Hello dear Reddit buddies,
I recently am encountering an issue with my insurance company. My insurance company denied one of my medical services (81229) for the reason they think its an experimental. I checked out with them for a detailed reason, they said the Dx O28.0 my OB provided is not a covered Dx.
But I checked out my insurance that procedure 81229 is 100% covered by my insurance plan, Also, this procedure was suggested to do by my OB because I failed my NIPT test (no cell result for 2 times). My OB suggested that test failure is associated with an increased risk of aneuploidy, providing additional genetic counseling, and offering comprehensive ultrasound evaluation and diagnostic testing. So my OB sent me to do amniocentesis and sent my sample to a lab to do the analytics tests.
What should I do to deal with this issue?? I don't know which one is the right Dx that can be covered and I think my provider submitted this Dx is based on her professional medical experience which I don't think can be changed easily.
Advice needed, please. Thanks to all of you.
Hey guys , does anyone know of a lab that has a microarray reader than can scan/image an entire microscope slide? I'm looking for an instrument like the Innoscan microarray scanner or something similar to it. Thanks.
Thought I would update! For those of you who don’t know my story, I had the NIPT done at 11+3. My results came back with no result on Monosomy X (atypical results on sex chromosomes) but everything else came back low risk. I had a consultation with a genetic counselor. Once I had my results I had to rush to get an NT scan done (and almost didn’t get in before the cutoff). Everything came back normal but I still decided to have an amniocentesis done for peace of mind.
My amnio went off without a hitch and I didn’t have any issues afterwards. The procedure was quick but I did cramp every time they drew fluid out with the syringe (which made me nervous). After they got the sample, they checked the baby and she was doing great so I was released.
FISH results came back normal about 3 days later. About a week and a half later, I had my anatomy scan and that came back normal as well. Now I finally have my microarray results (about 3 weeks after the amnio procedure) and I’m so happy to say that those are normal, too!
This whole process has been extremely stressful but I’m so thankful for this sub. It saved my sanity on soo many different occasions. I was blown away by the amount of false positives and atypical results that turned out to be nothing but I’m very happy to say that this was the case for me. I really everyone stuck in limbo gets some resolution soon!
I am trying to analyse gene expression data from a dietary intervention RCT of two groups fed two different diets. I have the gene expression data pre and post the diet from these two groups of individuals. I want to determine genes that are differentially expressed in the intervention group compared to the control group and I want to adjust for the "baseline gene expression" values that were initially measured just before the start of the trial. How can I do this in limma? The way limma works it seems we provide it with a covariate matrix that I am adjusting for. But here for each gene there would be an individual "baseline gene expression" value. Can someone advice me if this can be done in the limma package?
Hi all. I updated my previous post but I’m re-posting to get more input.
I got an amnio mainly to rule out possible abnormal sex chromosomes. My NIPT was otherwise fine, and after a few stressful weeks waiting for said amnio, FISH came back normal too and with normal sex chromosomes. YAY!
But wait. Just got a call from MFM and they need both myself and my husband to come in for a blood draw. It sounds like they need more info from us to understand or rule out something they found in the microarray.
They were intentionally vague, and said “we need to see if baby gets it from you or dad.. but it could be nothing.” But wouldn’t tell me what they ARE looking at.
My anxiety does worse with less info rather than more. Any ideas? 😣
UPDATE: ok it was a balanced inversion, and it seems to be of unknown significance? But they tested me and my husband and I have the same thing as baby, so sounds like they are not too worried. Genetic counseling next week. I think this is… good?
Anything else anyone thinks I should know or be prepared for?
UPDATE 2: Ok, they found that I have the same balanced inversion…. So they just said they aren’t worried about it? I have genetic counseling appt tomorrow so I guess I can clarify?
On top of that, now I’m be told (reminded?) that my NT is thickened which I knew from the 12 week scan, but no new # was given to me but they told me they are now testing my amniotic fluid for noonan’s syndrome. I already tested negative for this on the Natera Vistara test.
So… thickened NT but ruled out trisomies on the amnio.
I’m so exhausted of being worried and them finding more and more thing to test me for. And waiting for results. I should have asked the 20 week NT measurement I guess, ugh. Why didn’t they just test for this the first time?
Welcome, dear r/genomics community!
This is my first post here, so forgive me in case of any mistakes.
Together with my friend who works as a Scientist in The Independent Clinical Epigenetics Laboratory Szczecin, Poland. We have built an application
https://app.geneintelligence.io/
Our tool uses AI and ML techniques to select significantly associated markers with the examined traits. In contrast to classic statistical methods, our model takes into account multifactorial interactions between markers and phenotype. As a result, the marker-trait relation can be extracted even from very noisy data.
It's totally free to use.
We already have several successful collaborations with research teams, we help them in cancer and covid research.
More detailed information about it https://geneintelligence.io/
Currently, we are able to analyze and process EPIC/450K data. In the meantime, we are building the module responsible for RNA-seq data processing. And we hope it will be released within the next 2-3 weeks. However, if you have experience in any other "omics" fields, we can cooperate and build a module adjusted for this type of data.
We are very keen to get feedback from specialists from the industry :) We just started and we would like to reach out to as many scientists as we can.
As I mentioned already the software is free, I really encourage you to try it and give us your feedback :)
The documentation page you can find it here - https://geneintelligence.io/documentation/
PS.
