Sun-Wei Guo

Performing the exact test of Hardy-Weinberg proportion for multiple alleles

The Hardy-Weinberg law plays an important role in the field of population genetics and often serves as a basis for genetic inference. Because of its importance, much attention has been devoted to tests of Hardy-Weinberg proportions (HWP) over the decades. It has long been recognized that large-sample goodness-of-fit tests can sometimes lead to spurious results when the sample size and/or some genotypic frequencies are small. Although a complete enumeration algorithm for the exact test has been proposed, it is not of practical use for loci with more than a few alleles due to the amount of computation required. We propose two algorithms to estimate the significance level for a test of HWP. The algorithms are easily applicable to loci with multiple alleles. Both are remarkably simple and computationally fast. Relative efficiency and merits of the two algorithms are compared. Guidelines regarding their usage are given. Numerical examples are given to illustrate the practicality of the algorithms.

Recurrence of endometriosis and its control

BACKGROUND Although surgery is currently the treatment of choice for managing endometriosis, recurrence poses a formidable challenge. To delay or to eliminate the recurrence is presently an unmet medical need in the management of endometriosis. To this end, proposals to investigate patterns of recurrence, to develop biomarkers for recurrence and to carry out biomarker-based intervention have been made. METHODS Publications pertaining to the recurrence of endometriosis and its related yet unaddressed issues were identified through MEDLINE. The reported recurrence rates, risk factors for recurrence, the effects of post-operative medication and causes of recurrence were reviewed and synthesized. In addition, several poorly explored issues such as time hazard function and mechanisms of recurrence were reviewed. Approaches to the development of biomarkers for recurrence and future intervention are discussed. RESULTS The reported recurrence rate was high, estimated as 21.5% at 2 years and 40-50% at 5 years. Few risk factors for recurrence have been consistently identified, and the evidence on the efficacy of the post-operative use of medication was scanty. The investigation on the patterns of recurrence may provide us with new insight into the possible mechanisms of recurrence and its control. The attempt to identify biomarkers for recurrence has started only very recently. CONCLUSIONS Much research is needed to better understand the patterns of recurrence and risk factors, and to develop biomarkers. One top priority is to develop biomarkers for recurrence, which may provide much needed clues to the possible mechanisms underlying recurrence and would allow the identification of patients with high recurrence risk, and permit for targeted intervention.

Affected-sib-pair interval mapping and exclusion for complex genetic traits: Sampling considerations

We describe an extension of Rischs [(1990a,b) Am J Hum Genet 46:222–228, 229–241] method of linkage detection and exclusion for complex genetic traits. The method uses interval mapping to infer disease locus identity‐by‐descent (IBD) sharing for affected sib pairs (ASPs) based on marker information for the ASP and other genotyped family members. The method is likelihood based, and makes use of Rischs parameterization in terms of recurrence risk ratios for relatives. We describe specific linkage detection and exclusion tests for use as genome screening tools to prioritize genomic regions for further study. We also examine issues of optimal study design.

Promoter Hypermethylation of Progesterone Receptor Isoform B (PR-B) in Endometriosis

The physiological effects of progesterone (P) is mediated by two isoforms of progesterone receptors (PRs): PR-A and PR-B. Progestins have long been used in the treatment of endometriosis but unfortunately the relief of pain is relatively short-term. In addition, about 9% of women with endometriosis simply do not respond to progestin therapy due to reasons unknown. In fact, a general tendency for relative progesterone resistance within eutopic and ectopic endometrium of women with endometriosis and the downregulation of PR-B, but not PR-A, in endometriosis have been noted. Since promoter hypermethylation is well-documented to be associated with transcriptional silencing, we sought to determine the methylation status of the PR-A and PR-B promoter regions in the epithelial component of endometriotic implants using a combination of laser capture microdissection (LCM), methylation specific PCR, and bisulfite sequencing. We found that the promoter region of PR-B, but not PR-A, is hypermethylated in endometriosis as compared with controls. In addition, the PR-B expression was significantly reduced in the ectopic endometrium. Our finding suggests that progesterone resistance in endometriosis in general and the down-regulation of PR-B, but not PR-A, in particular, are a result of promoter hypermethylation of PR-B, but not PR-A. This, in conjunction with our reported aberrant methylation of HOXA10 in the eutopic endometrium of women with endometriosis, strongly suggests that endometriosis is an epigenetic disease. This perspective should potentially open up new avenues for the delineation of pathogenesis of endometriosis, and might also lead to novel ways to treat the disease through reversing aberrant methylation via pharmacological means.

