Introduction England has one of the lowest breastfeeding rates in Europe. Initiation rates are 83... more Introduction England has one of the lowest breastfeeding rates in Europe. Initiation rates are 83% but within one week the rate of exclusive breastfeeding drops to 46% and by 6 months to only 1%.1 Lay and professional support, particularly if it is multi-faceted and spans pregnancy and birth, can prolong the duration and exclusivity of breastfeeding. The most beneficial interventions to promote breastfeeding include support by skilled peers and trained professionals. This study aims to evaluate women’s experiences of breastfeeding services within the North West London area. Methods and materials Data collected using questionnaire with statistical analysis of the results and a semi structured interview technique with content analysis. Study conducted within North West Thames. Questionnaire consisted of 57 questions examining demographic, economic, psychosocial experiences, antenatal and postnatal care. Results 50 questionnaires completed. 43/50 (86%) mothers intended to breastfeed during antenatal period, 2/50 (4%) bottlefeed, 2/50 (4%) combination of breast and bottle and 3/50 (6%) undecided. 34/50 (68%) did not feel confident that their GP could provide adequate advice and support. Of those 34, 4/34 (12%) would contact their health visitor for breastfeeding related concerns. Who they would contact for breastfeeding related questions or concerns is summarised in Figure 1. 7/50 (14%) felt pushed into a decision regarding breastfeeding, 43/50 (86%) did not, however 3 expressed that breastfeeding was “strongly” encouraged with a feeling of guilt towards bottlefeeding. 24/50 (48%) received conflicting advice from healthcare professionals at some point during the antenatal or postnatal period. 14/50 (28%) identified conflicting advice around technique specifically. Conclusion Training healthcare staff is a key source to improve experiences as they are commonly the first port of call for mothers with breastfeeding issues. With limited healthcare resources, expectations must however be managed. With consistent advice from knowledgeable staff, breastfeeding support and experiences can be improved. Maximising support within the community was highlighted as the most appropriate and preferable route, through the use of more face to face time with health visitors but also increasing confidence with mother’s own GP’s.
<p>Nephropathy prevalence calculated per group according to age in relation to the five yea... more <p>Nephropathy prevalence calculated per group according to age in relation to the five years duration for the total of 54,670 patients.</p
With the increasing adoption of next generation sequencing technology in the medical practice, th... more With the increasing adoption of next generation sequencing technology in the medical practice, there is an increasing demand for faster data processing to gain immediate insights from the patient’s genome. Due to the extensive amount of genomic information and its big data nature, data processing takes long time and delays are often experienced. In this paper, we show how to exploit in-memory platforms for big genomic data analysis, with focus on the variant analysis workflow. We will determine where different in-memory techniques are used in the workflow and explore different memory-based strategies to speed up the analysis. Our experiments show promising results and encourage further research in this area, especially with the rapid advancement in memory and SSD technologies.
International journal of geoinformatics, Mar 1, 2009
Because diabetes is an extremely common disorder in Saudi Arabia, the National Diabetes Registry ... more Because diabetes is an extremely common disorder in Saudi Arabia, the National Diabetes Registry was designed by King Saud University Hospital, Diabetes Center in collaboration with King Faisal Specialist Hospital and Research Center in the year 2001. The registry was designed to provide information on the extent and nature of specific types of diabetes, diabetes complications and treatment of diabetes in Saudi Arabia. Using a secured login module, over 41,000 cases have been registered in the web-based registry database as of December 31, 2007. In order to give a better, geographical insight into the registry data, an Internet mapping facility has been incorporated into the registry software. This Internet Mapping Service allows the users to query the distribution of diabetes patients within the Kingdom of Saudi Arabia along with spatial data. The key feature is the availability of “real-time” patient data for patient-related queries, which was made possible by establishing a direct connection “Open Database Connectivity” with the SQL Server database.
