Identifying the combination of genetic factors that determine susceptibility to cervical cancer

[[abstract]]Cervical cancer is common among women all over the world. Although infection with high-risk types of human papillomavirus (HPV) has been identified as the primary cause of cervical cancer, only some of those infected go on to develop cervical cancer. Obviously, the progression from HPV infection to cancer involves other environmental and host factors. Recent populationbased twin and family studies have demonstrated the importance of the hereditary component of cervical cancer, associated with genetic susceptibility. Consequently, single-nucleotide polymorphism (SNP) markers and microsatellites should be considered genetic factors for determining what combinations of genetic factors are involved in precancerous changes to cervical cancer. This study employs a Bayesian network and four different decision tree algorithms, and compares the performance of these learning algorithms. The results of this study raise the possibility of investigations that could identify combinations of genetic factors, such as SNPs and microsatellites, that influence the risk associated with common complex multifactorial diseases, such as cervical cancer. The web site associated with this study is http://140.115.155.8/FactorAnalysis/

Data Mining in Healthcare: A Survey of Techniques and Algorithms with its Limitations and Challenges

The large amount of data in healthcare industry is a key resource to be processed and analyzed for knowledge extraction. The knowledge discovery is the process of making low-level data into high-level knowledge. Data mining is a core component of the KDD process. Data mining techniques are used in healthcare management which improve the quality and decrease the cost of healthcare services. Data mining algorithms are needed in almost every step in KDD process ranging from domain understanding to knowledge evaluation. It is necessary to identify and evaluate the most common data mining algorithms implemented in modern healthcare services. The need is for algorithms with very high accuracy as medical diagnosis is considered as a significant yet obscure task that needs to be carried out precisely and efficiently

Prevalence of high risk human papilloma virus in symptomatic women attending our gynaecology OPD

