Genetic associations in preterm birth: a primer of marker selection, study design, and data analysis

Protein interaction networks define the genetic architecture of preterm birth

The likely genetic architecture of complex diseases is that subgroups of patients share variants in genes in specific networks sufficient to express a shared phenotype. We combined high throughput sequencing with advanced bioinformatic approaches to identify such subgroups of patients with variants in shared networks. We performed targeted sequencing of patients with 2 or 3 generations of preterm birth on genes, gene sets and haplotype blocks that were highly associated with preterm birth. We analyzed the data using a multi-sample, protein–protein interaction (PPI) tool to identify significant clusters of patients associated with preterm birth. We identified shared protein interaction networks among preterm cases in two statistically significant clusters, p < 0.001. We also found two small control-dominated clusters. We replicated these data on an independent, large birth cohort. Separation testing showed significant similarity scores between the clusters from the two independent cohorts of patients. Canonical pathway analysis of the unique genes defining these clusters demonstrated enrichment in inflammatory signaling pathways, the glucocorticoid receptor, the insulin receptor, EGF and B-cell signaling, These results support a genetic architecture defined by subgroups of patients that share variants in genes in specific networks and pathways which are sufficient to give rise to the disease phenotype.

Genetic variation associated with preterm birth in African-American women

BACKGROUND

Preterm birth is considered a multifactorial condition; however, emerging evidence suggests that genetic variation among individuals may have an important role. Prior studies have suggested that single-nucleotide polymorphisms associated with genes related to the immune system, and particularly the maternal inflammatory response, may be associated with an increased risk of preterm delivery.

OBJECTIVE

The objective of the study was to identify single-nucleotide polymorphisms associated with spontaneous preterm birth <37 weeks within a cohort of African-American women.

STUDY DESIGN

This is a secondary analysis of a randomized trial that evaluated periodontal disease and preterm birth. Women were enrolled between 6 and 20 weeks' gestation at 3 prenatal care clinics between 2004 and 2007. Maternal DNA samples were collected and analyzed using a custom 1536 single-nucleotide polymorphismgenotyping array designed to assess genes involved in inflammation. Women were included in this study if they self-identified as African American. We excluded women with a multiple gestation or an indicated preterm delivery. We performed allele- and genotype-based analyses to evaluate the association between spontaneous preterm birth and tag single-nucleotide polymorphisms. We used a logistic regression to adjust for prior preterm birth in our genotype-based analysis. In a subgroup analysis, we compared women who delivered at <34 weeks' gestation to women who delivered at term. Within the microarray, we identified ancestry informative markers and compared global ancestry estimates among women who delivered preterm with those who delivered at term.

RESULTS

Of the 833 African-American women in the study with genotype data, 77 women (9.2%) had a spontaneous preterm birth, whereas 756 women delivered at term. In an allele-based analysis, 4 single-nucleotide polymorphisms related to the genes for protein kinase C-α (PRKCA) were associated with increased risk of spontaneous preterm birth <37 weeks, whereas a single single-nucleotide polymorphism related to fms-related tyrosine kinase 1 (FLT1) was associated with spontaneous preterm birth <34 weeks. A genotype-based analysis revealed similar associations between single-nucleotide polymorphisms related to the PRKCA genes and spontaneous premature delivery. Additionally, single-nucleotide polymorphisms related to matrix metalloproteinase-2 (MMP2), tissue inhibitor of matrix metalloproteinase-2 (TIMP2), and interleukin 16 (IL16) genes were associated with spontaneous preterm birth <37 weeks in genotype-based analysis. Genetic variants related to MMP2, matrix metalloproteinase-1 (MMP1), and leukemia inhibitory factor receptor antisense RNA 1 (LIFR-AS1) genes were associated with higher rates of preterm birth <34 weeks. Ancestry estimates were similar between the women who had a spontaneous preterm birth and those who delivered at term.

CONCLUSION

We identified tag single-nucleotide polymorphisms related to 7 genes that are critical to inflammation, extracellular remodeling, and cell signaling that were associated with spontaneous preterm birth in African-American women. Specifically, we found a strong association with the PRKCA gene. Genetic variation in these regions of the genome may be important in the pathogenesis of preterm birth. Our results should be considered in the design of future genomic studies in prematurity.

