увеличивать число копий этого гена путем дупликации и вставки или уменьшать его путем делеции, что приводит к нулевому генотипу.
Поэтому у некоторых особей может быть две или даже более копий гена, или вообще не быть копий. Например, некоторые люди европейского генетического происхождения могут нести две копии гена группы крови резуса, RHD, в то время как некоторые могут иметь только одну, а другие вообще не иметь ни одной.  
ХНВ может влиять на фенотипы, которые зависят от количества функциональных копий генов. В европейско-американских и азиатских регионах, где распространены диеты на основе крахмала, популяция демонстрирует более высокое число копий гена AMY1, гена, который участвует в метаболизме крахмала.
ХНВ также связаны с несколькими заболеваниями, такими как псориаз, болезнь Паркинсона, и поведенческими расстройствами, такими как аутизм и шизофрения.
В то время как CNV обычно охватывают большие вариации последовательностей ДНК, однонуклеотидные полиморфизмы или SNP представляют собой случайные замены одного основания, обнаруженные по всему геному.
Такие замены оснований происходят один раз на 1000 нуклеотидов, однако не все из них квалифицируются как SNP. Как правило, только нуклеотидная вариация, которая встречается более чем у 1% населения, называется SNP.
SNP могут вызывать различные заболевания, такие как диабет или рак. Например, у пациентов с серповидноклеточной анемией замена одного основания с аденина на тимин в определенном локусе гена бета-глобина вызывает образование серповидных эритроцитов.

<ol>
	<li>Ли, Чарльз и Стивен В. Шерер. "Клинический контекст вариации числа копий в геноме человека." Экспертные обзоры в молекулярной медицине 12 (2010).</li>
	<li>Будоул, Брюс и Анжела Ван Даал. "Криминалистически значимые классы SNP." Биотехники 44, No5 (2008): 603-610.</li>
</ol>

Сравнение вариантов количества копий и snp

Секвенирование человеческого генома открыло несколько сокровенных тайн генома. Ученые выявили тысячи вариаций генома, существующих в популяции. Эти вариации могут представлять собой один нуклеотид или более крупную хромосомную вариацию. Вариации числа копий или CNV — это структурные вариации, которые охватывают более 1 КБ последовательности ДНК. С другой стороны, однонуклеотидный полиморфизм (SNP) представляет собой изменение одного нуклеотида или точечную мутацию, которая обнаруживается более чем у 1% населения. И CNV, и SNP чрезвычайно ценны в исследованиях генетического скрининга и анализе родства. <h4>Формы CNV. </h4> Существует пять форм CNV. Первый называется удалением. Потеря сегмента ДНК может уменьшить количество копий гена или группы генов. Второй вариант называется тандемным дублированием. Здесь копия хромосомного сегмента вставляется в соседний регион. Третий называется несмежным дублированием. Здесь хромосомный сегмент дублируется и вставляется в отдаленную хромосомную область или другую хромосому. Четвертая форма называется мультиаллельной CNV. Сегмент ДНК дублируется несколько раз, что приводит к образованию множества аллелей гена. Пятая форма называется сложной перегруппировкой. Здесь сегмент ДНК дублируется и инвертируется, прежде чем снова вставиться в ту же или другую хромосому. <h4>Однонуклеотидный полиморфизм</h4> Однонуклеотидный полиморфизм или SNP — это еще один тип геномной вариации, включающий изменения в одном нуклеотидном основании. Ученые идентифицировали тысячи SNP по всему геному человека, и они регулярно используются в качестве генетических маркеров для наследственных заболеваний и судебно-медицинской экспертизы. По способу применения SNP делятся на четыре типа. SNP для проверки личности используются для дифференциации людей и исключения людей из семейных связей. SNP, информативные о происхождении, представляют собой тесно связанные SNP, которые помогают идентифицировать пропавших без вести людей в семейном анализе. Информационные SNP о происхождении помогают установить происхождение человека и связать его с его фенотипическими характеристиками. Информационные SNP о фенотипе устанавливают вероятность наследования определенного фенотипа, например цвета кожи, цвета глаз и т. д.

Сравнение вариантов количества копий и SNP

Секвенирование генома человека открыло несколько наиболее тщательно охраняемых секретов генома. Ученые выявили тысячи вариаций генома, которые существуют...

Education

JoVE Core

Molecular Biology

Молекулярная биология

Unit 2

Раздел 2

Genomes and Evolution

Геномы и эволюция

KEY TERMS AND CONCEPTS

ОСНОВНЫЕ ТЕРМИНЫ И ПОНЯТИЯ

genome variation in cnvs and snps

Genome variation in CNVs and SNPs shows how DNA can differ across people in a population. These differences may involve a single nucleotide, which is one DNA base, or a larger chromosomal change. Scientists study them to understand inherited variation in the human genome.

