Ask HN: How to be my own genetic disease researcher for my partner?

Promethease [1] is a great resource

[1] https://www.promethease.com/

Bioinformatician here. What are you hoping to find? If you just want to search for variants, and your VCF file is germline variants and annotated appropriately, yeah that will work. You may need to annotate the VCF.

As far as discovering new associations or causal relationships from a single WGS, you are probably not going to have any luck there.

If you truly think this is a rare disease, it's very likely that there's just one single causal mutation in your partner's genome. The easiest way to find that is to:

1. Search for variants in that genome where the allele frequency is close to 0 in a very large population e.g. https://gnomad.broadinstitute.org/

2. Look into variant effects for those you prioritized in step 1 using https://www.ensembl.org/info/docs/tools/vep/index.html

Rare diseases are typically due to a coding mutation that alters the protein coding sequence in some significant way.

If you need help contact details are on my profile. I do this for a living at a university.

rsIDs are a minefield as they change often, there are synonyms and probably you won't have all loci properly annotated. Don't rely on that too much unless you really know what you are doing.

If it's not a rare disease, this gets quite more difficult. Also, depending on the whole genome sequencing platform you have used, many structural variants (e.g. deletions or insertions of large chunks of DNA) won't be easy to measure.

Other comments have suggested Promethease, which will give you a bit of help if it's not a rare disease (e.g. if it's an autoimmune one, it's good at imputing HLA and finding risk haplotypes).

My whole comment is a bit of an oversimplification, but I think these suggestions are a good starting point.

  - A mild case of Becker's Nevus
  - Single palmar crease 
  - A somewhat smaller shoulder blade (suggesting a Sprengel diformity?)

Not directly an answer to your question, but if you're not already aware of it, another thing that might be worth pursuing in parallel is having your doctor refer you to the Undiagnosed Disease Network, if the case meets the criteria for that [1].

Another avenue might be a crowdsourced rare disease research organization like [2]

I have no relation to any of the above but read a book about the UDN that may be of interest to you: [3]

[1] https://undiagnosed.hms.harvard.edu/apply/

[2] https://www.researchtothepeople.org/

[3] https://www.goodreads.com/en/book/show/53317420-the-genome-o...

Which condition is this?

Matt Might chronicled experiences with his son's rare genetic disease. Perhaps that will give you some ideas.

Hunting down my son's killer: https://matt.might.net/articles/my-sons-killer/

You may also want to email him. Anecdotally, I believe the rare disease research community is small and willing to listen to outliers.

University department page: https://www.uab.edu/medicine/pmi/matt-might

(Edit: fixed urls, typos, grouping.)

Specific plug for Will Byrd's mediKanren and Matt Might's group in general they are the real deal. (source: I have worked for other deals).

For more just start learning the tools... I have not checked in on them for years now but "BioStars Handbook" was up & coming

[] https://github.com/webyrd/mediKanren [] https://biostar.myshopify.com/

maybe call around and try to find a genetic counselor who would be willing to work with a patient who has the resources and capability to contribute to research efforts.

would recommend trying to find supervision from an expert rather than just diving in alone. every field has its nuance.

Here's a post I made on reddit about how to do exactly this:

https://www.reddit.com/r/Nebulagenomics/comments/nhjfpa/how_...

You use the VCF and a java project called the Exomiser, and it will give you output files with all the pathogenic variants marked

In my case and is the case with a lot of rare diseases you could have unique pathology and mutations in a certain gene but that don't show up as pathogenic in clin var. For example my family has a lot of autoimmune diseases and as expected my HLA genes are totally trashed. However none of these mutations have ever been seen and flagged before especially was WGS is so new.