Background The clinical utility of exome sequencing is now well documented. Rapid exome sequencin... more Background The clinical utility of exome sequencing is now well documented. Rapid exome sequencing (RES) is more resource-intensive than regular exome sequencing and is typically employed in specialized clinical settings wherein urgent molecular diagnosis is thought to influence acute management. Studies on the clinical utility of RES have been largely limited to outbred populations. Methods Here, we describe our experience with rapid exome sequencing (RES) in a highly consanguineous population. Clinical settings included intensive care units, prenatal cases approaching the legal cutoff for termination, and urgent transplant decisions. Results A positive molecular finding (a pathogenic or likely pathogenic variant that explains the phenotype) was observed in 80 of 189 cases (42%), while 15 (8%) and 94 (50%) received ambiguous (variant of uncertain significance (VUS)) and negative results, respectively. The consanguineous nature of the study population gave us an opportunity to obser...
The main aim of this study is to determine the prevalence and risk factors of ischemic stroke amo... more The main aim of this study is to determine the prevalence and risk factors of ischemic stroke among diabetic patients registered in the Saudi National Diabetes Registry (SNDR) database. A cross-sectional sample of 62,681 diabetic patients aged ≥25 years was used to calculate ischemic stroke prevalence and its risk factors. Univariate and multivariate logistic regression analyses were used to assess the roles of different risk factors. The prevalence of ischemic stroke was 4.42% and was higher in the older age group with longer diabetes duration. Poor glycemic control and the presence of chronic diabetes complications were associated with a high risk of ischemic stroke. History of smoking and type 2 diabetes were more frequent among stroke patients. Obesity significantly decreased the risk for ischemic stroke. Regression analysis for ischemic stroke risk factors proved that age ≥45 years, male gender, hypertension, coronary artery disease (CAD), diabetes duration ≥10 years, insulin u...
Family trio next-generation sequencing-based variant analysis was done to identify the genomic re... more Family trio next-generation sequencing-based variant analysis was done to identify the genomic reason on unexplained recurrent pregnancy loss (RPL). A family (dead fetus and parents) from Saudi Arabia with an earlier history of three unexplained RPLs at the ninth week of pregnancy was included in the study. Whole-genome sequencing (WGS) of a dead fetus and the parents was done to identify the pathogenic variation and confirmed through Sanger sequencing. WGS of dead fetus identifies a novel homozygous exonic variation (NM_017419.3:c.680G>T) in ASIC5 (acid-sensing ion channel subunit family member 5) gene; the parents are heterozygous. Newly designed ARMS PCR followed by direct sequencing confirms the presence of heterozygous in one subject and absence of homozygous novel mutation among randomly selected healthy Saudis. The second family with heterozygous was confirmed with three unexplained RPLs. Pathogenicity analysis of R227I amino acid substitution in ASIC5 protein through mole...
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with genetic and clinical... more Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with genetic and clinical heterogeneity. The interplay of de novo and inherited rare variants has been suspected in the development of ASD. Here, we applied whole exome sequencing (WES) on 19 trios from singleton Saudi families with ASD. We developed an analysis pipeline that allows capturing both de novo and inherited rare variants predicted to be deleterious. A total of 47 unique rare variants were detected in 17 trios including 38 which are newly discovered. The majority were either autosomal recessive or X-linked. Our pipeline uncovered variants in 15 ASD-candidate genes, including 5 (GLT8D1, HTATSF1, OR6C65, ITIH6 and DDX26B) that have not been reported in any human condition. The remaining variants occurred in genes formerly associated with ASD or other neurological disorders. Examples include SUMF1, KDM5B and MXRA5 (Known-ASD genes), PRODH2 and KCTD21 (implicated in schizophrenia), as well as USP9X and SM...
Advanced cholestatic liver disease is a leading referral to pediatric liver transplant centers. R... more Advanced cholestatic liver disease is a leading referral to pediatric liver transplant centers. Recent advances in the genetic classification of this group of disorders promise a highly personalized management although the genetic heterogeneity also poses a diagnostic challenge. Using a next-generation sequencing-based multi-gene panel, we performed retrospective analysis of 98 pediatric patients who presented with advanced cholestatic liver disease. A likely causal mutation was identified in the majority (61%), spanning many genes including ones that have only rarely been reported to cause cholestatic liver disease e.g. TJP2 and VIPAS39. We find no evidence to support mono-allelic phenotypic expression in the carrier parents despite the severe nature of the respective mutations, and no evidence of oligogenicity. The high carrier frequency of the founder mutations identified in our cohort (1 in 87) suggests a minimum incidence of 1:7,246, an alarmingly high disease burden that calls...
