Добавил:
Sekretar
kiopkiopkiop18@yandex.ru
t.me/Prokururor I Вовсе не секретарь, но почту проверяю
Опубликованный материал нарушает ваши авторские права? Сообщите нам.
Вуз:
Предмет:
Файл:Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_53_библиотеки_им_акад_М_И_Перельмана
.pdf
for more than 90% of all the human genetic variations and thus constitute an
important aspect of genetic variation exhibited by the human genome.
Keywords
Polymorphism · Mutations · Genome wide association studies · Single
nucleotide polymorphism · Genetic variations
Abbreviations
ACE Angiotensin-converting enzyme
CNPs Copy number polymorphisms
CNVs Copy number variants
DNA Deoxyribo nucleic acid
GP Genetic polymorphisms
GPC Genome project consortium
GVs Genetic variations
GWAS Genome wide association studies
HGP Human genome project
Indels Insertions or deletions
ISVs Intermediate-sized variants
lncRNAs Long noncoding RNAs
LCVs Large-scale copy number variants
mCNVs Multi-allelic copy number variants
MEIs Mobile element insertions
miRNA MicroRNA
NUMTs Nuclear mitochondrial sequences
SNP Single nucleotide polymorphism
UTR Untranslated regions
1.1 Introduction
Deoxyribonucleic acid (DNA) along with carbohydrates, lipids, and proteins consti-
tute four main classes of macromolecules, which are prerequisite for any form in
which life exists. DNA is the fundamental determinant of all cellular processes or
responses whether those associated with normal cellular physiology or those
associated with diverse pathophysiological conditions. DNA is fundamentally
responsible for all the known and expressed phenotype including the color of hair,
skin, and eyes, vulnerability to various diseases, response to various drugs, and
immune response to various pathogens and vaccines. DNA acts as the main control
center for determining how, when, what to do, or what will happen (Sukhumsirichart
2018).
2 A. S. Sameer et al.
https://t.me/medicina_free
The Human Genome Project (HGP), a global research project, was undertaken
from 1990 to 2003, with the primary aim to determine the sequence of nucleotides,
which constitute the human DNA, and to physically identify and map all the
estimated 100,000 genes, which make up the human genome and to decipher their
function (Salzberg 2018; Lander et al. 2001). The Human Genome Project (HGP)
has enabled us to have a peek into the intricacies of DNA and established that human
DNA contains about 3 billion base pairs, which are present in every human cell with
a nucleus (Ve nter et al. 2001; Lander et al. 2001). HGP established two important
facts: One, that the human genome has remained well conserved throughout the
period of human evolution with DNA of two individuals differing only by around
0.5%, which means that DNA of two individuals is almost 99.5% identical. Second,
that against an initially estimated number of 100,000, DNA actually contains much
less number of genes, approximately ~24,000 (International Human Genome
Sequencing Consortium I 2004; Salzberg 2018). However, since 2004 numerous
scientific teams have unearthed that human genome is more complex, dynamic, and
diverse in its structure (Karki et al. 2015). The total number of genes in human
genome database (HGDB) is around 43,162. Of these, 21,306 genes code for
proteins (coding genes), whereas 21,856 genes do not code for prote ins (noncoding
genes). The total number of transcripts is 323,824 and when compared with total
number of genes, the number of transcripts per gene comes out to be 7.5. However,
recently it has been proposed that the human genome database should be updated
and diversifie d to include almost 5000 new coding and noncoding genes in it. The
proposed list of new genes includes 4997 genes in total, of which 1178 are coding
genes and 3819 are noncoding genes. The proposed list also includes 97,511 new
transcripts or splice variants of coding genes (Pertea et al. 2018; Willyard 2018).
Box 1.1 Introduction to Human DNA
Human beings are diploid organisms, which mean humans have two sets of
chromosomes, each inherited from one of the parents. The nucleus of human
somatic cells contains 46 chromosomes organized into 23 chromosome pairs.
Out of these, 22 pairs are autosomes or non-sex chromosomes with each pair
containing two identical copies of a specific chromosome. The remaining pair
consists of two identical or non-identical allosomes or sex chromosomes. In
females, the allosome pair consists of two identical copies of X-chromosome,
whereas in males, the allosome pair consists of one copy each of
X-chromosome and Y-chromosome. In addition, mitochondria, an important
cellular organelle also contains its own DNA, present as 16-kilobase pair
(16 kb) mitochondrial genome.
