Human Genetics Basics

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Human Genetics Basics

• Kate Garber
• Director of Education
• Department of Human Genetics
• kgarber_at_genetics.emory.edu

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Medical Genetics

• Syndrome named after an old guy
• Gene name, which is some meaningless abbreviation
• Pathway
• Genetic test

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Variable Human Traits
Qualitative Traits Discrete traits Receding
hairline Bushy eyebrows Gray hair
Quantitative Traits Measurable traits IQ Blood
pressure Height
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Genes versus Environment
Rare Simple genetics High recurrence risk
Common Complex genetics Low recurrence risk
Sickle cell disease
Scurvy Infectious diseases Gunshot wound
Hypertension Heart disease Diabetes Asthma Behavio
ral disorders
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Why might someone want to seek genetic services?

• Get information about their family history and
  any genetic risk factors
• The diagnosis of a genetic disorder by physical
  examination and/or genetic laboratory testing
• How/why a disorder occurred (in most cases)
• The chance for the disorder to reoccur in the
  family
• The chance for other family members to have the
  disorder or pass it on
• The management and treatment of the disorder
• Support groups for the disorder
• Connections to other families who have a child
  with a similar/same disorder

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• Types of genetic testing
• 1. Diagnostic testing - establish or confirm a
  diagnosis
• 2. Carrier testing - screen adults to determine
  if they are carriers of mutations so that their
  risk of having a child with a genetic defect can
  be calculated
• 3. Prenatal testing - determine if a fetus is
  affected with a genetic disorder (also includes
  PGD testing).
• 4. Presymptomatic testing - determine if a
  currently asymptomatic individual will become
  affected with a genetic disease in the future.
• 5. Population screening - screening of the entire
  population for a genetic disorder so that these
  individuals can be identified and treated before
  the onset of symptoms

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Chromosome Variation

• Karyotype
• 23 pairs autosomes, 2 sex chromosomes
• Each chromosome has a characteristic banding
  pattern
• What is the most common genetic variation you see
  in karyotypes from a normal population?

46, XX versus 46, XY
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Variation in Chromosome Number

• Trisomies 13, 18, and 21 are the only non-mosaic
  trisomies for an entire autosome that are
  compatible with postnatal survival
• Monosomy X is the only monosomy that is viable

Trisomy 13
Trisomy 18
Turnpenny Ellard, 2007
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Variation in chromosome structure

• Translocations
• Inversions
• Duplications
• Deletions

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• Chromosome abnormalities
• microscopically visible changes in the number or
  structure of chromosomes occur in
• Approximately 1 of all live births
• 23 of congenital anomalies with MR
• 13 of congenital heart defects
• 60 of spontaneous first trimester abortions
• Examples
• Down syndrome - caused by an additional copy of
  chromosome 21
• Unbalanced translocations - partial monosomy for
  one region of the genome and partial trisomy for
  another region of the genome
• 22q11.2 deletion interstitial deletion of 3Mb
  removing several genes

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When to order cytogenetic testing (i.e. standard
of care) Multiple congenital anomalies Mental
retardation of unknown origin or associated with
minor or major malformations Multiple
unexplained spontaneous abortions Ambiguous
genitalia Prenatal testing Abnormal prenatal
screen Ultrasound abnormalities
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Fluorescence In Situ Hybridization (FISH)
G A T T
Metaphase cell
Denatured probe DNA
Denatured target DNA ds ssDNA
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FISH probes
Unique sequence probes - single copy probes (1 kb
feasible). Useful for microdeletions/dups,
specific telomeres.
A shows a normal chromosome 15 B shows a
deletion at the end of the other chromosome 15
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Copy Number Polymorphism

• Large chunks of DNA (1000s-1 Mb) that are present
  in a variable number of copies in different
  people
• Can affect the number of copies of a gene that
  are present in a person
• Even if they dont contain a complete gene, they
  can affect the level of gene expression

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Comparative Genome Hybridization

• Fragments of sample and reference DNA labeled
  with different fluorescent dyes
• Labeled DNAs are denatured and incubated with
  metaphase chromosomes or on DNA arrays
• The DNAs compete for binding to the target DNA
• Resulting relative fluorescence is measured
• If theres an equal sequence between sample and
  reference,you get a yellow signal. If not you get
  red or green.

