Ebb&Flo (Project 2 + 3) by Abidur Rahman https://padlet.com/abidurrahman3/rb4yyw244nfn96x0 en-us 2022-11-28 08:05:16 UTC 2025-11-01 16:24:06 UTC hello@padlet.com Quick facts about Endometriosis abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2399824775 Endometriosis is a systemic & chronic inflammatory disease where endometrial cells grow outside the uterus. 

Classical symptoms include pain during periods & sexual intercourse, chronic pelvic pain, nausea, fatigue, and sometimes depression, anxiety, and infertility.

The golden standard of diagnosis and treatment is Laparoscopy - a surgical procedure to remove the aberrant lesions. ]]> 2022-11-28 08:07:13 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2399824775 The Global Incidence of Endometriosis abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2399834174 190 million of women and girls suffer from endometriosis globally and there is an average delay of 6-12 years from having symptoms to getting diagnosed.]]> 2022-11-28 08:16:34 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2399834174 The Ongoing Challenges with Endometriosis abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2399850560 This delay is due to 3 key challenges : 
1. Very heterogeneous symptom presentation 
2. Great overlap with other diseases (e.g. pelvic pain with ovarian cysts) 
3. The lack of accessible diagnostics as laparoscopy can cost about $5000 and is highly reliant on surgical skills & equipment access. ]]> 2022-11-28 08:31:49 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2399850560 ebb&flo : A revolutionary end-to-end approach to endometriosis care abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2399856406 Seeing how millions of women are being failed by current care approaches, Kelly Goldfeder founded ebb&flow - 
a health & biotechnology company that provides marginalized groups with personalized care from chronic diseases, including endometriosis. 

Our first project looked at creating a low-cost, accessible & accurate diagnostic kit for endometriosis. ]]> 2022-11-28 08:37:16 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2399856406 Our kit development process abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402584958 1) Find appropriate biomarkers for endometriosis
2) Find an appropriate biological sample that covers these biomarkers and a standard way to collect it
3) Incorporate a standard assay to detect these biomarkers ]]> 2022-11-29 21:00:08 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402584958 Step 1 : Biomarker selection abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402595971 The literature review for endometriosis-related biomarker selection had 3 selection criteria: 
1) The study needs to report the specificity & sensitivity of the biomarker clearly. 
2) The study cannot focus on only 1 type of endometriosis.
3) The study should use either serum or menstrual blood as its initial samples, as biopsy or tissue-based samples would be similar to laparoscopy. ]]> 2022-11-29 21:13:29 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402595971 Finalized list of biomarkers abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402637448 As we went through our literature review, we came across 2 lines of research : 1) classical biomarkers like the IL-6 cytokine 2) recent bank of research focusing on microRNAs in reliably detecting different forms of endometriosis.

Here, we present a list of the biomarkers, common sources to obtain them from the human body, and the sensitivity* and specificity** of the biomaker.

*Sensitivity percentages reflect the ability of a test to correctly identify patients with a disease

**Specificity percentages reflect the ability of a test to correctly identify people without the disease

More info:
  • IL6: inflammatory marker successful in detecting endometriosis
  • IGFBP-1: altered levels successful in detecting ovarian endometriosis
  • CA125: significantly higher levels due to endometrial tissue growth outside the uterus in endometriosis patients

For their potential in the identification of endometriosis in participants with inflammatory symptoms, 3 biomarkers with elevated serum levels chosen -
  • IL-8
  • IL-1B
  • TNF-a
]]> 2022-11-29 22:07:09 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402637448 Introduction : We are failing patients with endometriosis abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402639977 2022-11-29 22:10:17 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402639977 Our Kit Development Process : Nifty bacteria, old antibodies and a tale of microRNA power abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402640897 2022-11-29 22:11:46 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402640897 Step 2 : Sample Selection & Collection abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402673310 We decided to select serum separated from peripheral blood as our ideal sample for 4 reasons: 
1) Almost all of our biomarkers are studied in serum samples. 
2) Past studies show that pro-inflammatory cytokines e.g. IL‐6, IL‐1β are significantly different and higher in menstrual blood versus peripheral blood.
3) It is more invasive & expensive (e.g. menstrual cups, tampons) to extract menstrual blood.  
4) Hormones and biomarkers need to pass
 the salivary gland membranes to be detected. ]]> 2022-11-29 23:01:10 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402673310 Step 1: Researching Medications rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402691905 We went through research papers and patient forums to learn more about the different types of medications endometriosis patients are prescribed or take. Medication for Endometriosis patient include contraceptives, Hormones and Antineoplastics, Progestins, Sex Hormones, Gonadotropin Releasing Hormones, Antigonadotropic agents, and Gonadotropin-releasing hormone antagonists. 

