ME:680.712 Phenotyping for Functional Genetics

Johns Hopkins Mouse Pathobiology and Phenotyping Short Course
♦ Rigor and Reproducibility in Translational Research 


NEXT SHORT COURSE: July 13-17, 2020

REGISTRATION (Click ⇒ Links for registration forms; email completed forms to

⇒ Registration Form for ALL JHU registrants (JHU GRAD STUDENTS, POSTDOCS, FACULTY, STAFF, CORES)
⇒ Tuition Remission Form (for JHU Faculty & Staff –$600 for any/all lectures, labs, tours, slide conference, Monday reception
⇒ NON JHU Registration Form  Until June 15, 2020: $600. for lectures only; $800. For Lectures + 4 hands on laboratory sessions.
​       ♦ After June 15 CALL for AVAILABILITY: $800. for lectures only; $1000. For lectures + labs (space permitting).
⇒  EXHIBIT Registration Form July 13-14 Turner Concourse (includes access to course lectures activities throughout the week)


Target Audience: Graduate students and postdocs, as well as research faculty and staff, who currently work with, or expect to work with mouse models and genetically engineered mice.

Since 2010 this has been offered in a short course format, largely for continuity of the practical laboratory training experience.

Faculty from JHU School of Medicine and Bloomberg School of Public Health introduce students to mouse biology, pathology, genetics, normal 'phenotypes', phenotyping concepts, and to new and established phenotyping capabilities in multiple disciplines.  JHU cores and resources are highlighted. See previous course programs/schedules below.

>35 contact hours: ~11hr Laboratory sessions; ~24 hr Lectures; also poster sessions, laboratory tours, interactive quiz.
33hr Approved RACE CE credit.
Four (4) hands-on laboratory sessions (~11 hours total)  include clinical and physical examination of mice, specimen collection, clinical pathology and anatomic pathology
(Familiarity with basic anatomy is EXPECTED for participation in laboratory sessions).

Syllabus material is provided:   Hard copy laboratory manual is provided to all enrolled in laboratory sessions.  Lecture and laboratory syllabus material is provided electronically as pdf's linked to the program.   It is NOT necessary to purchase a text book.

(JHUSOM graduate school ME 680.712) Course credit and grades are based on:

  1. Attendance and participation in lecture and laboratory sessions  Monday morning through Friday noon, and
  2. Exam ('take home', Open book, JHU honor code applies), distributed Monday at the beginning of the course, and Due Friday, 5pm.  
    The exam is intended to be practical and relevant to diverse research.       
  3. ONLY Students registered to take this course FOR CREDIT may participate in laboratory sessions.
    Graduate students who AUDIT the course, also postdocs, faculty, staff, may wait list to participate in laboratory sessions if space is available. CONTACT to request to wait list.
    Familiarity with basic anatomy is EXPECTED for participation in laboratory sessions.  

Course Co-Directors: Cory Brayton, DVM, Dip. ACLAM, ACVP, Julie Watson, MA, VetMB, Dip ACLAM, Kinta Diven, MS.

Laboratory Coordinator: Nadine Forbes McBean, MS -

Course Administrator: Wendy Elza - - 410 502 3050
Graduate students and postdocs in JHU institutions OTHER THAN SOM should contact Wendy for assistance.


MONDAY            July 13, 2020           Welcome, Intro, Posters, Exhibits 
8am-5pm             Registration – Turner Concourse
845-10am            Brayton  – Introduction: Phenotyping & Famous Mice
10-11    Brayton  –  Common Phenotypes & Disease (Spontaneous /NON infectious)
11-12    Watson   –  Environmental influences on phenotypes What is in your mouse environment?
12-1    LUNCH   –  POSTERS, Meet the Cores
1-2        Resources for Rigor and Validity in PreClinical Research
2-3        Brayton  –  Microbial & infectious phenotypes in our research
3-4        Brayton  –  Immunovariability in (immune sufficient and immune deficient) mice
4-5        Hutchinson – Research relevant social life and behaviors of mice
5-7pm   RECEPTION,  POSTERS, Meet the Cores
TUESDAY           July 14, 2020          GEM & Multidisciplinary Phenotyping
9-10        Hawkins/Reeves – Making Mice - traditional and new transgenic technologies
10-11      Aja – Metabolic Phenotypes and Phenotyping
11-12      Mitzner – Pulmonary/Respiratory Phenotypes & Phenotyping  
12-130   LUNCH & TOURS –  CMOR (metabolic) & BRB Imaging, Behavioral + visit Cores/posters
130-230    Doyle – Ophthalmic Phenotypes and Phenotyping
230-330    Kim/Lauer – Auditory Phenotypes and Phenotyping
330-430    Foss/Gabrielson – IMAGING for Phenotyping
430-530    TBA – Digital Pathology: options for image analysis and quantitative pathology
WEDNESDAY    July 15, 2020          Practical Phenotyping 1
9-10        Brayton - Clinical Pathology – oversimplified
10-11      Watson - Clinical / Physical Exam – Modified SHIRPA
11-1130   Adelaja - Applied Imaging Mass Spectrometry - AIMS Core
1130-1230   LUNCH BREAK (on your own) & Tours – CMOR (metabolic) & BRB Imaging, Behavioral
1230-230  LAB 1: Watson / Forbes & al Clinical Examination
 230-5       LAB 2: Forbes / Brayton & al Clinical Pathology and Specimen collection
JH Phenotyping Laboratory Manual 5th ed 2019  (PDF 58p  ~6MB)
THURSDAY       July 16, 2020           Practical Phenotyping 2
9-1030            Brayton/Forbes- Anatomic Pathology Phenotyping  – Necropsy + trimming
1030-1130      Brayton – Microscopic Anatomy & Pathology – interactive Quiz format
1130-1230      LUNCH BREAK (on your own)
1230-430        LAB 3: Forbes / Brayton & al.  Anatomic Pathology – Necropsy, tissue collection
FRIDAY             July 17, 2020           Practical Phenotyping 3 Advanced Pathology
9-11       LAB 4: Forbes / Brayton & al. Anatomic Pathology – Tissue Trimming for histology
11-12     Comparative Anatomy/Pathology (human/mouse) – interactive Quiz format
12-1       LUNCH BREAK (on your own)
1-2         A Meeker  –  Immunohistochemistry - principles and protocol development
2-3         B Karim, N Pate – NCI Pathology in Preclinical Cancer Research
3-4         TBA – Embryo and Developmental Phenotyping 

5pm        Quizzes Due ! for course ME680.712


Phenotyping Core
Johns Hopkins Phenotyping and Comparative Pathology Core (MRB)
iLAB information and submission

Animal Care and Use Committee (ACUC)

Behavioral Core School of Medicine
Rodent Behavioral Phenotyping (MRB)
CSMR Centralized Services for Metabolism Research
Indirect calorimetry, food intake (Rangos)

MRB Molecular Imaging Service Center and Cancer Functional Imaging Core
MRI, PET, CT, SPECT, IVIS, Optical Imaging, Ultrasound (MRB)

OTS Oncology Tissue Services Core
TMA, IHC, Slide Scanning, Histology core labs at SKCCC
iLAB information and submission

Laboratory Manual and Previous Programs



Radaelli, Santagostino, Sellers, Brayton. 2019. Immune Relevant and Immune Deficient Mice: Options and Opportunities in Translational Research. IlarJ.