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Indications for array CGH

• Patients with normal chromosome analysis and
• Unexplained developmental delay or mental
  retardation
• Dysmorphic features or congenital anomalies
• Autism spectrum disorders, seizures, or a
  clinical presentation suggestive of a chromosomal
  syndrome
• Patients with a previously identified chromosome
  abnormality
• To size deletions or duplications and identify
  genes involved
• For apparently balanced rearrangements and an
  abnormal clinical phenotype, oligo array analysis
  can be used to test for cryptic
  deletions/duplications at the breakpoints

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Changes to DNA sequence

• CTCGAGGGGCCTAGACATTGCCCTCCAGAGAGAGCACCCAACACCCTCCA
  GGCTTGACCGGCCAGGGTGTCCCCTTCCTACCTTGGAGAGAGCAGCCCCA
  GGGCATCCTGCAGGGGGTGCTGGGACACCAGCTGGCCTTCAAGGTCTCTG
  CCTCCCTCCAGCCACCCCACTACACGCTGCTGGGATCCTGGATCTCAGCT
  CCCTGGCCGACAACACTGGCAAACTCCTACTCATCCACGAAGGCCCTCCT
  GGGCATGGTGGTCCTTCCCAGCCTGGCAGTCTGTTCCTCACACACCTTGT
  TAGTGCCCAGCCCCTGAGGTTGCAGCTGGGGGTGTCTCTGAAGGGCTGTG
  AGCCCCCAGGAAGCCCTGGGGAAGTGCCTGCCTTGCCTCCCCCCGGCCCT
  GCCAGCGCCTGGCTCTGCCCTCCTACCTGGGCTCCCCCCATCCAGCCTCC
  CTCCCTACACACTCCTCTCAAGGAGGCACCCATGTCCTCTCCAGCTGCCG
  GGCCTCAGAGCACTGTGGCGTCCTGGGGCAGCCACCGCATGTCCTGCTGT
  GGCATGGCTCAGGGTGGAAAGGGCGGAAGGGAGGGGTCCTGCAGATAGCT
  GGTGCCCACTACCAAACCCGCTCGGGGCAGGAGAGCCAAAGGCTGGGTGT
  GTGCAGAGCGGCCCCGAGAGGTTCCGAGGCTGAGGCCAGGGTGGGACATA
  GGGATGCGAGGGGCCGGGGCACAGGATACTCCAACCTGCCTGCCCCCATG
  GTCTCATCCTCCTGCTTCTGGGACCTCCTGATCCTGCCCCTGGTGCTAAG
  AGGCAGGTAAGGGGCTGCAGGCAGCAGGGCTCGGAGCCCATGCCCCCTCA
  CCATGGGTCAGGCTGGACCTCCAGGTGCCTGTTCTGGGGAGCTGGGAGGG
  CCGGAGGGGTGTACCCCAGGGGCTCAGCCCAGATGACACTATGGGGGTGA
  TGGTGTCATGGGACCTGGCCAGGAGAGGGGAGATGGGCTCCCAGAAGAGG
  AGTGGGGGCTGAGAGGGTGCCTGGGGGGCCAGGACGGAGCTGGGCCAGTG
  CACAGCTTCCCACACCTGCCCACCCCCAGAGTCCTGCCGCCACCCCCAGA
  TCACACGGAAGATGAGGTCCGAGTGGCCTGCTGAGGACTTGCTGCTTGTC
  CCCAGGTCCCCAGGTCATGCCCTCCTTCTGCCACCCTGGGGAGCTGAGGG
  CCTCAGCTGGGGCTGCTGTCCTAAGGCAGGGTGGGAACTAGGCAGCCAGC
  AGGGAGGGGACCCCTCCCTCACTCCCACTCTCCCACCCCCACCACCTTGG
  CCCATCCATGGCGGCATCTTGGGCCATCCGGGACTGGGGACAGGGGTCCT
  GGGGACAGGGGTCCGGGGACAGGGTCCTGGGGACAGGGGTGTGGGGACAG
  GGGTCTGGGGACAGGGGTGTGGGGACAGGGGTGTGGGGACAGGGGTCTGG
  GGACAGGGGTGTGGGGACAGGGGTCCGGGGACAGGGGTGTG