Here, we present a few drugs endometriosis patients might take. The ones stated are a current list of the most common Hormones and Antineoplastics taken]]> 2022-11-29 23:14:30 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402691905 Step 3: Researching Gene-Drug Interactions rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402693258 One of the goals of ebb&flo is to be able to give patients a list of suggested treatments that is tailored to their own biology. When ebb&flow sends out a genetic testing kit, they are not only searching for Endometriosis susceptibility through biomarkers, they are also looking at other genes that might affect the way one's biology reacts to treatment. 

Through advance literature research, our group went through every medication we had sourced from patient forums and literature reviews in Step 2 and researched their chemical compositions. From there, the drugs were researched to see whether any particular genes caused additional side effects or simply did not work for a person. This allows us to have a comprehensive list of genes and gene variants ebb&flo would need to test in order to suggest the best possible solution for a patient. ]]> 2022-11-29 23:16:39 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402693258 Introducing SerumDPTs! abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402747721 SerumDPT provides real-time separation of serum from plasma in a low-cost manner without using centrifuges. 

The SerumDPT tube has two evacuated chambers and the blood enters the collection chamber through a flow regulator. This chamber also houses a micro-fibres-based filtration system that separates cells and clotting factors from the blood. 

SerumSTAT delivers a minimum of 250 microlitres of serum from 2mL of drawn blood in a minute. ]]> 2022-11-30 00:26:57 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402747721 Step 3 : Diagnostic Kit Development abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402759588 Th iGEM kit involves 2 components :
1) A lateral flow assay (LFA)
2) Production of antibodies for the lateral flow assay

Design Principle :
Initially described in 1960 and now widely used, a lateral flow assay detects the presence of target proteins (in our case, endometriosis-related biomarkers) in a liquid sample (in our case, serum from patients) . At the sample pad, where the separated serum is applied, we have a fixed concentration of labelled primary antibodies. These primary antibodies are either labelled with dyes or gold nanoparticles. As the sample flows to the end (where the test strip is), the labeled primary antibodies bind to the biomarkers. Once our samples reach the test line, the target molecules bound to another secondary, immobilized antibodies. Free labeled primary antibodies can continue to travel down the strip to a control line (Sajid et al., 2015).(Teerinen et al., 2014).]]> 2022-11-30 00:37:21 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402759588 Production of antibodies in bacteria abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402848097 Generating antibodies in animals or cell lines is a very expensive and laborious process, with a variety of ethical concerns.

Recent research has shown how we can produce over 70 different types of full-length antibodies in a specific E.coli strain called SHuffle (Robinson et al., 2015). This strain is equipped with a modified oxidative cytoplasm, so we can have disulfide bond formation and thus proper folding and conformation of the antibodies. The strain also has extra chaperones (e.g.  GroEL/S systems) to guide this folding process (Lobstein 2012 et al., 2012). (Robinson et al., 2015)]]> 2022-11-30 01:59:02 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402848097 Future Outlook & Analysis abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402891162 2022-11-30 02:36:59 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402891162 Empowering patients with our pharmacogenomic databases abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402894343 2022-11-30 02:39:47 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402894343 Step 4: Research Drug-Drug Interactions abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402897530 While patients are prescribed many medications, they are not fully aware of side-effects with co-administered drugs e.g. Advil for pain. 
Ebb&flo believes in full-transparency and patient empowerment and one of our sub-projects was to create a drug-drug interactions database. 

