The whole lab is closing and so as the sales team of BGI Health AU. The reasons are including economic downturn and ongoing loses. The director is wrong doing on several important strategic decisions. Also the director has conflicts of interest with her partner who is in charge of the finance and working under her, as being in a secret relationship.

Hi everyone,

I'm new to bioinformatics and currently working on a project where I need to use fastp. I want to go beyond just running the basic command—I’d like to adjust parameters to filter my data effectively and retain only the highest-quality data.

Since I’ve never used fastp before, I was wondering if anyone could recommend helpful resources, tutorials, or example workflows for getting started with it? Any tips or best practices for customizing fastp parameters would also be greatly appreciated!

Thanks in advance for your help!

At the nos3 gene according to my tesr i likely have lower NOS3 activity

For example the rs1799983 i have TT genotype And rs2070744 CC genotype.

Im afraid this will make me have cardiovascular problems and high blood pressure. Anyone know more than me that can explain if this is a big deal or nothing to worry about.

I had sequencing done by Nebula, but didn't download my files. It appears now that I'm out of luck. I tried importing it with sequencing.com, but it failed. I have an appointment with a geneticist at Johns Hopkins on February 3rd, and I'd love to have my data available for that meeting (I likely have CMT disease and am seeking to better understand my prognosis and options).

Should I just have it redone at sequencing.com? For about $1300 they promise 2-3 week turnaround... What do you folks think? Any other options to consider?

MYNZ (Mainz Biomed) is pleased to announce the appointment of cancer survivor and healthcare advocate Petra Smeltzer Starke as its new Brand Ambassador. With her personal experience overcoming cancer, Petra is perfectly positioned to advocate for MYNZ’s cutting-edge early detection technologies. These advancements aim to revolutionize cancer care by identifying cancer in its earliest stages, improving survival rates and empowering healthcare providers worldwide. Petra’s involvement will raise global awareness about the importance of early screenings, promoting proactive health measures and encouraging the adoption of innovative diagnostic tools. This collaboration highlights the critical role of personal stories in amplifying the impact of healthcare innovations, making life-saving technologies more accessible and transforming cancer care for future generations.

I went through a rather long and expensive process in my country to be tested for EDS. It got me thinking about establishing a direct to consumer gene testing operation as an alternative for someone wanting a diagnosis.

I'm aware that many of these outfits exist around the world. No one in my country seems to be doing it properly however, all the companies seem to focus on a panel of non specific genes mostly catering to those who aren't looking for anything in particular but just want to tick a box and say they had gene testing done.

My idea is to partner with a lab who does clinical grade testing and offer a handful of the more in demand panels including BRCA, EDS etc. However, I don't have a background in genetic medicine or healthcare. I don't know as an example how responsive a lab would be in offering me their services or whether I may run into any local regulatory issues. These are some of the complications I've come up with.

For those involved in the industry, are you able to provide an opinion on this idea? Have I overlooked something substantial that may be making this idea redundant?

Thank you.

I understand that for the majority of genes, one can be fine with one functioning copy. In other cases, some genes are highly intolerant to loss of function (LoF) of one allele due to dosage sensitivity. This loss-of-function intolerance typically shows up in annotations in ClinVar, or in other places such as gnomAD.

GnomAD lists three scenarios regarding loss of function: "null (tolerant; where loss-of-function variation – heterozygous or homozygous - is completely tolerated by natural selection), recessive (where heterozygous variants are tolerated but homozygous ones are not), and haploinsufficient (where heterozygous loss-of-function variants are not tolerated)".

However, there is one specific gene which I am having trouble figuring out if a rare loss-of-function allele could potentially have had an impact, or not, (i.e. which of the above categories does it belong). The gene is AREL1: https://gnomad.broadinstitute.org/gene/ENSG00000119682?dataset=gnomad_r4

I understand that pLI is typically used to predict loss of function intolerance. AREL1 has a pLI of 0, which indicates tolerance. However, gnomAD also considers observed/expected (o/e) loss-of-function variants as another potential gauge of loss-of-function intolerance. AREL1's o/e is 0.60 (60 observed LoF SNVs over 100.7 expected LoF SNVs).

I also understand that the 90% confidence interval is important, particularly the upper bound (LOEUF). AREL has a LOEUF = 0.74. gnomAD recommends a LOEUF score < 0.6 as a threshold for Mendelian cases.

I guess my question is: with all these different metrics, is AREL1 loss-of-function intolerant or not, and if so, what category does it fall into?

(also, please forgive me if I've confused any terminology here, I took genetics over 30 years ago so I'm a bit rusty).

Am I missing something here?

I've been trying to load .cram and .crai files like an error message says I need to do whenever I load one of those, but there's no way for me to add the second file. How do I load these two files?

Hello. I want to get my whole genome sequencing Next Gen. My goal is to be able to run several popular software myself on the data so I can find interesting aspects myself. Which of the several vendors would you recommend? Obviously price matters but I also want to make sure I can run most recent software projects on them.

https://www.classaction.org/news/class-action-claims-nebula-secretly-shares-genetic-test-results-with-facebook-google-microsoft

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Can anyone download or analyze their genome on Nebula's site?

