FCM GENETICS

Role of genetics in medicine

To understand the underlying principles of human genetics

To give patients and their families the full benefit of expanding genetic knowledge

To explore gene-gene and gene-environment interactions in disease

genetics is important to

know the role in cancer mutation and aging

prenatal dx

pre-symptomatic testing

population screening

to develop new gene based therapies

DNA to mRNA is called

transcription

- occurs in nucleus

RNA to proteins is called

translations

- occurs in the ribosomes

75% of the human genome is

unique, single copy DNA

Junk DNA

no recognized function

less than 10% of our DNA is responsible for

encodes things that make us unique and individual from one another

Heterochromatin is _________

Euchromatin is ________

heterochromatin is NOT transcribed

Euchromatin is transcribed

25% of the human genome is___

repetitive DN

purines

adenine, guanine

Pyrimidines

cytosine, thymine

Exons

DNA that is transcribed into RNA

Transcribed into messenger RNA is what can give us those different products

Introns

Non coding intervening sequences that are not transcribed

5' and 3' untranslated regions are

Transcribed but not translated regions, that are important in gene regulation

Untranslated ends on both 5 prime and 3 prime of that helix = allows transcription factors to bind onto messenger RNA to transcribe it

RNA polymerase

Initiates transcription

Makes mRNA copy of single strand of DNA

Introns are excised by

splicing

Translation

Mature mRNA translated in the ribosomes

Precursor protein undergoes cleavage into smaller active peptides

further modified in the golgi body

somatic cells

46 chromosomes (23 pairs)

44 autosomes

2 sex chromosomes

cell division in somatic cells

mitosis

cell division in germ line cells

meiosis

germline cells

Cell line from which gametes are derived

23 chromosomes

Haploid

cytogenetics

The study of chromosomes, their structure, and their inheritance as applied to the practice of medical genetics

tissues commonly used in cytogenetic studied

Peripheral blood

Saliva wash

Buccal swab

Skin fibroblasts

Amniotic fluid cells (skin cells off the baby)

Chorionic villi

Products of conception

clinical indications for chromosome analysis

Specific phenotypes

Problems of early growth and development

Stillbirth and neonatal death

Fertility problems

Family history of known or suspected chromosome abnormality

Neoplasia

Pregnancy in a women of advanced age

Chromosomal Analysis

getting a karyotype

When looking at a chromosomal analysis or a karyotype is telling you what’s missing and what is not

ring chromosome

Deletion of the normal telomere with fusion of the ends to form a circular chromosome

Normal phenotype/mild abnormalities

Apparalent “balanced ring”

Deletion and duplication syndromes are described by

location or eponym

Van de Woude syndrome presents with

LIP PITS

monosomy means

deletion occurred

trisomy means

duplication occurred

phenotypic abnormalities are more commonly seen in deletion syndromes than duplication syndromes (T/F)

True

truly hyper-nasal speech is seen in which chromosomal deletion

22q

autosomal microdeletions

Dysmorphic syndromes associated with very small deletions

Contiguous gene syndromes

May require FISH for diagnosis

FISH

FISH = Fluorescent in Situ Hybridization

Performed on metaphase chromosomes or interphase nuclei

Detects deletions of chromosomes too small to see using conventional karyotyping analysis

Useful to identify or confirm the common deletion and duplication syndromes as well as subtle chromosomal rearrangements

Indications for Prenatal FISH for Aneuploidy (missing or extra chromosome)

Trisomy risk = X,Y, 13,18,21 = commonly done

Abdominal ultrasound (abnormal)

Maternal anxiety

Limitations of FISH

Adequate additional specimen

False positives:

Microarray Technology

DNA chip technology

Used primarily to study gene expression (but now done to quickly assess if DNA pieces are missing or not)

Proband

(index case): affected family member through whom a family with a genetic disorder is first brought to attention

