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Genetics rotation goals and objectives
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UIC Department of Pediatrics
Division of Genetics
Genetics Rotation Goals and Objectives
The genetics rotation exposes residents and medical students to the principles of genetic diagnosis,
management, and counseling. Residents and students will be exposed to patient and family historytaking in the context of genetic disorders, will gain experience in the dysmorphology examination, and
will observe genetic counseling sessions. Residents and students will also gain knowledge and
experience in the diagnosis and management of patients with metabolic disorders.
The goals and objectives of this rotation are formulated on the basis of the core ACGME competencies.
A clinic schedule and specifics goals for knowledge are also outlined in this document.
1.
Competency 1: Patient care (PC). Residents are expected to provide patient care in a
compassionate, appropriate, and effective manner for the promotion of health, prevention of
illness, treatment of disease, and at the end of life. Residents and student s will:
a. Demonstrate the ability to gather a three-generation family history for genetic disorders
and identify risks when present. By the end of the rotation, the resident will
demonstrate some proficiency in drawing a pedigree.
b. Demonstrate physical examination skills that are appropriate for patients across all age
ranges, emphasizing the identification and description of major and minor anomalies.
c. Develop an assessment and diagnostic/management plan for the patient based on
personal and family history and physical exam findings.
2. Competency 2: Medical knowledge (MK). Residents must demonstrate knowledge of
established and evolving biomedical, clinical, epidemiological and social-behavioral sciences,
as well as the application of this knowledge to patient care. They will demonstrate
proficiency in obtaining knowledge through didactic sessions, discussions on rounds or in
clinic, and self-guided education. Residents and students will:
a. Demonstrate knowledge of key concepts regarding genome structure, molecular
and cytogenetics techniques, and common patterns of Mendelian and nonMendelian inheritance.
b. Demonstrate knowledge of common methods for genetic diagnosis such as
chromosome analysis, microarray CGH analysis, single gene analysis, and carrier
screening. Residents and students should understand applications and limitations of
these techniques.
c. Demonstrate knowledge about the etiology of major and minor malformations:
chromosomal, single gene, teratogen exposure, maternal factors, and multifactorial.
d. Describe the indications for genetic testing for genetic or metabolic disorders in the
primary care setting.
e. Demonstrate knowledge of key concepts related to testing for carrier state (ie,
how race/ethnicity and carrier frequency play a role in carrier screening) and for
adult-onset disorders such as cancer, hemochromatosis, Huntington disease.
Genetics rotation goals and objectives
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f. Describe the settings and reasons in which prompt diagnosis of certain
chromosome abnormalities is necessary (Trisomy 13 and 18).
g. Discuss evaluation and management of individuals with a positive newborn
screen.
h. Describe the diagnosis and management of the more common genetic disorders
such as Down syndrome, Turner syndrome, Klinefelter syndrome,
Neurofibromatosis type I, Noonan syndrome, Fragile X syndrome, Marfan
syndrome, osteogenesis imperfecta, etc.
3. Competency 3: Practice-based learning and improvement (PBL). Residents must
demonstrate the ability to investigate and evaluate their care of patients, to appraise
and assimilate scientific evidence, and to continuously improve patient care based on
constant self-evaluation and life-long learning. Residents are expected to develop skills
and habits to be able to meet the following goals:
a. identify strengths, deficiencies, and limits in one’s genetics knowledge and
expertise;
b. set learning and improvement goals by means of self-directed learning, readings
from the genetics reading file, and completion of the weekly genetics problem
set;
c. identify and perform appropriate learning activities as outlined above;
d. systematically analyze practice using quality improvement methods, and
implement changes with the goal of practice improvement;
e. incorporate formative evaluation feedback into daily practice.
4. Competency 4: Interpersonal and communications skills (CS). Residents must
demonstrate interpersonal and communication skills that result in the effective exchange of
information and collaboration with patients, their families, and health professionals.
Residents are expected to:
a. communicate effectively with patients, families, and the public, as appropriate,
across a broad range of socioeconomic and cultural backgrounds;
b. demonstrate empathetic and supportive behavior to patients and families when
delivering or discussing difficult news;
c. demonstrate the ability to provide genetic counseling and education to patients and
families in an approachable and easily-understandable manner;
d. understand the appropriate use of interpreting services;
e. communicate effectively with physicians, other health professionals, and health
related agencies;
f. work effectively as a member or leader of a health care team or other professional
group;
g. act in a consultative role to other physicians and health professionals; and,
h. maintain comprehensive, timely, and legible medical record from clinic and
consultations.
