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1.  Implementing competency based admissions at the Albert Einstein College of Medicine 
Medical Education Online  2016;21:10.3402/meo.v21.30000.
The Albert Einstein College of Medicine (Einstein) was founded in 1955 during an era of limited access to medical school for women, racial minorities, and many religious and ethnic groups. Located in the Bronx, NY, Einstein seeks to educate physicians in an environment of state-of-the-art scientific inquiry while simultaneously fulfilling a deep commitment to serve its community by providing the highest quality clinical care. A founding principle of Einstein, the basis upon which Professor Einstein agreed to allow the use of his name, was that admission to the student body would be based entirely on merit. To accomplish this, Einstein has long used a ‘holistic’ approach to the evaluation of its applicants, actively seeking a diverse student body. More recently, in order to improve its ability to identify students with the potential to be outstanding physicians, who will both advance medical knowledge and serve the pressing health needs of a diverse community, the Committee on Admissions reexamined and restructured the requirements for admission. These have now been categorized as four ‘Admissions Competencies’ that an applicant must demonstrate. They include: 1) cocurricular activities and relevant experiences; 2) communication skills; 3) personal and professional development; and 4) knowledge. The purpose of this article is to describe the process that resulted in the introduction and implementation of this competency based approach to the admission process.
PMCID: PMC4742465  PMID: 26847852
diversity; competency; admissions; access; community service
2.  Motivation to Pursue Genetic Testing in Individuals with a Personal or Family History of Cardiac Events or Sudden Cardiac Death 
Journal of genetic counseling  2014;23(5):849-859.
Genetic testing is becoming increasingly available for cardiac channelopathies, such as long QT syndrome and Brugada syndrome, which can lead to sudden cardiac death. Test results can be used to shape an individual’s medical management and to identify at-risk family members. In our qualitative study, all participants had a personal or family history of a diagnosed cardiac arrhythmia syndrome or sudden cardiac death. Open-ended interviews were conducted individually and in focus groups. Interviews were audio recorded, transcribed verbatim, and analyzed using a qualitative grounded-theory approach. Of 50 participants, 37 described their motivations for pursuing genetic testing for long QT syndrome or another cardiac channelopathy. Participants’ motivations included: to find an explanation for a family member’s sudden death, to relieve uncertainty regarding a diagnosis, to guide future medical management, to allay concern about children or other family members, and to comply with recommendations of physicians or family members. Perceived reasons not to pursue genetic testing included denial, fear, and lack of information. The genetic counseling and informed consent process can be enhanced by understanding and addressing an individual’s internal and external motivations either for or against pursuing genetic testing.
PMCID: PMC4157088  PMID: 24664857
genetic testing; sudden cardiac death; long QT syndrome; motivation; channelopathy; genetic counseling
3.  What Parents Want to Know about the Storage and Use of Residual Newborn Bloodspots 
Many state newborn screening programs retain residual newborn screening bloodspots for a variety of purposes including quality assurance, biomedical research, and forensic applications. This project was designed to determine the information that prospective parents want to know about this practice.
Eleven focus groups were conducted in four states. Pregnant women and their partners and parents of young children (N=128) were recruited from the general public. Focus group participants viewed two educational movies on newborn screening and DBS retention and use. Transcripts were analyzed with qualitative methods and the results were synthesized to identify key information items.
We identified 14 categories of information from the focus groups that were synthesized into seven items prospective parents want to know about residual DBS. The items included details about storage, potential uses, risks and burdens, safeguards, anonymity, return of results, and parental choice.
For those state programs that retain residual dried bloodspots, inclusion of the seven things parents want to know about residual dried bloodspots in educational materials may improve parental understanding, trust, and acceptance of the retention and use of stored bloodspots.
PMCID: PMC4205184  PMID: 25131714
newborn screening; dried bloodspots; education; research; public health
4.  Psychological stress associated with cardiogenetic conditions 
Personalized medicine  2014;11(7):631-640.