In humans, a copy of genome, organized into 23 pairs of chromosomes, has
an estimated length of about 3.2 gigabase pairs and contains around 43,162
genes. Of these, 21,306 genes code for proteins (coding genes), whereas
21,856 genes do not code for proteins (noncoding genes). Protein coding
(continued)
1 Mutations and Polymorphisms: What Is The Difference? 3
https://t.me/medicina_free
Box 1.1 (continued)
genes comprise only about 1.0–1.5% of the total human DNA. The major
portion (98.5–99%) of the total human DNA is noncoding and does not code
for proteins. The non-coding DNA consists of telomeres, introns, and various
gene regulatory sequences including promoters, enhancers, silencers, and
insulators. It also contains sequences, which provide instructions for the
production of various types of noncoding ribonucleic acid (RNA) molecules
including transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), long noncoding
RNAs (lncRNA s), microRNAs (miRNA), small nuclear RNAs (snRNAs),
small nucleolar RNAs (snoRNAs), small interfering RNAs (siRNAs), small
temporal RNAs (stRNAs), and heterogeneous nuclear RNAs (hnRNAs).
The human genome exhibits a dynamic variation between different individuals
and across different geographical and/or racial/ethnical populations. However, this
genetic variation accounts for only 0.1–0.4% of the total genomic DNA or genome
(Jorde and Wooding 2004; Karki et al. 2015). 1000 Genomes Project Consortium
(1KGPC/1000GPC) identified more than 88 million genetic variations based on the
study of high-quality individual haplotypes from 26 different populations across
different regions of the world including Europe (EUR), Africa (AFR), Americas
(AMR), East Asia (EAS), and South Asia (SAS). These genetic variations include
84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/
deletions (indels), and 60,000 structural variations (SVs) (Auton et al. 2015).
An integrated map of six types of structural variations, linking population genet-
ics with the functional impact of SVs, has been constructe d through the analysis of
2504 genomes from 26 different populations. The analysis identified 2929 multi-
allelic copy number variants (mCNVs), 6025 biallelic duplications, 42,279 biallelic
deletions, 16,631 mobile element insertions (MEIs), 786 inversions, and
168 insertions in nuclear mitochondrial sequences (NUMTs) (Fig. 1.1) (Sudmant
et al. 2015). The 1000 Genomes Project, an international research project, which was
completed in 7 years (2008–2015), concluded that human genome has an abundance
of structural variations and a single diploid genome contains a median of 18.4 Mbp
of structural variations (>50 kb). These structural variations aris e due to a series of
complex evolutionary processes (Birney and Soranzo 2015).
Of all the known genetic variations present in the human genome, polymorphism
especially the single nucleotide polymorphism (SNP) represents the most common
type of sequence variation and accounts for more than 90% of all the human genetic
variations (Ding 2007; Orr and Chanock 2008; Risch 2000).
4 A. S. Sameer et al.
https://t.me/medicina_free
Box 1.2 Definitions of Common Terms Used in Genetics
Genome: The sum of all the DNA or complete set of chromosomes present in a
viable cell (of an individual).
Genetic variation: The variation of the sequence or structure in the gene
and alleles thereof. It is because of them that an individual acquires uniqueness
from the others within the population. The term variant defines a specific
region of the human genome, which differs between two genome samples.
Genetic marker: A specific region of DNA or a DNA sequence with a
known chromosomal location, which shows variation or is polymorphic in
nature and can be used in identification of different individuals or species or
mapping of genes involved in specific diseases.
Locus: The location of a DNA marker or a specific gene within a specific
chromosome.
Allele: Different version of the same gene or gene variant.
Genotype: The genetic constitution (whole DNA) of the living organism
(Cell).
Phenotype: External visible characters of the living organism. It is
governed by the genotype and the environment in which organism lives.
Homozygous: An individual, which possess identical alleles for a particular
trait.
Heterozygous: An individual, which contains both dominant and recessive
alleles of the particular trait.
Penetrance: Ability of a gene (or genes) to be expressed phenotypically to
any degree.
(continued)
Genetic/
Structural
Variations
Deletions
Duplications
mCNVs
MEIs
Insertions
in
NUMTs
Inversions
Fig. 1.1 Different types of
genetic/structural variations
reported by 1000 genomes
project. mCNVs multi-allelic
copy number variants,
NUMTs nuclear mitochondrial
sequences, MEIs mobile
element insertions
1 Mutations and Polymorphisms: What Is The Difference? 5
https://t.me/medicina_free
Box 1.2 (continued)
Polymorphism: The phenomenon by which a specific DNA sequence or a
gene exists in one of the two or more variant forms with each form capable of
expressing itself as an alternative phenotype.
Mutation: A heritable and often deleterious change in a DNA sequence or a
gene, which usually has higher penetrance (expressivity) and hence higher
ability to affect phenotype.