Copy number variations, or CNVs, are structural changes that cover more than 1 kb of DNA sequence. A CNV can change the number of copies of a gene or a group of genes. The main forms are deletion, tandem duplication, noncontiguous duplication, multiallelic CNV, and complex rearrangement.

A deletion removes a DNA segment and can lower gene copy number. In tandem duplication, a copied chromosomal segment is inserted next to the original region. In noncontiguous duplication, the copied segment moves to a distant chromosomal region or even a different chromosome. Multiallelic CNV creates several copies and can produce multiple alleles of a gene. In complex rearrangement, a segment duplicates and inverts before it is inserted back into the same or a different chromosome.

Single nucleotide polymorphism, or SNP, is another genomic variation that changes one nucleotide base. A SNP is a point mutation found in more than 1% of the population. Scientists have identified thousands of SNPs across the human genome, and they are widely used as genetic markers in studies of inherited disease and forensic analysis.

SNPs are grouped by use into four types. Identity-testing SNPs help distinguish people and exclude familial connections. Lineage informative SNPs are tightly linked SNPs that help identify missing individuals in family analysis. Ancestry informative SNPs help connect a person's ancestry with related phenotypic traits. Phenotype informative SNPs help estimate the chance of traits such as skin color or eye color.

Genome Variation in CNVs and SNPs

evolutionary relationships through genome comparisons

evolutionary-relationships-through-genome-comparisons

Tracing Evolution with Genome Data

Genome data helps scientists trace how organisms are related over time. When two species share a common feature, it is often encoded by DNA sequences that have stayed conserved in both species. As genome sequencing improved in the late 20th century, researchers gained a better way to compare conserved domains across species and use that evidence to infer evolutionary relationships. Genome comparison can show evolutionary relationships at three levels. At the broadest level, it highlights...

genome copying errors

DNA Replication Error Checks

DNA replication includes built-in error checks that protect the genome during cell division. Even though this process copies millions of base pairs with high fidelity, a wrong base or a longer stretch of wrong bases can still be added to the daughter strands. If these mistakes are not corrected, cells may build up mutations that can threaten survival. One level of repair is proofreading. DNA polymerase enzymes, which build the new DNA strand, can make about 1 incorrect nucleotide per 100,000...

phylogenetic trees

Reading Evolution in Phylogenetic Trees

Phylogenetic trees show how organisms are related through evolution. They map branching patterns that trace common ancestry and help scientists compare species over time. A phylogenetic tree can be read like a family tree for life. Each branch point marks a split from a shared ancestor, and the pattern of branches shows how closely related different organisms are. These trees are used to organize biological information and to study evolutionary change. They can also help scientists understand...

synteny and evolution

Chromosome Rearrangements and Synteny

Chromosome rearrangements and synteny show how shared gene order can reveal evolutionary history. Synteny means genes are found on the same chromosome, even if they are not genetically linked. John H. Renwick coined the term in 1971. Species with common ancestry often keep conserved syntenic regions. Scientists use synteny to compare the evolutionary relationship between species. Human and mouse lineages split from a common ancestor about 80 million years ago. Since then, the ancestral...

multi-species conserved sequences

Conserved DNA Across Species

Conserved DNA across species shows how some genome regions stay nearly unchanged over time. Next-generation sequencing has built large genome databases for many animals and plants. Since the Human Genome Project, scientists have compared the genomes of primates, mammals, and other distant species. These large studies have helped reveal evolutionary relationships between organisms. Although species genomes differ greatly, a few DNA sequences are highly conserved. Conserved DNA sequences found...

gene duplication and divergence

How Duplicate Genes Shape Evolution

Gene duplication helps drive evolution by creating extra copies of DNA that can change over time. The seminal work of Ohno in 1970 helped popularize this idea. DNA sequence comparisons show that many genes in bacteria, archaebacteria, and eukaryotes came from duplication and later divergence, which makes this process important in evolution. The duplicated copies of a gene are called paralogs. When paralogs have similar sequences and functions, they form a gene family. Many gene families have...

exon recombination

How Exons Mix to Form New Genes

Exon recombination helps new genes form by mixing exons from the same gene or from different genes. This process is also called exon shuffling or domain shuffling. It has been seen in vertebrates, invertebrates, and some plants, including potatoes and sunflowers. During exon recombination, exons join in new exon-intron combinations. These new combinations may later become new genes. Exon shuffling follows splice frame rules, which means the exons must fit the reading frame correctly. Each...

comparing copy number variations and snps

Genome variation in CNVs and SNPs shows how DNA can differ across people in a population. These differences may involve a single nucleotide, which is one DNA base, or a larger chromosomal change. Scientists study them to understand inherited variation in the human genome. Copy number variations, or CNVs, are structural changes that cover more than 1 kb of DNA sequence. A CNV can change the number of copies of a gene or a group of genes. The main forms are deletion, tandem duplication,...

key terms and concepts

Explore how copy number variations and SNPs change the human genome, from deletions and duplications to ancestry, identity, and phenotype markers.

