Study reveals rate at which key genetic deletions contribute to male infertility

Electron micrograph of egg and sperm

Electron micrograph of egg and sperm.

Image: Courtesy of HHMI

October 25, 2012

Tags: Page LabGenetics + Genomics

CAMBRIDGE, Mass. — A large-scale analysis of Y chromosomes from more than 20,000 men finds that two spontaneously recurring deletions along a complex region of the Y chromosome are responsible for approximately 8% of cases of failed sperm production.

Although previous research had identified deletions in the region of the Y known as AZFc (for azoospermia factor c) as causing severe spermatogenic failure (SSF), this latest analysis, conducted by Whitehead Institute Director David Page and colleagues, is the first to determine how prevalent these deletions are in the general population.

According to the study, published in the November issue of the American Journal of Human Genetics, the deletion known as b2/b4 is found in one of every 2,300 men, increases the risk of SSF 145 times, and is responsible for roughly 6% of cases.

“This deletion almost always results in spermatogenic failure, so it would be extremely rare for it to be transmitted from father to son without medically assisted reproduction,” says Page. “Because of this, we can conclude that its prevalence in the population essentially reflects the rate at which this deletion arises spontaneously in men.”

“Medically relevant population genetics studies are well established for most of the human genome, but this is the first study of this kind for the Y chromosome,” says Steven Rozen, an associate professor at Duke-NUS Graduate Medical School Singapore and first author of the study.

Page notes that this study would not have been possible without the unique sequencing method he developed with collaborators at Washington University in St. Louis to help navigate the structural complexities of the Y chromosome. As Page reported years ago, the Y comprises several regions of large palindromes—areas of mirror-imaged genetic sequences. Such regions render conventional sequencing approaches incapable of detecting extremely subtle genetic differences found hidden among the “mirrors.” In response, Page and colleagues developed an approach known as SHIMS (single-haplotype iterative mapping and sequencing) to establish a definitive reference DNA sequence of the Y chromosome.

Such structural complexity is not exclusive to the Y chromosome, however. Smaller “halls of mirrors” can be found scattered throughout the human genome, and these areas are likely to be as unstable and prone to mutation as those on the Y chromosome. While the effects of the known deletions of the AZFc region appear to be limited to sperm production, substantially more harmful health effects are apt to arise from mutations elsewhere. Given the inherent challenges of obtaining accurate and complete DNA sequences of mirrored regions, Page believes that the current reference sequence of the human genome is missing potentially meaningful detail—and that the time has come to apply SHIMS broadly.

“The key to SHIMS starts with the realization that there are areas of the human genome that are almost perfectly mirrored repeated sequences that are greater than 99% identical,” says Page, who is also an investigator of the Howard Hughes Medical Institute. “When you assemble a sequence from multiple unrelated chromosomes, as was done with the human genome, you cannot make sense of minute but critical differences.”

“The human genome reference is a consensus sequence, which is a politically wonderful outcome,” he adds. “But in mirrored regions, consensus doesn’t really represent anything. A complete and accurate assembly of the human genome will answer questions we do not even know to ask.” 


This work was supported by the National Institutes of Health, the Howard Hughes Medical Institute, and the Singapore Ministry of Health and Agency for Science, Technology, and Research.


Written by Matt Fearer  


David Page’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also a professor of biology at Massachusetts Institute of Technology and an investigator of the Howard Hughes Medical Institute.


Full Citation:

“AZFc Deletions and Spermatogenic Failure: A Population-Based Survey of 20,000 Y Chromosomes”

American Journal of Human Genetics, November 2, 2012 (in print)

Steven G. Rozen (1,2), Janet D. Marszalek (1,3), Kathryn Irenze (4), Helen Skaletsky (1,3), Laura G. Brown (1,3), Robert D. Oates (5), Sherman J. Silber (6), Kristin Ardlie (4,7), and David C. Page (1,3,8)

1. Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.

2. Duke-NUS Graduate Medical School, Singapore 169857, Singapore.

3. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.

4. Genomics Collaborative, SeraCare Life Sciences, Cambridge, MA 02139, USA.

5. Department of Urology, Boston University School of Medicine, Boston Medical Center, Boston, MA 02118, USA.

6. Infertility Center of St. Louis, St. Luke’s Hospital, St. Louis, MO 63017, USA.

7. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

8. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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