Human genetics and genomics | Quizlet

how many bases does human genome approx. has?

3,000,000,000 bases(

how many chromosomes are there per normal cell?

23 chromosome pairs/cell

how many genes are approximatly in human genome?

App. 25.000 genes

how do we get a protein from a DNA?

DNA is transcribed to mRNA

mRNA is translated to polypeptide

The polypeptide forms a functional protein after posttranslational processing

what's a gene?

functional unit of DNA encoding a protein sequence

how does the cell know when and where to perform splicing?

Splicing positions are encrypted in DNA/RNA code

what is necessary to transcribe a gene(besides enzymes)?

gene can be transcribed only if specific repressors and promoters assume their specific position

what is an Alternative splicing?

Alternative splicing = different functional proteins from the same DNA sequence

also Posttranslational modifications add to diversity(cleavage(proteolysis),Glycosylation(addition of sugars),Phosphorylation

how is it possible that 25.000 genes lead to 100.000 - 300.000 proteins?

Alternative splicing = different functional proteins from the same DNA sequence

also Posttranslational modifications add to diversity(cleavage(proteolysis),Glycosylation(addition of sugars),Phosphorylation

what are functions of Functions non-coding DNA?

• > 98% "Junk DNA"

• Portion of noncoding DNA is read into functional noncoding RNA molecules (eg transfer RNA, ribosomal RNA, and regulatory RNAs)

• ENCODE project: 80% of DNA in the human genome "serves some purpose, biochemically speaking"

• Regulatory functions: promoter sequence, enhancers, silencers etc.

Every individual is 99.9% equal to another individual what are two greatest sourses of variation in human population?

- Recombination

- Origin of mutations

what is genetic Recombination?

During meiosis crossing-over occurs between homologous chromosomes.Resulting in genetic recombination (new combinations of genes) and thus higher genetic diversity.

what are germline mutations?

Replication is not correct during meisosis

what are somatic mutations?

Replication is not correct during mitosis(often mosaic mutations)

what are mosaic mutations?

what are 4 types genetic diseases?

• Chromosomal abnormalities

• Monogenic disorders

-often rare

-caused by 1-2 strong mutations

• Multifactorial (polygenic) disorders

-often common

-combination of multiple genetic and environmental causes

-caused by many weak mutations

• Mitochondrial disorders

what are consequences of numerical chromosomal abnormalities(trisomy/monosomy)

Loss of a chromosome or an extra chromosome is often incompatible with life and is the main cause of spontaneous abortions (50%).

However following trisomies are not necessary aborted and are compatible with life:

Down Syndrome 21

Patau Syndrome 13,

Klinefelter's Syndrome XXY

Name 3 trisomies that can result in viable pregnancies and are compatible with life in general?

Down Syndrome 21

Patau Syndrome 13,

Klinefelter's Syndrome XXY

what are Numerical Chromosomal Aberrations?give examples

Numerical:

-aneuploidi= extra or missing chromosome

-poly-ploidy= extra complete set

what is aneuploidy?

extra or missing chromosome

What is poly ploidy?

extra complete set/sets of chromosomes

what are Structural Chromosomal abnormalities?

translocations

inversions

deletions

duplications

what is Aneuploidy?

name sex chromosomal abberations

• Male

- Kelnifelter (47,XXY) • 1/1000 males

• Female :

- Turner (45,X) • 1/2500 females

- Triple X syndrome

what is Reciprocal translocation?

it's when two different chromosomes(4 and 20 for example) exchange fragments

- breaks in two different chromosomes

- both chromosomes exchange fragments

what is Robertsonian translocation?

Chromosomes break at centromere(approx."center") and exchange "halves"

- 2 long (q) arms of two different acrocentric chromosomes (13, 14, 15, 21 and 22) merge.

- The two short (p) arms of these chromosomes are usually lost (no essential information)

- carriers often phenotypically normal

what is balanced (reciprocal) translocation?

