Transcript End of Quarter Review Genetics 202

END OF QUARTER REVIEW
GENETICS 202
Jon Bernstein
Department of Pediatrics
November 19th, 2015
Session Outline

Final exam logistics

Review
◦ Major topics since first review session
◦ Overview of genetic testing methods and strategies
◦ Practice questions

Announcements
Final Exam Information
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Wednesday December 9th; 9:30a to 12:30p
◦ LKSC 120 and LKSC 130
◦ Room assignments TBA
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Multiple choice format administered on CourseWork
◦ Approximately 75 questions
◦ Students will take the exam on computers provided by EdTech
◦ Some questions based on clinical vignettes some not
◦ Paper copy of exam will be available
Final Exam Information
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Two sections to final exam
◦ “Multiple Choice Questions”
◦ “Using Electronic Resources” questions
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You can use OMIM, GeneReviews (selected articles) and the UCSC genome browser for the entire exam
What you may bring
◦ Notes

Notes may be on paper or electronic
 You may bring your iPad or laptop
◦ It may be difficult to access files on CourseWork while taking the exam
◦ Some questions will require calculations

Consider bringing a piece of scratch paper and/or a pencil
Final Exam Make-Up Policy
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As per course policy, a written Dean’s excuse is
required
Types of Material Covered in Course
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Definitions (Lectures, course reader)
◦ e.g. - chromosome, sequencing, CGH, heteroplasmy, epigenetic, GWAS
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Problem solving skills (Lectures, course reader, problem sets, small-group sessions)
◦ e.g. - Bayes theorem/conditional probability, variant assessment, selecting laboratory tests, risk
assessment (includes pedigree analysis, Hardy-Weinberg equation, multifactorial inheritance),
using electronic resources
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Communication strategies and skills (Lectures, problem sets, small-group sessions)
Current areas of research (Lectures, course reader, problem sets)
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Epigenetics and the microbiome
Personalized medicine in oncology
Therapy for mitochondrial disorders
Strategies for iPS cell construction
Linkage and Association
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Two methods of developing evidence for a relationship between a
genetic locus and a trait/disease
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Linkage
◦ Calculate odds ratio for the observed pattern of segregation in a pedigree
at a given recombination frequency
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Association
◦ Calculate a p-value for the likelihood that the observed relationship
between genotype and phenotype occurred by chance
GWAS versus Rare variant association studies
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In GWAS one is looking for associations
between genetic markers identifying
haplotypes (ancestral chromosome
segments) and phenotypes
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In whole genome/exome sequencing
one is looking for associations between
predicted mutations of variable ages
and phenotypes
http://hapmap.ncbi.nlm.nih.gov/originhaplotype.html.en
Reproductive genetics
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Carrier testing, Universal carrier testing
◦ Importance of pre and post-test probability
Non-invasive prenatal testing
 Preimplantation genetic diagnosis
 Chorionic villus sampling
 Amniocentesis
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Reproductive genetics
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Teratology
◦ Critical period for exposure
◦ Dose-response relationship
◦ Plausible mechanism
Microbiome and Epigenome
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Technological advance has driven down the cost of acquiring large
genomic and other “omic” data sets
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Gene regulation at the level of the epigenome may result from
congenital and somatic variation
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These data sets provide additional opportunity to identify cohorts
of patients with similar genotypic and/or phenotypic profiles that
may predict prognosis or response to therapy
Next-generation sequencing / Genomics – Ethical
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Genome scale testing is more likely to produce
secondary or incidental findings
◦ In the near term, also more likely to produce variants of
unknown significance
Biochemical Genetics / Interventional Genetics
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The prototypical metabolic pathway
Common biochemical laboratory tests
◦ Plasma amino acids
◦ Urine organic acids
◦ Acylcarnitine profile
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Newborn screening
Therapy (Indications for and limitations of)
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Dietary therapy
Cofactor therapy
Enzyme replacement therapy
Organ transplantation
Cell and Gene Therapy
•
Delivery
• Targeting appropriate tissue
• Viral and non-viral vectors
• Duration of expression
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Immune response
Side effects/Toxicity
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Advantages and disadvantages of
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• Integrating and non-integrating vectors
• Stem cell and iPS cell therapies
Clinical genetics
Integrating clinical and laboratory findings
 Dysmorphology
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◦ Malformation
◦ Deformation
◦ Disruption