Targeted Sequencing and Meta-Analysis of Preterm Birth

Understanding the genetic contribution(s) to the risk of preterm birth may lead to the development of interventions for treatment, prediction and prevention. Twin studies suggest heritability of preterm birth is 36-40%. Large epidemiological analyses support a primary maternal origin for recurrence of preterm birth, with little effect of paternal or fetal genetic factors. We exploited an "extreme phenotype" of preterm birth to leverage the likelihood of genetic discovery. We compared variants identified by targeted sequencing of women with 2-3 generations of preterm birth with term controls without history of preterm birth. We used a meta-genomic, bi-clustering algorithm to identify gene sets coordinately associated with preterm birth. We identified 33 genes including 217 variants from 5 modules that were significantly different between cases and controls. The most frequently identified and connected genes in the exome library were IGF1, ATM and IQGAP2. Likewise, SOS1, RAF1 and AKT3 were most frequent in the haplotype library. Additionally, SERPINB8, AZU1 and WASF3 showed significant differences in abundance of variants in the univariate comparison of cases and controls. The biological processes impacted by these gene sets included: cell motility, migration and locomotion; response to glucocorticoid stimulus; signal transduction; metabolic regulation and control of apoptosis.

Cluster analysis of spontaneous preterm birth phenotypes identifies potential associations among preterm birth mechanisms

OBJECTIVE

We sought to use an innovative tool that is based on common biologic pathways to identify specific phenotypes among women with spontaneous preterm birth (SPTB) to enhance investigators' ability to identify and to highlight common mechanisms and underlying genetic factors that are responsible for SPTB.

STUDY DESIGN

We performed a secondary analysis of a prospective case-control multicenter study of SPTB. All cases delivered a preterm singleton at SPTB ≤34.0 weeks' gestation. Each woman was assessed for the presence of underlying SPTB causes. A hierarchic cluster analysis was used to identify groups of women with homogeneous phenotypic profiles. One of the phenotypic clusters was selected for candidate gene association analysis with the use of VEGAS software.

RESULTS

One thousand twenty-eight women with SPTB were assigned phenotypes. Hierarchic clustering of the phenotypes revealed 5 major clusters. Cluster 1 (n = 445) was characterized by maternal stress; cluster 2 (n = 294) was characterized by premature membrane rupture; cluster 3 (n = 120) was characterized by familial factors, and cluster 4 (n = 63) was characterized by maternal comorbidities. Cluster 5 (n = 106) was multifactorial and characterized by infection (INF), decidual hemorrhage (DH), and placental dysfunction (PD). These 3 phenotypes were correlated highly by χ(2) analysis (PD and DH, P < 2.2e-6; PD and INF, P = 6.2e-10; INF and DH, (P = .0036). Gene-based testing identified the INS (insulin) gene as significantly associated with cluster 3 of SPTB.

CONCLUSION

We identified 5 major clusters of SPTB based on a phenotype tool and hierarch clustering. There was significant correlation between several of the phenotypes. The INS gene was associated with familial factors that were underlying SPTB.

Entropy-based selection for maternal-fetal genotype incompatibility with application to preterm prelabor rupture of membranes

Background

Maternal-fetal genotype incompatibility (MFGI) is increasingly reported to influence human diseases, especially pregnancy-related complications. In practice, it is challenging to identify the ideal incompatibility model for analysis, since the true MFGI mechanism is generally unknown. The underlying MFGI mechanism for different genetic variants can vary, and to use a single incompatibility model for all circumstances would cause power loss in testing MFGI.

Results

In this article, we propose a practical 2-step procedure that incorporates a model selection strategy based on an entropy measurement to select the most appropriate MFGI model represented by data and test the significance of the MFGI effect using the chosen model within the generalized linear regression framework.

Conclusions

Our simulation studies show that the proposed two-step procedure controls the type I error rate and increase the testing power under various scenarios. In a real data application, our analysis reveals genes having an MFGI effect, which may not be detected with a non-model selection counterpart.