A balanced or chromosomal translocation is a condition in which part of a chromosome has broken off and reattached in another location. In other words, it means that sections of two chromosomes have switched places. Translocations can be completely harmless or they can cause serious health problems, depending on the circumstances.

what are possible consequences for a child is to have a parent with balanced translocation?

partial monosomy or partial trisomy

a parent is considered a balanced carrier

consequences of having a balanced translocation

A balanced translocation usually does not cause any problems for the person himself. These people can, however, pass on the balanced translocation, unbalanced, to their children.

How do deletions - duplications cause the disease?

Summary chromosomal diseases

• Different types of chromosomal abnormalities - Complete chromosomes

- Structural variations

• Chromosomal abnormalities can be detected with karyotyping, FISH, array CGH, SNP arrays

- (lecture 2 techniques)

name characteristicas of Monogenic disorders

• often rare

• caused by 1-2 strong mutations

Variants by which only one nucleotide is altered

- Most frequently occurring type of variation

- Mostly unknown function in non protein coding parts of genome (neutral?)

- Highly diverse effects in coding parts of genome

What are silent mutations?

have no effect on the amino acid produced by a codon because of redundancy in the genetic code

most of mutations in genetic code are silent.what does it mean?

have no effect on the amino acid produced by a codon because of redundancy in the genetic code

if a person has partial or mosaic form o 21st chromosome trisomy what are consequences of it?

milder forms of Downs syndrome

what are consequences if mutation which happened was a promotor deletion

the whole gene may have been marked inactive

What is a Missense mutation?

Point mutation in which a single nucleotide is changed, resulting in a codon that codes for a different amino acid.

What is a Nonsense mutation?

Point mutation in which a single nucleotide is changed, resulting in a premature stop codon,so protein is not fully synthesised

what is a frameshift mutation?

all amino acids are changed beyond insertion or deletion point(if number of bases can not be divided by 3)

What is Beckwith-Wiedemann syndrome?

macrosomia, macroglossia, visceromegaly (liver and kidneys), omphalocele, hypoglycemia, hyperinsulinemia

have a increased risk of neoplasms such as Wilms' tumor, hepatoblastoma, and gonadoblastoma

what are Splice site mutations?

A splice site mutation is a genetic mutation that inserts, deletes or changes a number of nucleotides in the specific site at which splicing takes place during the processing of precursor messenger RNA into mature messenger RNA. Splice site consensus sequences that drive exon recognition are located at the very termini of introns. The deletion of the splicing site results in one or more introns remaining in mature mRNA and may lead to the production of abnormal proteins. When a splice site mutation occurs, the mRNA transcript possesses information from these introns that normally should not be included.

or

-> dysfunctional mRNA and thus (no) protein

Name the types of mendelian inheritance patterns

- Autosomal dominant

- Autosomal recessive

- Sex-linked: X-linked or Y-linked autosomal and recesssive

give characteristics of Autosomal recessive inheritance

Both alleles are defective

The patient's parents do not have the condition

The patient's parents are usually asymptomatic carriers

More common among genetically related parents (e.g. cousin)

Disorder occurs equally to men and women

For each subsequent child of the same parents, recurrence risk is 25%

give characteristics of Autosomal dominant inheritance

1 allele is defective

affected person usually (!) has at least 1 affected parent

disorder occurs equally to men and women

is passed on by both men and women

for each subsequent child of the same parents, recurrence risk is 50% (if the affected parent is heterozygous)

give characteristics of Autosomal de novo dominant inheritance

1 allele is defective

affected person has no affected parent

disorder occurs equally in men and women

originates in a germline cell of 1 of the parents

very low recurrence risk for every subsequent child of the same parents

give characteristics of X-linked recessive inheritance

2 alleles are defective (however men only have 1 X)

Almost only boys get symptoms of illness

Parents of the patient are usually not affected

Mother is often an asymptomatic carrier and may have affected male family members

Women can be affected if the father is affected and the mother is a carrier

give characteristics of X-linked (sex-linked) dominant inheritance

1 allele is defect

very rare

disorder occurs in men and women, but more often in women (often spontaneous miscarriage of male fetuses) child of an affected mother has a 50% chance of developing the disorder

only all daughters of an affected father get the condition

give characteristics of Y-linked inheritance

only men are affected

affected men always have an affected father (or there must be a de novo mutation)

only inheritance from man to man

all the sons of an affected man are affected

what is rduced Penetrance?

