Genomics and World Health - Prof. Sir David Weatherall
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This document discusses genomics and world health, with a focus on birth defects, genetic disorders of hemoglobin like sickle cell anemia and thalassemia, and the population genetics and control of these disorders, especially in developing countries. It notes that 7.9 million births per year have defects, with 25% comprised of 5 main diseases. Partnerships between countries and organizations are needed to support control programs through screening, education, and capacity building. Genomics can help prevention, management, and may enable gene and cell-based therapies in the future.
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This document provides an update on research into Fabry disease. Some key points:
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DEFINITION:
Dna analysis can be used for the identification of carriers of hereditary disorders.
For prenatal diagnosis of serious genetic conditions yearly diagnosis before the onset of symptoms is done MOLECULAR DIAGNOSIS OF GENETIC DISEASE
CYSTIC FIBROSIS:
Cystic fibrosis is a genetic disease that affect mostly lungs and also the pancreas.
Screening test:
It is a complex process
Large number of genetic alterations have to be done.
For eg : It is the one of the most common lethal autosomal recessive disorder in Europe.
It is caused by mutations to cystic fibrosis transmembrane conductance regulator(CFTR) gene .
Screening individuals who may be at risk for cystic fibrosis for 500 different mutations is a daunting task.
Diagnosis test that screen for a large number of mutations of a single gene in one assay being developed.
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It is a disorder where red blood cells become rigid and sticky and are shaped like “sickle”.
This irregularly shaped cells stucks in small blood vessels which can slow and block the blood flow and oxygen to all the parts of the body.
There’s no cure for sickle cell anemia.
Screening for sickle cell anemia:
SCA is a genetic disease that is the result of a single nucleotide change in the codon for the sixth aminoacid of the β- chain of the hemoglobin molecule.
The anemia is caused by the inability of the mutated hemoglobin to carry sufficient oxygen.
Target – probe hybridasation is done.
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Genetic diseases
Hemophilia is a genetic disease where males have excessive bleeding due to failures in blood clotting. Symptoms include prolonged bleeding after procedures like circumcision or vaccinations. Treatment involves regular injections of clotting factor replacements. Diabetes is caused by the body's inability to properly metabolize or respond to insulin, leading to excessive urination and thirst. It has both genetic and environmental causes. Sickle-cell anemia causes red blood cells to take on a sickle shape, which can block blood flow and lead to infection before age 20 if untreated. It predominantly affects those of African descent.
Genetic Disorders
A genetic disorder is a disease caused by a different form of a gene called a variation,
or an alteration of a gene called a mutation. Many diseases have a genetic aspect. Some,
including many cancers, are caused by a mutation in a gene or group of genes in a person's
cells. These mutations can occur randomly or because of an environmental exposure such as
cigarette smoke.
Other genetic disorders are inherited. A mutated gene is passed down through a family
and each generation of children can inherit the gene that causes the disease. Still other
genetic disorders are due to problems with the number of packages of genes called
chromosomes. In Down syndrome, for example, there is an extra copy of chromosome 21.
If you know that you have a genetic problem in your family, you can have genetic testing to see if your baby could be affected.
NIH: National Human Genome Research Institute
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As long as knowledge on inherence, diagnosis and preventive measures are limited to very few people, it is difficult to control the spread of the genetic anomaly in our population. Apart from lack of comprehensive knowledge, The findings in this study showed a high level of general awareness about the existence of SCD but comprehensive knowledge about the cause and prevention was low and associated with vast misconceptions. A large percentage did not see its importance in influencing their marital decisions. Perhaps simple interventions that worked in the western countries can also work in India.
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Genetic variants associated with common diseases like diabetes and obesity have small individual effects but can combined to generate a polygenic risk score. While this score can help identify higher risk individuals, on its own the predictive ability of currently known genetic loci is limited. Integrating genetic data with clinical and other biological factors has not proven to significantly improve prediction of diseases like type 2 diabetes compared to non-genetic models alone. Large genome-wide studies continue to discover new loci to help better understand disease pathogenesis and potentially increase predictive power over time.
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The document provides information about hereditary spherocytosis, an inherited blood disorder where red blood cells take on an abnormal spherical shape. It discusses how the condition is caused by defects in red blood cell membrane proteins and is diagnosed through blood tests and examination of red blood cell shape under a microscope. Signs and symptoms include anemia, jaundice, and an enlarged spleen. Treatment options include removing the spleen through surgery to prevent red blood cell destruction, or supplements for mild cases.
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Genetic disorders are an important cause of disease and community medicine plays a role in their prevention and control. Screening programs can help detect genetic disorders during pregnancy or in newborns to allow for early treatment or intervention. Genetic counseling educates families about the risks and options for conditions with a genetic basis. Prevention strategies include screening, counseling, and public health efforts like vaccination or nutrition programs. Community medicine aims to understand and reduce the impact of genetic diseases through population-level interventions.
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- Anaemia is very common in cancer patients, occurring in 20-60% at presentation and increasing with chemotherapy cycles.
- Anaemia can be caused by the cancer itself, chemotherapy, radiotherapy, blood loss from surgery. It adversely impacts quality of life through fatigue and other symptoms.
- More severe anaemia is associated with worse survival outcomes and prognosis. This may be due to tumour hypoxia enhancing progression.