1 change every 1,000 bases 99.9 identical
from person to person
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What is the effect of a DNA change?
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DNA change can lead to different results
Deleterious
???
mutation
polymorphisms
Neutral variation
height, weight response to certain drugs, hair,
skin, eye color
Inborn errors of metabolism, cystic fibrosis,
sickle cell anemia, cancer
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Mutation can occur in different places across a
gene
1 2 3 4 5
X
X
X
X
promoter
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Clinicians often dont use pedigrees

• Although there are several obstacles, ... a
  common underestimation by clinicians of the value
  of the family history,

Blue 57 - no significant family hx Red 33 -
one chronic condition Yellow 8 - two Pink 2
- three or more

• (3) Scheuner, et al. Am J Med Genet 1997,
  71315-324.

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Pedigree vs. Questionnaire

• Focus on individuals by asking about each person
  in family
• Trigger patient memory
• Easier to see patterns
• Use to explain patterns
• Demonstrates biological relationships
• Amount of genetic information shared
• Reveals social relationships

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Family history can provide the basis for

• Making a diagnosis
• Determining who is at risk and level of risk
• Assessing needs for education and psychosocial
  support

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Rules

• Squares for males
• Circles for females

• Relationship line (horizontal) connects
  partners double slash equals separation
• Line of descent (vertical)
• Sib-ship line (horizontal)

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Information to collect

• Initials or first name particularly affected
• Ages or dates (year) of birth
• Decades for adult onset concerns okay
• Unaffected just as important as affected
• If affected, note age of onset
• Deceased slash age and cause include lost
  pregnancies

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More information to collect

• Physical and mental health of each individual
• Birth defects, developmental delay, mental
  retardation, inherited disorders, chronic
  conditions?
• Build key shading, patterns, etc.
• Watch abbreviations add to key as you go
• Date pedigree, Where and who collected
• Who reported information - Historian

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What to look for

• Early age of onset
• Multiple affecteds
• Individuals who are affected multiple times
• Particular constellations of features
• Pattern of inheritance

• Mental retardation/
• developmental delay
• Birth Defects
• Obvious genetic conditions
• Infertility/miscarriage

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90
82
Dx 48 d. 50
82
63
62
60
Dx 42 58
61 Type 2 diabetes Dx. 45
28
35 33 30
Breast cancer

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90
82
Dx 75 d. 77
Dx 76 80
Dx 68 d. 75 MI
63
62
60
58
28
35 33 30
Breast cancer

30
90
d. 86 Prostate ca
d. 35 Car accident
Dx 54 d. 78
70
63
d. 40 MI
60
58
Dx 51 51
28
35 33 30
Breast cancer

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• Autosomal Dominant
• Responsible gene on autosome
• Only 1 copy of mutation needed - normal allele
  not sufficient to compensate for mutant allele
• Heterozygotes and homozygotes are both affected

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Characteristics of Autosomal Dominant Disorders

• appears in every generation
• each affected person has an affected parent
  (exceptions!)
• each child of an affected parent has 50 risk to
  inherit trait.
• unaffected family members dont transmit
  phenotype to children (exceptions again).
• males and females equally likely to transmit the
  trait, to children of either sex.
• male-to-male transmission
• new mutations relatively common

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• Autosomal Recessive
• Responsible gene on autosome
• Both alleles of the gene must be defective.
• Frequently due to loss of function (gene is
  inactivated)
• Heterozygotes are unaffected carriers

Medium chain acyl CoA dehydrogenase (MCAD)
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Characteristics of Autosomal Recessive Disorders

• If disorder appears gt1 family member, typically
  found within a sibship, not across generations.
• The recurrence risk for each sib of the proband
  is 25.
• More common with consanguinity, especially for
  rare diseases.
• Males and females are equally likely to be
  affected.
• New mutation is almost never a consideration.