Single Nucleotide Polymorphism: The most common type of genetic varia-
tion, which results from a single base pair substitution within the DNA
sequence. It is abbreviated as SNP and pronounced as snip.
SNPs, as the name indicates, result from a single base pair substitution within the
DNA sequence. The other common type of genetic variation is the insertion or
deletion polymorphism, often known as indel polymorphism (Robert and Pelletier
2018). Various studies have established that sequence variations, especially SNPs in
coding or noncoding regions, of the human genome may predict or indicate predis-
position to certain diseases and modulate the response to drugs (Karki et al. 2015;
Kruglyak 1999). Therefore, the deep understanding of the polymorphism as impor-
tant genetic variation and in particular SNPs becomes imperative for the evolution-
ary and population geneticists not only to understand the disease mechanisms but
also to effect the development of the precision (personalized) medicine.
1.2 Mutations
Mutations (Lit. change) are the basic events, which are responsible for the generation
of almost all genetic variations (GVs). In its contextual definition, as endorsed by
many scientists, mutation is defined as the irreversible sequence variation in the
DNA which essentially encompasses all types of variations occurring in the human
genome spontaneously or non-spontaneously (Beaudet and Tsui 1993; Beutler 1993;
den Dunnen and Antonarakis 2000). However, the persistence of the GVs in the
genome is heavily dependent upon the interactions of numerous factors including
environment. The single simple definition of the mutation is a contentious one and
mutation is always defined based on their contextual effects and penetrance within
the individual (den Dunnen and Antonarakis 2000).
Therefore, a mutation in context to its penetrance usually represents a rare change
in sequence of the gene, which usually manifests in the diseases causing attribute
(Condit et al. 2002; Karki et al. 2015). The polymorphism has therefore been
essentially meant to represent a neutral or harmless mutation present in a popula tion
with a frequency of 1% or more (Condit et al. 2002).
Mutations can be further classified either as germline if they are inherited from
parents or as somatic if they are acquired over the life mainly because of environ-
mental effects. The germline mutations are present or arise in the gametes, sperm,
6 A. S. Sameer et al.
https://t.me/medicina_free
ovum, or both. When the affected gametes (sperm and ovum) fuse, the mutations are
passed onto the zygote and can be found in each cell of the progeny derived from this
zygote. The soma tic mutations, however, are important in the disease processes
including carcinogenesis (Karki et al. 2015). Depending upon the severity or extent
of change in the DNA, a mutation can also be categorized as point, if it involves the
change of single nucleotide, or gross, if it involves change of a stretch of DNA or
entire chromosome change (GHR 2020). The classification of mutations is
summarized in Table 1.1.
1.3 Genetic Polymorphisms
Genetic polymorphism is the most common and dynamic form of genetic variation
present throughout the human genome. It is defined as the presence of two or more
alternative forms of an allele in the genome of any individual, which results in
distinct phenotypes in the same population (Singh and Kulathinal 2013). Therefore,
the gene locus (of the gene) should possess two or more alternative forms of an
allele, wherein the most common allele is present at a frequency of 99% or less and
Table 1.1 The generalized classification of the mutations
Type of
mutation Change and effect
Point/
substitution
Usually involves a change of single nucleotide
Silent New codon formed codes for the same amino acid because of codon
degeneracy. The change in DNA sequence therefore has no altering effect on
the amino acid sequence of the translated polypeptide
Missense New codon formed codes for a different amino acid. The change in DNA
sequence therefore results in substitution of one amino acid by another within
the polypeptide chain
Nonsense Codon changes to a stop codon. The change in DNA sequence therefore results
in premature truncation of polypeptide chain
Frameshift Insertion or deletion in codon changes everything beyond it and hence changes
the entire reading frame of the gene beyond the affected site
Gross
mutations
Usually explained in context to whole chromosome, hence involves many
genes
Duplications Involves duplication or copying of a part of the chromosome and generates
duplicate segments, which may result in increased gene expression
Inversions Involves removal of a segment of chromosome and its insertion back into the
chromosome but in reverse order
Deletions A portion or segment of a chromosome is completely removed or deleted. It
results in loss of genes contained within that segment
Insertions A portion or segment of one chromosome is removed and this removed
chromosomal segment is added onto another chromosome, which may alter the
DNA sequence and disrupt genes on both the affected chromosomes
Translocations Two chromosomes exchange chromosomal portions or segments, which may
alter the DNA sequence and disrupt genes on both the affected chromosomes
1 Mutations and Polymorphisms: What Is The Difference? 7
https://t.me/medicina_free
the less common allele present at a frequency of 1% or more (Brookes 1999; Singh
and Kulathinal 2013). The lower limit of the frequency of the most common allele
should not be beyond 95% (Singh and Kulathinal 2013). With the advent of
technology and availability of the cheap next generation sequencing (NGS) an
accelerated annotation of the genetic variations has been made possible since the
completion of HGP almost two decades ago (Srinivasan et al. 2016; Sudmant et al.