Penetrance of the gene: percentage of the gene carriers that show abnormalities(may differ)

which pattern of inheritance does Huntington has?

autosomal dominant

which pattern of inheritance does Duchenne Muscular Dystrophy (DMD) have?

Xcarried recessive

What is pleiotropy?

The ability of a single gene to have multiple effects:

1 gene mutation leads to more than 1 phenotype

what is Variable expression of a mutation?

what is Lynch syndrome

Hereditary nonpolyposis colorectal cancer (HNPCC) or Lynch syndrome is an autosomal dominant genetic condition that is associated with a high risk of colon cancer as well as other cancers including endometrial cancer (second most common), ovary, stomach, small intestine, hepatobiliary tract, upper urinary tract, brain, and skin. The increased risk for these cancers is due to inherited mutations that impair DNA mismatch repair. It is a type of cancer syndrome.

what is Hereditary nonpolyposis colorectal cancer (HNPCC)?

Hereditary nonpolyposis colorectal cancer (HNPCC) or Lynch syndrome is an autosomal dominant genetic condition that is associated with a high risk of colon cancer as well as other cancers including endometrial cancer (second most common), ovary, stomach, small intestine, hepatobiliary tract, upper urinary tract, brain, and skin. The increased risk for these cancers is due to inherited mutations that impair DNA mismatch repair. It is a type of cancer syndrome.

what can Variable expression of a genetic disorder can be caused by?

• Environmental factors

• Modifier genes (genes that influence expression of other genes)

• Allelic heterogeneity (different types of mutations on the same disease focus)

what is Genetic Heterogeneity?give an example

Genetic Heterogeneity =a phenomenon in which a single phenotype or genetic disorder may be caused by any one of a multiple number of alleles or non-allele mutations. This is in contrast to pleiotropy, where a single gene may cause multiple phenotypic expressions or disorders

Lynch syndrome

what is pleiotropy?

pleiotropy=a single gene may cause multiple phenotypic expressions or disorders

Lynch syndrome is an example of ?

Genetic Heterogeneity =a phenomenon in which a single phenotype or genetic disorder may be caused by any one of a multiple number of alleles or non-allele mutations. This is in contrast to pleiotropy, where a single gene may cause multiple phenotypic expressions or disorders

Summary monogenic diseases

• Mendelian inheritance: autosomal dominant, recessive and sex-linked

• (point) mutations:

- nonsense

- misssense

- indels (insertions and deletions)

- splice site

• Single nucleotide variants can be detected with sequencing

Making a diagnosis can be difficult because of:

• Pleiotropy

• Incomplete penetrance

• Variable expression

• Genetic heterogeneity• Pleiotropy=a single gene may cause multiple phenotypic expressions or disorders

• Incomplete penetrance=Penetrance of the gene: percentage of the gene carriers that show abnormalities(may differ)

• Variable expression=all kind of factors may influence phenotype even if n allele is the same

• Genetic heterogeneity=a phenomenon in which a single phenotype or genetic disorder may be caused by any one of a multiple number of alleles or non-allele mutations. This is in contrast to pleiotropy, where a single gene may cause multiple phenotypic expressions or disorders

why Making a diagnosis for some monogenetic deseases can be difficult ?