- While red blood cell transfusions are used to treat anaemia, over a third of anaemic cancer patients receive no treatment. Recombinant erythropoietin can increase hemoglobin levels and
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The document discusses the management of venous thromboembolism (VTE) in patients with cancer. It notes that cancers of the breast, colon, and lung are most commonly associated with VTE, though cancers of the pancreas, ovary, and brain have the strongest association when adjusted for prevalence. It recommends long-term anticoagulation with low molecular weight heparin over vitamin K antagonists or heparin for VTE in cancer patients. Extensive cancer screening in patients with idiopathic VTE is not routinely warranted, as it does not improve survival outcomes.
Molecular diagnosis of genetic disease ppt for students
DEFINITION:
Dna analysis can be used for the identification of carriers of hereditary disorders.
For prenatal diagnosis of serious genetic conditions yearly diagnosis before the onset of symptoms is done MOLECULAR DIAGNOSIS OF GENETIC DISEASE
CYSTIC FIBROSIS:
Cystic fibrosis is a genetic disease that affect mostly lungs and also the pancreas.
Screening test:
It is a complex process
Large number of genetic alterations have to be done.
For eg : It is the one of the most common lethal autosomal recessive disorder in Europe.
It is caused by mutations to cystic fibrosis transmembrane conductance regulator(CFTR) gene .
Screening individuals who may be at risk for cystic fibrosis for 500 different mutations is a daunting task.
Diagnosis test that screen for a large number of mutations of a single gene in one assay being developed.
SICKLE CELL ANEMIA:
It is a disorder where red blood cells become rigid and sticky and are shaped like “sickle”.
This irregularly shaped cells stucks in small blood vessels which can slow and block the blood flow and oxygen to all the parts of the body.
There’s no cure for sickle cell anemia.
Screening for sickle cell anemia:
SCA is a genetic disease that is the result of a single nucleotide change in the codon for the sixth aminoacid of the β- chain of the hemoglobin molecule.
The anemia is caused by the inability of the mutated hemoglobin to carry sufficient oxygen.
Target – probe hybridasation is done.
Genetic risk of uterine fibroid and its disparity
Uterine fibroids are benign tumors that develop in the uterus and disproportionately affect black women. Genetic factors contribute to uterine fibroid risk, as evidenced by familial clustering and higher concordance rates in monozygotic twins compared to dizygotic twins. While the MED12 gene is commonly mutated in fibroids, no single genetic variant fully explains racial disparities. Genome-wide association studies have identified some associated loci but failed to find differences between black and other ethnic groups. Determining the genetic underpinnings of uterine fibroids may help reduce the healthcare burden through improved screening and treatments.
Case study - gaucher disease
Gaucher disease is an inherited disorder caused by mutations in the GBA gene, resulting in deficient activity of the enzyme glucocerebrosidase. This causes glucocerebroside and other fatty substances to accumulate abnormally in tissues and organs like the spleen, liver and bone marrow. There are three main types of Gaucher disease, with type 1 being the most common. Symptoms vary but can include enlarged organs, bone pain and fractures, anemia, and neurological problems depending on the type. Treatment options include enzyme replacement therapy to supplement glucocerebrosidase or substrate reduction therapy to decrease glucocerebroside production.
Gaucher disease
Gaucher disease is a multisystemic lipidosis characterized by hematologic abnormalities, organomegaly, and skeletal involvement. There are three clinical subtypes delineated by the absence or presence and progression of neurologic manifestations. Treatment of type 1 includes enzyme replacement therapy to reverse symptoms. Types 2 and 3 also involve neurologic deterioration and have a poorer prognosis, though enzyme replacement may help with visceral symptoms in type 3.
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This document discusses several single-gene disorders including cystic fibrosis, sickle cell anemia, fragile X syndrome, Huntington's disease, and muscular dystrophy. It provides details on the genetics, symptoms, inheritance patterns, and impact of each disorder. References are also included at the end related to catastrophic antiphospholipid syndrome.
6.2 Human Genetic Disorders 2019
Genetic disorders can be caused by changes in genes or chromosomes. There are two major types - those caused by mutations in DNA sequences and those caused by changes in chromosome structure or number. Some examples of genetic disorders discussed include Down syndrome, Klinefelter syndrome, Turner syndrome, sickle cell anemia, cystic fibrosis, hemophilia, muscular dystrophy, Huntington's disease, ALS, diabetes, color blindness, albinism, achondroplasia, and hairy ears syndrome. Pedigrees and karyotypes are tools used to study genetics and inheritance patterns of traits and disorders.
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Examples of Hereditary Diseases, Cystic Fibrosis, Thalassemia, Diabetes, Down Syndrome, Obesity, and its symptoms, causes and treatments for it.
Case study
A 20-year-old female presented with fever, abdominal pain, altered mental status, and was found to have a blood sugar level of 21.9 and temperature of 34 degrees. On examination, she had a blood pressure of 85/60, heart rate of 110, cool pale dry skin, and was alert. Key findings included anxious appearance, clear lung sounds, heart rate of 110, respiratory rate of 28, and labored breathing. Differential diagnoses included sepsis, diabetic ketoacidosis (DKA), and amphetamine use. Though amphetamines could affect insulin control, the presenting problems and further lab results at the emergency department make DKA the most likely diagnosis, potentially representing the first presentation of type 1
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quick review of most common genetic disorders ,, with special regards , thanks and appreciation to slide sharers who inspire me to do such ppt ,, i should give thanx to a slide sharer i dont know his name , i made the outline of my ppt from his ppt because i like it too much ,, thnx to all followers and special thanx to slideshare.net
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Periodontal disease doesn’t exactly occupy the same “pedestal” as diseases like cancer. And yet, it’s a valid health condition that needs urgent attention. There is more than enough research connecting periodontitis (aka gum disease) to general health. For instance, diabetes is confirmed to be a major risk for periodontitis, according to researchers from England, Spain, and Germany.