Localization of a major susceptibility locus influencing preterm birth

Preterm birth (PTB) is a complex trait, but little is known regarding its major genetic determinants. The objective of this study is to localize genes that influence susceptibility to PTB in Mexican Americans (MAs), a minority population in the USA, using predominantly microfilmed birth certificate-based data obtained from the San Antonio Family Birth Weight Study. Only 1302 singleton births from 288 families with information on PTB and significant covariates were considered for genetic analysis. PTB is defined as a childbirth that occurs at <37 completed weeks of gestation, and the prevalence of PTB in this sample was 6.4%. An ∼10 cM genetic map was used to conduct a genome-wide linkage analysis using the program SOLAR. The heritability of PTB was high (h(2) ± SE: 0.75 ± 0.20) and significant (P = 4.5 × 10(-5)), after adjusting for the significant effects of birthweight and birth order. We found significant evidence for linkage of PTB (LOD = 3.6; nominal P = 2.3 × 10(-5); empirical P = 1.0 × 10(-5)) on chromosome 18q between markers D18S1364 and D18S541. Several other chromosomal regions (2q, 9p, 16q and 20q) were also potentially linked with PTB. A strong positional candidate gene in the 18q linked region is SERPINB2 or PAI-2, a member of the plasminogen activator system that is associated with various reproductive processes. In conclusion, to our knowledge, perhaps for the first time in MAs or US populations, we have localized a major susceptibility locus for PTB on chromosome 18q21.33-q23.

Candidate gene linkage approach to identify DNA variants that predispose to preterm birth

BACKGROUND

The aim of this study was to identify genetic variants contributing to preterm birth (PTB) using a linkage candidate gene approach.

METHODS

We studied 99 single-nucleotide polymorphisms (SNPs) for 33 genes in 257 families with PTBs segregating. Nonparametric and parametric analyses were used. Premature infants and mothers of premature infants were defined as affected cases in independent analyses.

RESULTS

Analyses with the infant as the case identified two genes with evidence of linkage: CRHR1 (P = 0.0012) and CYP2E1 (P = 0.0011). Analyses with the mother as the case identified four genes with evidence of linkage: ENPP1 (P = 0.003), IGFBP3 (P = 0.006), DHCR7 (P = 0.009), and TRAF2 (P = 0.01). DNA sequence analysis of the coding exons and splice sites for CRHR1 and TRAF2 identified no new likely etiologic variants.

CONCLUSION

These findings suggest the involvement of six genes acting through the infant and/or the mother in the etiology of PTB.

Pathway-based genetic analysis of preterm birth

Preterm birth in the United States is now 12%. Multiple genes, gene networks, and variants have been associated with this disease. Using a custom database for preterm birth (dbPTB) with a refined set of genes extensively curated from literature and biological databases, we analyzed GWAS of preterm birth for complete genotype data on nearly 2000 preterm and term mothers. We used both the curated genes and a genome-wide approach to carry out a pathway-based analysis. There were 19 significant pathways, which withstood FDR correction for multiple testing that were identified using both the curated genes and the genome-wide approach. The analysis based on the curated genes was more significant than genome-wide in 15 out of 19 pathways. This approach demonstrates the use of a validated set of genes, in the analysis of otherwise unsuccessful GWAS data, to identify gene-gene interactions in a way that enhances statistical power and discovery.

Associations between genetic polymorphisms of beta-2 adrenergic receptor and preterm delivery in Korean women

PROBLEM

We investigated genetic polymorphisms to understand the etiology of preterm delivery, which involves inflammatory cytokines and uterine contraction. Maternal polymorphisms of ADRB2, iNOS, and eNOS were examined, and associations between these and the risk of preterm delivery were sought.

METHOD OF STUDY

This study was performed on 166 Korean women who underwent preterm delivery and 289 normal controls. Logistic regression analyses were carried out to identify single genes and haplotypes that affect the risk of preterm delivery.

RESULTS

The G/G haplotype of ADRB2-rs1042713 and -rs1042714 was found to be associated with the risk of preterm delivery (OR = 1.90, 95% CI = 1.08-3.33, P-value = 0.0252). The genotype frequency of G allele in ADRB2-rs1042714 was associated with increased the risk of preterm delivery. However, after the adjustment of multiple comparison corrections, the association with preterm delivery was not remained significantly.

CONCLUSION

These findings possibly aid our understanding of the pathogenesis of preterm delivery and suggest that a haplotype with variants in maternal genes involved in adrenergic activation may lead to the dysregulation of uterine contractility and increase the risk of preterm delivery.