INTRODUCTION: Invasive cancer of cervix is considered as a preventable disease because it has a long preinvasive state, cervical cytology screening programs are currently available and the treatment of preinvasive lesions is effective. Normally the lifetime probability for developing cervical cancer is 1:128.Although screening programs in US are well established, it is estimated that 30% of cervical cancer cases will occur in women who have never had a PAP test. In developing countries, this percentage approaches sixty. Human Papilloma Virus is the major aetiological agent for cervical cancer, the second common cancer among the women everywhere in the world (Munoz et al 1994). This virus is also implicated in other anogenital cancers. HPV is among the most important viruses in causation of cancer. A large number of epidemiological, biological and chemical studies are underway to get to know the nature of this infection and its outcome. The prospects of HPV vaccine in preventing cervical cancer make it the most suitable target for studies in low resource settings with high morbidity and mortality from cervical cancer. Cervical cancer is the second most common cancer among women worldwide. The majority of the cases occur in the developing world, where in most countries, it is the leading cause of cancer mortality in women. An estimated 470,000 new cases of cancer cervix are diagnosed each year worldwide and 80% of these occur in the developing world. A quarter of the global burden is experienced in India, where about 126,000 new cases and 71000 deaths attributable to cervical cancer are estimated to occur each year. Cancer cervix constitutes15-51% of all female cancers and rates of age-standardised incidence range from 17.5 to 55% per 100,000 women in different regions of India. More than 80% are diagnosed at an advanced clinical stage and 5 year survival is less than 40%. In many developed countries a decline in the incidence and mortality caused by cervical cancer has been observed in the past 30 years as a result of screening by cytology. India has the burden of having the largest number of women with cervical cancer contributing to18% of world’s total number. One out of every 5 women in world suffering from cervical cancer is from India. AIM OF THE STUDY: The aim of the study is to determine the prevalence of high risk human papilloma viruses 16 and 18 in women with symptoms of chronic discharge per vaginum and those with cancer cervix attending our Gynaecology OPD. MATERIALS AND METHODOLGY: The study was conducted at the Institute of Obstetrics and Gynaecology, Egmore in collaboration with the Department of Biotechnology, Cancer Biology Lab, IIT, Chennai between 2008-2009. Study Design and Population: It is a hospital based study .300 Consenting women attending the Gynaecology OPD at our Institute were enrolled with 100 cases belonging to the symptomatic group and 100 belonging to cancer cervix and 100 cases who came to the OPD for other complaints. Inclusion Criteria: The women with the following criteria were included in the symptomatic group in our study 1. Age 16 to 70 years, 2. Patients with complaints of persistent vaginal discharge, 3. Patients with complaints of intermenstrual or postcoital bleeding, 4. Unhealthy cervix per speculum. Simultaneously 100 women with frank carcinoma cervix and 100 women who attended the Gynaecology OPD for other complaints who underwent total Hysterectomy due to complaints other than uterine cervical lesions such as uterine fibroid, endometriosis and so on were also studied for HPV prevalence. Exclusion Criteria: The women fulfilling the following criteria were excluded from the study 1. Pregnant women and puerperium, 2. Women with bleeding at the time of examination, 3. Clinical evidence of acute infection, 4. Unsatisfactory colposcopy, 5. Unmarried women, 6. Women undergoing radiotherapy or chemotherapy for cancer cervix, 7. Women with cancer cervix recurrence. Consent and Ethical Considerations: A written informed consent in local vernacular was obtained from each patient prior to enrolment in the study .Ethics Committee of the Institution approved the study protocol. METHODOLOGY: Relevant socioeconomic, obstetric, gynaecological, and medical history was obtained in a pretested, semi structured questionnaire. SUMMARY: This study was conducted in our Institute which comprises women attending the Gynaecology OPD for various reasons. 300 consenting women were enrolled with 100 belonging to the group of women who came with complaints of persistent vaginal discharge, 100 women who came for other complaints and 100 women with frank cancer cervix. A Pap smear was obtained in the index study and colposcopic guided biopsy of the cervical tissues was also obtained. Cervical tissue samples in subjects who underwent total hysterectomy due to complaints other than uterine cervical lesions such as uterine fibroids, endometriosis and so on, were obtained from theatres posted for fractional curettage after verifying the basic screening report .Cervical punch biopsy samples were taken in 100 women who came with frank cancer cervix. Cervical tissue samples were stored and Reverse Transcriptase Polymerase chain reaction (RT-PCR) was done to assay HPV DNA16 and 18. The prevalence of HPV 16 and 18 in each of the groups was analysed. We found that the prevalence of HPV 16 in the index study, in women with other symptoms and those with cancer cervix was 63%, 15%, and 97% respectively. HPV 18 prevalence in cancer cervix was 32%.HPV 16 prevalence was highest in the age group 30 – 40 years It was also high in women who got married at an early age, women belonging to the lower socioeconomic strata, and in the illiterate group. We did not observe any significant parity related difference in HPV 16 prevalence. The index study generated the prevalence data of subclinical high risk HPV infection in the symptomatic women. The limitation of the study is that being a hospital based study, the women enrolled visited the hospital with varied ailments and thus were not true representations of the community. In addition, the prevalence of high risk HPV, other than hpv 16 AND 18 was not evaluated. Cancer cervix screening practices are inconsistent in India. Use of Pap smear, as a sole indicator for screening has limitations. The cytological interpretation becomes faulty if the smear is inflammatory, a situation not infrequent among women from the lower socioeconomic background. In a scenario of infrequent screening, screening with a test of high sensitivity provides greater reassurance, that potential disease has not been missed in women who screened negative. It is an irony that the middle and high socioeconomic women, who can afford HPV screening by molecular techniques require it the least, owing to the low prevalence. High risk HPV DNA screening appears to be a valid option in mass cervical screening programmes in the developed countries. In a resource poor country, it is not feasible to offer a universal molecular testing for high risk HPV, till HPV screening is made cheaper. Identification of population at risk will enable focused screening, with a greater cost effective utilization of resources. Screening preferentially should be directed to the target population for the optimal utilization of resources. Needless to say, health education, promotion of condom usage, and need to follow healthy hygienic practices is the most cost effective approach in reducing the incidence of cervical carcinoma in resource-crunched societies