Genetic testing now makes it possible to identify specific mutations that may lead to life-threatening cardiac arrhythmias. This article presents data from a qualitative research study that explored the subjective experiences of individuals and families with cardiogenetic conditions. We focus on describing patients’ experiences of psychological stresses associated with having a cardiogenetic condition, illustrating the importance of integrating psychological and medical care. This integration of care is particularly important as personalized genomic medicine continues to evolve and the implications of genetic testing have a profound effect on individuals and families.
The researchers interviewed 50 participants from 32 families. The research team used a systematic, grounded theory procedure to code and analyze interview and focus group transcripts, incorporating multiple coders at several stages of the data analysis process.
Three major themes emerged: a bereavement trajectory associated with sudden death in the absence of prior symptoms; high anxiety about transmitting a genetic mutation; and resilience reflected in positive lifestyle changes and participation in support groups.
This article identifies patient perspectives on personalized genomic medicine in cardiogenetics that can improve clinical care, including: specialized bereavement counseling; improving education about cardiogenetic conditions for medical professionals; parent guidelines for discussing cardiogenetic conditions with their children; information about support groups; and the routine inclusion of clinical psychologists in interdisciplinary treatment teams. Given recent advances in technology and decreasing costs, whole-genome sequencing is likely to become common practice in the near future. Therefore, these recommendations are likely to be relevant for other genetic conditions, as well as the entire field of personalized genomic medicine.
PMCID: PMC4242419  PMID: 25431604
cardiogenetic conditions; genetic testing; interdisciplinary treatment; long QT syndrome; personalized genomic medicine; psychological stress and genetic testing; sudden death
5.  Translating Advances in Cardiogenetics Into Effective Clinical Practice 
Qualitative health research  2014;24(10):1315-1328.
In this article we describe a qualitative research study in which we explored individuals’ subjective experiences of both genetic testing and cardiogenetic disorders. Using a grounded theory approach, we coded and analyzed interview and focus group transcripts from 50 participants. We found that just under half of the participants who received their diagnosis during the study reported difficulty understanding information about both the purpose of genetic testing and their cardiac disease. A high level of anxiety about genetic testing and cardiac symptoms exacerbated individuals’ cognitive confusion. Participants reported both positive and negative interactions with the medical community, depending on health care professionals’ knowledge of cardiogenetic disorders. Overall, participants expressed a range of attitudes—positive, negative, and ambivalent—toward genetic testing. We conclude with a discussion of the barriers to achieving effective clinical care for genetic conditions and offer suggestions for improving collaborative decision making between physicians and patients.
PMCID: PMC4487807  PMID: 25114027
communication; medical; genetics; heart health; health care; interprofessional; health care; teamwork
6.  An interdisciplinary approach to personalized medicine: case studies from a cardiogenetics clinic 
Personalized medicine  2013;10(1):73-80.
In the genomic age, the challenges presented by various inherited conditions present a compelling argument for an interdisciplinary model of care. Cardiac arrhythmias with a genetic basis, such as long QT syndrome, require clinicians with expertise in many specialties to address the complex genetic, psychological, ethical and medical issues involved in treatment. The Montefiore–Einstein Center for CardioGenetics has been established to provide personalized, interdisciplinary care for families with a history of sudden cardiac death or an acute cardiac event. Four vignettes of patient care are presented to illustrate the unique capacity of an interdisciplinary model to address genetic, psychological, ethical and medical issues. Because interdisciplinary clinics facilitate collaboration among multiple specialties, they allow for individualized, comprehensive care to be delivered to families who experience complex inherited medical conditions. As the genetic basis of many complex conditions is discovered, the advantages of an interdisciplinary approach for delivering personalized medicine will become more evident.
PMCID: PMC3564672  PMID: 24496296
cardiogenetics; interdisciplinary; long QT syndrome; multidisciplinary; personalized medicine
7.  Newborn Screening and the Obstetrician 
Obstetrics and gynecology  2012;120(4):908-917.