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5. Competency 5: Professionalism (P). Residents must demonstrate a commitment to
carrying out professional responsibilities and an adherence to ethical principles.
Residents are expected to demonstrate:
a. compassion, integrity, and respect for others;
b. responsiveness to patient needs that supersedes self-interest;
c. respect for patient privacy, confidentiality, and autonomy;
d. accountability to patients, society and the profession; and,
e. sensitivity and responsiveness to a diverse patient population, including but not
limited to diversity in gender, age, culture, race, religion, disabilities, and sexual
orientation.
f. the ability to identify and discuss ethical issues in genetic testing and counseling,
including testing of asymptomatic/presymptomatic minors.
6. Competency 6: Systems-based practice (SBP). Residents must demonstrate an
awareness of and responsiveness to the larger context and system of health care, as
well as the ability to call effectively on other resources in the system to provide optimal
health care. Residents are expected to:
a. work effectively with the genetics team, including attendings, genetic
counselors, and metabolic dietitians;
b. coordinate patient care within the UIC health care system as it is relevant to the
patient;
c. incorporate considerations of cost awareness and risk-benefit analysis in patient
and/or population-based care as appropriate, including choosing the appropriate
type of testing and considerations of genetic testing versus a clinical diagnosis
with supportive evidence when appropriate;
d. advocate for quality patient care and optimal patient care systems;
e. work in interprofessional teams to enhance patient safety and improve patient
care quality; and
f. participate in identifying system errors and implementing potential systems
solutions.
g. locate, appraise, and assimilate evidence from scientific studies related to their
patients’ health problems;
h. use information technology to optimize learning; and,
i. participate in the education of patients, families, students, residents and other
health professionals.
Genetics rotation goals and objectives
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Knowledge goals for the genetics rotation
1ºcompetency Level of
domain
competence
Teaching Evaluation
methods methods
Understand the role of the primary care
provider in the identification of developmental
or physical problems
PC,MK
PGY1
1,3,4,5
A,b,c
PC, MK,
PBL,SBP
PGY1
1,3,5
A,b,c
MK
PGY1
1,2,3,4,5
A,b,c
PC,PBL,MK
PGY2
1,2,3,4,5
A,b,c
MK, PBL
PGY1
1,2,3,4,5
A,b,c
a.
Know the basic investigations for speech
delay
b. Know the basic investigations for
developmental delay
c. Know the basic investigations for major and
/or minor malformations
Understand the role of the primary care
provider in a referral to a geneticist
a.
Know some of the indications for referral
based on personal history of a condition
(overgrowth, hemihypertrophy, hearing loss,
major malformations, failure to thrive)
b. Know some of the indications for referral
based on family history of a condition
(multiple pregnancy losses, hearing loss, early
deaths, family history of a specific genetic
condition)
c. Provide some basic counseling to patients and
families regarding the reason for the referral
Understand patterns of Mendelian and nonMendelian inheritance (autosomal
dominant/recessive, X-linked, mitochondrial,
imprinting)
a.
b.
c.
d.
Understand the concept of co-dominance
and incomplete dominance in AD disease
(example: homozygous achondroplasia)
Know that carriers of X-linked disorders may
manifest some aspects of disease, and
understand the reasons for this.
Understand the role of imprinting in disease
that is maternally vs. paternally inherited.
Know the concepts of variable penetrance
and expressivity.
Understand basic concepts in the etiology of
chromosomal/genomic/single gene disorders
(cytogenetically-visible deletions/duplications vs.
microdeletions/microduplications, aneuploidy,
inversions, balanced vs. unbalanced translocations,
Robertsonian translocations,
missense/nonsense/frameshift mutations)
Understand the basic limitations of genetic
testing methodologies, including chromosome
analysis, microarray analysis, FISH, and gene
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sequencing.
Understand the role and limitations of carrier
screening in genetic counseling and family
planning
Understand the concept of newborn screening,
have basic knowledge of the methodologies
used in newborn screening (substrate
quantification, measurement of enzyme activity,
HPLC, tandem mass spectrometry).
a.
b.
c.
a.
b.
c.
d.