Identification of disease related significant SNPs

Single nucleotide polymorphisms (SNPs) are DNA sequence variations that occur when a single nucleotide in the genome sequence is altered. Since, variations in DNA sequence can have a major impact on complex human diseases such as obesity, epilepsy, type 2 diabetes, rheumatoid arthritis; SNPs have become increasingly significant in identification of such complex diseases. Recent biological studies point out that a single altered gene may have a small effect on a complex disease, whereas interactions between multiple genes may have a significant role. Therefore, identifying multiple genes associated with complex disorders is essential. In this spirit, combinations of multiple SNPs rather than individual SNPs should be analyzed. However, assessing a very large number of SNP combinations is computationally challenging and due to this challenge, in literature there exist a limited number of studies on extracting statistically significant SNP combinations. In this thesis work, we focus on this challenging problem and develop a five step "disease-associated multi-SNP combinations search procedure" to identify statistically significant SNP combinations and the significant rules defining the associations between SNPs and a specified disease. The proposed five step multi-SNP combinations procedure is applied to the simulated rheumatoid arthritis data set provided by Genetic Analysis Workshop 15. In each step, statistically significant SNPs are extracted from the available set of SNPs that are not yet classified as significant or insignificant. In the first step, the genome wide association analysis (GWA) is performed on the original complete multi-family data set. Then, in the second step we use the tag SNP selection algorithm to find a smaller subset of informative SNP markers. In literature most tag SNP selection methods are based on the pair wise (two-markers) linkage disequilibrium (LD) measures. But in this thesis, both the pair wise and multiple marker LD measures have been incorporated to improve the genetic coverage. Up to the third step the procedure aims to identify individual significant SNPs. In the third step a genetic algorithm (GA) based feature selection method is performed. It provides a significant combination of SNPs and the GA constructs this combination by maximizing the explanatory power of the selected SNPs while trying to decrease the number of selected SNPs dynamically. Since GA is a probabilistic search approach, at each execution it may provide different SNP combinations. We apply the GA several times to obtain multiple significant SNP combinations, and for each combination we calculate the associated pseudo r-square values and apply some statistical tests to check its significance. We also consider the union and intersection of the SNP combinations, identified by the GA, as potentially significant SNP combinations. After identifying multiple statistically significant SNP combinations, in the fourth and fifth steps we focus on extracting rules to explain the association between the SNPs and the disease. In the fourth step we apply a classification method, called Decision Tree Forest, to calculate the importance values of individual SNPs that belong to at least one of the SNP combinations found by the GA. Since each marker in a SNP combination is in bi-allelic form, genotypes of a SNP can affect the disease status. Different genotypes of SNPs are considered to define candidate rules. Then utilizing the calculated importance values and the occurrence percentage of the candidate rule in the data set, in the fifth step we perform our proposed rule extraction method to select the rules among the candidate ones. In literature there are many classification approaches such as the decision tree, decision forest and random forest. Each of these methods considers SNP interactions which are explanatory for a large subset of patients. However, in real life some SNP interactions that are observed only in a small subset of patients might cause the disease. The existing classification methods do not identify such interactions as significant. However, of the proposed five-step multi-SNP combinations procedure extracts these interactions as well as the others. This is a significant contribution to the research on identifying significant interactions that may cause a human to have the disease

Análisis de polimorfismos de nucleótido simple (SNPs) en genes asociados a la infección por el virus del papiloma humano (VPH) y la progresión neoplásica: un modelo poligénico de susceptibilidad al cáncer cervical