A bioinformatics approach to preterm birth

A vast body of literature has suggested genetic programming of preterm birth. However, there is a complete lack of an organized analysis and stratification of genetic variants that may indeed be involved in the pathogenesis of preterm birth. We developed a novel bioinformatics approach to identify the nominal genetic variants associated with preterm birth. We used semantic data mining to extract all published articles related to preterm birth. Genes identified from public databases and archives of expression arrays were aggregated with genes curated from the literature. Pathway analysis was used to impute genes from pathways identified in the curations. The curated articles and collected genetic information are available in a web-based tool, the database for preterm birth (dbPTB) that forms a unique resource for investigators interested in preterm birth.

dbPTB: a database for preterm birth

Genome-wide association studies (GWAS) query the entire genome in a hypothesis-free, unbiased manner. Since they have the potential for identifying novel genetic variants, they have become a very popular approach to the investigation of complex diseases. Nonetheless, since the success of the GWAS approach varies widely, the identification of genetic variants for complex diseases remains a difficult problem. We developed a novel bioinformatics approach to identify the nominal genetic variants associated with complex diseases. To test the feasibility of our approach, we developed a web-based aggregation tool to organize the genes, genetic variations and pathways involved in preterm birth. We used semantic data mining to extract all published articles related to preterm birth. All articles were reviewed by a team of curators. Genes identified from public databases and archives of expression arrays were aggregated with genes curated from the literature. Pathway analysis was used to impute genes from pathways identified in the curations. The curated articles and collected genetic information form a unique resource for investigators interested in preterm birth. The Database for Preterm Birth exemplifies an approach that is generalizable to other disorders for which there is evidence of significant genetic contributions.

The contribution of maternal stress to preterm birth: issues and considerations

Preterm birth represents the most significant problem in maternal-child health, with maternal stress identified as a variable of interest. The effects of maternal stress on risk of preterm birth may vary as a function of context. This article focuses on select key issues and questions highlighting the need to develop a better understanding of which particular subgroups of pregnant women may be especially vulnerable to the potentially detrimental effects of maternal stress, and under what circumstances and at which stages of gestation. Issues related to the characterization and assessment of maternal stress and candidate biologic mechanisms are addressed.

Insights into the multifactorial nature of preterm birth: proteomic profiling of the maternal serum glycoproteome and maternal serum peptidome among women in preterm labor

OBJECTIVE

The purpose of this study was to identify peptide classifiers that predict spontaneous preterm birth (SPTB) among women in preterm labor (PTL) and to demonstrate specific protein pathways that are activated in PTL.

STUDY DESIGN

Serum from 110 women with PTL between 20 weeks and 33 weeks 6 days of gestation was subjected to glycoprotein purification, matrix-assisted laser desorption ionization time-of-flight mass spectrometry peptide profiling, 2-dimensional liquid chromatography tandem mass spectrometry, and pathway analysis. Women were divided into 2 groups: delivery at <34 weeks' gestation (SPTB group) and delivery at > or =34 weeks' gestation (PTL group).

RESULTS

Twenty-three peptide masses were identified that discriminated PTL from SPTB in 97% of cases. Fifty-two proteins were present differentially between PTL and SPTB; 48 of 52 proteins were classified into 1 of 4 functional pathways that were involved with PTL: (1) complement/coagulation cascade, (2) inflammation/immune response, (3) fetal-placental development, and (4) extracellular matrix proteins.

CONCLUSION

Among women in PTL, proteomic analysis of serum peptides and glycoproteins classifies women who will deliver preterm and identifies specific protein pathways at work among individuals with "idiopathic" PTL.

Geographic ancestry and markers of preterm birth

Several biomarkers associated with spontaneous preterm birth (PTB) have been discovered over the last decade. Many of these markers, such as cytokines, are associated with infection and inflammation. As such, these biomarkers represent biologically plausible candidates for assessing those at risk of PTB. However, in the early association studies of biomarker-pregnancy outcome, the geographic ancestry of subjects was not considered. Based on more recent data, it is becoming increasingly evident that these biomarkers, and a universal approach that uses a single biomarker, fail to provide adequate assessment of risk in all subjects. Rather, recent data support the conclusion that some markers associate in subjects of African descent and another nonoverlapping set associates in subjects of European descent. These data indicate that diagnostic or predictive tests will have to use different biomarkers for different sets of subjects. If this is true, it poses severe restrictions on how to predict outcome or perform tests of association, and may make it impossible to determine risk or provide proper intervention. An alternative is presented that, although not yet proven, may make it possible to use a common set of biomarkers and their relationships to assess risk.

