GENETIC TESTING IN INDIVIDUALS AND IN POPULATION

8/7/2019 GENETIC TESTING IN INDIVIDUALS AND IN POPULATION

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GENETIC TESTING IN

INDIVIDUALS AND IN

POPULATION


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INTRODUCTION

Genetic testing is a type of medical test that identifies

changes in chromosomes, genes, or proteins.

Most of the time, testing is used to find changes that are

associated with inherited disorders.


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WHY GENETIC TESTING?

The results of genetic testing may help

Diagnose a disease.

Find genetic difference that may increasethe individuals risk of getting a disease.

Find genetic diseases that could be

passed onto the individuals children.Guide the health care provider to choose

the best treatment for diagnoses.


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SAMPLES FOR GENETIC TESTING

Genetic test are performed on a sample of

Blood

Cells swabbed from the mouth

SalivaSkin

Hair

TumorsAmniotic fluid/ chorionic villus samples.

Urine


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Genetic diagnosis can be made in two essentially different

ways

Direct testing:

a sample from the consultand is tested to see whether he has acertain genotype or not, typically a pathogenic mutation in a certaingene. IT IS THE TEST OF AN INDIVIDUAL.

Gene tracking:

linked markers are used in family studies to discover whether or notthe consultand inherited the high risk chromosome from aheterozygous parent. IT IS TEST OF THE FAMILY.

gives information about the segregation of the chromosomalsegment in the family.


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Two Main Types of Genetic Tests

Constitutional

Tests for mutations that affect ALL CELLS in

the body, and have been there since

conception

Acquired

Tests for changes that affect only certain cells

or cell types in the body, and that occurredlater in life


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Genetic Tests forConstitutional Mutations

Molecular Tests

Cytogenetic Tests

Biochemical Tests


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Molecular Test: Example

Analysis of DNA sequence in patient with arare inherited disease Muscular Dystrophy

Gene: DMD Clinical Picture

1 in 3500 male births

progressive muscle weakness starting in early childhood

wheelchair by age 12 death in 20s


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Molecular Test: Muscular Dystrophy

Obtain blood sample from child

Read the DNA sequence of the DMD gene

Identify the mutation that caused thedisease


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How is this information useful?

Can test Mom Is she an unaffected carrier ofthe mutation? Is she at risk to have morechildren with this disease?

Can test siblings of affected child Can offer prenatal diagnosis in Moms next

pregnancy OR

Can offer pre-implantation genetic diagnosis

Can provide information about prognosis


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Cytogenetic Test: Example

Karyotype to examine the chromosomal

complement of an individual including

number, form, and size of the

chromosomes.

Frequently used for children who present

with multiple anomalies, developmental

delay, autism.


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Cytogenetic Test: Child with MCA

and autism

Obtain a blood

sample from baby

Look at

chromosomes


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CGH


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ARRAY CGH


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Can determine exactly which genes areinvolved

Can test parents and siblings of affected child

to see if they carry the abnormality Can offer prenatal diagnosis in next pregnancy

OR

Can offer pre-implantation genetic diagnosis

Can provide information about prognosis


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Biochemical Test

Analyzes the quantity of a downstream

product of a gene (e.g. not looking directly

at the gene, or the chromosome).

Example: Newborn Screening

Mandated in all 50 states

Twenty primary targets that all states do

Over 4 million newborns tested each year


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Biochemical Test: PKU

Phenylketonuria Inherited metabolic

disorder If untreated, leads tomental retardation

Affects 1 in 20,000newborns

Missing enzyme:phenylalaninehydroxylase.

Measures the amount ofphenylalanine in blood.