1,2,3,4,5
A,b,c
PC,MK, PBL
PGY2
1,2,3,4,5
A,b,c
PC,MK
PGY2
1,2,3,4,5
A,b,c
PC, MK
PGY2
1,2,3,4,5
A,b,c
Know the major features and
management of common chromosomal
conditions such as Down syndrome,
Trisomy 13 and 18, Turner, cri du chat
Know the major features and
management of common genomic,
imprinting, and single gene disorders
such as Velocardiofacial syndrome,
Williams syndrome, Fragile X, Prader
Willi and Angelman, Beckwith
Wiedemann, osteogenesis imperfecta,
and Duchenne Muscular Dystrophy.
Know the manifestations of common
embryopathies, such as valproate,
warfarin, and phenytoin
Understand multifactorial inheritance in
cleft lip/palate, club foot, neural tube
defects, autism
Understand when to suspect and the screening
laboratories to do for inborn errors of
metabolism (IEM)
b.
PGY1
Know the limitations of newborn screening
Know the resources for contacting a
department of public health and how to find
out the scope of a particular newborn
screening program
Understand how to respond to notification of
an abnormal newborn screen and
online/community resources for information
Understand the etiology of major and minor
malformations, including chromosomal, single
gene, teratogen exposure, maternal factors, and
multifactorial.
a.
MK, PBL
Know the difference between the different
categories and presentation of IEM (amino
acid disorder, organic acidemia, fatty acid
oxidation disorder, urea cycle disorder)
Understand the basic goals of treatment of
IEM
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Codes for teaching activities
1. Clinical encounters
2. Lecture
3. Small group discussion/problem sets
4. Assigned reading
5. Web-based module
Codes for evaluation methods
a. Direct observation
b. New Innovations
c. Participation in small group discussion
Clinic attendance and completion of consults will address the majority of these knowledge goals. We
have also compiled a reading file that includes a variety of articles related to the knowledge goals.
Residents are expected to also pursue self-directed reading and learning during the rotation.
There will be a weekly review of cases on Thursdays at 2pm, and the resident is expected to briefly
present one interesting case a week.
A weekly problem set will be available for the resident to work on in advance and will be discussed
Tuesdays at 2pm.
Each resident is expected to do a 20 minute presentation on an interesting topic of choice during case
review on the last Thursday of the rotation.
In addition, the resident is directed to the following online resources for learning:
1.
2.
3.
4.
5.
6.
7.
8.
9.
Gene Clinics: www.geneclinics.org. A comprehensive resource for peer-reviewed information
on a variety of syndromes. Follow the link on the home page labeled “Educational materials” for
extensive information about genetic services.
Online Mendelian Inheritance (OMIM):
http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM&itool=toolbar (Can also access by going
to www.pubmed.gov and clicking on OMIM link).
SimulConsult: http://www.simulconsult.com/ Good website for generating a differential
diagnosis for disorders with neurological symptoms.
American College of Medical Genetics ACT sheets: www.acmg.net, follow the link labeled “ACT
sheets and confirmatory algorithms.” An excellent resource for determining the conditions
encompassed by an abnormal analyte on newborn screening and how to proceed.
National Newborn Screening and Genetics Resource Center: http://genes-r-us.uthscsa.edu/
Contains information on the state level regarding conditions included in newborn screening per
state and state contact information.
The Illinois newborn screening program contains Illinois-specific information:
http://www.idph.state.il.us/HealthWellness/genetics.htm’
The Region 4 Genetics Collaborative, which includes Illinois, has an online course for healthcare
providers about newborn screening. You will need to register. The course is available at:
http://www.region4genetics.org/online_learning/online_learning_home.aspx
The American Academy of Pediatrics, Committee on Genetics publishes health supervision
guidelines for various genetic conditions:
http://aappolicy.aappublications.org/cgi/collection/committee_on_genetics
Neuromuscular disorders webpage through Washington University in St. Louis:
http://neuromuscular.wustl.edu/ Good website for working through a differential diagnosis.
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Feedback will be given during the rotation and at the end based on attendance in clinic, completion of
consults, baseline knowledge, self-directed learning, and observation of patient and family interactions
by the genetics staff. Written feedback will be submitted by appropriate staff through New Innovations.
Residents are encouraged to offer feedback and suggestions as well for continued improvement of the
rotation.