It's not a marketing post, we are young and really into science. We just want to collect feedback from the scientific area. We would like to help scientists in their research make it faster and more robust!
So I am looking for a software or a website that allows me to simulate different microarray images with different parameters such as noise, so that I can compare with my algorithms. Any ideas please?
Protein microarray (or protein chip) is an emerging technology that provides a versatile platform for the characterization of hundreds of thousands of proteins in a highly parallel and high-throughput way. Two major classes of protein microarrays are defined to describe their applications: analytical and functional protein microarrays.
The chip consists of a support surface such as a glass slide, nitrocellulose membrane, bead, or microtitre plate, to which an array of capture proteins is bound. Probe molecules, typically labeled with a fluorescent dye, are added to the array. Any reaction between the probe and the immobilized protein emits a fluorescent signal that is read by a laser scanner. Protein microarrays are rapid, automated, economical, and highly sensitive, consuming small quantities of samples and reagents. Learn more: https://www.leadingbiology.com/article-858.html
Hello everybody.
I read a lot of guides but I can still not understand why we need linear models for differential expression and how to use them. Most of the guides just talk about the mathematical part and other just briefly explain the reason.
At the end of the day I have my idea but I can not find nothing to confirm what I understood.
Here below my supposition:
- Let's suppose I have 3 replicates from condition A and 3 replicates from condition B and I want to study expression of just one gene.
- I can draw a scatter plot using expression values (normalized) from condition A that will be my X-axis and expression values from B that will be my Y-axis
- I can now compute the linear regression
What I have to do now ( or what R packages as limma does) ?
I think that I have to project the values on the linear regression and use these new values for a moderated t-test between the two groups.
Is that right?
What is the purpose and advantages of doing that?
Thanks for helping
I'm pretty noob to Bioinformatics
I have downloaded a matching Expression (RNA-seq) and Genotype (microarray) data with the aim to call eQTL using the downloaded data.
I kinda get the RNA-seq data analysis part, But....
I'm totally not experienced when it comes to analysing Genotype data: I have hundreds of idat files, I guess this is the raw data file capturing the fluorescent of the probes or something?
Anyway, there are too many questions since I basically have close to zero knowledge of how to process this dataset, my question is:
- Do you guys know of any resources or books that I can read to jumpstart my knowledge of how to process the genotype data? I have tried reading review papers but they usually focus on one aspect of the workflow and since I have zero knowledge I don't know how to contextualize them.
I'm looking for some practical guides, maybe a book? or a comprehensive blog? Maybe something similar to the book "RNA-seq Data Analysis: A Practical Approach" (which helps me tremendously when it comes to RNA-seq data analysis) but for genotype or array data?
Thank you!!
SNP microarrays are routinely used in breeding programmes of cattle, sheep, goat and pigs with outstanding success. SNP #microarrays are now also used for fish in #aquaculture. Read how microarrays aid fish breeding for improved growth, thermal tolerance, lipid metabolism and resistance to diseases at https://the-dna-universe.com/2021/09/30/microarrays-accelerate-blue-biotechnology-to-the-next-stage/
https://preview.redd.it/q1flt4wekmq71.jpg?width=1200&format=pjpg&auto=webp&s=db9b975219cda1db2d20f8438f5b8d3fe12d41c3
I received a no result on monosomy x and am currently in limbo right now (i.e. atypical result on sex chromosomes - however NIPT determined baby is a girl). I have my amnio on Monday and I know for sure my doctor ordered a FISH and microarray. What will the initial FISH results be able to tell me? Will that be able to rule out Turner’s or XXX? Or will I have to wait until the full microarray comes back? I’m just wondering how confident I can be after receiving the initial FISH results.
So far there are no physical markers that would suggest anything is going on from the ultrasound. NT scan came back and baby is perfect but I know that a baby can still have Turner’s without any physical indicators.
Welcome, dear r/biotechnology community!
This is my first post here, so forgive me in case of any mistakes (I'm new to Reddit).
Together with my friend who works as a Scientist in The Independent Clinical Epigenetics Laboratory Szczecin, Poland. We have built an application
https://app.geneintelligence.io/
Our tool uses AI and ML techniques to select significantly associated markers with the examined traits. In contrast to classic statistical methods, our model takes into account multifactorial interactions between markers and phenotype. As a result, the marker-trait relation can be extracted even from very noisy data.
It's totally free to use.
We already have several successful collaborations with research teams, we help them in cancer and covid research.
More detailed information about it https://geneintelligence.io/
Currently, we are able to analyze and process EPIC/450K data. In the meantime, we are building the module responsible for RNA-seq data processing. And we hope it will be released within the next 2-3 weeks. However, if you have experience in any other "omics" fields, we can cooperate and build a module adjusted for this type of data.
We are very keen to get feedback from specialists from the industry :) We just started and we would like to reach out to as many scientists as we can.
As I mentioned already the software is free, I really encourage you to try it and give us your feedback :)
The documentation page you can find it here - https://geneintelligence.io/documentation/
PS.
It's not a marketing post, we are young and really into science. We just want to collect feedback from the scientific area. We would like to help scientists in their research make it faster and more robust!
We are in process of creating the publication of it in a journal with IF. We will let you know once we complete it.