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Can diagnose the baby in time to treat and

avoid all clinical consequences of the

disease

Treatment: Restrict phenylalanine in the diet

Can test siblings of affected child to see if

they are carriers for the disease (1 in 70 in

the general population are carriers)


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Genetic Tests forAcquired Mutations

Molecular Tests

Cytogenetic Tests


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Molecular Test for Acquired Disease

KRAS gene test on tumor tissue from

patients with colorectal cancer

Obtain tumor from patient

Extract DNA; treat with enzyme that allows

visualization of the mutation


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Patients whos colon tumors do not have a

KRAS mutation are much more likely to

respond to Cetuximab therapy

Identifies patients most likely to benefit

from specific therapies

Allows choice of alternative therapies (and

saves time and money) for patients

unlikely to respond


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Cytogenetic Test for Acquired

Disease: Example

Her-2/neu gene amplification in Breast

Cancer

Occurs early in oncogenesis

Seen in up to 1/3 of breast cancers

Associated with poor prognosis

Responds to Herceptin (trastuzumab)

treatment Does not respond to Tamoxifen treatment


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Assists in selection of patients for

chemotherapy, and which therapy to use

Predicts response to adjuvant therapy

Increases survival

Allows choice of alternative therapies (and

saves time and money) for patientsunlikely to respond.


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TYPES OF GENETIC TESTING

Newborn screening

Carrier testing

Diagnostic testing

Preimplantation testing

Predictive testing/ presymptomatic testing


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NEWBORN SCREENING

Used just after birth to identify genetic disorders that canbe treated early in life.

Look forabnormal arrangements of chemical bases in

the gene itself while other test detect inborn errors ofmetabolism.

Millions are infants are tested each year in united states

forphenylketonuria and congenital hypothyroidism.


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CARRIER TESTING

Used to identify people who carry one copy of gene

mutation that, when present in two copies causes a

genetic disorder

Offered to individuals who have a family history of a

genetic disorder and to people in certain ethnic groups

with an increased risk of specific genetic conditions.

If both parents are tested, the test can provide

information about a couples risk of having a child with

genetic condition.


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DIAGNOSTIC TESTING

Used to identify / rule out a specific

genetic chromosomal condition

Genetic testing is used to confirm a

diagnosis when a particular condition is

suspected based on physical signs and

symptoms.


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PRENATAL TESTING

To detect changes in a fetus genes/

chromosomes before birth.

Offered during pregnancy if there is an

increased risk that the baby will have a

genetic / chromosomal disorder.


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PREIMPLANTATION TESTING

Used to detect changes in the embryos

that were created using assisted IVF.

Small number of cells are taken from the

embryos and tested for certain genetic

changes

Embryos without these changes are

implanted in the uterus to initiate a

pregnancy.


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PREDICTIVE/PRESYMPTOMATIC

TESTING

Used to detect gene mutations associated with

disorders that appear often later in life.

Predictive testing- identify mutations that

increase a persons risks of developing diseaseswith genetic basis, such as certain type of

cancer.

Presymptomatic testing- determine whether a

person will develop a genetic disorder, before

any signs or symptoms appear.


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MUTATION SCANNING METHODS

Detection of known genetic mutations Allele Specific Oligonucleotide (ASO)

Amplification Refractory Mutation System ( ARMS)

Oligonucleotide Ligation Assay (OLA)

Detection of unknown genetic mutations Denaturing high performance liquid chromatography (DHPLC)

Single strand conformation an polymorphism(SSCP)

Denaturing gradient gel electrophoresis (DGGE )

DNA microarray

Protein truncation test (PTT)


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OLIGONUCLEOTIDE LIGATION ASSAY


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ALLELE SPECIFIC OLIGONUCLEOTIDE


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AMPLIFICATION REFACTORY MUTATION SYSTEM


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PROTEIN TRUNCATION TEST


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DHPLC

Most sensitive method that provides a high degree of automation

and throughput.

Detects successfully single nucleotide substitutions, small deletions,

insertions within 2.5 minutes in unpurified amplicons as large as 1.5

kb

Detects mutation on the basis of mismatches between amplified

chromosomal fragments that results in the formation of

heteroduplex.

stationary phase-polystyrene divinyl benzene

Ion pairing reagent- triethylammonium acetate Mobile phase-acetonitrle

Sensitivity doesn't drop over a size of150-700 bp.


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DGGE

DNA MICROARRAY


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DNA MICROARRAY


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GENE TRACKING

Steps involved

Distinguish the two chromosomes in

relevant parents i.e. to find closely linked

marker for which they are heterozygous.

Determine phase

Work out which chromosome the

consultand received.


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RFLP


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Thank you

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