Newborn screening is the largest genetic screening program in the United States, with approximately four million infants screened yearly. It has been available and in continuous development for over 50 years. Each state manages, funds, and maintains its own individual program, which encompasses newborn screening as well as the diagnosis and coordination of care for affected infants and children. The ideal disorder for screening is one in which newborn intervention prevents later disabilities or death for infants who may appear normal at birth. There are 31 core conditions that are currently recommended for incorporation into state screening programs. To obtain a sample, several drops of blood are collected from the newborn’s heel and applied to filter paper. Although testing for core disorders is fairly standardized, more extensive screening varies by state and the rigorous evaluation of new disorders for inclusion in state screening panels is ongoing. As genomic medicine becomes more accessible, screening newborns for chronic diseases that may affect their long-term health will need to be addressed, as well the use of the residual blood spots for research. Obstetric providers should, at some time during pregnancy, review the basic process of newborn screening with parents to prepare them for this testing in the neonatal period. This information can be reviewed as it best suits incorporation in an individual’s practice; verbal discussion and the distribution of written materials with resources for further information is encouraged.
PMCID: PMC3459237  PMID: 22996108
8.  Reproductive Decision Making and Genetic Predisposition to Sudden Cardiac Death 
AJOB primary research  2012;3(3):30-39.
With current genetic technology, it is possible to detect mutations associated with long QT syndrome (LQTS), a hereditary cardiac arrhythmia syndrome. As a result, prospective parents diagnosed with LQTS will have to decide whether or not to prevent its transmission to future generations, either by not procreating or through the use of assisted reproductive technologies or prenatal testing. This paper explores how a hereditary predisposition to sudden cardiac death can influence reproductive decision making.
This study draws from interviews and focus groups with individuals who have personal or family histories of cardiac arrhythmia or sudden death. A keyword search was conducted on interview transcripts to identify quotes for analysis.
Participants expressed complex, often ambivalent attitudes about the prospect of having a child with a predisposition to sudden cardiac death. Their comments reveal conflicting understandings of genetic responsibility and reflect the variable effects of personal experience on reproductive decision making. This paper compares attitudes towards LQTS and other genetic conditions in analyzing the themes that emerged in interviews and focus groups.
The “disability critique” of prenatal testing should be applied carefully to a context of genetic predisposition to sudden cardiac death in order to understand reproductive decision making. Firsthand experience with the condition, among other factors, can weigh heavily in those decisions.
PMCID: PMC3400258  PMID: 22822470
LQTS; sudden cardiac death; reproductive decision making; genetic responsibility; parental responsibility; prenatal testing
9.  A qualitative study of the experience of CenteringPregnancy group prenatal care for physicians 
BMC Pregnancy and Childbirth  2013;13(Suppl 1):S6.
This study sought to understand the central meaning of the experience of group prenatal care for physicians who were involved in providing CenteringPregnancy through a maternity clinic in Calgary, Canada.
The study followed the phenomenological qualitative tradition. Three physicians involved in group prenatal care participated in a one-on-one interview between November and December 2009. Two physicians participated in verification sessions. Interviews followed an open ended general guide and were audio recorded and transcribed. The purpose of the analysis was to identify meaning themes and the core meaning experienced by the physicians.
Six themes emerged: (1) having a greater exchange of information, (2) getting to knowing, (3) seeing women get to know and support each other, (4) sharing ownership of care, (5) having more time, and (6) experiencing enjoyment and satisfaction in providing care. These themes contributed to the core meaning for physicians of “providing richer care.”
Physicians perceived providing better care and a better professional experience through CenteringPregnancy compared to their experience of individual prenatal care. Thus, CenteringPregnancy could improve work place satisfaction, increase retention of providers in maternity care, and improve health care for women.
PMCID: PMC3561144  PMID: 23445867
10.  The All Our Babies pregnancy cohort: design, methods, and participant characteristics 
BMC Pregnancy and Childbirth  2013;13(Suppl 1):S2.