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Division of Genetics clinic schedule
Monday
Tuesday
Wednesday
Thursday
Friday
Morning report
0800-0900
Morning report
0800-0900
Morning report
0800-0900
Morning report
0800-0900
Morning report
0800-0900
Genetics Clinic
0830-1200
GEH
Genetics Clinic
0830-1200
LP
Genetics Clinic
0830-1200
CH
Genetics Clinic
0830-1200
AH
LP
Noon conference
1200-1300
Genetics Clinic
1200-1600
GEH
Noon conference
1200-1300
Eye clinic (4th
Tuesday, Eye &
Ear Infirmary)
1230-1600
AH
Noon conference
1200-1300
Patient review
1400
12th floor
840 S. Wood
Noon conference
1200-1300
Noon conference
1200-1300
Genetics Clinic
1230-1600
GEH
Neurocutaneous
Clinic (1st Wed, 2nd
floor Eye & Ear
Infirmary)
1230-1630
LP
MDA Clinic (1st &
3rd Thursday, OCC
4E)
RD or JZ
Inpatient consults: LP 1st half of month, AH 2nd half of month
GEH: George Hoganson
AH: Allen Horwitz
CH: Catharine Harris
LP: Loren Pena
RD: Rich Dineen
JZ: Jamie Zdrodowski
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Problem set
Week 1
1.
You receive a call from the department of public health with abnormal newborn screening
results for a patient of yours. Your patient had a galactose level of 9mg/dL (normal less than
6.5) and reduced GALT activity.
a. How do you proceed?
b. How do you interpret these results?
c. If the galactose is 1.5mg/dL and GALT activity is absent, how do you interpret the
results? What specific questions do you ask the parents in order to interpret the
results?
d. If the galactose level is 12mg/dL and GALT activity is present, and you know the patient
received a blood transfusion, how do you interpret these results?
2. You receive another call from the department of public health with abnormal newborn
screening results. The person reports that the patient had a “very elevated level of C3
acylcarnitines”? You scratch your head and wonder what the person is talking about.
a. What resources would you consult in order to interpret this result?
b. Once you understand what the results mean, you realize that this is your next patient to
be seen in clinic. Delineate the next steps in your management of this patient.
3. Illinois is one of the states that screens for cystic fibrosis. You receive a letter stating that your
patient had “an IRT greater than 150 and one delta F508 mutation identified.”
a. What do these results mean?
b. What’s the next step in the management of this patient?
4. Mr and Mrs Smith are interested in starting a family, and they come to see you for genetic
counseling. Mrs Smith relates that she had some learning problems at school that required
special education. Her parents were healthy, and she had a brother and a sister. Her brother
and a male cousin through the maternal aunt had mental retardation. Mr Smith is an only child
of healthy parents with no family history of learning disabilities or mental retardation. Mr and
Mrs Smith are interested in finding out what the family history may reflect and whether it can
be “passed on” in the family.
a. Draw the pedigree
b. Comment on the most likely pattern of inheritance
c. Generate a differential diagnosis and possible testing strategies for your differential.
d. How would you counsel this couple?
Genetics rotation goals and objectives
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Problem set
Week 2
1.
You are rotating through the NICU and are called to a delivery in the middle of the night. A full
term infant weighing 3kg is born. As you resuscitate the baby, you notice that he has bilateral
cleft lip and palate, a cardiac murmur, and an imperforate anus.
a. You decide to call genetics the next morning, but you want to look good by having a
differential diagnosis and diagnostic plan in place before you call. Where would you
look for ideas, and what testing, if any, would you propose?
2.
On your next call in the NICU, you are called to a delivery of a child who was noted to have
“lung hypoplasia” and short humeri and femurs on prenatal ultrasound. After delivery, you
notice a very very small thoracic cavity, length <5th percentile for gestational age, and short
extremities. Baby is having respiratory distress.
a. Once you go through the ABCs and the patient is stabilized, you reflect on how small
the chest and how short the extremities are. You decide to call genetics the next day,
but in the meantime, what kind of investigations can you do to investigate the physical
findings in this child?
b. You meet mom the next day – she appears to have short stature and a narrow chest,
while dad is of normal stature. What kind of inheritance does this family history
suggest?
c. The parents seem surprised that baby was born with these problems, and they ask you
whether this can occur in a future pregnancy – what do you tell them?
d. If you meet the parents and they are both short, and they tell you that they both have
achondroplasia, how would you counsel them regarding a prognosis for this baby and
recurrence risk in a future pregnancy?
