Welcome to Frontiers in Reproductive Technology!

Schedule

Week Date Homework In-class Discussion Topics Readings
1 April 1 Select a project Readings for next class Course Overview
New datasets, new technologies, new opportunities in fertility technology 		Summary of course goals, topics covered, expectations, project descriptions, students meet each other and form teams.
New datasets: UK Biobank
New technologies: single cell sequencing, robotics, computer vision
New opportunities: strategies to make IVF more affordable, less invasive, for infants to be born with fewer diseases
1 April 3 Readings for next class IVF I Guest Lecture with Dr. Ruben Alvero, MD - Professor of Obstetrics and Gynecology (Reproductive Endrocrinology and Infertility) at Stanford Medical Center
2 April 8 Readings for next class Cost and Coverage of IVF in the US & Abroad Disparities in cost and quality of IVF domestically and internationally
Classes of companies in the IVF/infertility/fertility preservation space
    TBA
2 April 10 Readings for next class A Crash Course in Reproductive Biology and Embryology Guest lecture with Vikrant Reddy - Embryologist, Fertility & Reproductive Health, Stanford Medicine and Ogi Badamjav, Clinical Embryologist (Andrology), Stanford Healthcare
    Textbook of Clinical Embryology - Edited by Kevin Coward and Dagan Wells
    Chapters 3, 4, 10, 11, 23, 24, 26, 27, 28, 30, 31 and 34.
3 April 15 Readings for next class GWAS and Polygenic Risk Scores I Broad vs. narrow sense heritability
Mathematical modelling of gene vs environmental variables, flaws and limitations
3 April 17 Mid-quarter progress report due next week GWAS and Polygenic Risk Scores II PRS- How are they computed? How accurate are they?
GWAS successes/failures. Missing heritability problem.
4 April 22 Mid-quarter progress report due Wednesday at midnight In vitro gametogenesis (IVG) Guest lecture: Vittorio Sebastiano Assistant Professor of Obstetrics & Gynecology - Reproductive and Stem Cell Biology
4 April 24 Mid-quarter progress report due at midnight SNP chips, cfDNA, and single cell sequencing Overview of wet lab techniques, basic chemistry and protocols
How is the data generated (and cleaned) to arrive at a diagnosis or risk score?
Strengths? Limitations? Cost? Sensitivity/specificity.
    TBA
5 April 29 Readings for next class Measuring Embryo Health Guest Lecture with Barry Behr - Professor of Obstetrics and Gynecology (Reproductive Endrocrinology and Infertility) at Stanford Medical Center
Visit to Stanford's IVF Lab (optional, after clearance)
5 May 1 Readings for next class Egg Harvesting and Cryopreservation Guest Lecture with Barry Behr - Professor of Obstetrics and Gynecology (Reproductive Endrocrinology and Infertility) at Stanford Medical Center
Deep dive into embryo fertilization, biopsy, selection protocols used today
Opportunities to improve selection
6 May 6 Readings for next class Setting up an IVF lab from scratch Guest Lecture with Barry Behr - Professor of Obstetrics and Gynecology (Reproductive Endrocrinology and Infertility) at Stanford Medical Center
Visit to Stanford's IVF Lab (optional, after clearance)
6 May 8 Readings for next class Prenatal Genetic Diagnosis Overview of tests currently available, costs, market penetration, sensitivity/specificity
Single gene disorders, chromosomal abnormalities
Tradeoffs in obtaining data from a 3rd party vs. developing a lab in house
Quality measures, regulation, cost
7 May 13 Readings for next class New technologies applied to IVF Roboticization, microfluidics, computer vision for egg selection
7 May 15 Readings for next class Ethics of Embryo Selection and Editing Student debate on the ethics and implications of embryo selection based on phenotypes as genetic testing technology improves
8 May 20 Readings for next class Prenatal Diagnostics Guest lecture with Jie Deng - Reproductive Endocrinologist and Infertility Physician at Stanford University
8 May 22 Final presentations next week! Setting up a genomics lab from scratch Guest Lecture: Danny Desloover from Color Genomics
9 May 27 Final Project Presentations due this week
Code, supplementary write ups due end of Week 10
No Class Holiday
    None.
9 May 29 Final Project Presentations due this week
Code, supplementary write ups due end of Week 10
Final Project Presentations and Feedback Student projects!
    None.

Logistics

Organizers
Noor Siddiqui (nfs (at) stanford (dot) edu)
Office Hours: By appointment.
Course Project Mentors

To be announced

Honor Code

(From the Office of Community Standards): The Honor Code is the university's statement on academic integrity written by students in 1921. It articulates university expectations of students and faculty in establishing and maintaining the highest standards in academic work. The Honor Code is an undertaking of the students, individually and collectively: that they will not give or receive aid in examinations; that they will not give or receive unpermitted aid in class work, in the preparation of reports, or in any other work that is to be used by the instructor as the basis of grading; that they will do their share and take an active part in seeing to it that others as well as themselves uphold the spirit and letter of the Honor Code. The faculty on its part manifests its confidence in the honor of its students by refraining from proctoring examinations and from taking unusual and unreasonable precautions to prevent the forms of dishonesty mentioned above. The faculty will also avoid, as far as practicable, academic procedures that create temptations to violate the Honor Code. While the faculty alone has the right and obligation to set academic requirements, the students and faculty will work together to establish optimal conditions for honorable academic work.

Disclaimer
  • The schedule is subject to change.

Feedback
  • Anonymous Feedback is greatly appreciated. This is the first time this course is being offered and we'd love to tailor it to your interests. Compliments, complaints, and recommendations for topics to add are all fair game :)

Required Work

Participation

Attendance will be taken at the start of each class, and will be mandatory.

Summary of Deadlines

Week 1: Select a project and propose a midterm (week 4) milestone to achieve
Week 4: Submit a mid-quarter progress report
Week 9: Final project presentations
Week 10: Submit final project

Final grade computation
  • 50% Final Project
  • 30% Attendance and Participation
  • 20% Paper Review and Presentation
Credit
  • Website Design from CS124 course staff. Used with permission from Dan Jurafsky.
  • Video credit

FAQ

Can I audit the class?
  • The room is quite small, so this will have to be on a case-by-case basis. Please email nfs [at] stanford.edu if you would like to audit the course. .
Is this class about how to build a designer baby?
  • No.
What is a student initiated course?
  • Stanford has a pathway for students to propose and teach courses after review, accompanied by faculty sponsorship. This couse is sponsored by Russ Altman. This is our first time offering the course, and we greatly appreciate your feedback!
Will lectures be recorded?
  • Unfortunately not. Please contact the teaching staff if you would like a copy of the slides etc., but most of the course readings/material is listed above.