2015).
Four different types of genetic variations have been annotated until now. These
include single nucleotide polymorphisms (SNPs), copy number variants (CNVs),
insertions or deletions (indels), and structural variants (Srinivasan et al. 2016).
Human genome is composed of almost 3.3 billion nucleotides and the current
knowledge about it demonstrates that almost 98.5% of it is noncoding i.e., does
not code for any protein and only about 1.5% of the genome comprises protein
coding sequences (Lander 2011). It has been estimated that human genome harbors
one genetic variation for every 100–300 base pairs, which is inherent to the DNA
copying mechanism (Gonzaga-Jauregui et al. 2012; Lander 2011; Srinivasan et al.
2016). Further, a typical individual possesses around 150 rare variants of coding
genes, which affect around 1% of the genes (Lander 2011; Sudmant et al. 2015).
1.3.1 Types of Polymorphisms
As already mentioned, four different types of genetic variations have been annotated
until now and these include single nucleotide polymorphisms (SNPs), copy number
variants (CNVs), insertions or deletions (indels), and structural variants (Srinivasan
et al. 2016).
Copy number variations (CNVs) are important GVs, which occur, frequently in
the human genome, as well as in other mammalian species (Auton et al. 2015;
Freeman et al. 2006; Jorde and Wooding 2004) (Fig. 1.2). A CNV is a DNA segment
or a sequence, one kilobase (kb) or larger in size, which is present in different copy
numbers in a particular genome in comparison to the normal reference genome
(Redon et al. 2006). A CNV in its sequence and structure may consist of simple
tandem duplication (Fig. 1.3a) or may be segmental, which involves a complex,
multi-site structural loss or gain of homologous sequenc es (Fig. 1.3b) (Freeman et al.
2006; Redon et al. 2006).
CNVs have been reported to cover around 12% of the human genome, which
constitutes around 360 megabases distributed across 1500 identified sites (Clancy
2008). In an individual, CNVs are distributed across almost whole of the genome
and around 6–19% of the chromosomes are known to contain CNVs (Redon et al.
2006). CNVs are present in the genome in any of the three important structural
variant forms, which include large-scale copy number variants (LCVs),
intermediate-sized variants (ISVs), and copy number polymorphisms (CNPs). How-
ever, the DNA segments containing retroposonal insertions are not included in
CNVs (Freeman et al. 2006).
8 A. S. Sameer et al.
https://t.me/medicina_free
CNVs lead to drastic changes in the gene sequence and overall gene structure and
therefore exert a strong influence on the expression, phenotypic variation, and
adaptation in an individual. CNVs have been reported to cause various microdeletion
and microduplication diseases and increase predisposition to lethal genetic variations
and complex traits (Buckland 2003; Freeman et al. 2006; Inoue and Lupski 2002;
Lupski and Stankiewicz 2005; McCarroll et al. 2006). CNVs also affect expression
of genes through position effects, which often result from translocation and through
varied chromosomal changes, CNVs contribute to the process of evolution (Freeman
et al. 2006; Redon et al. 2006).
Insertion/deletion (indel—I/D) polymorphism constitutes the type of genetic
variation whereby a specific nucleotide sequence of varied length (1–100 bps) is
inserted into or deleted from the affected DNA sequence or gene. Indels are
distributed extensively across the human genome and affect many important
genes. 1000 Genomes Project Consortium (1KGPC/1000GPC) identified around
3.6 million short insertions/deletions (indels) (Auton et al. 2015). A simplest and
classical example of indel polymorphism is the 287 bp Alu repetitive sequence or
element present in the intron 16 of the gene coding for angiotensin-converting
enzyme (ACE). This indel produces three genotypes: insertion/insertion
(II) homozygote, insertion/deletion (ID) heterozygote, and deletion/deletion
(DD) homozygote (Pinto and van Gilst 1999; Sameer et al. 2010) (Fig. 1.4).
The 287 bp Alu element indel polymorphism has been reported to cause differ-
ential ACE serum concentration and activity with D allele associated with increased
ACE serum activity. The DD homozygous genotype or absence of 287 bp Alu
element has been associated with two times increased mean plasma concentration
and activity of ACE in comparison to II homozygous genotype or presence of 287 bp
Alu element (Rigat et al. 1990).