3. As the senior resident on the floor, you get a call from the ER regarding a 4 day old infant that
was just brought in for lethargy and hypotonia. Per the ER, baby was initially feeding well but
has become less responsive in the last 24 hrs, and is now barely arousable. A dexi in the ER was
undetectable. The ER has initiated resuscitation and a septic workup. However, a palpable liver
was noted by the staff, and, since all the UIC geneticists are on vacation, they are interested in
your input regarding whether any “genetic problems” are possible, and if so, how they could
investigate.
a. Comment on possible “genetic” etiologies, their symptoms, and diagnostic workup for
each.
b. Assuming this is a weekday, are there any resources available that you could contact
regarding the above symptoms in the newborn?
Genetics rotation goals and objectives
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Problem set
Week 3
1.
You get a frantic phonecall from Mrs Jones to let you know that she is unexpectedly pregnant
and just found out. She estimates that she is 5-6 weeks along. She had a previous child with
congenital adrenal hyperplasia who had ambiguous genitalia and died early in infancy during an
adrenal crisis. She remembers that part of the counseling involved taking a medication early in
her next pregnancy, and is scared that she is already too late.
a. What is the recurrence risk for congenital adrenal hyperplasia in a couple who
previously had an affected child?
b. What enzyme is deficient, what are some of the possible symptoms, and how do you
manage an affected child?
c. Mrs Jones comes to see you the next day. Enumerate the management steps that you
recommend for this pregnancy, and compare the management plans for a male and a
female fetus.
2. The Stein family comes to see you in clinic. While Mrs Stein is a healthy woman, Mr Stein has a
family and personal history of Familial Adenomatous Polyposis (FAP) and had a subtotal
colectomy in his 30s for thousands of polyps. However, he has not had genetic testing. They
have 3 children, who are 5, 7, and 12 years old. They are interested in finding out whether their
children have FAP.
a. What is the inheritance pattern of FAP?
b. How can you establish the diagnosis?
c. How can you establish whether the Stein children are affected? Would you defer
diagnosing the kids to a later age?
3. Mrs Blatt has an extensive history of breast and ovarian cancer in her family – her mother had
ovarian cancer in her 40s, and two of her sisters had breast cancer in their late 30s. She is in her
early 40s and has received genetic counseling regarding hereditary breast and ovarian cancer
syndromes, but has declined genetic testing for herself. She comes to see you in clinic because
she is interested in BRCA testing for her 10 year old daughter, as she feels this information is
important for the daughter to have.
a. Draw the pedigree
b. How would you approach genetic testing in the family?
c. How are BRCA1 and BRCA2-related hereditary ovarian cancer syndromes inherited?
d. Would you offer testing for the 10 year old daughter? Explain your rationale.
Genetics rotation goals and objectives
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Problem set
Week 4
1.
You are seeing a patient in your continuity clinic for the first time, and notice dysmorphic facies
that resemble those of Down Syndrome. As part of the gestational history, mom offers that she
had some sort of blood test that was abnormal, but she declined additional testing.
a. What kind of blood test during pregnancy is she referring to? Describe the specifics of
the test.
b. If above test is abnormal, what additional diagnostic testing can be offered to the
expectant mother?
c. What kind of testing can you send to confirm your suspicion about your patient?
d. A diagnosis of Down Syndrome is confirmed, and the family is back for counseling. Are
there any resources at your disposal to discuss the management of this patient? List the
more common types of complications observed through childhood and as adults in
patients with Down syndrome.
2. The Mendoza family comes to see you because of a family history of a very rare autosomal
recessive disorder. The couple has 3 children who are affected, in addition to another 4 children
in the family who are also affected. While the estimated incidence of this disorder is about 1:5
million, you are puzzled that there are so many kids affected with the same disorder in this
family.
a. How do you interpret this family history? What are the possible scenarios that could
account for such a high incidence rate in the family?
b. The Mendozas are adamant that they are not related, and that there are no
consanguineous marriages in the family. What are some alternative explanations for
this family history?
c. How can you approach genetic testing for this family? Would you start with the
parents, the unaffected, or the affected kids?
d. How can they use the results of genetic testing in their family planning?
3. A couple with a child who has cleft lip and palate seek genetic counseling regarding recurrence
of cleft lip and palate in a future pregnancy.
a. What kind of recurrence risk would you quote them?
b. What other sorts of medical history would help you in your counseling?
c. During the session, you notice that the mother has a number of small pits on her lower
lip. Are you concerned? Does this change your risk estimate?
Updated on 2/3/10