Epigenetics of endometriosis

Endometriosis is a common gynecologic disorder with an enigmatic etiopathogenesis. Although it has been proposed that endometriosis is a hormonal disease, an autoimmune disease, a genetic disease, and a disease caused by exposure to environmental toxins, our understanding of its etiopathogenesis is still inadequate, as reflected by recent apparent setbacks in clinical trials on endometriosis. In the last 5 years, evidence has emerged that endometriosis may be an epigenetic disease. In this article, the evidence in support of this hypothesis is reviewed, and its diagnostic, therapeutic and prognostic implications discussed. Publications, up to the end of June 2009, pertaining to epigenetic aberration in endometriosis were identified through PubMed. In addition, publications on related studies were also retrieved and reviewed. Epigenetics appears to be a common denominator for hormonal and immunological aberrations in endometriosis. Epigenetics also appears to have a better explanatory power than genetics. There is accumulating evidence that various epigenetic aberrations exist in endometriosis. In vitro studies show that histone deacetylase inhibitors may be promising therapeutics for treating endometriosis. In conclusion, several lines of evidence suggest that epigenetics plays a definite role in the pathogenesis and pathophysiology of endometriosis. As such, endometriosis is possibly treatable by rectifying epigenetic aberrations through pharmacological means. DNA methylation markers may also be useful for diagnostic and prognostic purposes. It is also possible that the delineation of the epigenetic changes accompanied by the genesis and progression of endometriosis could lead to interventions that reduce the risk of developing endometriosis.

Fine-Scale Genetic Mapping Based on Linkage Disequilibrium: Theory and Applications

Linkage-disequilibrium mapping (LDM) recently has been hailed as a powerful statistical method for fine-scale mapping of disease genes. After reviewing its historical background and methodological development, we present a general, mathematical, and conceptually coherent framework for LDM that incorporates multilocus and multiallelic markers and mutational processes at the marker and disease loci. With this framework, we address several issues relevant to fine-scale mapping and propose some efficient computational methods for LDM. We implement various LDM methods that incorporate population growth, recurrent mutation, and marker mutations, on the basis of a general framework. We demonstrate these methods by applying them to published data on cystic fibrosis, Huntington disease, Friedreich ataxia, and progressive myoclonus epilepsy. Since the genes responsible for these diseases all have been cloned, we can evaluate the performance of our methods and can compare ours with that of other methods. Using the proposed methods, we successfully and accurately predicted the locations of genes responsible for these diseases, on the basis of published data only.

Nuclear Factor-κB (NF-κB): An Unsuspected Major Culprit in the Pathogenesis of Endometriosis That Is Still at Large?

Endometriosis, defined as the ectopic presence of endometrial glandular and stromal cells outside the uterine cavity, is a common benign gynecological disorder with an enigmatic pathogenesis. Many genes and gene products have been reported to be altered in endometriosis, yet some of them may not be major culprits but merely unwitting accomplices or even innocent bystanders. Therefore, the identification and apprehension of major culprits in the pathogenesis of endometriosis are crucial to the understanding of the pathogenesis and would help to develop better therapeutics for endometriosis. Although so far NF-ĸB only has left few traces of incriminating fingerprints, several lines of investigation suggest that NF-ĸB, a pivotal pro-inflammatory transcription factor, could promote and maintain endometriosis. Various inflammatory agents, growth factors, and oxidative stress activate NF-ĸB. NF-ĸB proteins themselves and proteins regulated by them have been linked to cellular transformation, proliferation, apoptosis, angiogenesis, and invasion. Interestingly, all existing and nearly all investigational medications for endometriosis appear to act through suppression of NF-ĸB activation. In endometriotic cells, NF-ĸB appears to be constitutively activated, and suppression of NF-ĸB activity by NF-ĸB inhibitors or proteasome inhibitors suppresses proliferation in vitro. Viewing NF-ĸB as a major culprit, an autoregulatory loop model can be postulated, which is consistent with existing data and, more importantly, can explain several puzzling phenomena that are otherwise difficult to interpret based on prevailing theories. This view has immediate and important implications for novel ways to treat endometriosis. Further research is warranted to precisely delineate the roles of NF-ĸB in the pathogenesis of endometriosis and to indict and convict its aiders and abettors.