The only functional aspect of their site seems to be the worthless "Traits" and "Ancestry" sections.

Mainz Biomed has named Petra Smeltzer Starke, a cancer survivor and advocate, as their new Brand Ambassador. Petra will play a key role in promoting the company’s groundbreaking early cancer detection technologies, which have the potential to significantly improve survival rates and healthcare outcomes.

Petra’s personal experience with cancer provides her with a unique perspective on the importance of early detection, and her passion for healthcare innovation makes her an ideal representative for Mainz Biomed. Her advocacy for better access to early detection tools aligns perfectly with the company’s mission to make life-saving diagnostic technologies more accessible to everyone.

This partnership marks an exciting step in raising awareness about the potential of early cancer detection to change lives. By leveraging Petra’s voice, Mainz Biomed hopes to not only amplify their message but also encourage more individuals to prioritize their health and explore new diagnostic options.

What do you think of the role personal stories play in advancing healthcare initiatives? Do you believe brand ambassadors can genuinely help increase awareness and support for vital medical innovations?

Hello everybody,

I want to sequence and assemble the genome of the plant Artemisia absinthium (4.324 GB) with PacBio HiFi. I am looking for a solid kit or protocol to obtain high molecular weight DNA. The PacBio PanDNA kit seems good, but requires nuclei pellet, and I have no clue how to achieve that (there was a kit from PacBio that is not available anymore). Any recommendations? Thank you!

Next-Level Screening: Mainz Biomed (NASDAQ: MYNZ) partners with Thermo Fisher Scientific to revolutionize colorectal cancer diagnostics with cutting-edge tools for early detection.
Raising Awareness: With Petra Smeltzer Starke as its ambassador, Mainz Biomed is advocating for the importance of regular cancer screenings to save lives.
Global Commitment: Focused on equitable healthcare, Mainz Biomed’s mission is to ensure advanced screening solutions reach patients everywhere.

Leading Innovation: Mainz Biomed (NASDAQ: MYNZ) partners with Thermo Fisher Scientific to redefine colorectal cancer screening with advanced technology for early diagnosis.
Awareness Through Advocacy: With Petra Smeltzer Starke as its ambassador, Mainz Biomed is driving education campaigns to underscore the life-saving power of early detection.
Global Health Equity: Dedicated to reducing cancer’s impact, Mainz Biomed is advancing accessible, effective diagnostic solutions to benefit patients everywhere.

Reimagining Early Diagnosis: Mainz Biomed (NASDAQ: MYNZ) has partnered with Thermo Fisher Scientific to develop state-of-the-art solutions for colorectal cancer screening. This innovative collaboration is poised to set new benchmarks in early detection, offering patients a better chance at timely and effective treatment.

Raising Awareness Through Advocacy: With Petra Smeltzer Starke as Brand Ambassador, Mainz Biomed is leading efforts to promote the life-saving benefits of early cancer detection. By driving education and awareness, the company aims to inspire widespread adoption of proactive health screenings.

A Vision for Global Health Equity: Committed to tackling colorectal cancer worldwide, Mainz Biomed is harnessing cutting-edge technology to make early detection more efficient and accessible. This mission reflects the company’s dedication to reducing cancer rates and improving health outcomes for communities everywhere.

Anyone else having issues with Nebula ?

Human genome project, 1000 genome project and HapMap have ended.

What are ongoing genome projects (December 2024) that you know?

First things that comes to my mind are 100k Pathogen project, Neanderthal genome project and Human microbiome project.

Years ago I did the Ancestry.com genome test. I got the raw data processed by Promethease. From here: how I get it interpreted to me as a non-geneticist? Can I just take my raw data to a genetics counselor? How does one find one of those?

I've been curious about this for awhile and was hoping someone could shed some light on it. There are lots of methods for doing scRNA-seq and they typically involve dissociating the tissue to single cell suspension or some form of pre-processing. How do we know the cells don't totally change their expression profiles during the time they are being processed? How can we trust the genes we see being expressed are not just a response to all the new and foreign signals the cells are receiving during pre-processing? I work with human PBMCs which are usually frozen, washed several times, stained for cell sorting, etc. Doesn't that drastically change the transcriptional activity of the cells?

I'll start this by saying I have no genetic background. My ancestry DNA shows I have rsID397515515 at position 155208421 alleles 1 and 2 are both A. How does this translate to Gaucher's disease? Is this enough information to tell that I'm a carrier or have the disease? Looking into this for my son's sake.

Anyone know how to ID extra copies of a gene in Cravat? I assumed this is possible in sequence ontology (pseudogenes) but not certain. Looking for extra copies of TPSAB1 in a WGS VCF file.

Could polygenic gene therapy be invented?

I am trying to determine if multiple copies of TPSAB1 exist in a Nebula VCF file. Is there an easy tool for detecting?