• Pleiotropy=a single gene may cause multiple phenotypic expressions or disorders

• Incomplete penetrance=Penetrance of the gene: percentage of the gene carriers that show abnormalities(may differ)

• Variable expression=all kind of factors may influence phenotype even if n allele is the same

• Genetic heterogeneity=a phenomenon in which a single phenotype or genetic disorder may be caused by any one of a multiple number of alleles or non-allele mutations. This is in contrast to pleiotropy, where a single gene may cause multiple phenotypic expressions or disorders

Multifactorial (polygenic) disorders how is it a spectrum?

• Interaction of various mutated genes and environmental factors

• Complex heredity patterns

• Relatively frequent occurrence (5 to 200 per 10,000)

Genes and environmental factors are in balance Behavior (e.g. smoking) can disrupt this balance, however: There is not 1 specific factor that causes the disease

sometimes it's hard to say wherever the disorder is caused by an environment or an allele

why are Multifactorial (polygenic) disorders so complex?

• Interaction of various mutated genes and environmental factors

• Complex heredity patterns

• Relatively frequent occurrence (5 to 200 per 10,000)

Genes and environmental factors are in balance Behavior (e.g. smoking) can disrupt this balance, however: There is not 1 specific factor that causes the disease.effect of 1 single gene ois small but if there are many->phenotype is formed

How do you find genes for complex diseases?

• linkage analysis in families

• candidate gene studies based on gene function

• hypothesis-free approach: GWAS

effect of 1 single gene ois small but if there are many->phenotype is formed

name types of genetic variants in complex diseases

• spread accross the genome

• common in the population

• small effect sizes: odds ratios low

• effects on e.g. gene expression are limited

effect of 1 single gene ois small but if there are many->phenotype is formed

characterise Mitochondrial disorders

• Caused by mutations in mitochondrial DNA that affect the function of mitochondria

• Inherited(only) from the mother

• Effects very heterogeneous due to different number of copies per cell

What is karyotyping?

Ranking of cut out chromosomes photographed during cell division (mitosis) on the basis of:

•Length

•Location of the centromere

•Banding pattern

Cytogenetics / genome diagnostics: what matherial is taken for investigation?

• Prenatal material (chorionvilli or flakes, amniotic fluid)

• Postnatal material (blood, skin, abortion material, cheek mucosa)

• Bone marrow, lymphomas and tumors

which genetic abnormalities can be detected by using Chromosome testing (karyotyping)?

• Numerical abnormalities (e.g. trisomy 21 or Down syndrome, trisomy 13/18, Turner syndrome)

• Structural deviations (such as deletions, duplications, translocations and inversions)

• Submicroscopic and other "cryptic" abnormalities (via molecular cytogenetics, FISH)

name Karyotyping features

Characteristics:

• analysis per individual cell

• (tumors have a lot of heterogeneity)

Benefits:

• visualization chromosomes

• balanced deviations are shown

• cheap, no expensive equipment needed

Cons:

(*) resolution 550 bands = 5-10 Mb

(**) dividing cells required

Solutions:

(*) (multicolor) FISH

(**) CGH/SNP array

What is the FISH technique?

Fluorescence In Situ Hybridisation

Principle: Detection presence or absence of a certain genomic region with fluorescently labeled DNA (probe). Probe binds to specific position on the chromosome

Can be used to detect

• Detection of microdeletion syndromes(~ 1 Mb)

• Detection of structural deviations

• Detection of numerical deviations

BUT:

• Limited resolution (~ 1Mb)*

• Only testing of known translocations

how is multicolor FISH(Fluorescence In Situ Hybridisation) is superior to ordinary FISH in some aspects and inferior in other?

Direct recognition of small translocations and marker chromosomes. Inversions are invisible

Also: Coloring per chromosome arm and even coloring per band

Very expensive: only little applied

what can FISH(Fluorescence In Situ Hybridisation) technique be used for?

Can be used to detect

• Detection of microdeletion syndromes(~ 1 Mb)

• Detection of structural deviations

• Detection of numerical deviations

BUT:

• Limited resolution (~ 1Mb)*

• Only testing of known translocations

what are SNP arrays?