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This document provides an overview of genetic diseases and inheritance patterns. It discusses several types of genetic disorders including single gene inheritance, multifactorial inheritance, chromosomal abnormalities, and mitochondrial inheritance. Specific genetic diseases are described for each category, such as cystic fibrosis, sickle cell anemia, and Alzheimer's disease. The roles of genes, chromosomes, and mitochondria in the development and transmission of genetic traits and diseases are also summarized.
GVHD & transplantation
Transplantation of organs and tissues has become common for treating diseases. Complications include graft-versus-host disease (GVHD) and increased risk of infection and cancer due to lifelong immunosuppression. GVHD occurs when transplanted immune cells attack the recipient's body, commonly affecting the skin, bowel and liver. Opportunistic infections are frequent due to weakened immunity, including viruses like CMV and fungi such as Candida. Cancer risk is elevated 100-fold, with lymphoproliferative disorders, Kaposi's sarcoma and skin cancers being most common.
Fabry Disease Ppt.Cyrus & Jukie
Fabry disease is a rare genetic disorder caused by deficient activity of the enzyme alpha-galactosidase A. This enzyme breakdown lipids in the body. Its deficiency leads to a buildup of lipids in blood vessels, kidneys, and other organs. Symptoms include skin lesions, pain, kidney failure, and increased risk of heart disease. Treatment involves enzyme replacement therapy via intravenous infusion to help break down the buildup of lipids. However, this treatment does not cure the condition but only manages symptoms.
Genetic diseases
Hemophilia is a genetic disease where males have excessive bleeding due to failures in blood clotting. Symptoms include prolonged bleeding after procedures like circumcision or vaccinations. Treatment involves regular injections of clotting factor replacements. Diabetes is caused by the body's inability to properly metabolize or respond to insulin, leading to excessive urination and thirst. It has both genetic and environmental causes. Sickle-cell anemia causes red blood cells to take on a sickle shape, which can block blood flow and lead to infection before age 20 if untreated. It predominantly affects those of African descent.
Genetic Disorders
A genetic disorder is a disease caused by a different form of a gene called a variation,
or an alteration of a gene called a mutation. Many diseases have a genetic aspect. Some,
including many cancers, are caused by a mutation in a gene or group of genes in a person's
cells. These mutations can occur randomly or because of an environmental exposure such as
cigarette smoke.
Other genetic disorders are inherited. A mutated gene is passed down through a family
and each generation of children can inherit the gene that causes the disease. Still other
genetic disorders are due to problems with the number of packages of genes called
chromosomes. In Down syndrome, for example, there is an extra copy of chromosome 21.
If you know that you have a genetic problem in your family, you can have genetic testing to see if your baby could be affected.
NIH: National Human Genome Research Institute
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Molecular diagnosis of genetic disease ppt for students
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As long as knowledge on inherence, diagnosis and preventive measures are limited to very few people, it is difficult to control the spread of the genetic anomaly in our population. Apart from lack of comprehensive knowledge, The findings in this study showed a high level of general awareness about the existence of SCD but comprehensive knowledge about the cause and prevention was low and associated with vast misconceptions. A large percentage did not see its importance in influencing their marital decisions. Perhaps simple interventions that worked in the western countries can also work in India.
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The document discusses various genetic diagnostic tests including cytogenetic tests, molecular tests, and molecular diagnostics for infectious diseases and genetic identification. It describes tests for genetic diseases including somatic rearrangements in cancer, genetic risk factors, pharmacogenetics, and mutations in monogenic diseases. Specific tests and diseases are discussed, along with factors that impact diagnosis such as disease mutations, technology, cost, and organization.
15 Genetic Diseases
Genetic diseases are increasing due to factors like environmental pollution and improved diagnostic techniques. In China, it is estimated that 1 million new patients develop inherited disorders each year. Genetic diseases can be classified as chromosomal abnormalities, single gene disorders, and polygenic disorders. While most genetic diseases cannot be cured, treatment options include dietary restrictions, removing harmful substances, supplementing lacking substances, and gene therapy shows promise for some conditions. Prevention involves genetic counseling and prenatal testing.
헬스케어 빅데이터로 무엇을 할 수 있는가?
Healthcare big data can be used to gain insights into human health and disease through various data sources like genetics, electronic health records, insurance claims, medical images, and sensor data. This data when analyzed using techniques like genome-wide association studies, transcriptomics, proteomics, and metabolomics can provide novel findings and reveal genetic and environmental factors influencing common and rare diseases. Integrating these different types of omics data offers opportunities for more precise diagnosis, treatment and prevention strategies in precision medicine.
Genomics in CVD
Functional genomics has led to an improvement of our understanding of CVD and can be translated to clinical utility. Gene-based pre-symptomatic prediction of illness, finer diagnostic sub-classifications and improved risk assessment tools will permit earlier and more targeted intervention. Pharmacogenetics will guide our therapeutic decisions and monitor response to therapy. Personalised medicine requires the integration of clinical information, stable and dynamic genomics and molecular phenotyping.