Maternal and fetal genetic associations of PTGER3 and PON1 with preterm birth

OBJECTIVE

The purpose of this study was to identify associations between maternal and fetal genetic variants in candidate genes and spontaneous preterm birth (PTB) in a Norwegian population and to determine the effect size of those associations that corroborate a previous study of PTB.

METHODS

DNA from 434 mother-baby dyads (214 cases and 220 controls) collected from the Norwegian Mother and Child Cohort (MoBa) was examined for association between 1,430 single nucleotide polymorphisms in 143 genes and PTB. These results were compared to a previous study on European Americans (EA) from Centennial Women's Hospital in Nashville, TN, USA. Odds ratios for SNPs that corroborated the Cenntennial study were determined on the combined MoBa and Centennial studies.

RESULTS

In maternal samples the strongest results that corroborated the Centennial study were in the prostaglandin E receptor 3 gene (PTGER3; rs977214) (combined genotype p = 3x10(-4)). The best model for rs977214 was the AG/GG genotypes relative to the AA genotype and resulted in an OR of 0.55 (95% CI = 0.37-0.82, p = 0.003), indicating a protective effect. In fetal samples the most significant association in the combined data was rs854552 in the paraoxonase 1 gene (PON1) (combined allele p = 8x10(-4)). The best model was the TT genotype relative to the CC/CT genotypes, and resulted in an OR of 1.32 (95% CI = 1.13-1.53, p = 4x10(-4)).

CONCLUSIONS

These studies identify single locus associations with preterm birth for both maternal and fetal genotypes in two populations of European ancestry.

Prostanoid DP receptor (PTGDR) variants in mothers with post-coital associated preterm births: preliminary observations

OBJECTIVE

To describe prostanoid DP receptor (PTGDR) variants in women with preterm births who admitted to coital activity (CA) within 24 h of labor.

STUDY DESIGN

To achieve >80% statistical power, a pilot case-control study compared 24 premature births from mothers with CA (Group 1), 30 mothers of premature infants who did not have CA (Group 2 non-coital activity) and 95 non-coital activity mothers with term births (Group 3 controls). Four functional PTDGR single nucleotide polymorphisms (SNPs) were evaluated: T-549C, C-441/T, T-197C and G+1044A. PHASE 2.0.2 and SAS 9.2 were used for analysis.

RESULT

All SNPs were in Hardy-Weinberg equilibrium in controls. The C-441/T genotype frequency was significantly increased among Group 1 women relative to Group 2 and 3 women (odds ratio (OR): 30.1, 95% confidence interval (CI) 6.9-191 and 25.7 95%CI 25.7-not computible, respectively). Of the possible haplotypes among the groups, the TCTG haplotype (T-549C, C-441/T, T-197C and G+1044A) was significantly more frequent in Group 1 women compared with the control groups (OR 53.4, 95%CI 10.3-554.8).

CONCLUSIONS

A differential genomic pattern of PTGDR polymorphisms was identified in a sub-set of mothers which was associated with an increased risk of post-coital preterm birth.

Chorioamnionitis--a complex pathophysiologic syndrome

Chorioamnionitis, inflammation of the amniochorionic membrane (fetal membranes) is a very common disease but a complex syndrome associated with pregnancy. It presents a clinical impasse due to lack of knowledge of specific etiologies associated with this condition making confident clinical interventions difficult. Recent reports provide insight into genetic, epigenetic, behavioral, psychosocial, molecular and pathophysiological factors that are associated with chorioamnionitis. However, a coordinated approach in understanding causality and lack of early indicators (clinical and biomarkers) has hampered gaining knowledge about the disease status preventing proper intervention. Several reviews have provided in-depth analysis of the histologic and clinical evidence associated with chorioamnionitis. In this review, we provide a novel perspective on chorioamnionitis based on recent evidences from scientific literature on inflammation, apoptosis and genetics.