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• Sex-Linked
• Responsible gene on X chromosome (also called
  X-linked)
• Usually for females, both copies of the X
  chromosome must be affected
• Males, hemizygous for the X chromosome, much more
  likely to be affected

X-linked mental retardation
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Genetics and Prenatal Care

• Diagnostic Tests
• Chorionic Villus Sampling (CVS)
• Amniocentesis
• Testing for single gene defects

• Screens
• Combined first trimester screen
• Triple screen/Quad screen

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Genetics and Prenatal Care

• Diagnostic Tests
• Chorionic Villus Sampling (CVS)
• Amniocentesis

• Screens
• Combined first trimester screen
• Triple screen/Quad screen

Is 35 a magic age cut-off for screening versus
testing?
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From Thompson Thompson Genetics in Medicine
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For an autosomal recessive disorder, what is the
family history likely to be?
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Carrier Testing
The frequency of Tay-Sachs (prior to the onset of
widespread carrier screening among Ashkenazim )
was about 1/360,000 live births for
non-Ashkenazi North Americans, and 1/3,600
for North American Ashkenazi Jews Carrier
frequencies are therefore about 1/300 for
most North Americans, and 1/30 for North
American Ashkenazi Jews
And within a certain population, particular
mutations tend to predominate
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Carrier Testing

• Ashkenazi Jewish
• Tay-Sachs
• Canavan Disease
• 1 in 40
• Gaucher Disease
• 1 in 13
• Familial Dysautonomia
• 1 in 30
• Cystic fibrosis
• 1 in 25
• Fanconi anemia
• 1 in 90
• Niemann-Pick Disease
• 1 in 90
• Bloom syndrome
• 1 in 100

• African Americans
• Sickle cell disease
• 1 in 10
• Caucasians
• Cystic fibrosis
• 1 in 25

What does a negative result tell you?
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For an autosomal recessive disorder, what is the
family history likely to be?
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Newborn Screening
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Newborn Screening WHY ?

• Detect an affected infant before before symptoms
  to prevent or reduce morbidity and mortality
• Provide parents and family reproductive options
  for future pregnancies
• Avoid diagnostic odyssey

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http//genes-r-us.uthscsa.edu
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www.acmg.net/resources Look under reference
materials
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Algorithm for MCAD positive newborn screen
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MCAD ACT Sheet
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Adults who might seek genetic services

• Those with reproductive problems
• Those with a known genetic disorder in the family
• Those with symptoms of a genetic disorder
• Those with family history of cancer

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Case Study

• At the time of her annual physical, your patient,
  a 30-year old woman, asks about the breast
  cancer gene. She is Jewish and has been reading
  in the paper that Jewish women may be more likely
  to have this gene. She has two older sisters,
  aged 33 and 35, who are also worried about their
  risks.

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Cancer risk assessment
Sporadic cancer
Familial cancer
Red Flags
Hereditary cancer
Early onset cases Individuals affected with
multiple tumors Particular patterns of
tumors Breast and ovarian
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90
82
Dx 48 d. 50
82
63
62
60
Dx 42 58
61 Type 2 diabetes Dx. 45
28
35 33 30
Breast cancer

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Genetic testing for BRCA1/2

• All testing in North America performed by a
  single lab, Myriad
• Exons and adjacent regions sequenced. Also look
  for large duplications and deletions.
  Mutation-specific testing is also available.
• Possible results
• Mutation positive
• Mutation negative (known mutation in family)
• Variant of unknown significance (This happens
  10 of the time)
• No mutation found
• Preferable procedure is to do test on an affected
  family member first

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If our patient tests negative for a BRCA1/2
mutation, what are the possible explanations?

• No BRCA1/2 mutation in the family
• Increased risk
• She didnt inherit the mutation in the family
• Population risk (1 in 8)
• There is a mutation in our patient but we cant
  detect it using our testing method.
• High risk
• How can we avoid some of this confusion?
• Identify a familial mutation
• Try to test aunt first or test archived tissue
  sample from grandmother, if available.

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What if the test is positive?

• Provide psychosocial support
• Review cancer risks and management options
• Identify at-risk relatives
• Plan for follow-up

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Cancer risks with BRCA mutations
www.myriad.com
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Personal risk reduction following BRCA1/2
mutation detection

• Increased surveillance
• Selective estrogen receptor modulators
  (tamoxifen)
• Prophylactic mastectomy
• Prophylactic oophorectomy (usually recommended)

Finch et al. (2006) JAMA 286185-192
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ASCO Guidelines for Hereditary Cancer Testing

• Cancer predisposition testing should be offered
  only when
• There is a personal or family history suggesting
  a genetic susceptibility to cancer
• The test can be adequately interpreted
• The test result will aid in diagnosis or
  influence medical management of the patient or
  family members

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Why might somebody who has already had cancer
want genetic testing?