In molecular biology, SNP array is a type of DNA microarray which is used to detect polymorphisms within a population. A single nucleotide polymorphism (SNP), a variation at a single site in DNA, is the most frequent type of variation in the genome. Around 335 million SNPs have been identified in the human genome,[1] 15 million of which are present at frequencies of 1% or higher across different populations worldwide

The basic principles of SNP array are the same as the DNA microarray. These are the convergence of DNA hybridization, fluorescence microscopy, and solid surface DNA capture. The three mandatory components of the SNP arrays are

1.An array containing immobilized allele-specific oligonucleotide (ASO) probes.

2.Fragmented nucleic acid sequences of target, labelled with fluorescent dyes.

3.A detection system that records and interprets the hybridization signal.

The ASO probes are often chosen based on sequencing of a representative panel of individuals: positions found to vary in the panel at a specified frequency are used as the basis for probes. SNP chips are generally described by the number of SNP positions they assay. Two probes must be used for each SNP position to detect both alleles; if only one probe were used, experimental failure would be indistinguishable from homozygosity of the non-probed allele

Single nucleotide polymorphisms:

• population frequency >5%

• catalogus: Hapmap database

what are usual result of SNP arrays?

Usually there are 3 clusters of genotypes (because a SNP has only 2 forms):

Homozygotes for the major allele (AA)

Homozygotes for the minor allele (BB)

Heterozygotes (carrying a minor and a major allele, AB)

what are advantages of SNP arrays(Single nucleotide polymorphisms)?

• Higher resolution due to more measuring points (currently 1.5 million SNPs per array)

• Ability to do homozygosity mapping and linkage in families

ability to detect From large (structural) variation to single nucleotide variations

what is Polymerase chain reaction (PCR)?

What is qRT-PCR?

what to do after mutation has been identified?

• What is the function of the gene?

• What is the effect of the mutation on the gene?

• Functional studies!

How to start:

• Often with effect of mutation on mRNA expression (qRT-PCR, whole genome)

• in vitro systems: overexpression, down regulation, etc

• knock-out mice

name steps of The genetic approach of a disease

1.Identification of loci/ genes associated with disease

2.Identification of DNA variants associated with disease

3.Demonstrating functional link between DNA variant and pathology

4."Early prediction":Find genetic profiles to identify individuals with a high risc

&"Early prevention/ treatment":Develop new strategies to intervene in the disease process

DNA screening is done for Acquired defects.name example of deceases and tissues taken for analysis

• Haematological disease

o Bone marrow

o Lymph node (proliferation)

o Solid tumour

DNA screening is done for birth defects in prenatal screening.name tissues taken for analysis

o Chorion villi

o Amniotic fluid

describe Principle of DNA isolatie from blood(prosedure)

• Both red and white blood cells are "inflated" by cell lysis buffer

• DNA is in a solution of broken blood cells

• Magnetic beads are added

• Buffers are added

• DNA sticks to the beads due to the chemical composition of the solution

• A magnet removes beads with DNA from the solution

• After washing DNA, the DNA is ready to be used

• DNA is released from beads by changing the composition of the buffer

what is a purpose of Postnatal diagnostics?

Confirm/ exclude diagnosis

• Eg. suspected genetic syndrome, or suspected hereditary breast cancer, heart disease, cystic fibrosis

• Correct diagnosis important for treatment and prognosis

• Enable carrier testing, presymptomatic testing, and prenatal testing in the family

what is the clinical picture of RETT syndrome?