Spontaneous preterm birth in African Americans is associated with infection and inflammatory response gene variants

OBJECTIVE

The objective of the study was to study the genetic risk factors of spontaneous preterm birth (PTB) in African Americans.

STUDY DESIGN

Case-control analyses were performed using maternal and fetal deoxyribonucleic acid from 279 African American birth events (82 PTB and 197 term) and 1432 single-nucleotide polymorphisms from 130 candidate genes. Single-locus association and haplotype analyses were performed.

RESULTS

The most significant associations were in the maternal interleukin (IL)-15 (rs10833, allele P = 2.91 x 10(-4), genotype P = 2.00 x 10(-3)) gene and the fetal IL-2 receptor B (IL-2RB) (rs84460, allele P = 1.37 x 10(-4), genotype P = 6.29 x 10(-4)) gene. The best models for these markers were additive (rs10833, odds ratio [OR], 0.30; 95% confidence interval [CI], 0.14-0.62; P = 1.0 x 10(-3); rs84460, OR, 2.32; 95% CI, 1.47-3.67; P < 1.0 x 10(-3)). The largest number of significant associations was found in genes related to infection and inflammation. There were overall a larger number of significant associations in infants than in mothers.

CONCLUSION

These results support a strong role for genes involved in infection and inflammation in the pathogenesis of PTB, particularly IL-12 and IL-12RB, and indicate that in African Americans there may be complementarity of maternal and fetal genetic risks for PTB.

Preterm birth and inflammation-The role of genetic polymorphisms

Spontaneous preterm labour and preterm births are still the leading cause of perinatal morbidity and mortality in the developed world. Previous efforts to prevent preterm birth have been hampered by a poor understanding of the underlying pathophysiology, inadequate diagnostic tools and generally ineffective therapies. Clinical, epidemiological and experimental studies indicate that genito-urinary tract infections play a critical role in the pathogenesis of preterm birth. Moreover, intrauterine infection increases perinatal mortality and morbidity, such as cerebral palsy and chronic lung disease, significantly. It has recently been suggested that gene-environment interactions play a significant role in determining the risk of preterm birth. Polymorphisms of certain critical genes may be responsible for a harmful inflammatory response in those who possess them. Accordingly, polymorphisms that increase the magnitude or the duration of the inflammatory response were associated with an increased risk of preterm birth. In contrast polymorphisms that decrease the inflammatory response were associated with a lower risk of preterm birth. This article will review the current understanding of pathogenetic pathways in the aetiology of preterm birth.

Oxidative stress-related gene interactions with preterm delivery in Korean women

OBJECTIVE

We hypothesized that the cytochrome P450IA1 (CYP1A1), glutathione S-transferases mu 1 (GSTM1), and theta 1 (GSTT1) polymorphisms are associated with the risk for preterm delivery. This study was undertaken to identify gene-gene interactions and haplotypes that increase the risk of preterm delivery.

STUDY DESIGN

This case-control study was performed in Korea on 145 women with preterm birth and 120 normal controls. Logistic regression and multifactor dimensionality reduction analysis were used to explore single genes and gene-gene interactions, which have an impact on the risk of preterm delivery, respectively.

RESULTS

The GSTM1 null genotype and the interaction between the CYP1A1-I462V and GSTM1 null type conferred a risk of preterm birth. The association between preterm delivery and the CYP1A1-T6235C/I462V haplotype plus GSTM1 null type was verified.

CONCLUSION

The interaction between the CYP1A1-I462V and GSTM1 null genotype were found to increase the risk for preterm birth in Korean women. This finding provides evidence of a gene-gene interaction, which has an impact on preterm delivery.

Born too soon: the continuing challenge of preterm labor and birth in the United States

Prematurity is the single greatest cause of morbidity and mortality in obstetrics. Families, health care services, and education systems experience the impact of prematurity for the lifetime of the preterm-born child. Health care providers have tried to lower the preterm birth rate with prevention both before and during pregnancy and intervention for symptomatic women. The inability of the health care system to significantly decrease the incidence of preterm birth continues to be a challenge. To further complicate the situation, new data shows that infants born between 34 and 37 weeks' gestation who were thought to have minimal long-term effects of preterm birth may be more at risk than previously appreciated. This article reviews evidence-based risk identification, prevention, and management of women experiencing preterm labor and birth.