• They would be at increased risk of other
  additional primary tumors
• Could influence patient management
• Could help family members

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Genetic counseling/risk assessment

• When a patient is not interested in or is not a
  good candidate for cancer genetic testing,
  genetic counseling and risk assessment are still
  valuable when there is
• A suggestive pattern of cancers in the family or
  individual
• High anxiety
• A mixture of cancers in the family (suggestive of
  a cancer syndrome)

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Mendelian versus complex traits

• Mendelian traits
• Are determined by the independent action of a
  single major gene
• Mutation in this gene is necessary and sufficient
  for phenotype
• Have predictable inheritance patterns

Cystic fibrosis
Risk to each sib is 25 and we can do prenatal
testing
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Mendelian versus complex traits

• Complex traits
• Exhibit familial clustering but not predictable
  inheritance patterns

Cleft palate
Recurrence risk is 3 (compared to population
risk of 0.1)
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Benefits to determining genetic factors that
influence a complex trait

• Provide a molecular definition of the trait
• Improve understanding of disease etiology and
  mechanism
• Can offer early risk assessment
• Aids in discovery of new, targeted drugs
• Can be utilized for disease prevention

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How do we find genes for complex traits?
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Association studies

• Search for the occurrence of specific genetic
  variation at a higher frequency among affected
  individuals compared to unaffected individuals
• Strength of association is measured by an odds
  ratio
• we identified a variant in the CDKAL1 gene that
  was associated with T2D in individuals of
  European ancestry (odds ratio (OR) 1.20)
  Steintorsdottir et al. (2007)
• In contrast to studies of Mendelian traits in
  which you look for mutations throughout a gene
  that that are inherited with a trait, association
  studies look for one specific allele that is
  overrepresented in the case population
• An allele is the specific genetic variation in a
  gene
• The sickle cell mutation is an allele of the beta
  globin gene
• We reserve the term mutation for alleles that
  cause disease and are very rare

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Association and allele frequency in populations
Association with allele 1
Note the disease-associated allele is found in
the control population!
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Case Study

• A 53-year old African American male has an annual
  check-up. He is 510 and 220 lbs. He reports
  feeling well. Family history indicates a history
  of diabetes in his mother that was diagnosed at
  age 45. She died at age 58 from complications of
  diabetes after 3 years on dialysis.

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An immediate practical consequence of the
discovery, said Decodes chief executive, Kari
Stefansson, would be to develop a diagnostic test
to identify people who carry the variant gene. If
people knew of their extra risk, they would
have an incentive to stay thin and exercise, he
said.
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TCF7L2 and Type 2 Diabetes

• 38 of people examined are heterozygous for the
  TCF7L2 risk allele
• Relative risk if you are heterozygous for the
  TCF7L2 risk allele is 1.4.
• 26 of people in the group without the risk
  allele had T2D
• 38 of people in the group heterozygous for the
  risk allele had T2D
• General population risk for T2D is 33

Grant et al. (2006) Nature Genetics 38 320-323
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Why is this study important?

• There was no prior evidence that TCF7L2 was
  involved in diabetes. This gives us a new way to
  look at the process by which diabetes develops.
• Could ultimately lead to new treatments
• We may find other genes that, in combination with
  TCF7L2, help us fully understand genetic
  contributions to diabetes.

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Evaluating Association Studies

• Has the result been replicated in an independent
  population?
• How predictive is the genetic variation of
  disease?
• How do environmental risk factors interact with
  this genetic risk factor? Does the environmental
  risk have a much bigger role?
• Would a genetic test for this variation give us
  more accurate risk assessment than one based on
  general family history and lifestyle factors?

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Unique Aspects of Genetic Medicine

• Youre really treating a family, not an
  individual
• Testing individuals can reveal information about
  other family members
• Testing can be predictive
• Especially as we move toward genomic tests, we
  may find things were not looking for

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Genetic Resources

• National Society of Genetic Counselors
• http//www.nsgc.org/
• Genetics Home Reference
• http//ghr.nlm.nih.gov/
• NIH website with consumer-oriented information on
  genetic variation and genetic disease
• Gene Tests/Gene Reviews
• http//www.geneclinics.org/
• Current reviews of genetic disorders
• Labs that offer testing for each, if available
• Genetic clinics by geographic location
• Emory Genetics
• http//www.genetics.emory.edu/egl/index.php