It is now possible to systematically search the entire human genome for common variants that are associated with a particular phenotype. (HGP, HAP MAP)
Genetic counselling - a review
https://userupload.net/06gt5zcwvh90
Genetic counseling is the process of advising individuals and families affected by or at risk of genetic disorders to help them understand and adapt to the medical, psychological and familial implications of genetic contributions to disease.[1] The process integrates:
Interpretation of family and medical histories to assess the chance of disease occurrence or recurrence
Education about inheritance, testing, management, prevention, resources
Counseling to promote informed choices and adaptation to the risk or condition.
Strategies To Reduce The Incidence Of Genetic Disorders In The Arab World By ...
Noor Conference | Global Knowledge Forum | http://www.noor.org.sa | Day 2 - Panel 3 - Strategies To Reduce The Incidence Of Genetic Disorders In The Arab World By Prof. Hossam E. Fadel, Noor
MLGG_for_linkedIn
1) Manuel L. Gonzalez-Garay presented research projects at UTHealth from 2009-2015 investigating rare genetic disorders using next-generation sequencing and metabolomics.
2) An experimental design involved whole exome sequencing of 81 healthy volunteers from the Young Presidents' Organization to explore the practical value and challenges of genomic information for healthy individuals.
3) Analysis of the sequencing data and metabolomics profiles identified several disease-causing variants and metabolic deficiencies, demonstrating the potential for precision medicine approaches in volunteers of normal health.
20160119 디지털 헬스케어 의사모임 1월 전체 파일 v3
디지털 헬스케어 의사모임 1월 모임에서 발표되었던 파일들을 묶었습니다.
토픽은
1. 지난 한달 간의 디지털 헬스케어 토픽 리뷰
2. 빅데이터 분석: 유전체 정보와 개인 라이프로그 정보 활용
3. CES 2016 간단 리뷰
4. 네오팩트 회사 소개
입니다.
Lymphadenopathy in general
The article discusses the evaluation of peripheral lymphadenopathy in primary care patients. While the majority of cases are benign, malignancy can occasionally be the cause. The risk of malignancy increases with age and duration of lymphadenopathy greater than two weeks. Key factors suggesting malignancy include firm or fixed nodes, supraclavicular location, and associated symptoms like weight loss or night sweats. A thorough history of exposures, medications, travel, and review of systems can help determine the etiology. For unexplained cases, observation for one month is reasonable before further testing or biopsy. Knowledge of risk factors guides the management of lymphadenopathy to identify serious underlying conditions.
Sub-regional and Global SCD Networks - Jacques Elion
The document discusses the establishment of sub-regional and global networks for sickle cell disease (SCD). It notes the large disease burden of SCD globally and the disparity in resources and outcomes between wealthy and poor countries. Successful regional networks in Africa, the Caribbean, and other areas are highlighted. The creation of the Global SCD Network is outlined, with the goals of facilitating international partnerships on research, training, education and clinical programs. Priority areas of focus for the network include natural history studies, infectious disease interactions, hydroxyurea trials in developing countries, and understanding genetic factors in phenotypic diversity.
Non communicable diseases (final)
1. Non-communicable diseases (NCDs) such as cardiovascular diseases, cancers, diabetes and chronic respiratory diseases account for a large burden of disease in Nepal. NCDs represent over 80% of outpatient cases and over 88% of inpatient cases based on national data.
2. Risk factors for NCDs such as tobacco use, harmful alcohol consumption, unhealthy diet, and physical inactivity are highly prevalent in Nepal. Surveys show over one-third of the population uses tobacco and over one-quarter consumes alcohol harmfully.
3. While Nepal has drafted an NCD policy and strategy, urgent action is needed to implement prevention and control efforts for NCDs given their growing burden
Cyprus: a case study - Carsten W. Lederer
(1) Cyprus established a successful national prevention program for beta-thalassemia that reduced expected cases from over 50 births annually to less than 5 through population-wide carrier screening, counseling, and prenatal diagnosis. (2) Key factors in Cyprus's success included a small, homogeneous population; strong social support networks; and dedicated diagnostic and counseling centers. (3) Maintaining prevention efforts remains challenging as society changes and awareness declines in younger generations who have never seen the impacts of untreated thalassemia.
Similar to Genomics and World Health - Prof. Sir David Weatherall (20)
GG2020 Developing capacity for variant data sharing in low- and middle-income...
GG2020 Developing capacity for variant data sharing in low- and middle-income...
Strategies To Reduce The Incidence Of Genetic Disorders In The Arab World By ...
Strategies To Reduce The Incidence Of Genetic Disorders In The Arab World By ...