- Incidence: 1 in 10.000/15.000 girls - X-linked dominant inheritance - Extremely rare with boys - Developmental disorder of the nervous system in particular brain stem - Average life expectancy above 40 years

1. Normal development in the first 6 months

2. Head circumference growth rate slows down at 6-18 months of age

3. After 0.5-2.5 years, coarse and fine motor skills deteriorate (atactic motion image)

4. Originate of stereotypical hand movements such as hand rubbing or pinching, clapping or hand-mouth movement

5. Dyspraxia: difficult to control all body movements such as limbs, head but also eye movements and speech

6. Loss of communication eg. of learned words (no autism)

7. Serious disruption of autonomous functions due to developmental disorder of brain stem. Breathing disruption such as hyper / hypoventilation, breathing pauses and excessively supported breathing

Why is this important for parents to know if mutation in child is de novo?

to wherever there is a chance of their next children have a chance to aquire same genetic diorder(if oarents are carriers)

what is purpose of Presymptomatic Postnatal diagnostics ?

- Eg. diagnostics for healthy sister of the BRCA2 mutation carrier

- Gain knowledge on the own risc of getting the disease known in the family

- Prophylactic treatment, intensive check ups/ no further check ups

- Available for many hereditary diseases: eg. breast cancer, colon cancer, heart defects, spinocerebellar ataxia

discribe a procedure for Procedure for presymtomatic testing

• Counseling interview

• Decision-making interview at least 4 wk after 1st interview

• Diagnostic result interview

• Follow up after a bad result

• Discussions together with a genetic consultant and social work

what is SCA(SpinoCerebellar Ataxia)?

SpinoCerebellar Ataxia (SCA) is a rare neurodegenerative disorder in the small brain where the nerve cells do not properly transmit their signals to the muscles. SCA is a hereditary disease that can be caused by several genes. Because the nerves no longer pass on their signals to the muscles correctly, problems arise in the motor actions. That's why someone with SCA walks weird, like he's drunk. He also often talks unclear and drops things out of his hands.

what is SCA?

SpinoCerebellar Ataxia (SCA) is a rare neurodegenerative disorder in the small brain where the nerve cells do not properly transmit their signals to the muscles. SCA is a hereditary disease that can be caused by several genes. Because the nerves no longer pass on their signals to the muscles correctly, problems arise in the motor actions. That's why someone with SCA walks weird, like he's drunk. He also often talks unclear and drops things out of his hands.

which tissues are used for prenatal(invasive) testing?

chorionic villi or amniotic fluid cells

why diagnostics using chorionic villi or amniotic fluid cells during pregnacy is rapid?

so parents have time to terminate pregnansy

there is an Increase in the risk of nondisjunction leading to trisomy 21 with increasing age in wemen.after which "threashold" does it start to increase rapidly?

after 35 y.o.

what is a combined non-invasice test for trisomy 21?

Combination of two tests:

1. a blood test in the pregnant woman, between 9 and 14 weeks of pregnancy;

2. the foetal nuchal fold measurement. This is done with an ultrasound that is made between 11 and 14 weeks of pregnancy.

The results of blood test and nuchal fold measurement, in combination with the age of the mother and the exact duration of the pregnancy determine the likelihood of a child with a trisomy 13, 18 and 21.

what are advantages and disadvantages of non-invasive tests?

Advantages: No chance of a spontaneous abortion Possible for all pregnancies

Disadvantage: Chance of false positive and false negative results

what are advantages of non-invasive tests?

No chance of a spontaneous abortion Possible for all pregnancies

what are disadvantages of non-invasive tests?

Chance of false positive and false negative results

what is QF-PCR(Prenatal diagnostic method)?

• QF-PCR stands for quantitative-fluorescent polymerase chain reaction

• QF-PCR regards amplification, detection and analysis of short tandem repeat (STR) markers, which are chromosome specific

• STRs can differ in length between the parental chromosomes and are inherited as alleles

• PCR amplification of several STRs on chromosomes 13/18/21/X/Y is performed with fluorescence PCR

• PCR fragments are separated based on size at a capillary sequencer

• Comparison of the copy number of the chromosomes is possible due to the fluorescent signal: the degree of fluorescence is a measure of the number of chromosomes

what is coverage of sequensing?

what is sequencing read?