The prospective cohort study design is ideal for examining diseases of public health importance, as its inherent temporal nature renders it advantageous for studying early life influences on health outcomes and research questions of aetiological significance. This paper will describe the development and characteristics of the All Our Babies (AOB) study, a prospective pregnancy cohort in Calgary, Alberta, Canada designed to examine determinants of maternal, infant, and child outcomes and identify barriers and facilitators in health care utilization.
Women were recruited from health care offices, communities, and through Calgary Laboratory Services before 25 weeks gestation from May 2008 to December 2010. Participants completed two questionnaires during pregnancy, a third at 4 months postpartum, and are currently being followed-up with questionnaires at 12, 24, and 36 months. Data was collected on pregnancy history, demographics, lifestyle, health care utilization, physical and mental health, parenting, and child developmental outcomes and milestones. In addition, biological/serological and genetic markers can be extracted from collected maternal and cord blood samples.
A total of 4011 pregnant women were eligible for recruitment into the AOB study. Of this, 3388 women completed at least one survey. The majority of participants were less than 35 years of age, Caucasian, Canadian born, married or in a common-law relationship, well-educated, and reported household incomes above the Calgary median. Women who discontinued after the first survey (n=123) were typically younger, non-Caucasian, foreign-born, had lower education and household income levels, were less likely to be married or in a common-law relationship, and had poor psychosocial health in early pregnancy. In general, AOB participants reflect the pregnant and parenting population at local and provincial levels, and perinatal indicators from the study are comparable to perinatal surveillance data.
The extensive and rich data collected in the AOB cohort provides the opportunity to answer complex questions about the relationships between biology, early experiences, and developmental outcomes. This cohort will contribute to the understanding of the biologic mechanisms and social/environmental pathways underlying associations between early and later life outcomes, gene-environment interactions, and developmental trajectories among children.
PMCID: PMC3561154  PMID: 23445747
11.  Comparing CenteringPregnancy® to standard prenatal care plus prenatal education 
BMC Pregnancy and Childbirth  2013;13(Suppl 1):S5.
There is significant evidence to support the importance of prenatal care in preventing adverse outcomes such as preterm birth and low infant birth weight. Previous studies have indicated that the benefits of prenatal care are not evenly distributed throughout the social strata. In addition, emerging evidence suggests that among particular populations, rates of preterm birth are unchanged or increasing. This suggests that an alternate care model is necessary, one that seeks to addresses some of the myriad of social factors that also contribute to adverse birth outcomes. In previous studies, the group prenatal care model CenteringPregnancy® had been shown to reduce adverse birth outcomes, but to date, no comparison had been made with a model that included prenatal education. This study sought to investigate whether any significant difference remained within the comparison groups when both models accounted for social factors.
This analysis was based on survey data collected from a prospective cohort of pregnant women through the All Our Babies Study in Calgary, Alberta.
At baseline, there were significant differences between the comparison groups in their psychosocial health, with the women in the CenteringPregnancy® group scoring higher levels of depressive symptoms, stress and anxiety. At four months postpartum, the differences between the groups were no longer significant. Conclusions: These results suggest that CenteringPregnancy® can recruit and retain a demographically vulnerable group of women with a constellation of risk factors for poor pregnancy and birth outcomes, including poverty, language barriers and poor mental health. Post program, the rates of stress, anxiety and depression were similar to other women with more social and financial advantage. These findings suggest that CenteringPregnancy® may be a community based care strategy that contributes to improved mental health, knowledge, and behaviours to optimize outcomes for mothers and children.
PMCID: PMC3561159  PMID: 23445830
12.  Genome-wide association studies in preterm birth: implications for the practicing obstetrician-gynaecologist 
BMC Pregnancy and Childbirth  2013;13(Suppl 1):S4.