A person serving as the starting point for the genetic study of a family

consultant

person who brings the family to the attention of a genetics professional

kindred

entire family

consanguineous

couples who have one or more ancestors in common

gene

a hereditary unit

Alleles

alternative forms of a gene

wild type

normal allele

Mutant allele

gene with a permanent heritable change in DNA sequence

Polymorphism

two or more relatively common alleles at a locus in the population

phenotype

the observed biochemical, physiological, and morphological characteristics of an individual

genotype

the genetic constitution of an individual

Hemizygote

an individual with only one representative of a chromosome or chromosome segment

Homozygote

a person with a pair of identical alleles

Heterozygote

a person with alleles that are different

compound heterozygote

two different mutant alleles of the same gene are present

ex: Cystic Fibrosis

carrier

person who has one mutant and one wild-type allele for an autosomal recessive or X-linked gene

chromosomal disorders should be tested with

karyotyping

Microdeletion or Microduplication syndromes should be tested with

FISH

CGH

single gene disorders should be tested with

mutation analysis

DNA sequencing

and or deletion testing

mutlifactoral disorders should be tested with

none currently

epigenetic disorders should be tested with

methylation analysis

triple repeat disorders should be tested with

DNA testing for number of repeats

Microdeletion syndromes

22q11 deletion

Williams syndrome

methods of diagnosing genetic disorders pre-natal (invasive)

amniocentesis

chorionic villus sampling

cordocentesis (Percutaneous Umbilical Blood Sampling)

preimplantation genetic diagnosis

methods of diagnosing genetic disorders pre-natal (non-invasive)

maternal serum alpha-fetoprotein

maternal serum screen

ultrasonography

isolation of fetal cells from maternal circulation (NIPS)

NIPS

Cell-free fetal DNA (cffDNA) background

Cell-free fetal DNA is found in maternal plasma and is thought to be placental in origin.

There may be as much as >10% cell free fetal DNA in maternal blood.

All cffDNA clears from the woman’s blood within 2 hours after birth, ensuring that any detected fetal DNA is from the current pregnancy

caveat → fetal free fetal DNA has been found in males, but when they have an embryonic cancerous tumor (testicular cancer

indications for prenatal diagnosis by invasive testing?

advanced maternal age (M/C implication)

previous child with a de novo chromosome abnormality

presence of structural chromosome abnormality in one of the parents

family history of a genetic disorder that may be diagnosed or ruled out by biochemical or DNA analysis

family history of an X-linked disorder for which there is no specific prenatal diagnostic test

risk of a neural tube defect

fetal abnormalities detected by ultrasound or suspected, based on maternal serum screening

chrorionic villus sampling (CVS)

biopsy of tissue from the villous area of the chorion

transcervical OR transabdominal

10th – 12th gestational week

~1% risk of miscarriage

Amniocentesis

transabdominal removal of amniotic fluid

15th – 16th gestational week

0.5-1.0 % risk of miscarriage

chromosome analysis, DNA-based testing, biochemical studies (AFP)

what is whole genome sequencing?

“Reading” the DNA sequence of an individual’s entire genome"

Coding and non-coding regions

Does not provide information on actual gene expression or epigenetic factors

Mitochondrial inheritance

(it is only inherited maternally)

Often called the 24th chromosome

Each mitochondria contains its own genome in a circular piece of DNA

Some genes affecting the mitochondria are inherited in a autosomal recessive fashion

Bottleneck phenomenon

The number of mtDNA molecules within each oocyte (egg) is reduced, being subsequently amplified to the huge total seen in the mature oocyte.

The restriction and then subsequent amplification is termed bottle neck.

Mitochondria homoplasmy

>50% of the same type of mitochondrial DNA, offers no concern

mitochondria heteroplasmy

>25% but less than

mitochondrial disorders illustrate

reduced penetrance, variable expression and pleiotropy. The degree and distribution of heteroplasmy contributes significantly to the variability seen with mutations in mtDNA.

penetrance

The proportion of individuals with a disease genotype who have any actual signs or symptoms of the disease

Expression

The variable phenotypes caused by an abnormal gene.