El cáncer de cuello uterino es el séptimo cáncer más frecuente en la población general y el segundo más común entre las mujeres de todo el mundo. Numerosos estudios epidemiológicos y moleculares han establecido al Virus del Papiloma Humano (VPH) como el principal factor etiológico del cáncer cervical. Sin embargo, dada la alta prevalencia de la infección por VPH en la población general respecto de la incidencia del carcinoma cervical, se presume que la sola infección por este virus sería insuficiente para provocar la transformación neoplásica. Las diferencias genéticas del hospedador que influyan en la respuesta contra la infección viral podrían determinar un mayor riesgo de desarrollo de lesiones cervicales y progresión hacia un carcinoma invasor. De esta manera, los polimorfismos genéticos presentes en genes relacionados a la infección viral, a la respuesta inmune, a los sistemas de reparación del ADN y aquellos genes supresores de tumores, podrían influenciar y determinar un riesgo aumentado de desarrollo de la neoplasia cervical. El objetivo del presente trabajo fue determinar el efecto del componente genético en relación a la susceptibilidad de desarrollo de cáncer cervical y la infección por el Virus del Papiloma Humano. Se analizaron un total de 512 muestras cervicales de mujeres de la ciudad de La Plata, las cuales fueron clasificadas histológicamente en: 200 muestras de mucosa cervical normal (PapI/II), 100 Lesiones Intraepiteliales de Bajo Grado (LGSIL), 72 Lesiones Intraepiteliales de Alto Grado (HGSIL) y 140 muestras correspondientes a Carcinomas Cervicales Escamosos (SCC). La presencia de ADN del VPH fue examinada mediante PCR anidada y la genotipificación del virus por PCR-SSCP y PCR-EIA. La genotipificación de los Polimorfismos de Nucleótido Simple (SNPs) presentes en los genes FASL (-844 T/C), IL10 (-1082 G/A), p53 (Arg72Pro), INFG (+ 874 T/A) y RNASEL (Arg462Gln) se llevó a cabo mediante la tecnología de Pirosecuenciación, mientras que el análisis de los SNPs Arg399Gln y Arg194Trp de XRCC1, -308 (G/A) y -238 (G/A) de TNF-α y -670 del gen FAS se realizó utilizando la técnica de PCR-RFLP. La prevalencia de la infección por VPH en el grupo control fue del 36,5%. El tipo viral más prevalente fue el VPH-16 (51,2%). Del total de los controles, el 29,3% correspondió a mujeres mayores a 30 años infectadas con VPH-16 y/o VPH-18. Los polimorfismos presentes en las regiones promotoras de los genes TNF-α (-308 (G/A) y -238 (G/A)), IL-10 (-1082 (G/A)) y FASL (-844 (T/C)), así como el SNP + 874 (T/A) del gen Interferon gamma, no presentaron diferencias entre casos y controles. De manera similar, no hubo asociación entre dichos polimorfismos y la presencia del ADN del VPH. Sin embargo, se registró un incremento significativo en el riesgo de desarrollo de cáncer cervical otorgado por los genotipos homocigota AA del gen FAS (OR=2,25; p=0,035), heterocigota CG del gen p53 (OR=2,43; p=0,004) y el genotipo TT+TC del gen XRCC1 codon 194 (OR=2,26; p=0,02). Por otra parte, los genotipos homocigota AA de RNASEL (OR=0,31; p=0,034) y heterocigota AG de XRCC1 codon 399 (OR=0, 48; p=0,023) otorgaron una menor susceptibilidad frente al desarrollo de la neoplasia cervical. En el caso del gen FAS, el genotipo homocigota AA (OR=2,53; p=0,035) se encontró asociado con un incremento en la susceptibilidad a la infección por VPH. En cuanto a las lesiones cervicales, se observó que tanto el alelo Gln (A) (OR=3,03; p=0,001) como el genotipo homocigota Gln/Gln (AA) (OR=5,34; p=0,000) de XRCCI Arg399Gln otorgaron un incremento significativo en el riesgo de desarrollo de lesiones de bajo grado (LSIL). Por el contrario, el genotipo heterocigota Gln/Arg (AG) de este mismo polimorfismo estuvo asociado con una disminución en el riesgo de desarrollo de este tipo de lesiones (OR=0, 25; p=0,009). Por último, el análisis de los polimorfismos a través del algoritmo MDR reveló que existe una interacción sinérgica entre ellos, presentando el modelo de cuatro-factores (cuatro-loci), conformado por FASL-P53-RNASEL-XRCC1399, una asociación significativa con la neoplasia cervical (TA=0,61; p<0,05). De acuerdo a los resultados obtenidos se observa que la asociación encontrada entre los Polimorfismos de Nucleótido Simple y el carcinoma cervical apoya el rol de la susceptibilidad genética del hospedador en la etiología de esta enfermedad. En base a esto se sugiere que la utilización de estos polimorfismos podría resultar muy conveniente en la identificación de aquellos individuos que se encuentran con mayor riesgo de desarrollo de lesiones cervicales y progresión hacia un carcinoma invasor.Facultad de Ciencias Médica