Introduction England has one of the lowest breastfeeding rates in Europe. Initiation rates are 83... more Introduction England has one of the lowest breastfeeding rates in Europe. Initiation rates are 83% but within one week the rate of exclusive breastfeeding drops to 46% and by 6 months to only 1%.1 Lay and professional support, particularly if it is multi-faceted and spans pregnancy and birth, can prolong the duration and exclusivity of breastfeeding. The most beneficial interventions to promote breastfeeding include support by skilled peers and trained professionals. This study aims to evaluate women’s experiences of breastfeeding services within the North West London area. Methods and materials Data collected using questionnaire with statistical analysis of the results and a semi structured interview technique with content analysis. Study conducted within North West Thames. Questionnaire consisted of 57 questions examining demographic, economic, psychosocial experiences, antenatal and postnatal care. Results 50 questionnaires completed. 43/50 (86%) mothers intended to breastfeed during antenatal period, 2/50 (4%) bottlefeed, 2/50 (4%) combination of breast and bottle and 3/50 (6%) undecided. 34/50 (68%) did not feel confident that their GP could provide adequate advice and support. Of those 34, 4/34 (12%) would contact their health visitor for breastfeeding related concerns. Who they would contact for breastfeeding related questions or concerns is summarised in Figure 1. 7/50 (14%) felt pushed into a decision regarding breastfeeding, 43/50 (86%) did not, however 3 expressed that breastfeeding was “strongly” encouraged with a feeling of guilt towards bottlefeeding. 24/50 (48%) received conflicting advice from healthcare professionals at some point during the antenatal or postnatal period. 14/50 (28%) identified conflicting advice around technique specifically. Conclusion Training healthcare staff is a key source to improve experiences as they are commonly the first port of call for mothers with breastfeeding issues. With limited healthcare resources, expectations must however be managed. With consistent advice from knowledgeable staff, breastfeeding support and experiences can be improved. Maximising support within the community was highlighted as the most appropriate and preferable route, through the use of more face to face time with health visitors but also increasing confidence with mother’s own GP’s.
<p>Nephropathy prevalence calculated per group according to age in relation to the five yea... more <p>Nephropathy prevalence calculated per group according to age in relation to the five years duration for the total of 54,670 patients.</p
With the increasing adoption of next generation sequencing technology in the medical practice, th... more With the increasing adoption of next generation sequencing technology in the medical practice, there is an increasing demand for faster data processing to gain immediate insights from the patient’s genome. Due to the extensive amount of genomic information and its big data nature, data processing takes long time and delays are often experienced. In this paper, we show how to exploit in-memory platforms for big genomic data analysis, with focus on the variant analysis workflow. We will determine where different in-memory techniques are used in the workflow and explore different memory-based strategies to speed up the analysis. Our experiments show promising results and encourage further research in this area, especially with the rapid advancement in memory and SSD technologies.
International journal of geoinformatics, Mar 1, 2009
Because diabetes is an extremely common disorder in Saudi Arabia, the National Diabetes Registry ... more Because diabetes is an extremely common disorder in Saudi Arabia, the National Diabetes Registry was designed by King Saud University Hospital, Diabetes Center in collaboration with King Faisal Specialist Hospital and Research Center in the year 2001. The registry was designed to provide information on the extent and nature of specific types of diabetes, diabetes complications and treatment of diabetes in Saudi Arabia. Using a secured login module, over 41,000 cases have been registered in the web-based registry database as of December 31, 2007. In order to give a better, geographical insight into the registry data, an Internet mapping facility has been incorporated into the registry software. This Internet Mapping Service allows the users to query the distribution of diabetes patients within the Kingdom of Saudi Arabia along with spatial data. The key feature is the availability of “real-time” patient data for patient-related queries, which was made possible by establishing a direct connection “Open Database Connectivity” with the SQL Server database.
