Precision medicine

 Precision Medicine for Investigators, Practitioners and Providers

Many topics under the same umbrella:

Table of Contents

Introduction

2. Role of genomics in precision medicine

3. High throughput omics in the precision medicine ecosystem

4. Infant gut microbiome

5. Paraprebiotics

6. Fecal transplantation in autoimmune disease

7. Drug pharmacomicrobiomics

8. CRISPR technology for genome editing

9. Engineering microbial living therapeutics

10. Organ on a chip

11. Multicellular in-vitro organ systems

12. The role of biobanks in biomarker development

13. Translational interest of immune profiling

14. Organoid pharmacotyping

15. Large datasets for genomic investigation

16. Modern applications of neurogenetics

17. Genomic profiling in cancer

18. Genomics in pediatrics

19. Genomics of gastric cancer

20.  Genomics of prostate cancer

21. MicroRNAs and inflammation markers in obesity

22. MiRNA sequencing for myocardial infarction screening

23. Cell free DNA in hepatocellular carcinoma

24. Non coding RNA in cancer

25. Germline variants and childhood cancer

26. Pharmacogenomics in cancer

27. Proteomic biomarkers in vireoretinal disease

28. Proteomics in respiratory diseases

29. Cardiovascular proteomics

30. Host genetics, microbiome, and inflammatory bowel disease

31. Sampling, Analyzing, and Integrating Microbiome ‘omics Data in a Translational Clinical Setting

32. Omics and microbiome in sepsis

33. Molecular and omics methods for invasive candidiasis

34. Lipid metabolism in colorectal cancer

35. Salivary volatolome in breast cancer

36. immunodiagnosis in leprosy

37. decision support systems in breast cancer

38. Electronic medical records and diabetes phenotyping

39. Clinical signature of suicide risk

40. Machine learning and cluster analysis in critical care

41. Artificial intelligence in gastroenterology

42. Algorithms for epileptic seizure prediction

43. Precision medicine in ophthalmology

44. Phenotyping COPD

45. Lifestyle medicine

46. Precision medicine for a healthier world

47. Aging and clustering of functional brain networks

48. Nutrigenetics

49. Genome editing in reproductive medicine

50. MRI guided prostate biopsy

51. Precision Nutrition

52. Theranostics in precision oncology

53. Precision medicine in daily practice

54. Imaging in precision medicine

55. Organoid for drug screening

56. Printing of personalized medication using binder jetting 3D printer

57. 3 D printing in orthopedic trauma

58. Consumer genetic testing tools in depression

59. The future of wearables

60. Tumor heterogeneity and drug development

61. Smartphone based clinical diagnosis

62. Smartphone biosensing for point of care use

63. Data security and patient protection

64. Blockchain solutions for healthcare

65. Ethical questions in gene therapy

66. Pitfalls of organ on a chip technologies

67. Regulatory issues of artificial intelligence in radiology

68. Academic industrial alliance

69. The future of precision medicine

70. Precision Medicine Glossary

71. Useful internet sites

Approaching the golden age of epigenomics and epitranscriptomics

A new twist on epigenetics

If epigenomics is crucial to discard the genetic predestination paradigm, now we can add a new 'omics to the paradigm: epitranscriptomics. Last February, Nature published interesting news related to recent scientific developments:

The epigenome helps to explain how cells with identical DNA can develop into the multitude of specialized types that make up different tissues. The marks help cells in the heart, for example, maintain their identity and not turn into neurons or fat cells. Misplaced epigenetic marks are often found in cancerous cells.

 Chuan He and Tao Pan are two researchers that have been working on new ways of controlling gene expression

He and others have shown that a methyl group attached to adenine, one of the four bases in RNA, has crucial roles in cell differentiation, and may contribute to cancer, obesity and more. In 2015, He’s lab and two other teams uncovered the same chemical mark on adenine bases in DNA (methyl marks had previously been found only on cytosine), suggesting that the epigenome may be even richer than previously imagined.

The team had shown for the first time that RNA methylation was reversible, just like the marks found on DNA and histones.

Methylated adenine bases are the focus of research on gene expression.

Medicine as a data science

THE PATIENT WILL SEE YOU NOW
The Future of Medicine Is in Your Hands

Maybe the title is the most confounding factor of the new great book written by Eric Topol.  Once you have finished reading it, you'll be convinced that he set the expectations to high, ordinary people should develop certain skills beyond their capabilities to apply such concept. I would say that a greater part of the medicine is in your hands, not medicine at all. The rationale behind the book is that medicine digitization allows patients to know more about their disease and how to "manage" it in certain cases. The most important thesis is that future medicine has to be considered a data science. And this is exactly the impact of the digitization of diagnostic and treatment: pervasive application of Bayes theorem in clinical practice, using big data and analytics.(Remember my archimedes posts, surprisingly Topol forgot it).
The book includes many topics that those that follow this blog it would sound familiar, i.e. ch. 4 about Angelina Jolie and BRCA genetic tests, a must read. And chapter 5 is a journey on the new omics of the medicine, a topic that I have also covered in the blog.
Nowadays, Eric Topol is the writer that is able to capture what's going on in medicine and its impact on society. That's why this book is a key reference of our time and I strongly recommend it.

PS. If you don't believe me, check Forbes, NYT, WP, WSJ.
PS. The book is also an invitation to change the current academic programmes for life sciences universities. Better now than later.

