Module 9

STR- Short tandem repeats

The allele is based on the length of the DNA segment, with different alleles having different lengths because they have different numbers of copies of a short, repeated DNA sequence.

Polymorphic- important bc unlikely that two ppl will have same profile

VNTR

Variable Number of Tandem Repeats

Gel electrophoresis

Put samples in wells of gel

Run electrical current through sample (DNA is negatively charged)

Separates DNA based on SIZE

Small pieces move faster than big pieces

Microsatellite regions

Polymerase Chain Reaction

Denature DNA by heating to 95^oC

Strands separate

Each strand is template for replication

Primers anneal to identify target that will be identified
Taq polymerase adds nucleotides to 3’ end of primer

Repeat many times

Who won nobel prize for PCR?

Kary Mullis

PCR Limitations

•Must know something about sequence surrounding gene of interest in order to use PCR to clone a gene

•PCR reactions are easily contaminated from other DNA in the lab

•Taq polymerase does not proofread and correct errors (error rate about 1 in 20,000 bp)

•Fragments amplified by PCR are relatively small (2000 bp standard, modified reactions up to 50,000 bp)

CODIS- Combined DNA Index System

Database funded by FBI

Uses 20 polymorphic regions

Loci assort independently- product rule applies

13 mil profiles from offenders and 3 mil from arrestees

845,000 from crime scenes

415,000 hits

Ethical Issues

Partial Matches and familial DNA searching

The Innocence Project

•There have been ~350 people who were falsely convicted released from prison and ~149 alternative perpetrators identified

SNP- Single Nucleotide Polymorphism

•a specific site in the genome where the DNA base varies in at least 1% of the population.

SNPS near each other are haplotype

TagSNPS= few SNPS used to identify a haplotype

SNPs in association studies

Can be correlated with genetic disorders

Quicker to identify DNA sequences between individuals than sequencing whole genomes

Ecogenetics

Study of genetic variation that affects responses to environmental chemicals

Risk of exposure to a chemical depends on the genetics involved in:

Transport of chemical

Metabolism of chemical

Excretion of chemical

Sensitivity to pesticides example

Parathion breaks down into toxic chemical paraoxan

Ppl with RR genotype detoxify 10x faster than those with QQ

Different populations have different QQ frequencies

Drug Sensitivities and Genetics

Individuals break down drugs at different rates

-Can lead to toxic (even fatal) complications

Eg. Suxamethonium

Muscle relaxant, short-acting anesthetic

• Most people take minutes to recover from small dose

• Autosomal recessive condition- takes HOURS to recover from small dose

• Can cause paralysis of respiratory system and death

Breast Cancer and Tamoxifen

Tamoxifen mimics the shape of estrogen, but, unlike estrogen does not stimulate the cells to divide

-helps with breast cancer

CYP2D6 gene metabolizes it

women with poor metabolism higher risk of cancer resurgence

Warfarin

Anti-coagulant

Greater than 10-fold inter-individual variability in the dose required to attain a therapeutic response

Required dose also varies depending on individual’s diet and is not the same for each person

What 2 genes influence effective Warfarin dose?

CYP2C9 (warfarin metabolic enzyme)

VKORC1 (Vitamin K epoxide reductase complex 1)

DTC Testing

The lab extracts and amplifies your DNA

Samples are placed on a gene chip that has 500,000 SNP probes

Your DNA binds to complementary probes

Computer identifies which SNPs are present in you and correlates your SNPs to those that are used for ancestry analysis.

DTC Testing differences from medical testing

SNPs used in DTC testing are limited and do not do as thorough a test as the medical testing conducted by genetic counselors and physicians.

Genomics ethical questions

How do you control/regulate the spread of use of your genetic information?

Is the information going to make life simpler or more complex?

Who has access to your genetic information?

Genetic counseling

Helping people understand and adapt to genetic disease

• Analyzing family and medical histories

• Education

• Risk assessment

• Counseling to help people reach decisions

• Psychological support

Genetic counselors responsibilities

• Obtaining medical history

• Assessing risk and assist in determining diagnosis

• Providing education about the disorder

• Reviewing options available to patient

• Facilitating genetic testing

• Assist in getting services covered by health insurance

• Providing referrals to support groups, medical and social service agencies

Non directive counseling

The genetic counselor shares his/her expertise, knowledge and experiences

But the patient and the patient’s family members are responsible for making the decision that they feel is best for their situation

Prenatal Genetic Counseling

Positive results on screening tests

High risk pregnancies due to age (>35)

Anomalies seen on ultrasound

Those interested in diagnostic testing

Family history of genetic disorder

Individuals with fertility problems or repeat pregnancy loss

Prenatal exposures

Screening vs diagnostic meaning

Screening is estimate for risk

Diagnostic is a specific diagnosis

Screening vs Diagnostic tests in pregnancy

Screening

1st tri screening (ultrasound and protein levels)

Maternal serum screening (levels of 4 proteins)

Cell-free DNA screening (baby’s DNA in mother’s blood)

Ultrasound- morphological appearance

Diagnostic

CVS

Amniocentesis

Karyotype and Microarray analysis

Prenatal microarray is now offered to anyone who undergoes a diagnostic procedure

Informed consent is crucial

• Consanguinity

• VUS (variant of unknown significance)

Pediatric Genetic Counseling used for children and adults with

Children with a family history of genetic disorders to rule out or diagnose suspected syndromes

Children with Developmental or Intellectual Delay

Babies with abnormal newborn screening tests.

Children with teratogenic exposures

Children with dysmorphic (atypical) features

NICU consultations

PICU consultations

Known diagnoses

Failure to thrive

Autism

Cancer Genetic Counseling

Family history of cancer

Been diagnosed with cancer at a young age

Been diagnosed with multiple cancers

Individuals who need more information to make decisions regarding their medical care

A known family cancer syndrome or mutation

Genetic Counseling Career Opportunities

Clinical Genetic Counselor

Laboratory Counselor

Public Health Counselor

Health Educator

Public Policy Consultant

University Faculty Member

Private Healthcare Company Employee

Science Researcher

How to Become a Genetic Counselor

Bachelor's degree

Shadowing a genetic counselor

Master’s degree in Genetic Counseling from an ABGC accredited program

Board certification