Preterm birth has the highest mortality and morbidity of all pregnancy complications. The burden of preterm birth on public health worldwide is enormous, yet there are few effective means to prevent a preterm delivery. To date, much of its etiology is unexplained, but genetic predisposition is thought to play a major role. In the upcoming year, the international Preterm Birth Genome Project (PGP) consortium plans to publish a large genome wide association study in early preterm birth. Genome-wide association studies (GWAS) are designed to identify common genetic variants that influence health and disease. Despite the many challenges that are involved, GWAS can be an important discovery tool, revealing genetic variations that are associated with preterm birth. It is highly unlikely that findings of a GWAS can be directly translated into clinical practice in the short run. Nonetheless, it will help us to better understand the etiology of preterm birth and the GWAS results will generate new hypotheses for further research, thus enhancing our understanding of preterm birth and informing prevention efforts in the long run.
PMCID: PMC3561171  PMID: 23445776
13.  A Comparison Between Late Preterm and Term Infants on Breastfeeding and Maternal Mental Health 
Maternal and Child Health Journal  2012;17(8):1468-1477.
The objective of this study was to compare breastfeeding, postpartum mental health, and health service utilization between a group of late preterm (LP) maternal infant pairs and term counterparts. Data was drawn from a prospective community-based cohort in Calgary, Alberta. Bivariate and multivariable analyses were performed. LP infants were more likely to have had a longer median length of stay after birth (P < 0.001) and a higher re-hospitalization rate at 4-months (P < 0.001) compared to term infants. Mothers of LP infants were more likely to report immediate breastfeeding difficulties (P < 0.001) and earlier cessation of breastfeeding at 4-months postpartum (P = 0.008). Multivariable analyses revealed that LP status was an independent risk factor for excessive symptoms of maternal anxiety (OR = 2.07; 95 % CI = 1.08,3.98), but not for depression, stress, or low parenting morale. LP infants and their families are a vulnerable population with unique developmental trajectories. Further longitudinal research is required.
PMCID: PMC3785180  PMID: 23054457
Breastfeeding; Late preterm; Maternal mental health; Postpartum
14.  Strengthening the Reporting of Genetic Risk Prediction Studies (GRIPS): Explanation and Elaboration 
European journal of epidemiology  2011;26(4):313-337.
The rapid and continuing progress in gene discovery for complex diseases is fuelling interest in the potential application of genetic risk models for clinical and public health practice.The number of studies assessing the predictive ability is steadily increasing, but they vary widely in completeness of reporting and apparent quality.Transparent reporting of the strengths and weaknesses of these studies is important to facilitate the accumulation of evidence on genetic risk prediction.A multidisciplinary workshop sponsored by the Human Genome Epidemiology Network developed a checklist of 25 items recommended for strengthening the reporting of Genetic RIsk Prediction Studies (GRIPS), building on the principles established by prior reporting guidelines.These recommendations aim to enhance the transparency, quality and completeness of study reporting, and thereby to improve the synthesis and application of information from multiple studies that might differ in design, conduct or analysis.
PMCID: PMC3088812  PMID: 21424820
15.  Getting more than they realized they needed: a qualitative study of women's experience of group prenatal care 
Pregnant women in Canada have traditionally received prenatal care individually from their physicians, with some women attending prenatal education classes. Group prenatal care is a departure from these practices providing a forum for women to experience medical care and child birth education simultaneously and in a group setting. Although other qualitative studies have described the experience of group prenatal care, this is the first which sought to understand the central meaning or core of the experience. The purpose of this study was to understand the central meaning of the experience of group prenatal care for women who participated in CenteringPregnancy through a maternity clinic in Calgary, Canada.
The study used a phenomenological approach. Twelve women participated postpartum in a one-on-one interview and/or a group validation session between June 2009 and July 2010.
Six themes emerged: (1) "getting more in one place at one time"; (2) "feeling supported"; (3) "learning and gaining meaningful information"; (4) "not feeling alone in the experience"; (5) "connecting"; and (6) "actively participating and taking on ownership of care". These themes contributed to the core phenomenon of women "getting more than they realized they needed". The active sharing among those in the group allowed women to have both their known and subconscious needs met.