If you only have a list of genes and the genomizer will give you a list of the genes that are the most heaviy affected, you can put them into this app to get some further data and idea about what kind of tissue expression or rare disease spectrums you may be dealing with: https://maayanlab.cloud/Enrichr/

you can make informed decisions on it like for example I have a defect in my thiamine transport gene, so now I follow a b1 megadose protocol. A lot of people do that with the basic 23and me methylation reports but this is more in depth. So in my family maybe this looks like parkinsonanism, autism, diabetes, muscle disease, metaboloic syndrome, but we're understanding these diseases to be more like mitochondrial diseases that are more systemic. The answers you get are often really just too cutting edge for GPs or even specialists to deal with and you have better luck just researching, biohacking or talking to a natropath. Genetics doesn't really have that place in general practice yet unless it's something like a very very clear pathogenic marker which honestly isn't the case in a lot of cases, or alternatively you end up having a "pathogenic" marker that we had no idea even exists in people who aren't gravely disabled. For example I don't have lissencephaly regardless of what my pathogeniticty says. instead in that case you look at the gene, and see the big picture which that it's linked to neurodevelopmental disorders, and I have autism so that could be a factor there. But autism != lissencephaly. WGS is so new

sadly the reality is though you can have all that and it almost puts you at a disadvatnage with doctors because you look crazy and sus claiming you have some HLA mutation or whatever. Who told you that? Oh well I data mined it...uh huh sure....honestly to get it back into the medical system and to be taken seriously you'd probably have to get a doctor to retest it, for example I can can spin this up to get my HLA alleles from my fastq https://github.com/nf-core/hlatyping

But no doctor is going to put that in my medical record until I convince them to run a blood test for the same damn thing.

if anyone wants to help me with my own genetic search woes and help me out or know solutions please let me know. if you want to help me publish or add to that guide somewhere let me know - i asked nebula if they wanted to print it on the blog and they said the'd be interested but I just never cleaned it up

To add to what others have said, If they have blood relations that are willing to get sequenced you may be able to narrow things down by like looking for a recessive gene in both parents not shared by any siblings or otherwise looking at inheritance patterns.

In parallel to your own research, consider enrolling in a study like IDIOM at Scripps Health: https://www.scripps.edu/science-and-medicine/translational-i...

Other folks have mentioned CureFFI, but I would like to second that suggestion. This is a couple that has committed their lives to understanding and curing a rare condition that personally affects one of them.

https://www.cureffi.org/about/

Sonia: https://www.broadinstitute.org/bios/sonia-vallabh

Eric: https://www.broadinstitute.org/bios/eric-minikel

They are also hiring: https://broadinstitute.wd1.myworkdayjobs.com/broad_institute...

It was Great, Thanks

I do not want to be negative, but are you sure this is best use of your time? Hackers always see problem to chase, but real life may work differently. I still remember how HN folks, were trying to design ventilators out if common parts, that would kill 100% patients.

Genetics is very hard, and in very good case you may get 10% correlation. Then you will have to convince specialists to chase this weak possibility...

Working on this will consume your time, and put you under stress. This energy could be spend on your partner instead. You will need a lot of energy it it progresses.

Also there is always a big chance of misdiagnosis. Simple stuff like food alergy can be mistaken for many illnesses. Perhaps best first action is to verify this diagnosis. Get second opinion. Or change environment to rule out common triggers.

As a medicinal chemist (obviously biased), I would focus more on treatment and alleviation than the genetic component. This would usually mean looking at the metabolism or how the genetic mutation alters it. Is your partner lacking an enzyme, certain metabolites or intermediates etc.? These can at times be supplimented either directly or indirectly through food or vitamins/co-factors.

Biology and hence medicine is complex. You can not grok it in a day. You can not synthesize most drugs at home and you can not buy them without a license. There are therapies, side effects, treatments for side effects, interactions, ... It may be impossible to become an expert and find a cure in time for your partner. This is not your fault.

I strongly recommend that you start by consulting with multiple doctors until you find one or more who shows interest in your partner's case, understands probable causes, and demonstrates useful expertise in treatment. You may need to visit a larger hospital that is involved in research. Work the system. You are a recruiter.