Sub-regional and Global SCD Networks - Jacques Elion
Sub-regional and Global SCD Networks - Jacques Elion
More from Human Variome Project
ClinVar: Aggregating Data to Improve Variant Interpretation - Melissa Landrum
The rate of variant discovery continues to surpass the rate of clinicalgrade interpretation. This is a challenge for precision medicine, because fast, reliable access to variant interpretations is necessary to provide well-informed and timely interpretations of test results to patients. ClinVar is a public repository for interpretations of clinical significance and functional effects of variants in any gene and for any disease. Interpretations are submitted by many sources, including clinical testing laboratories, research laboratories, locus-specific databases, expert panels, practice guidelines, as well as OMIM® and GeneReviews™. Collecting variant interpretations in ClinVar depends on integrating data from these different sources, which has several benefits. First, data integration requires standardizing the data from each source. This improves the quality of the data in ClinVar as well as in each of the individual datasets. ClinVar staff validate HGVS expressions as a routine part of ClinVar submission processing. Submitters are encouraged to use standard terms in MedGen for diseases and phenotypes. Standard terms for clinical significance are used in ClinVar when available; for example, ClinVar uses the terms recommended by ACMG to classify variants for Mendelian diseases. Secondly, ClinVar aggregates all data for a variant defined by its genomic location. Therefore, HGVS descriptions on different transcripts or on different genomic sequences can be recognized as the same variant. Thirdly, integrating data from multiple submitters allows the evidence from all sources to be pooled together. This larger collection of evidence aids the re-evaluation of variant classifications, and is especially valuable for rare variants and novel gene-disease relationships. Fourthly, data integration means that variant interpretations from different sources can be viewed together and compared. Thus a ClinVar user has access to interpretations outside any internal system and knows when there is consensus in the interpretation or not. Submitting laboratories use reports of conflicting interpretations in ClinVar to prioritize variants that they should re-evaluate. ClinVar receives data from many data providers, and therefore provides clear attribution to each contributing group, including links to records in LSDBs. Each source may update their submission to ClinVar at any time. For example, a record may be updated when a variant is re-classified or when additional evidence is available to support the interpretation. Submitters may consider providing regular updates to ClinVar to prevent their interpretations from becoming out of date. Submissions to ClinVar describe variants that range in complexity from simple alleles with explicit sequence locations through copy number changes and cytogenetic rearrangements with fuzzy boundaries.
The BRCA Share(TM) Consortium - Christophe Beroud
The BRCA ShareTM Consortium is a public-private partnership that promotes sharing of BRCA genetic data. It has over 35,000 BRCA test results from US and French clinical labs. The goal is to accelerate BRCA research. It is a open user group co-founded by Inserm and Quest Diagnostics. BRCA ShareTM is well adopted internationally. In June 2016, it incorporated new data from private partners, increasing the number of known BRCA mutations. The consortium of French experts helps curate and reclassify variants of unknown significance based on multiple lines of evidence. This benefits all partners through improved annotation of shared variants.
Establishing validity, reproducibility, and utility of highly scalable geneti...
Establishing validity, reproducibility, and utility of highly scalable geneti...Human Variome Project
Background: New technologies and increased competition have, and will continue to improve the cost-effectiveness of genetic testing, making genetic analysis more accessible to medical practices worldwide. However, challenges remain to establishing the validity of such tests. Moreover many patients harbor rare or novel variants and classification is likely to remain a bottleneck in broader deployment of genetic medicine.The PhenX Toolkit: Standard Measures for Collaborative Research - Wayne Huggins
The PhenX Toolkit: Standard Measures for Collaborative Research - Wayne HugginsHuman Variome Project
Introduction and Background: The Web-based PhenX Toolkit (consensus measures for Phenotypes and eXposures, https://www. phenxtoolkit.org/) is a catalog of standard measures designed to facilitate collaborative biomedical research. PhenX measures help ensure that phenotypes from different studies are collected and represented in a consistent format. This consistency can enable data comparability across sites in large cohorts (e.g., Precision Medicine Initiative) and facilitates combining data to validate clinically actionable variants, increase statistical power (e.g., studies of rare genetic conditions or gene-enviroment interactions), or compare treatments and outcomes between patients.Legal and regulatory challenges to data sharing for clinical genetics and ge...
Legal and regulatory challenges to data sharing for clinical genetics and ge...Human Variome Project
There are many factors that impede genomic variant sharing in the UK, despite it becoming a necessary part of clinical care. These include the lack of a designated infrastructure or mechanism aggravated by the complexity of laws that apply, and fragmented and variable advice from local ‘Caldicott guardians’ who guide NHS trusts on their responsibilities concerning data protection and confidentiality. Since the legitimacy of data sharing in the UK is framed in terms of ‘personal data’ being shared for ‘direct care’ (subject to legal exceptions), the blurred boundaries between clinical care and research, and the spectrum of identifiability of data also lead to differing interpretations resulting in inconsistent practices.
In a multidisciplinary collaboration, the PHG Foundation and the UK’s Association for Clinical Genetic Science co-hosted a workshop to examine the clinical necessity for sharing variant data and associated phenotypic information, the technical feasibility and the legal and regulatory impediments to such sharing. Delegates included clinicians, laboratory scientists, and key policy makers, including the National Data Guardian for Health and Care and representatives from the 100,000 Genomes Project, a pioneering research project which promises to build a legacy for future genomics services in the UK. The key finding from our work was that current arrangements for sharing genomic variants within the NHS are unsatisfactory and inconsistent practices are compromising safety and quality. Our workshop report [1] highlights the urgent need for (i) national agreement to optimise sharing within the NHS and develop consensus on the legitimacy of data sharing, (ii) standardised operational processes, including a designated sustainable database or mechanism for sharing, and (iii) strong leadership by the multiple relevant health organisations to demonstrate the benefits and risks associated with sharing and not sharing data.