Women's experience of group prenatal care reflected strong elements of social support in that women had different types of needs met and felt supported. The findings also broadened the understanding of some aspects of social support beyond current theories. In a contemporary North American society, the results of this study indicate that women gain from group prenatal care in terms of empowerment, efficiency, social support and education in ways not routinely available through individual care. This model of care could play a key role in addressing women's needs and improving health outcomes.
PMCID: PMC3364900  PMID: 22436393
Canada; Prenatal care; Pregnant women; Women's health; Social support
16.  Challenges of genetic testing in adolescents with cardiac arrhythmia syndromes 
Journal of Medical Ethics  2011;38(3):163-167.
The ability to sequence individual genomes is leading to the identification of an increasing number of genetic risk factors for serious diseases. Knowledge of these risk factors can often provide significant medical and psychological benefit, but also raises complex ethical and social issues. This paper focuses on one area of rapid progress: the identification of mutations causing long QT syndrome and other cardiac channel disorders, which can explain some previously unexplained deaths in infants (SIDS) and children and adults (SUDS) and prevent others from occurring. This genetic knowledge, discovered posthumously in many cases, has implications for clinical care for surviving family members who might carry the same mutations. The information obtained from genetic testing, in the context of personal and family history, can guide individually tailored interventions that reduce risk and save lives. At the same time, obtaining and disclosing genetic information raises difficult issues about confidentiality and decision making within families. We draw on the experience of the Montefiore-Einstein Center for Cardiogenetics, which has played a leading role in the genetic diagnosis and clinical management of cardiac channel diseases, to explore some of the challenging ethical questions arising in affected families with adolescent children. We focus on the related issues of (1) family confidentiality, privacy and disclosure and (2) adolescent decision making about genetic risk, and argue for the value of interdisciplinary dialogue with affected families in resolving these issues.
PMCID: PMC3258368  PMID: 21955955
17.  Strengthening the reporting of genetic risk prediction studies (GRIPS): explanation and elaboration 
The rapid and continuing progress in gene discovery for complex diseases is fueling interest in the potential application of genetic risk models for clinical and public health practice. The number of studies assessing the predictive ability is steadily increasing, but they vary widely in completeness of reporting and apparent quality. Transparent reporting of the strengths and weaknesses of these studies is important to facilitate the accumulation of evidence on genetic risk prediction. A multidisciplinary workshop sponsored by the Human Genome Epidemiology Network developed a checklist of 25 items recommended for strengthening the reporting of Genetic RIsk Prediction Studies (GRIPS), building on the principles established by previous reporting guidelines. These recommendations aim to enhance the transparency, quality and completeness of study reporting, and thereby to improve the synthesis and application of information from multiple studies that might differ in design, conduct or analysis.
PMCID: PMC3083630  PMID: 21407270
18.  Strengthening the reporting of genetic risk prediction studies (GRIPS): explanation and elaboration 
European Journal of Epidemiology  2011;26(4):313-337.
The rapid and continuing progress in gene discovery for complex diseases is fuelling interest in the potential application of genetic risk models for clinical and public health practice. The number of studies assessing the predictive ability is steadily increasing, but they vary widely in completeness of reporting and apparent quality. Transparent reporting of the strengths and weaknesses of these studies is important to facilitate the accumulation of evidence on genetic risk prediction. A multidisciplinary workshop sponsored by the Human Genome Epidemiology Network developed a checklist of 25 items recommended for strengthening the reporting of Genetic RIsk Prediction Studies (GRIPS), building on the principles established by prior reporting guidelines. These recommendations aim to enhance the transparency, quality and completeness of study reporting, and thereby to improve the synthesis and application of information from multiple studies that might differ in design, conduct or analysis.