Genome Variation in CNVs and SNPs | JoVE K12

molecular biology

JoVE Core Molecular Biology showcases the molecular processes of the cell through clear and concise animated video lessons. Additionally, in scientist-in-action videos, these concepts' application is demonstrated through real experiments in modern laboratories.

ohios-learning-standards-and-model-curriculum

Ohio’s Learning Standards and Model Curriculum

9-12

Biology

Evolution

Speciation

Tennessee Academic Standards

Heredity

BIO1.LS3.2

Virginia  Standards of Learning

HIgh School

BIO.5

BIO.5.d

Minnesota Academic Standards in Science

Life Science

3.2.1 9L.3.2.1.3

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New Jersey Student Learning Standards for Science

Biological Evolution: Unity and Diversity

Arizona Science Standards

HS+B.L4

HS+B.L4U1.13

Next Generation Science Standards

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Heredity: Inheritance and Variation of Traits

HS-LS3-2

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New York State Science Learning Standards

Inheritance and Variation of Traits

HS-LS3-1.

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA ...

The Central Dogma

The central dogma explains the flow of genetic information from DNA nucleotides to the amino acid sequence of proteins.
RNA is the Missing Link Between ...

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations ...

genome-size-and-the-evolution-of-new-genes

Genome Size and the Evolution of New Genes

Gene Families

Gene Evolution - Fast or Slow?

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Types of Genetic Transfer Between Organisms

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 ...

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a ...

Phylogenetic Trees

Gene Duplication and Divergence

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 ...

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new ...

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist ...

Analyze and interpret scientific information that common ancestry and biological evolution are supported by multiple lines of empirical evidence. Emphasis is on a conceptual understanding of the role each line of evidence (e.g., similarities in DNA sequences, order of appearance of structure during embryological development, cladograms, homologous and vestigial structures, fossil records) demonstrates as related to common ancestry and biological evolution.

What is Natural Selection?

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Types of Selection

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Frequency-dependent Selection

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Limits to Natural Selection

Organisms that are well-adapted to their environment are more likely to survive and reproduce. However, natural selection does not lead to perfectly ...

Natural Selection

Fitness
Widespread variation of phenotypes in natural populations provides the raw material for evolution, which is the change in the inherited traits of ...

Simulating Natural Selection
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Simulating Natural Selection
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Artificial Selection

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Observing Artificial Selection in Plants
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Natural Selection and Adaptation

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...

Natural Selection and Mating Preferences

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Evolutionary ...

What is Population Genetics?

A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, ...

Genetic Drift

Natural selection&#x2014;probably the most well-known evolutionary mechanism&#x2014;increases the prevalence of traits that enhance survival and ...

Gene Flow

Gene flow is the transfer of genes among populations, resulting from either the dispersal of gametes or from the migration of individuals.

This ...

Construct an explanation based on evidence that biological diversity is influenced by (1) the potential for a species to increase in number, (2) the heritable genetic variation of individuals in a species due to mutation and sexual reproduction, (3) competition for limited resources, and (4) the proliferation of those organisms that are better able to survive and reproduce in the environment. Emphasis is on using evidence to explain the influence each of the four factors has on number of organisms, behaviors, morphology, or physiology in terms of ability to compete for limited resources and subsequent survival of individuals and adaptation of species. Examples of evidence could include mathematical models such as simple distribution graphs or proportional reasoning.

HS-LS4-2

Mutation, Gene Flow, and Genetic Drift

In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions ...

Hardy-Weinberg Principle

Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the ...

Apply concepts of statistics and probability to support explanations that populations of organisms adapt when an advantageous heritable trait increases in proportion to organisms lacking this trait. Emphasis is on analyzing shifts in numerical distribution of traits and using these shifts as evidence to support explanations for adaptations. Explanations could include basic statistical or graphical analysis.

HS-LS4-3

Understanding Species and Reproductive Barriers

A species is a group of organisms that interbreed and produce fertile offspring. Typically, individuals of the same species appear similar and share ...

Formation of Species

Speciation describes the formation of one or more new species from one or sometimes multiple original species. The resulting species are discrete from the ...

Speciation Rates

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Genetics of Speciation

Speciation is the evolutionary process resulting in the formation of new, distinct species&#x2014;groups of reproductively isolated populations.The ...

Hybrid Zones

Hybrid zones are narrow regions where two closely related species interact, mate, and produce hybrids. Relative to either parent species, hybrids may ...

Extinction

The History of Life on Earth
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Diversity and Extinction during the Paleogene Epoch
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Evaluate evidence supporting claims that changes in environmental conditions can affect the distribution of traits in a population causing: (1) increases in the number of individuals of some species, (2) the emergence of new species over time, and (3) the extinction of other species. Emphasis is on determining cause and effect relationships for how changes to the environment such as deforestation, overfishing, application of fertilizers, drought, flood, and the rate of change of the environment affect distribution or disappearance of traits in species.

HS-LS4-5

Genome Variation in CNVs and SNPs

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