Since publication of the workshop report, the NHS Consortium (operating within the DECIPHER database) has reported a 120% increase in the number of cases shared, the 100,000 Genomes Project and associated data embassy have got underway and the EU Data Protection Regulation has been finalised. However research highlights continuing public reservations about some aspects of data sharing including commercial access and misgivings around secondary uses of data. Publication of the National Data Guardian’s long-awaited review of consent and security provisions to provide guidance on a new consent and opt-out model for sharing patient information in the NHS, has been delayed pending the results of the EU referendum being known. Against this backdrop, the imperative to develop robust, proportionate policies for genomic data sharing becomes increasingly acute.
Funding from the PHG Foundation and the Association for Clinical Genetic Science.Report from the International Confederation of Countries Advisory Council - M...
Report from the International Confederation of Countries Advisory Council - M...Human Variome Project
This document summarizes discussions from Session V of the Human Variome Project on Thursday June 2nd.
It provides information on 3 country nodes - Austria, Democratic Republic of Congo, and an interim node. For Austria, it outlines the genetic testing landscape, notes progress establishing a national genetic database, and plans for selecting database software in the next year. It also briefly mentions the Democratic Republic of Congo and an interim country node. The document discusses challenges around data sharing, quality, and submission across national databases.Human variome project quality assessment criteria for variation databases - M...
Human variome project quality assessment criteria for variation databases - M...Human Variome Project
This document discusses quality assessment criteria for variation databases that are developed by the Human Variome Project working group. It outlines two key components of quality - the contents, update frequency, and quality of numerous available variation databases. It also describes work done by the working group to produce guidelines for defining variation database quality, which includes evaluating databases based on criteria and providing feedback and an electronic seal to indicate quality. The document concludes by outlining next steps, which include beta testing the quality evaluation scheme with real databases, performing independent evaluations of databases, and refining the quality criteria over time through voluntary participation.HVP Country Node: Venezuela - Aida Falcon de Vargas
The Venezuelan Country Node was established in 2012 and is organized through a Steering Committee and Advisory Groups. It currently has 35 clinical laboratories, 60 clinicians, and genetic counseling is performed by clinicians. Genetic healthcare services are provided partially through the national health system and private sector, though the national system has insufficient budgeting. The Country Node is working to establish a national data repository and develop data collection, access, and ownership policies, though it currently lacks funding and only has data available within individual institutions. Its plans for the next year include continuing collaboration efforts and workshops to build databases and train professionals to develop the national genomic infrastructure.
Human Genetics of Infectious Diseases - Laurent Abel
This document discusses human genetics research into infectious diseases. It summarizes that:
1) Genetic factors contribute to variability in individual responses to infection exposure and clinical outcomes. Rare single gene mutations can cause highly selective predispositions to specific pathogens like Herpes simplex virus-1 or mycobacteria.
2) Research has identified genetic causes of severe infectious diseases like Herpes simplex encephalitis and Mendelian susceptibility to mycobacterial disease. Defects in the TLR3 and IL-12/IFN-γ pathways increase risk.
3) Genome-wide studies of common infections like tuberculosis have found limited roles for common variants but suggest searching for rare variants using deep sequencing. Gen
HVP Country Node: Malaysia - Zilfalil bin Alwi
The document summarizes information about the Malaysian Node of the Human Variome Project (MyHVP).
It provides details such as:
- MyHVP was established in 2010 and is funded by Universiti Sains Malaysia.
- It is linked to several national human genetics societies and has an ethical framework for privacy and consent approved by Universiti Sains Malaysia.
The document also outlines MyHVP's technical aspects including its national data repository, data sharing policies, and plans to increase engagement and publications over the next 12 months. It notes that continued funding is one challenge faced.
GENETIC HETEROGENEITY OF MITOCHONDRIAL DISORDERS - Agnès Rötig
1. Genetic heterogeneity of mitochondrial disorders is high, with mutations in over 250 nuclear genes and 13 mitochondrial genes known to cause primary mitochondrial disorders. 2. Complex I deficiency is a common presentation and has high genetic and clinical heterogeneity, with mutations in over 30 nuclear genes associated. 3. Mitochondrial translation deficiency is another common presentation, with mutations in over 30 genes encoding mitochondrial aminoacyl-tRNA synthetases and other translation factors associated.
The BRCA Challenge & Exchange: Progress and Plans - Gunnar Rätsch
The BRCA Challenge aims to improve care for patients at risk of breast and ovarian cancer through global data sharing and collaboration on BRCA1 and BRCA2 variants. It plans to:
1) Share BRCA variants publicly via the BRCA Exchange portal, displaying a curated list of variants interpreted through expert consensus.
2) Address challenges of global data sharing through its organization structure and subcommittees.
3) Create a model for data sharing and analysis for all disease genes.
Richard GH Cotton: He may have been a bit before his time - Michael Watson
A tribute to Dick Cotton from Michael Watson. Part 2 of the inaugural Richard Cotton Memorial lecture.
Professor Richard Cotton - Finlay Macrae
A tribute to Dick Cotton from Finlay Macrae. Part 1 of the inaugural Richard Cotton Memorial lecture.
HVP Country Node: Canada - Matthew Lebo
The document summarizes information about the Canadian Open Genetics Repository (COGR), which serves as the HVP Country Node for Canada. It provides details on clinical genetics resources in Canada, the structure and funding of COGR, its data sharing policies and technical capabilities. COGR's data holdings have doubled in the past year and it plans to strengthen genomic data sharing by publishing findings and seeking additional funding. The primary challenges are obtaining funding and data from all sites.