PMCID: PMC3088812  PMID: 21424820
Genetic; Risk prediction; Methodology; Guidelines; Reporting
19.  All Our Babies Cohort Study: recruitment of a cohort to predict women at risk of preterm birth through the examination of gene expression profiles and the environment 
Preterm birth is the leading cause of perinatal morbidity and mortality. Risk factors for preterm birth include a personal or familial history of preterm delivery, ethnicity and low socioeconomic status yet the ability to predict preterm delivery before the onset of preterm labour evades clinical practice. Evidence suggests that genetics may play a role in the multi-factorial pathophysiology of preterm birth. The All Our Babies Study is an on-going community based longitudinal cohort study that was designed to establish a cohort of women to investigate how a women's genetics and environment contribute to the pathophysiology of preterm birth. Specifically this study will examine the predictive potential of maternal leukocytes for predicting preterm birth in non-labouring women through the examination of gene expression profiles and gene-environment interactions.
Collaborations have been established between clinical lab services, the provincial health service provider and researchers to create an interdisciplinary study design for the All Our Babies Study. A birth cohort of 2000 women has been established to address this research question. Women provide informed consent for blood sample collection, linkage to medical records and complete questionnaires related to prenatal health, service utilization, social support, emotional and physical health, demographics, and breast and infant feeding. Maternal blood samples are collected in PAXgene™ RNA tubes between 18-22 and 28-32 weeks gestation for transcriptomic analyses.
The All Our Babies Study is an example of how investment in clinical-academic-community partnerships can improve research efficiency and accelerate the recruitment and data collection phases of a study. Establishing these partnerships during the study design phase and maintaining these relationships through the duration of the study provides the unique opportunity to investigate the multi-causal factors of preterm birth. The overall All Our Babies Study results can potentially lead to healthier pregnancies, mothers, infants and children.
PMCID: PMC3022739  PMID: 21192811
20.  Genome-Wide Association Studies, Field Synopses, and the Development of the Knowledge Base on Genetic Variation and Human Diseases 
American Journal of Epidemiology  2009;170(3):269-279.
Genome-wide association studies (GWAS) have led to a rapid increase in available data on common genetic variants and phenotypes and numerous discoveries of new loci associated with susceptibility to common complex diseases. Integrating the evidence from GWAS and candidate gene studies depends on concerted efforts in data production, online publication, database development, and continuously updated data synthesis. Here the authors summarize current experience and challenges on these fronts, which were discussed at a 2008 multidisciplinary workshop sponsored by the Human Genome Epidemiology Network. Comprehensive field synopses that integrate many reported gene-disease associations have been systematically developed for several fields, including Alzheimer's disease, schizophrenia, bladder cancer, coronary heart disease, preterm birth, and DNA repair genes in various cancers. The authors summarize insights from these field synopses and discuss remaining unresolved issues—especially in the light of evidence from GWAS, for which they summarize empirical P-value and effect-size data on 223 discovered associations for binary outcomes (142 with P < 10−7). They also present a vision of collaboration that builds reliable cumulative evidence for genetic associations with common complex diseases and a transparent, distributed, authoritative knowledge base on genetic variation and human health. As a next step in the evolution of Human Genome Epidemiology reviews, the authors invite investigators to submit field synopses for possible publication in the American Journal of Epidemiology.
PMCID: PMC2714948  PMID: 19498075
association; database; encyclopedias; epidemiologic methods; genome, human; genome-wide association study; genomics; meta-analysis
21.  GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique 
BMC Bioinformatics  2008;9:205.
Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM), a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies.
The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts requiring individual review by the database curator. The tool also ascertained 47 articles that were missed by the traditional literature screening process during the 4-week test period. We examined the literature on genetic associations with preterm birth as an example. Compared with the traditional, manual process, the GAPscreener both reduced effort and improved accuracy.
GAPscreener is the first free SVM-based application available for screening the human genetic association literature in PubMed with high recall and specificity. The user-friendly graphical user interface makes this a practical, stand-alone application. The software can be downloaded at no charge.
PMCID: PMC2387176  PMID: 18430222

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