Patterns of and risk factors for recurrence in women with ovarian endometriomas.

OBJECTIVE: To identify risk factors for and the patterns of recurrence of endometrioma and of dysmenorrhea in women with ovarian endometrioma. METHODS: We evaluated 710 consecutive patients operated on for ovarian endometriomas who were followed up for an average of 22.4 months. Twenty factors were examined to assess their effect on risk of recurrence of endometrioma and of dysmenorrhea using survival analysis. Hazard rate also was estimated to examine recurrence patterns. RESULTS: For recurrence of endometrioma, the revised American Fertility Society (rAFS) score, younger age at surgery, and previous medical treatment of endometriosis were identified to be risk factors. For recurrence of dysmenorrhea, rAFS score was the only risk factor. For both recurrences, there was a constant hazard rate in the first 28–30 months after surgery, indicating that the recurrence in that period is completely random. After that period, the hazard rate increased dramatically. CONCLUSION: The total rAFS score, but not rAFS stage, is a risk factor for recurrence of both endometrioma and dysmenorrhea, indicating that the rAFS stage has little prognostic value. The existence of a completely random recurrence period may be a universal phenomenon, with its duration and the magnitude of recurrence risk determined by patient characteristics and quality of care. The second phase of much higher recurrence risk may reflect successful reseeding, reimplantation, and regrowth of ectopic endometrium. Therefore, the identification of risk factors as well as patterns of recurrence should shed better light on possible causes for recurrence, which is now poorly understood. LEVEL OF EVIDENCE: II

Resolution of clonal origins for endometriotic lesions using laser capture microdissection and the human androgen receptor (HUMARA) assay

OBJECTIVE To determine the clonal origins of endometriotic lesions using laser capture microdissection and PCR-based HUMARA assay. DESIGN Molecular genetic study of human tissue. SETTING Molecular genetics laboratory in an academic setting. PATIENT(S) Twenty patients with endometriosis. Forty specimens of endometriotic lesions from these patients and one specimen of normal endometrium were analyzed. INTERVENTION(S) Laser capture microdissection was used to harvest epithelial cells from single and multifocal endometrial lesions from paraffin-embedded and frozen tissues, and their clonality was determined with the HUMARA assay. MAIN OUTCOME MEASURE(S) Polymerase chain reaction-based HUMARA assay of clonality. RESULT(S) Thirty-eight specimens were polymorphic and thus informative. Most specimens were monoclonal, as determined by the HUMARA assay. In four specimens of multifocal lesions, polyclonality was detected, but upon more refined microdissections and further analyses, we found that each focus was monoclonal individually. CONCLUSION(S) Previously reported polyclonality is very likely to be attributed to the pooling of multifocal lesions or contamination of normal tissues. These results suggest that endometriotic lesions were monoclonal in origin, and in the case of multifocal lesions, each focus originates monoclonally; hence, different foci have independent origins. The monoclonality of endometriotic lesions suggests that they may carry neoplastic potentials, and the apparent independent origins of multifocal lesions suggest that reconstruction of individual lesion histories may help us to understand the initiation and progression of endometriosis.

Inflation of Sibling Recurrence-Risk Ratio, Due to Ascertainment Bias and/or Overreporting

One widely used measure of familial aggregation is the sibling recurrence-risk ratio, which is defined as the ratio of risk of disease manifestation, given that ones sibling is affected, as compared with the disease prevalence in the general population. Known as lambdaS, it has been used extensively in the mapping of complex diseases. In this paper, I show that, for a fictitious disease that is strictly nongenetic and nonenvironmental, lambdaS can be dramatically inflated because of misunderstanding of the original definition of lambdaS, ascertainment bias, and overreporting. Therefore, for a disease of entirely environmental origin, the lambdaS inflation due to ascertainment bias and/or overreporting is expected to be more prominent if the risk factor also is familially aggregated. This suggests that, like segregation analysis, the estimation of lambdaS also is prone to ascertainment bias and should be performed with great care. This is particularly important if one uses lambdaS for exclusion mapping, for discrimination between different genetic models, and for association studies, since these practices hinge tightly on an accurate estimation of lambdaS.