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The increasing role of data sharing in establishing
genetic pathogenesis
Cancer Genetics
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Genetic testing has an important role in guiding care of at risk family
members
◦ Can also impact management of affected individuals
 Both germline and somatic genetic variation can be predictive of therapeutic response
 Screening for predictable complications and prophylactic surgery can in improve outcomes
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Tumors of common origin and type often share similar somatic
mutations
Test youngest, affected individuals first to increase the likelihood of
obtaining informative negative test results due to age dependent
penetrance
Pharmacogenomics
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Pharmacokinetics
◦ Key examples
 Thiopurine metabolism
 Codeine metabolism
Pharmacodynamics
 Opportunities for clinical implementation
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◦ PharmGKB, CPIC Guidelines
Ethics and Communication
The same information can mean different things to different
people
 Different people may want to know about different types of
health/risk information
 The duty to warn at risk family members can conflict with
the requirement to protect patient confidentiality as well as
patient autonomy.
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◦ Primary vs secondary (incidental) findings
Considerations in genetic problem solving
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What is the known or suspected mode(s) of inheritance?
◦ Does the number of mutations/variants identified match that
expected for the mode of inheritance?
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Who has been tested? Are they affected or
unaffected? What tissue was tested?
◦ Should mosaicism be considered?
Considerations in genetic problem solving
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Who is the best person in the family to test and what
tissue is most appropriate to test?
◦ Test affected family members first when possible
◦ Consider the possibility of germline mosaicism, somatic
mosaisicm, tumor genotype versus non-tumor genotype,
recent transfusion, stem cell transplantation
Considerations in genetic problem solving
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Has the testing performed to date evaluated for all
potentially relevant changes/variation in the patient's
DNA?
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Do the results I have show variants or definite
mutations?
Considerations in genetic problem solving
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Interpretation of variants of unknown significance/Variant
curation
◦ Bioinformatics
 Effects on protein structure/function
 Effects on mRNA splicing
◦ Databases, medical literature
◦ Segregation analysis
 Consider mode of inheritance, possibility of age-dependent or
incomplete penetrance as well as possibility of mosaicism
Considerations in genetic problem solving
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Test characteristics
◦ What are the technical capabilities and limitations of the test
being ordered.
Summary of Cytogenetic Techniques
Summary of Molecular Techniques
Summary of next generation methods
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Strengths and limitations of NGS in detecting SNVs
◦ Difficulty with repetitive sequences
◦ Difficulty with non-unique sequences
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Strategies and limitations of NGS for detecting SVs (Hint:
approaching clinical level of accuracy for deletions)
◦ Analysis of paired-end reads
◦ Analysis of split reads
◦ Read depth analysis
Numerical chromosome abnormality
Chromosomal deletion or duplication
FISH*
Karyotype
Translocation, Inversion
Ring chromosome
Microdeletion or microduplication (CNV)
Single nucleotide variant%
Indel (Small insertion of deletion)
MLPA+
Array CGH
Next gen sequencing
Sanger sequencing
Deletion of a single or multiple exons of a gene
Uniparental disomy (involving an imprinted region)
Epimutation
Methylation Testing
Notes: Solid lines indicate the most common use(s) of each test. Dotted lines indicate abnormalities that may also be detected. * Each
FISH probe typically corresponds to only one region of the genome, if the probes do not correspond to the loci involved by an abnormality
it may not be detected. % DNA sequencing at typically performed examines exons, exon intron boundaries and sometimes promoter
sequences. Deep intronic sequences and other non-coding elements may not be assessed. + MLPA probe sets are most commonly used to
detect deletions and duplications at a single locus of size intermediate to that detectable by sequencing and that detectable by array CGH.
Electronic Resources
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Be able to access and utilize
◦ OMIM
 Searchable by multiple means including by clinical findings, comprehensive listing of
genes, phenotypes, and gene-phenotype associations, information on modes of
inheritance
◦ GeneReviews
 Information on Diagnosis/Testing, Management, Natural History and Genetic
Counseling for select conditions
◦ UCSC Genome Browser
 Information on location of elements within genome
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Know what types of information are accessible in each resource and be able to
locate it
Clinical Case
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What are possible
mode(s) of inheritance?
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What would the
recurrence risk be for the
couple’s next child?
Clinical Case
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How might an autosomal
dominant condition
result in this pedigree?