Use of open, curated variant databases: ethics? Liability? - Bartha Knoppers
Translation of genomics into medicine and drug development requires comprehensive, high-quality, genomic variant databases. To support translation, there is a movement towards sharing clinical annotations of variants (e.g., benign, unknown, pathogenic) internationally via open access. Despite the growing popularity of variant databases, ethical issues and liability risks have received scant attention. Ethical priorities for variant databases include 1) competence – ensuring that data is responsibly managed, curated, and used; 2) confidentiality – ensuring appropriate safeguards for patient data; 3) communication – clearly describing the purpose, quality standards, and data handling practices to contributing patients and potential users; and 4) continuous oversight to adapt database governance in a rapidly evolving environment. How can database managers fulfill these obligations when these responsibilities are increasingly distributed along the clinical pipeline? Legal issues include medical liability based on potential harm to patients; liability based on third-party intellectual property or privacy rights in the data; and regulatory risks as variant data is integrated into genetic tests or devices. Can these risks can be managed through appropriate governance structures – including adequate consents, access processes, contributor agreements, and disclaimers – while still facilitating sharing and clinical use?
HVP6: Final Thoughts - John Burn & Raj Ramesar
This document summarizes discussions from a workshop on developing capacity for gene variant data sharing in low and middle income countries. It outlines sessions on understanding the challenges, the current situations in different global regions, ELSI issues, funding and partnerships. Key outcomes include practical steps to develop LOVD databases, recommendations on hemoglobinopathies, and plans to facilitate networks through WHO collaborating centers and a future meeting in sub-Saharan Africa. The overall goal is to strengthen global collaboration and data sharing for conditions like sickle cell disease and thalassemias.
Report from the International Scientific Advisory Committee - John Burn
The document summarizes a report from the International Scientific Advisory Committee meeting of the Human Variome Project held from June 11-15, 2012 in Paris. It lists the voting and non-voting members of the committee and provides information on their accountabilities, remit, and domains. These include providing strategic scientific direction, approving publications, authorizing new initiatives, and making recommendations on behalf of the Human Variome Project Consortium. It also mentions functional classification of SNPs identified and goals of establishing standards, facilitating research, and strengthening capacity for sharing genomic data equitably and sustainably.
HVP Country Node: Italy - Domenico Coviello
The document summarizes Italy's HVP Country Node activities. It provides an overview of genetic services and resources in Italy, including 198 genetic diagnostic laboratories and approximately 200 clinicians. The HVP Country Node was established in 2014 and is endorsed by the national genetics society SIGU. However, it currently lacks formal policies and infrastructure for data sharing. Plans over the next 12 months include establishing a consortium to formalize collaboration for building a national website and installing LOVD software for a national database. The main challenges are a lack of financial and administrative support.
Rare and common variants contribute to the complex inheritance of Hirschsprun...
Rare and common variants contribute to the complex inheritance of Hirschsprun...Human Variome Project
1) The document discusses the genetic factors that contribute to Hirschsprung disease (HSCR), a congenital disorder caused by the lack of enteric nervous system in parts of the intestine.
2) It finds that both rare and common genetic variants contribute to the complex inheritance of HSCR. Common variants were identified in RET, NRG1 and SEMA3C-3D genes, with ethnic differences in frequencies.
3) Rare coding variants were also found to influence risk, suggesting HSCR has a complex genetic architecture involving both regulatory and coding changes across several loci. Understanding how these various genetic factors interact remains an area of ongoing research.More from Human Variome Project (20)
ClinVar: Aggregating Data to Improve Variant Interpretation - Melissa Landrum
ClinVar: Aggregating Data to Improve Variant Interpretation - Melissa Landrum
Establishing validity, reproducibility, and utility of highly scalable geneti...
Establishing validity, reproducibility, and utility of highly scalable geneti...
The PhenX Toolkit: Standard Measures for Collaborative Research - Wayne Huggins
The PhenX Toolkit: Standard Measures for Collaborative Research - Wayne Huggins
Legal and regulatory challenges to data sharing for clinical genetics and ge...
Legal and regulatory challenges to data sharing for clinical genetics and ge...
Report from the International Confederation of Countries Advisory Council - M...
Report from the International Confederation of Countries Advisory Council - M...
Human variome project quality assessment criteria for variation databases - M...
Human variome project quality assessment criteria for variation databases - M...
HVP Country Node: Venezuela - Aida Falcon de Vargas
HVP Country Node: Venezuela - Aida Falcon de Vargas
Human Genetics of Infectious Diseases - Laurent Abel
Human Genetics of Infectious Diseases - Laurent Abel
GENETIC HETEROGENEITY OF MITOCHONDRIAL DISORDERS - Agnès Rötig
GENETIC HETEROGENEITY OF MITOCHONDRIAL DISORDERS - Agnès Rötig
The BRCA Challenge & Exchange: Progress and Plans - Gunnar Rätsch
The BRCA Challenge & Exchange: Progress and Plans - Gunnar Rätsch
Richard GH Cotton: He may have been a bit before his time - Michael Watson
Richard GH Cotton: He may have been a bit before his time - Michael Watson
Use of open, curated variant databases: ethics? Liability? - Bartha Knoppers
Use of open, curated variant databases: ethics? Liability? - Bartha Knoppers
Report from the International Scientific Advisory Committee - John Burn
Report from the International Scientific Advisory Committee - John Burn
Rare and common variants contribute to the complex inheritance of Hirschsprun...