Angiotensin-converting enzyme (ACE) gene, a 21 kb gene (chromosomal loca-
tion 17q23.3) consists of 26 exons and 25 introns. The indel polymorphism in the
Presence or
Absence of
Variations
Gene A
Gene A
Gene A
Gene A
Gene A
Gene C
Gene B
Gene B
Gene B
Gene B
Gene D Gene E
Gene D
Gene C
Gene C
Gene C
Gene C
Gene C
Gene D Gene D
Gene D
Gene D
Copy
Number
Variations
Normal
Reference
Chromosome
Chromosome 1
Chromosome 1
Chromosome 2
Chromosome 2
Chromosome 1
Fig. 1.2 The simple generalized representation of the copy number variations (CNV) in
chromosomes
1 Mutations and Polymorphisms: What Is The Difference? 9
https://t.me/medicina_free
intron 16 of ACE gene results from the insertion or deletion (presence or absence) of
287 bp Alu element and produces three genotypes: insertion/insertion
(II) homozygote, insertion/deletion (ID) heterozygote, and deletion/deletion
(DD) homozygote. D allele and DD genotype of ACE gene 287 bp Alu element
have been associated with increased ACE serum concentration and activity.
Single nucleotide polymorphisms (SNPs) represent the most common type of
genetic variation or sequence variation and accounts for more than 90% of all the
human genetic variations (Ding 2007; Orr and Chanock 2008; Risch 2000). SNPs
involve the substitution of a single nucleotide by another nucleotide at a specific
location within the genome. These substitutions are of two types, transition and
Gene A Gene B Gene C Gene CGene C
Gene A Gene B Gene C Gene D
Gene A Gene B Gene C Gene C
Gene A Gene B Gene C Gene D
Gene D
3x Tandem Repetition
2x Tandem Repetition
Chromosome 2
Chromosome 2
Chromosome 1
Genome 1
Genome 2
Chromosome 1
Gene D
Gene A Gene B Gene C Gene D
Gene A Gene B Gene C Gene D
Gene A Gene B Gene C Gene D
Gene A Gene B Gene C Gene D
Gene A Gene B Gene C
Segmental Duplication
No Segmental Duplication
Chromosome 2
Genome 2
Genome 1
Chromosome 1
Chromosome 2
Chromosome 1
a
b
Fig. 1.3 (a) The copy number variation (CNV) in tandemly duplicated Gene C in two genomes,
(b) the copy number variation (CNV) in segmental duplicated gene A, B, and C in chromosome 2 of
the genome 2 in comparison to genome 1. The depiction is for the same gene battery present in
different loci in different chromosomes
10 A. S. Sameer et al.
https://t.me/medicina_free
transversion, are usually stable, and not believed to have any drastic effect on the
organisms (Brookes 1999; Robert and Pelletier 2018; Shastry 2009). Transition
involves substitution of one purine (adenine or guanine) by another purine (guanine
or adenine) or substitution of one pyrimidine (cytosine or thymine) by another
pyrimidine (thymine or cytosine), whereas transversion involves substitution of
purines by pyrimidines and vice versa (Fig. 1.5).
Of the two SNP types, transitions are more common. SNPs being the most
common type of genetic variation are present at a frequency of 1% or more within
a given population (Brookes 1999; Robert and Pelletier 2018; Shastry 2009). Within
the human genome, about ten million SNPs have been identified, each of which
occurs at an interval of approximately 100–300 base pairs (bp) with an average
occurrence every 300 bp (Lander 2011; Orr and Chanock 2008; Risch 2000;
Sudmant et al. 2015). SNPs because of their abundance and wide distribution
throughout the human genome have emerged as important g enetic markers for
mapping of various human diseases and have proven to be a vital tool for under-
standing population genetics and uncovering mechanisms of evolution (Ismail and
Essawi 2012).
5′ UTR
Promoter
5′ 3′
Exon 16
Chromosome 17q23.3
287 bp A/u
Exon 17 Exon 26
Splice Site
Intron 16 Intron 25
Start Codon
Upstream
Enhancer
Intergenic
Region
Stop Codon
3′ UTR
Gene Structure - Exons 1–26 & Introns 1–25
Fig. 1.4 The insertion/deletion (Indel) polymorphisms in angiotensin-converting enzyme
(ACE) gene
Fig. 1.5 SNP of an allele and the effect on phenotype
1 Mutations and Polymorphisms: What Is The Difference? 11
https://t.me/medicina_free
Соседние файлы в папке Библиотека им академика М.И. Перельмана