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What would the
recurrence risk be?
Clinical Case
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What is the
patient’s risk to be
a carrier (assume
no new
mutations)?
What is her risk to
have an affected
child?
P
= Hemophilia A (X-linked
recessive)
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The patient is
interested in the
possibility of
prenatal testing.
What should your
next step be?
P
= Hemophilia A
Next steps
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Who to test?
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What test to order?
◦ (Where would you
look this up?)
P
= Hemophilia A
What if testing results were normal?
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Are there other tests to consider?
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What might explain the situation if these tests are also
normal?
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A) Mutation is in a regulatory element or intron
B) The clinical diagnosis is incorrect
C) The pedigree is incorrect
D) All of the above
Review Question
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A genetic marker has two forms. The frequency of the first
is 0.4 and of the second is 0.6. What percentage of
individuals with be heterozygous at this locus?
a) .16
b) .25
c) .36
d) .48
e) .50
Review Question
Assume that the concordance for twins with cleft lip is 0.40 for MZ pairs
and 0.05 for DZ pairs. For congenital heart disease, the figures are 0.05 for
MZ pairs and 0.05 for DZ pairs. Based on this information:
A. A large proportion of cleft lip shows Mendelian inheritance
B. A large proportion of congenital heart disease shows Mendelian
inheritance
C. Cleft lip is more common in twins than is congenital heart defect
D. There is evidence for polygenic/multifactorial inheritance in cleft lip
E. None of the above.
Review Question
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You are planning a GWAS study to identify genetic risk
factors for decreased lung size. Halfway through the study
you learn that the device being use to measure lung size
produces unpredictable results. This may lead to:
A) False positive results in the GWAS study
B) False negative results in the GWAS study
C) Population stratification
D) Failure to take advantage of genetic heterogeneity
Clinical case
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Given the presence of
an autosomal recessive
disease in the family
what is the risk that the
couple’s first pregnancy
will be affected.
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P
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Clinicial case
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If the couple has had 3
prior unaffected children
is their estimated risk
now higher, lower or the
same as was previously
predicted?
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P
Clinical Case
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2 ½ year old boy with dilated cardiomyopathy, presented at
age 2 with persistent cough. Diagnostic work-up does not
provide an explanation for the cardiomyopathy.
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The patient is now “…7 years of age and underwent heart
transplant [at age 4] for a dilated cardiomyopathy….”
Clinical case
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The family is expecting a second child
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“I did speak to his parents about counseling about the recurrence
of cardiomyopathy in the family. The fetus that mom is carrying
has been echo'd already, so we know at least at this point that
there is no evidence of cardiomyopathy. However, this can
develop at any age. I suggested that both of -- parents obtain
echocardiograms, something which was suggested to them …, but
which has not been followed up on….”
What is the risk of recurrence?
What if the parents were 1st cousins?
P
A baby brother is born.
 Newborn screening is now
running in California. He is
positive for decreased C0
(Carnitine).
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The suspected diagnosis is
primary carnitine deficiency.
How can this diagnosis be
confirmed?
P
Clinical case
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You are seeing a young adult for a history of psychosis.
A DNA sequencing panel covering several genes
associated with mitochondrial disease was sent.
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The following test result is available to you.
Test result
Clinical case
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“The child had a positive POLG gene mutation and a
very strong family history of schizophrenia in the
mother and developmental issues in the father.”
Clinical case
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2-year-old mostly healthy boy presenting to our clinic
with concerns for dwarfism/skeletal dysplasia
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…a presumed diagnosis of hypochondroplasia was
provisionally made; however, a SNP microarray was
normal by report.
TA Review Session and Office Hours

TA Review Session – Tuesday Dec 8th 1-5p LK 209

Jon – Thursday 12/3 9-10a LKSC Café
Paula Tuesday 12/1 12:15PM-1:15PM LKSC Cafe
 Grace Wednesday 12/2 9:30-10:30 AM LKSC Cafe
 Additional TA office hours TBA
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Teaching Assistants for 2015
Please let course director or a TA know if you are
interested.
 5, 20% TAships will be available.
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Course Evaluations
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Will be distributed by evaluation group soon
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Your course evaluations are essential to guide course
development, please complete them
Good luck on the final exam!