Pick the primary doctor who will coordinate your partner's treatment. This doctor will be your partner's primary line of defense, and they will mentor you in any investigations you do. They will guide you through the maze of therapies, palliative care, research, social workers, and other forms of support. They will connect you to other specialists who can help.

Good luck!

The global locus outside of the USA for rare disease research is Orphanet https://www.orpha.net/consor/cgi-bin/index.php I would start there to find people and companies working on your partner's disease. No idea if there's a US equivalent.

If the disease is genetic (error in a gene) or genomic (error in the large scale structure of the genome), a very important thing to do would be to also sequence the parents (preferably WGS [Whole Genome Sequencing]). Doing such a trio sequencing experiment allows you to determine, for every gene and even base pair, from what parent it came and this allows you to assess what is normal (assuming the parents are not affected). This way you may find out if your partner is homozygous for an aberration both parents are heterozygous for. This could mean that is THE affected gene/chromosome. You may also find what we call "de novo" aberrations, these are aberrations that are not present in the parents at all and arose in you partner. These aberrations are very suspect (again, because both parents are not affected).

You may find something, you may not, a lot is unknown and regions outside of the genes may be affected and even the cause of the phenotype, but we still understand very little of this.

Depending on where you live, genomic counseling is free and trio sequencing is usually part of it.

This is not really my expertise (more in oncology) but feel free to ask more questions.

If you have BAM (or CRAM + reference genome) files for parents and your partner, you could download a trial of VarSeq [0] to do a more GUI based analysis of the results.

"Is it sufficient to identify variants by searching for the SNP string (e.g. "rsXXXXXX") in the VCF file?" If the variants have been associated with the same phenotype as your partner's, then yes, it is interesting. If there is no phenotype, perhaps you can track down the source publication and try to talk to the authors.

There are probably groups online with people in the same situation, try to find them, they can probably help you a lot more.

[0]: https://www.goldenhelix.com/products/VarSeq/index.html

A few notes to help you in this journey.

As for the data, I assume you've done Illumina sequencing. Your files are as follows:

FASTQ: short reads of the genome. CRAM: the reads aligned against a reference genome. VCF: small (probably <50bp, mostly SNPs) variants between your partner's genome and the reference, including your partner's genotypes (We are diploid, so there are two homologous copies of almost all loci in the genome, so you can have a variant that's in homozygosis---same alleles-- or heterozygosis--- different alleles.) The other files are index files that trivially describe the layout of these.

A substantial fraction of rare genetic disease (maybe 20%) relates to alleles found in the exome (the portion of the genome that directly codes for proteins in a 1:1 manner). You can look for rare variants that have significant effect on proteins. In most Illumina data sets, the significant majority of these will be genotyping or variant detection errors. Even ones that seem to lie in genes that are important for the etiology of your partner's phenotype are likely to be errors.

Other posters have linked to tools that might you predict the effect of given variants. You might also look at the variant effect predictor (VEP): https://grch37.ensembl.org/info/docs/tools/vep/index.html. This will classify the predicted effects of variants based on extremely detailed annotations of the genome. You can then find variants with high effect that are rare or nonexistent in the observed human population (using gnomad). Rare variants of highly deleterious functional effect with allele frequency >0% that your partner has in homozygosis may be candidates to follow up on. You will also want to look for variants that have AF=0% in the larger population and high effect size and your partner has in heterozygosis (they could be "dominant").

My impression is that most rare genetic disease is related to structural variation. This lies outside the scope of the short read resequencing which you've done. We don't even yet know the magnitude of this, because there are so few truly de novo assemblies of rare disease patients. The required technology has only come online in the past two years.

Between problems of observation of the genome and interpretation of the significance of variants, your job is not going to be easy. You will be confused by the signals you get, and probably follow many incorrect leads. Good luck.

As someone who has been trying to keep himself alive, it's definitely a battle.

We don't have to do everything ourselves.