We highlight the clinical trial of one such drug Elagolix(Orlissa) and its drug-drug interactions. ]]> 2022-11-30 02:42:47 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402897530 The Future of Endometriosis : miRNA detection? zshuha https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402903962
  • The study by Bendifallah et al found 86 miRNAs 
  • 10 of them have the greatest diagnostic potential, with miRNA 124-3p having been previously associated with endometriosis
  • most accurate signature provides a sensitivity of 96.8% and specificity of 100%
  • robust enough to replace the gold standard - diagnostic surgery
    • Recent studies, including one by Qui et al. used CRISPR-Cas9 combined with horseradish peroxidase to detect miRNAs in a very low-cost manner. This could be the future of endometriosis detection. 
    ]]>     2022-11-30 02:48:31 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402903962     Selecting miRNA biomarkers for diagnostic panel zshuha https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402904421 Let-7b: expression levels found to be significantly lower in endometriosis patients than in controls.
    miR-451a: expression shown to be decreased in eutopic endometrial tissues taken from endometriosis patient.
    miR-342-3p: higher levels shown to reduce the metabolic gene expression in adipocytes of endometriosis patients]]>     2022-11-30 02:48:54 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402904421     MicroRNA let-7b as a diagnostic biomarker zshuha https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402904632 Two studies demonstrated let-7 family is dysregulated in the serum f endometriosis patients. 
    Let-7 promotes cell differentiation and may act as a tumor suppressor. Meanwhile, let-7b is associated with cyclin D1, an estrogen-regulated gene involved in cell proliferation. 
    Another study showed the downregulation of let-7, which targets the KRAS gene. 
    The loss of this miRNA may initiate the progression of ectopic lesions. It may represent a link between inflammation and tumor-like growth in endometriosis.]]>     2022-11-30 02:49:01 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402904632     Lab Connection! abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402909300 We recently reached out to Alana Ogata, a professor in chemistry at the University of Toronto (Mississauga) who works in diagnostic pipelines for gynaecological diseases. 
    She has expressed interest in further discussions and potential collaboration!]]>     2022-11-30 02:53:10 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402909300     Future steps with our kit! abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402922966 1) Producing antibodies for at least some of our biomarkers 
    2) Comparing different dyes with gold nanoparticles, so the best option is used to label our biomarkers. 
    3) Trying out different flow rates of serum and pad sizes
    4) Comparing a prototype of our kit's accuracy with clinical standards (other flow assays, machine-learning based algorithms, laparoscopy) ]]>     2022-11-30 03:04:35 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402922966     Acknowledgements abidurrahman3 https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402925759 1) Introduction, Kit Development, Drug-Drug Interactions, Future Outlook - Abidur
    2) Introduction, Future Outlook, Kit Development (biomarker selection & figures) - Shuha
    3) Biomarker selection, Researching Drugs, Gene-Drug Interaction, Future Outlook - Rubaina]]>     2022-11-30 03:06:59 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402925759     References (Project 3) https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402939211
    Abo C, Biquard L, Girardet L, Chouzenoux S, Just P-A, Chapron C, Vaiman D, Borghese B. 2022. Unbiased in silico analysis of gene expression pinpoints circulating miRNAs targeting KIAA1324, a new gene drastically downregulated in ovarian endometriosis. Biomedicines. 10(9):2065. doi:10.3390/biomedicines10092065. [accessed 2022 Oct 22]. https://www.mdpi.com/2227-9059/10/9/2065/htm.

    Bendifallah S, Dabi Y, Suisse S, Jornea L, Bouteiller D, Touboul C, Puchar A, Daraï E. 2022. MicroRNome analysis generates a blood-based signature for endometriosis. Sci Rep. 12(1):4051. doi:10.1038/s41598-022-07771-7. [accessed 2022 Oct 31]. https://www.nature.com/articles/s41598-022-07771-7.

    Bendifallah S, Puchar A, Suisse S, Delbos L, Poilblanc M, Descamps P, Golfier F, Touboul C, Dabi Y, Daraï E. 2022. Machine learning algorithms as new screening approach for patients with endometriosis. Sci Rep. 12(1):639. doi:10.1038/s41598-021-04637-2. [accessed 2022 Nov 1]. https://www.nature.com/articles/s41598-021-04637-2.

    Chapron C, Lafay-Pillet M-C, Santulli P, Bourdon M, Maignien C, Gaudet-Chardonnet A, Maitrot-Mantelet L, Borghese B, Marcellin L. 2022. A new validated screening method for endometriosis diagnosis based on patient questionnaires. EClinicalMedicine. 44(101263):101263. doi:10.1016/j.eclinm.2021.101263. https://www.sciencedirect.com/science/article/pii/S2589537021005447.

    Moustafa S, Burn M, Mamillapalli R, Nematian S, Flores V, Taylor HS. 2020. Accurate diagnosis of endometriosis using serum microRNAs. Am J Obstet Gynecol. 223(4):557.e1-557.e11. doi:10.1016/j.ajog.2020.02.050. https://www.sciencedirect.com/science/article/pii/S0002937820303215.