Validesa i utilitat de l'òmica

Evolution of Translational Omics: Lessons Learned and the Path Forward

 L'"Òmica" és un terme que abasta múltiples disciplines moleculars, que impliquen la caracterització dels conjunts globals de molècules biològiques, com ara ADN, ARN, proteïnes, i metabòlits. Per exemple, la genòmica investiga milers de seqüències d'ADN, la  transcriptòmica investiga totes o moltes transcripcions de gens, la proteòmica investiga un gran nombre de proteïnes, i metabolòmica investiga grans conjunts de metabòlits.

Així comença el llibre de l'IOM sobre una qüestió fonamental de la medicina dels nostres dies.  I el més interessant és com explica la diferència entre l'òmica translacional i els biomarcadors. Malgrat la dificultat que presenta l'avaluació d'un biomarcador, els reptes al que s'enfronta l'òmica són molt superiors. Diu clarament a l'inici:

The complexity of omics research also makes data provenance more challenging and makes sharing of the complex data sets and computational models difficult, which limits the ability of other scientists to replicate and verify the findings and conclusions of omics research studies. Database repositories for genomic data sets are available, but data sharing is not routine, and  without access to the data sets or a precisely defined computational model, replication and  verification are more difficult than for single biomarker tests. While independent confirmation studies are expensive, the need for replication is beneficial in the omics field given the data  complexities that can lead to errors, from simple data management errors to incorrectly  designed computational models. This level of complexity does not exist for single-biomarker  test research, development, and validation.

Massa sovint es vol fer passar aquesta complexitat com inadvertida. I afegeix:

Many hope that the promise that omics science holds for medicine and public health will be realized. With the creation of high-throughput measurement technologies, it is now feasible to take a snapshot of a patient’s molecular profile at specific stages in the progression of disease pathology or at a given location in the body. However, the complexity of these technologies and of the resulting high-dimensional data introduces major challenges for the scientific community, as rigorous statistical, bioinformatics, laboratory, and clinical procedures are required to develop and validate these tests and evaluate their clinical usefulness.

Sobre el tipus de dades òmiques heu d'anar a la pàgina 40 i llegir-ho amb deteniment. Quan un acaba de comprendre el que s'explica de forma planera, aleshores s'adona que els que venen genoma i prou s'han quedat curts, la complexitat és notòria. I en especial la referent a l'epigenoma, del que ja n'he parlat repetidament en aquest blog. El capítol sobre avaluació de les proves esdevé clau. Només fa referència a validesa analítica i clínica, però és el principi sense el qual tots aquells que es plantegin fer cost-efectivitat no podran treballar. I cap al final trobo aquesta conclusió:

 A well-designed test development plan addresses a clinically meaningful question and employs rigorous test discovery, development, and validation procedures. This includes locking down all aspects of an omicsbased test prior to evaluation for clinical utility and use and avoiding overlap between discovery and validation specimens. Choosing an appropriate clinical/biological validation strategy and interacting with FDA prior to initiation of validation studies also reflect a well-designed test development plan. Making data and code available are critical aspects of test development because it enables external verification of the results and generation of additional insights that can advance science and patient care.

El rigor s'imposa i traduir la recerca en aplicacions obliga a comprendre el valor que aporten a la societat. El camí és llarg malgrat sovint apareix als diaris com que és bufar i fer ampolles.

PS. Es poden patentar les proves genòmiques? Avui un tribunal decideix, ho trobareu a WSJ.

PS. Ekaizer a 8TV, fonamental. I també a RAC1

PS. Al Diccionario RAE queda més clar encara: macarra. 1. adj. Dicho de una persona: Agresiva, achulada.

Eliseu Meifren, podeu veure'l a Sant Feliu de Guixols, paga la pena.

El naixement molecular d'una malaltia

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes
 
La pràctica de la medicina tal com l'hem coneguda fins avui tindrà una evolució natural mitjançant la incorporació de les disciplines òmiques. Si d'això se n'ha especulat des de fa anys, ara a Cell podeu trobar com un professor d'Stanford relata l'evolució del seu perfil òmic personal. Analitza què passa durant dos anys, com apareix una malaltia i quina és la reacció molecular del cos. Explica com descobreix el risc de diabetis i, quan es confirma la malaltia, què fa a partir d'aleshores. O també què succeeix davant una infecció viral.
És aquest "Integrative Personal Omics Profile- iPOP" el que permet comprendre què està passant al cos.Això és del tot nou i cal tenir present que la fascinació davant troballes com aquesta requereix tocar de peus a terra. Traduir aquest experiment cap una nova forma de medicina suposa uns canvis radicals, en citaré només dos de fonamentals. El primer és com el govern és capaç de posar ordre a la informació privada sobre la predisposició al risc d'emmalaltir. Si el Riskogram es manté com una caixa negra, aleshores cal estar preparats pel pitjor. Molts recursos abocats en una creació de valor incerta. Només un regulador proactiu obligant a difondre estàndars amb codi obert, limitarà un potencial d'una medicina opaca, ho he explicat repetidament en aquest blog (en aquest PS. per exemple). El segon es refereix a la necessitat de revisar organitzativament els serveis evitant monopolis de coneixement, és a dir que algú aprofiti l'òmica per objectius diferents dels que es pretenen. Algú hauria de reflexionar per exemple sobre què està passant amb el consell genètic i com caldria que s'organitzés en un sistema de salut.
Per sobre de tot això algú haurà d'explicar el cost-efectivitat  de les òmiques per al diagnòstic de malalties. I ho haurà de fer amb la solidesa necessària, perqùe la pressió per aplicar-les sense escrúpols serà més forta que mai.
Aquest relat del naixement molecular d'una malaltia és sens dubte el pròleg d'una altra medicina i un altre sistema de salut. Ho seguirem atentament.