Background The clinical utility of exome sequencing is now well documented. Rapid exome sequencin... more Background The clinical utility of exome sequencing is now well documented. Rapid exome sequencing (RES) is more resource-intensive than regular exome sequencing and is typically employed in specialized clinical settings wherein urgent molecular diagnosis is thought to influence acute management. Studies on the clinical utility of RES have been largely limited to outbred populations. Methods Here, we describe our experience with rapid exome sequencing (RES) in a highly consanguineous population. Clinical settings included intensive care units, prenatal cases approaching the legal cutoff for termination, and urgent transplant decisions. Results A positive molecular finding (a pathogenic or likely pathogenic variant that explains the phenotype) was observed in 80 of 189 cases (42%), while 15 (8%) and 94 (50%) received ambiguous (variant of uncertain significance (VUS)) and negative results, respectively. The consanguineous nature of the study population gave us an opportunity to obser...
The main aim of this study is to determine the prevalence and risk factors of ischemic stroke amo... more The main aim of this study is to determine the prevalence and risk factors of ischemic stroke among diabetic patients registered in the Saudi National Diabetes Registry (SNDR) database. A cross-sectional sample of 62,681 diabetic patients aged ≥25 years was used to calculate ischemic stroke prevalence and its risk factors. Univariate and multivariate logistic regression analyses were used to assess the roles of different risk factors. The prevalence of ischemic stroke was 4.42% and was higher in the older age group with longer diabetes duration. Poor glycemic control and the presence of chronic diabetes complications were associated with a high risk of ischemic stroke. History of smoking and type 2 diabetes were more frequent among stroke patients. Obesity significantly decreased the risk for ischemic stroke. Regression analysis for ischemic stroke risk factors proved that age ≥45 years, male gender, hypertension, coronary artery disease (CAD), diabetes duration ≥10 years, insulin u...
Family trio next-generation sequencing-based variant analysis was done to identify the genomic re... more Family trio next-generation sequencing-based variant analysis was done to identify the genomic reason on unexplained recurrent pregnancy loss (RPL). A family (dead fetus and parents) from Saudi Arabia with an earlier history of three unexplained RPLs at the ninth week of pregnancy was included in the study. Whole-genome sequencing (WGS) of a dead fetus and the parents was done to identify the pathogenic variation and confirmed through Sanger sequencing. WGS of dead fetus identifies a novel homozygous exonic variation (NM_017419.3:c.680G>T) in ASIC5 (acid-sensing ion channel subunit family member 5) gene; the parents are heterozygous. Newly designed ARMS PCR followed by direct sequencing confirms the presence of heterozygous in one subject and absence of homozygous novel mutation among randomly selected healthy Saudis. The second family with heterozygous was confirmed with three unexplained RPLs. Pathogenicity analysis of R227I amino acid substitution in ASIC5 protein through mole...
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with genetic and clinical... more Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with genetic and clinical heterogeneity. The interplay of de novo and inherited rare variants has been suspected in the development of ASD. Here, we applied whole exome sequencing (WES) on 19 trios from singleton Saudi families with ASD. We developed an analysis pipeline that allows capturing both de novo and inherited rare variants predicted to be deleterious. A total of 47 unique rare variants were detected in 17 trios including 38 which are newly discovered. The majority were either autosomal recessive or X-linked. Our pipeline uncovered variants in 15 ASD-candidate genes, including 5 (GLT8D1, HTATSF1, OR6C65, ITIH6 and DDX26B) that have not been reported in any human condition. The remaining variants occurred in genes formerly associated with ASD or other neurological disorders. Examples include SUMF1, KDM5B and MXRA5 (Known-ASD genes), PRODH2 and KCTD21 (implicated in schizophrenia), as well as USP9X and SM...
Advanced cholestatic liver disease is a leading referral to pediatric liver transplant centers. R... more Advanced cholestatic liver disease is a leading referral to pediatric liver transplant centers. Recent advances in the genetic classification of this group of disorders promise a highly personalized management although the genetic heterogeneity also poses a diagnostic challenge. Using a next-generation sequencing-based multi-gene panel, we performed retrospective analysis of 98 pediatric patients who presented with advanced cholestatic liver disease. A likely causal mutation was identified in the majority (61%), spanning many genes including ones that have only rarely been reported to cause cholestatic liver disease e.g. TJP2 and VIPAS39. We find no evidence to support mono-allelic phenotypic expression in the carrier parents despite the severe nature of the respective mutations, and no evidence of oligogenicity. The high carrier frequency of the founder mutations identified in our cohort (1 in 87) suggests a minimum incidence of 1:7,246, an alarmingly high disease burden that calls...
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