    Senocak GNC, Yapca OE, Yılmaz EPT, Ozturk N, Ozdes S, Kumtepe Y. 2022. May endocan be a new biomarker in the diagnosis of endometriosis? J Gynecol Obstet Hum Reprod. 51(7):102423. doi:10.1016/j.jogoh.2022.102423. https://www.sciencedirect.com/science/article/pii/S2468784722001064.

    Sivajohan B, Elgendi M, Menon C, Allaire C, Yong P, Bedaiwy MA. 2022. Clinical use of artificial intelligence in endometriosis: a scoping review. NPJ Digit Med. 5(1):109. doi:10.1038/s41746-022-00638-1. [accessed 2022 Nov 15]. https://www.nature.com/articles/s41746-022-00638-1.

    Anastasiu CV, Moga MA, Elena Neculau A, Bălan A, Scârneciu I, Dragomir RM, Dull A-M, Chicea L-M. 2020. Biomarkers for the noninvasive diagnosis of endometriosis: State of the art and future perspectives. Int J Mol Sci. 21(5):1750. doi:10.3390/ijms21051750. [accessed 2022 Nov 29]. http://dx.doi.org/10.3390/ijms21051750.

    Breitbach A. Milenia HybriDetect – A universal lateral flow development platform. Milenia Biotec. [accessed 2022 Nov 29]. https://www.milenia-biotec.com/en/universal-lateral-flow-development-tool/.

    Pokrovenko DA, Vozniuk V, Medvediev MV. 2021. MicroRNA let-7: A promising non-invasive biomarker for diagnosing and treating external genital endometriosis. J Turk Soc Obstet Gynecol. 18(4):291–297. doi:10.4274/tjod.galenos.2021.07277. [accessed 2022 Nov 30]. http://dx.doi.org/10.4274/tjod.galenos.2021.07277.

    Potential RNA markers of abnormal heart rhythms identified in circulating blood. 2018 Mar 19. Medical Xpress. [accessed 2022 Nov 29]. https://medicalxpress.com/news/2018-03-potential-rna-markers-abnormal-heart.html.

    Sun D, Wang Y, Wang L, Guo X. 2021. MicroRNA-342 promotes the malignant-like phenotype of endometrial stromal cells via regulation of Annexin A2. Anal Cell Pathol (Amst). 2021:1328682. doi:10.1155/2021/1328682. [accessed 2022 Nov 30]. http://dx.doi.org/10.1155/2021/1328682.
    ]]>     2022-11-30 03:20:10 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402939211     References (Project 2) rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402948296 Abo C, Biquard L, Girardet L, Chouzenoux S, Just P-A, Chapron C, Vaiman D, Borghese B. 2022. Unbiased in silico analysis of gene expression pinpoints circulating miRNAs targeting KIAA1324, a new gene drastically downregulated in ovarian endometriosis. Biomedicines. 10(9):2065. doi:10.3390/biomedicines10092065. [accessed 2022 Oct 22]. https://www.mdpi.com/2227-9059/10/9/2065/htm.

    Bendifallah S, Dabi Y, Suisse S, Jornea L, Bouteiller D, Touboul C, Puchar A, Daraï E. 2022. MicroRNome analysis generates a blood-based signature for endometriosis. Sci Rep. 12(1):4051. doi:10.1038/s41598-022-07771-7. [accessed 2022 Oct 31]. https://www.nature.com/articles/s41598-022-07771-7.

    Bendifallah S, Puchar A, Suisse S, Delbos L, Poilblanc M, Descamps P, Golfier F, Touboul C, Dabi Y, Daraï E. 2022. Machine learning algorithms as new screening approach for patients with endometriosis. Sci Rep. 12(1):639. doi:10.1038/s41598-021-04637-2. [accessed 2022 Nov 1]. https://www.nature.com/articles/s41598-021-04637-2.

    Chapron C, Lafay-Pillet M-C, Santulli P, Bourdon M, Maignien C, Gaudet-Chardonnet A, Maitrot-Mantelet L, Borghese B, Marcellin L. 2022. A new validated screening method for endometriosis diagnosis based on patient questionnaires. EClinicalMedicine. 44(101263):101263. doi:10.1016/j.eclinm.2021.101263. https://www.sciencedirect.com/science/article/pii/S2589537021005447.

    Moustafa S, Burn M, Mamillapalli R, Nematian S, Flores V, Taylor HS. 2020. Accurate diagnosis of endometriosis using serum microRNAs. Am J Obstet Gynecol. 223(4):557.e1-557.e11. doi:10.1016/j.ajog.2020.02.050. https://www.sciencedirect.com/science/article/pii/S0002937820303215.