Maybe you could find researchers working on his topic (your disease or the generic problem of identifying causal mutations for a disease) and pay them to work on your case?

You might fight your own parking ticket but you'd get a lawyer for your murder defence...

Computer people get paid a hella lot more than university medical research people, especially those outside big cities or in Europe or Asia. It's more efficient to work hard at making money and hire a few experts.

If you believe it a rare disease and your doctor confirmed so, one website you can try is https://rarediseases.info.nih.gov/. It might or might not be genetic or familial-related.

Some great advice here already. It is a little hard to be more specific without knowing what the disease is.

An important first step is to consider the probability that this is a condition with a genetic basis, based on what is already known about it.

I don't know much about the field but your post reminded me of this interview of Martine Rothblatt on the Tim Ferriss Show - https://tim.blog/2020/12/17/martine-rothblatt-transcript/

Her story might give you some pointers. All the best to you and your partner.

I'm working as a researcher/bioinformatician looking for the genetic causes of rare diseases. Your chances of success are ... complicated. However, there are various things you can do.

I'll second the suggestion to use Exomiser, or its more expansive version called Genomiser.

No, it is not sufficient to look up the RS numbers in the VCF file. There are two reasons for this:

1. The RS number just refers to the location. Different variants can exist at one location, so you aren't necessarily finding the same variant. Variants need to be matched by location and by the change that they cause.

2. RS numbers are typically given to locations that have common variants, although there are numerous exceptions. It is a universal rule of genetics that a rare monogenic disease cannot be caused by a common variant. This fact was so obvious, but it needed to be published [0] before people started taking it seriously. So mostly likely the variant that is causing the disease does not have an RS number.

The main problem you will face is the sheer quantity of data that you have been given. The average person has something like 3 million variants, so you need a way to whittle these down to a short list. The first thing you need to do is get rid of all the common variants, for the reason stated above. The easiest way to do this is to annotate the variants using software like VEP, Annovar, or alamut-batch. I'd recommend VEP because it is good, popular, and free. That will include in its output whether the variant has been found in the GnomAD project [1], which is a conglomeration of thousands of genome sequences, and can therefore say whether the variant is common or rare. For the variant to be considered rare, it shouldn't be present in GnomAD more than a couple of times.

Once you have the variants annotated, you should know for each variant whether it is inside a gene, which gene that is, and whether the variant has an effect on coding. If a variant is intronic, it is unlikely to be pathogenic (although it is never that simple). Common mechanisms of pathogenicity are:

1. If the variant changes the protein code (a missense variant). These are hard to interpret - they may be pathogenic but most are not.

2. If the variant changes the length of the coding DNA by a factor of three (an in-frame indel), which inserts/deletes amino acids from the protein. These are slightly more likely to be pathogenic than missense variants, but most are still not.

3. If the variant changes the length of the coding DNA by something other than a factor of three (a frameshift indel). This messes up the frame of the three-base code of the gene, making the rest of the gene gibberish. These are much more likely to be pathogenic, but only if the gene itself is actually important.

4. If the variant changes a protein codon into a "stop" codon (a "stop gain" or "nonsense" variant). These are as likely to be pathogenic as a frameshift.

5. If the variant interferes with splicing (a splicing variant). These variants are on the borders of the exons of genes and may change the way that the introns are cut out of the gene before translation into protein. These are fairly likely to be pathogenic.

The annotations should tell you which of these things a variant might be. A synonymous or intronic variant that doesn't affect splicing is very unlikely to be relevant.

You need to determine whether the disease is likely to be recessive or dominant. Recessive means that you need to have both copies of the gene broken in order to get the disease, whereas dominant means that you need just one copy broken in order to get the disease. If you look the disease or gene in ClinVar or OMIM [2] you can often find whether the gene is recessive or dominant. If it is recessive, you either need to find two pathogenic variants that are heterozygous, or you need to find a single pathogenic variant that is homozygous. In the VCF file, a variant is heterozygous if it says "0/1" and homo...