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We’ll kick things off by showcasing the most commonly used event-based triggers, introducing you to various automation workflows like manual triggers, schedules, directory watchers, and more. Plus, see how these elements play out in real scenarios.
Whether you’re tweaking your current setup or building from the ground up, this session will arm you with the tools and insights needed to transform your FME usage into a powerhouse of productivity. Join us to discover effective strategies that simplify complex processes, enhancing your productivity and transforming your data management practices with FME. Let’s turn complexity into clarity and make your workspaces work wonders!
Artificial Intelligence for XMLDevelopment
In the rapidly evolving landscape of technologies, XML continues to play a vital role in structuring, storing, and transporting data across diverse systems. The recent advancements in artificial intelligence (AI) present new methodologies for enhancing XML development workflows, introducing efficiency, automation, and intelligent capabilities. This presentation will outline the scope and perspective of utilizing AI in XML development. The potential benefits and the possible pitfalls will be highlighted, providing a balanced view of the subject.
We will explore the capabilities of AI in understanding XML markup languages and autonomously creating structured XML content. Additionally, we will examine the capacity of AI to enrich plain text with appropriate XML markup. Practical examples and methodological guidelines will be provided to elucidate how AI can be effectively prompted to interpret and generate accurate XML markup.
Further emphasis will be placed on the role of AI in developing XSLT, or schemas such as XSD and Schematron. We will address the techniques and strategies adopted to create prompts for generating code, explaining code, or refactoring the code, and the results achieved.
The discussion will extend to how AI can be used to transform XML content. In particular, the focus will be on the use of AI XPath extension functions in XSLT, Schematron, Schematron Quick Fixes, or for XML content refactoring.
The presentation aims to deliver a comprehensive overview of AI usage in XML development, providing attendees with the necessary knowledge to make informed decisions. Whether you’re at the early stages of adopting AI or considering integrating it in advanced XML development, this presentation will cover all levels of expertise.
By highlighting the potential advantages and challenges of integrating AI with XML development tools and languages, the presentation seeks to inspire thoughtful conversation around the future of XML development. We’ll not only delve into the technical aspects of AI-powered XML development but also discuss practical implications and possible future directions.
National Security Agency - NSA mobile device best practices
Threats to mobile devices are more prevalent and increasing in scope and complexity. Users of mobile devices desire to take full advantage of the features
available on those devices, but many of the features provide convenience and capability but sacrifice security. This best practices guide outlines steps the users can take to better protect personal devices and information.
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Genomics and World Health - Prof. Sir David Weatherall
- 1. Genomics and World Health David Weatherall Weatherall Institute of Molecular Medicine, University of Oxford
- 2. 2
- 3. Birth Defects (M of D, 2006) Frequency 7.9 million/yr. 3.3 million deaths 25% comprised of 5 diseases Congenital heart disease (1 m); Neural tube defect (324,000); Haemoglobinopathy (308,000); Down syndrome (217,000); G6PD deficiency (177,000) Relationship to GNI Low income 60.2% Middle income 33.5% High income 6.3% 3
- 4. Common Genetic Disorders of Haemoglobin Thalassaemia thalassaemia thalassaemia Structural variants Haemoglobin S Haemoglobin E Haemoglobin C 4
- 5. Annual births of severe disorders of haemoglobin Sickle cell anaemia Sub-Saharan Africa 240,932 Elsewhere 92,997 HbSC disease 54,736 Thalassaemia thalassaemia major 23,329 HbE thalassaemia 20,588 HbH disease 14,504 HbS thalassaemia 12,321 Hb Bart’s hydrops 5,183 5
- 8. Population genetics and dynamics of genetic disease in the developing countries 1) Natural selection 2) Consanguinity 3) Parental age 4) Population migration 5) Epidemiological transition 8
- 9. Organisation required for control of thalassaemia in the developing countries North/South and South/South partnerships Support by WHO, funding agencies, NGOs, Governments Definition of economic issues. GBD programme 9
- 10. Oxford-Sri Lanka North/South Partnership Joint research programme Capacity building National Thalassaemia Centre Central reference laboratory Molecular Medicine Centre National Thalassaemia Programme Education Screening Staff Training in Oxford 10
- 11. 11
- 12. 12
- 13. Genomics and Control of Haemoglobin Disorders Prevention Screening. PND Fetal blood/globin synthesis 1974-1989 13,921 cases DNA Analysis by CVS 1980 Improved Management Transfusion. Chelation. Hydroxyurea etc. 1960 Heterogeneity ‘Candidate’ genes. Linkage. Unusual phenotypes 1970 GWAS and related studies. Confirmed/extended No new modifiers Gene Therapy
- 14. Molecular Medicine (1950 - 2010) Monogenic (Mendelian) disease Diagnosis, prenatal diagnosis (therapy) Communicable disease Diagnosis, (therapy) Cancer Mechanisms, diagnosis, therapy Vascular disease, diabetes, dementia, rheumatic disease etc. Small (multigenic) components Pharmacogenomics Drug design, (personalised therapy) 14
- 15. The Future Data collection Genomics. GWS Transcriptomics Epigenomics Proteomics Metabolomics Phenomics Analysis Systems biology Cellmap 15
- 16. The Future Expansion of North-South partnerships Evolution of South-South partnerships Modification of medical education in rich countries Education of governments of rich countries and NGO’s regarding cost-effectiveness of partnerships