    Senocak GNC, Yapca OE, Yılmaz EPT, Ozturk N, Ozdes S, Kumtepe Y. 2022. May endocan be a new biomarker in the diagnosis of endometriosis? J Gynecol Obstet Hum Reprod. 51(7):102423. doi:10.1016/j.jogoh.2022.102423. https://www.sciencedirect.com/science/article/pii/S2468784722001064.

    Sivajohan B, Elgendi M, Menon C, Allaire C, Yong P, Bedaiwy MA. 2022. Clinical use of artificial intelligence in endometriosis: a scoping review. NPJ Digit Med. 5(1):109. doi:10.1038/s41746-022-00638-1. [accessed 2022 Nov 15]. https://www.nature.com/articles/s41746-022-00638-1.

    Shebley, M., Polepally, A. R., Nader, A., Ng, J. W., Winzenborg, I., Klein, C. E., Noertersheuser, P., Gibbs, M. A., & Mostafa, N. M. (2020). Clinical pharmacology of elagolix: An oral gonadotropin-releasing hormone receptor antagonist for endometriosis. Clinical Pharmacokinetics, 59(3), 297–309. https://doi.org/10.1007/s40262-019-00840-7

    Polepally, A. R., Ng, J. W., Salem, A. H., Dufek, M. B., Parikh, A., Carter, D. C., Kamradt, K., Mostafa, N. M., & Shebley, M. (2020). Assessment of clinical drug‐drug interactions of elagolix, a gonadotropin‐releasing hormone receptor antagonist. Journal of Clinical Pharmacology, 60(12), 1606–1616. https://doi.org/10.1002/jcph.1689

    Anastasiu CV, Moga MA, Elena Neculau A, Bălan A, Scârneciu I, Dragomir RM, Dull A-M, Chicea L-M. 2020. Biomarkers for the noninvasive diagnosis of endometriosis: State of the art and future perspectives. Int J Mol Sci. 21(5):1750. doi:10.3390/ijms21051750. [accessed 2022 Nov 29]. http://dx.doi.org/10.3390/ijms21051750.

    Breitbach A. Milenia HybriDetect – A universal lateral flow development platform. Milenia Biotec. [accessed 2022 Nov 29]. https://www.milenia-biotec.com/en/universal-lateral-flow-development-tool/.

    Pokrovenko DA, Vozniuk V, Medvediev MV. 2021. MicroRNA let-7: A promising non-invasive biomarker for diagnosing and treating external genital endometriosis. J Turk Soc Obstet Gynecol. 18(4):291–297. doi:10.4274/tjod.galenos.2021.07277. [accessed 2022 Nov 30]. http://dx.doi.org/10.4274/tjod.galenos.2021.07277.

    Potential RNA markers of abnormal heart rhythms identified in circulating blood. 2018 Mar 19. Medical Xpress. [accessed 2022 Nov 29]. https://medicalxpress.com/news/2018-03-potential-rna-markers-abnormal-heart.html.

    Sun D, Wang Y, Wang L, Guo X. 2021. MicroRNA-342 promotes the malignant-like phenotype of endometrial stromal cells via regulation of Annexin A2. Anal Cell Pathol (Amst). 2021:1328682. doi:10.1155/2021/1328682. [accessed 2022 Nov 30]. http://dx.doi.org/10.1155/2021/1328682.

    Tucci, F. C., Zhu, Y.-F., Struthers, R. S., Guo, Z., Gross, T. D., Rowbottom, M. W., Acevedo, O., Gao, Y., Saunders, J., Xie, Q., Reinhart, G. J., Liu, X.-J., Ling, N., Bonneville, A. K. L., Chen, T., Bozigian, H., & Chen. (2005). 3-[(2 R )-amino-2-phenylethyl]-1-(2,6-difluorobenzyl)-5-(2-fluoro-3-methoxyphenyl)- 6-methylpyrimidin-2,4-dione (NBI 42902) as a potent and orally active antagonist of the human gonadotropin-releasing hormone receptor. Design, synthesis, and in vitro and in vivo characterization. Journal of Medicinal Chemistry, 48(4), 1169–1178. https://doi.org/10.1021/jm049218c