Pleiotropy

Multiple phenotypic effects of a single gene or gene pair. Used especially when the effects are not obviously related.

mitochondrial diseases are multifactorial in that

BOTH additional genes and environmental factors influence level of expression.

all cancer is genetic but....

But not all cancer is inherited

most cancers occur in people

who have no family history of the cancer at all i.e. are "sporadic"

initiating mutations in sporadic cancers is caused by

an environmental insult, carcinogens, DNA replication errors

Hereditary Breast and ovarian cancer

Hereditary 7-10%

Familial 30%

Sporadic 60%

if someone has average risk for cancer (sporadic) you should recommend

Standard prevention recommendations

if someone is moderate risk (familial) for cancer you should recommend

Personalized prevention recommendation

if someone if high risk for cancer (inherited) you should recommend

Referral for genetic evaluation with personalized prevention recommendations

Who is at risk for sporadic cancer development (Average risk)?

No family history of breast or ovarian cancer

No other known risk factors for breast or ovarian cancer

Others who may be at average risk:

One 1st degree relative diagnosed >60 years

One or two 2nd degree relatives diagnosed >60 years

who is at risk for familial cancer (moderate risk)?

A few family members with the same cancer

Generally average age of onset of cancer

Individuals with cancer typically do not have more than 1 primary cancer

Risk to family members approx. 2-3 times the general population risk

Familial cancer is due to a combination of inherited and environmental factors

inherited cancer

Largely due to a mutation within a cancer susceptibility gene

Multiple family members with the same or related cancers (i.e. breast, ovarian)

Earlier than average ages at diagnosis

Rare cancers are more common

More than 1 primary cancer in a single individual

Cancer "passed" from generation to generation

a _________ genetic mutation is the single greatest factor in increasing an individual's risk of developing cancer

inherited

oncogene

Gene in which a genetic mutation is carcinogenic to a cell, even in the presence of a normal copy of the gene

tumor suppressor genes

A gene in which carcinogenesis results from the loss of both of the normal copies of that gene

2 hit hypothesis

Normal genes → prevent cancer

1st mutation → susceptible carrier

2nd mutation → leads to cancer

what gene is more common to see in inherited breast cancer?

BRCA1

consider testing for BRCA germline mutations in BRCA1 and BRCA2

Individuals with a personal or family history of breast cancer before age 50 or ovarian cancer at any age

Individuals with two or more primary diagnoses of breast and/or ovarian cancer

Individuals of Ashkenazi Jewish descent with a personal or family history of breast cancer before age 50 or ovarian cancer at any age

Individuals with a personal or family history of male breast cancer

Hereditary cancer risk can be ruled out if a known mutation is found in an affected family member and is not present in your patient. BUT

a negative test in the absence of a known mutation reduces the likelihood of hereditary cancer risk but cannot rule it out.

HNPCC (hereditary nonpolyposis colorectal cancer)

Also known as Lynch Syndrome; variants inclue Muir-Torre syndrome, Turcot syndrome

Up to 1/500 individuals affected with HNPCC

Most common inherited CRC syndrome; accounts for up to 6% of all cases of CRC

“Non-polyposis” a misnomer as precursor polyps (adenomas) are present

what is the most common inherited CRC syndrome

Lynch syndrome

FAP clinical features

100s-1000s of precancerous colonic polyps develop

Mean age of polyp development is 16

By age 35, 95% of affected individuals have polyps

Without colectomy, colon cancer is inevitable

FAP is due to mutations in

APC gene

What is juvenile polyposis

Predisposition to juvenile polyps of the GI tract

most affected by 20

9-50% risk of GI cancer due to malignant transformation of polyps

Genetic Information Nondiscrimination Act (GINA)

Prohibits US insurance companies and employers from discriminating on the basis of information derived from genetic tests

Forbids health insurance companies from discriminating through reduced coverage or pricing

Single gene disorders

Autosomal dominant

Autosomal recessive

X-linked recessive

X-linked dominant

Y-linked