    ]]>     2022-11-30 03:29:12 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402948296     Database Inspiration rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402980569 ebb&flo uses a very similar genetic testing and medicine suggestion platform used by many other companies thus far. Here are some of the companies ebb&flo took inspiration from:
    • DOTLAB 
    • Adyn
    • HERA 
    • ZRT Lab 
    • ROSE Endometriosis 
    • 23andMe 
    ]]>     2022-11-30 04:09:42 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2402980569     What is a Pharmacogenetic Database? rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408150735 A pharmacogenomics is the study of how genes affect a person's response to drugs. The database is used for personalising pharmacological therapy by understanding the impact of genetic variability on drug activity. In the case of ebb&flo, the database will be used to determine the best patient care for endometriosis patients and assist with early detecting through genetic testing - a non invasive solution to current methods. ]]> 2022-12-04 17:33:07 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408150735 Step 2: Researching Genes rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408156394 As ebb&flo's genetic testing kit wants to create a non-invasive solution to endometriosis detection, the database requires genes that should be tested to be able to detect endometriosis. A large reason for endometriosis patients not having genetic testing thus far is due to a lack of research in this field. Not all genes were promising in detecting endometriosis. Many were under-researched or require a large cohort study to be able to confidently be used as a detection gene. ]]> 2022-12-04 17:43:09 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408156394 Example Drug-Gene Interaction: Citalopram and CYP2C19 rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408158868 Citalopram
    • Brand name: Celexa 
    • Antidepressant of the selective serotonin reuptake inhibitor class
    • Used to treat major depressive disorder, obsessive-compulsive disorder, panic disorder, and social phobia
    CYP2C19 gene
    • Provides instructions for making an enzyme that is found primarily in liver cells
    ]]>     2022-12-04 17:47:58 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408158868     Why is this interaction important? rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408162155 In people who are rapid metabolizers, the CYP2C19 enzyme has high activity. This means that those who are rapid metabolizers break down some medicines quickly and may need different doses or a different medicine. The drug is eliminated too fast and does not achieve a high enough concentration in the blood to be effective. 

    Citalopram is metabolized by CYP2C19. If someone carried the CYP2C19*17 genotype, Citalopram would not be useful.]]>     2022-12-04 17:53:14 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408162155     Alternative solution: Fluvoxamine -> Not metabolized by CYP2C19 rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408163798 2022-12-04 17:55:54 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408163798 Why are drug-gene interactions important? rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408164222 2022-12-04 17:56:35 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408164222 Example Drug-Drug Interaction: Orlissa and Ketoconazole rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408167441 Orilissa (Elagolix)

    GnRH antagonist
    • competes for GnRH receptor occupancy with endogenous GnRH and blocks receptors upon binding
    Antagonism
    • Enters the pituitary and competes with GnRH to sit in the receptor
    LH/FSH
    • Suppresses luteinizing hormone (LH) and follicle-stimulating hormone (FSH)
    Estradiol
    •  Subsequent suppression of estradiol levels occurs
    ]]>     2022-12-04 18:01:54 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408167441     Results from drug-drug interaction trial rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408171358 Due to the mechanisms of the drug and other drug interactions, the dosage must be monitored. 

    Elagolix is a substrate for CYP3A; co-administration of elagolix with CYP3A inhibitors, such as ketoconazole, may increase elagolix plasma concentrations. 

    Solution: Decrease Elagolix dosage
    ]]>     2022-12-04 18:07:33 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408171358     Pharmacogenetic Database Creation rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408172981 As all the research has been collected, the next step would be to create the physical database. For Backend development, Python and SQL would be the best solution as they are the best-known programming languages to organize databases. For frontend development, which includes user interaction and UX/UI development, HTML and Python are most commonly used]]> 2022-12-04 18:10:21 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408172981 Continuing Research to expand database rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408175894 To increase the database, more research needs to be done. This can include researching more biomarkers that can be used to track endometriosis, more specifically gene indicators. Additionally, for the genes that have been under-researched, they can be researched with a larger cohort study. Lastly, more drug-gene and drug-drug interactions can be researched for both current and future drugs and discovered genes]]> 2022-12-04 18:15:31 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408175894 Inspiration from 23 and me rubainafarin https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408178203 ebb&flo plans to use a similar front end delivery for their patients which will show which gene variants they carry. This can further allow endometriosis detection and susceptibility. Additionally, the gene variants will be useful information for drug-drug and drug-gene interactions]]> 2022-12-04 18:19:40 UTC https://padlet.com/abidurrahman3/rb4yyw244nfn96x0/wish/2408178203