Informal Notes: Pathogenic Variant Risk for BRCA1/2 Mutations

[this set of notes branched out from this blog post] 

I think the estimates of 50% risk for breast cancer and 30% risk of ovarian cancer (in this infographic from the CDC) are in line with that I was expecting (although that doesn't capture mutations in BRCA1 being higher risk than BRCA2).  There is also this page with 60-75% risk for BRCA1 carriers and 50-70% risk for BRCA2 carriers (which I learned about from this Twitter reply).

Importantly, because of that Twitter communication, I read the book "Resurrection Lily" by Amy Byer Shainman.  I think this provides a very poignant perspective of what is like for yourself and/or your friends to go through either breast cancer treatment or prevention strategies (including up to preventive surgeries).  There are also multiple pages for risk estimates at the end of the book (pages 253 and 262-263 in my copy of the book).

Before I learned about that book, I think I would mostly typically refer to the Stanford BRCA Decision Tool (Kurian et al. 2012) that provides the variance of risk with a few options (although I'm not sure about the the intervals of screening, I don't know what is the relative effectiveness of hormonal therapies, and these estimates are at the gene level when I would expect some specific variants are higher risk than others).

While it is probably not going to be a problem in the future, there was a few days when the website was down.  So, I have attached some screenshots below (for BRCA1, and then BRCA2):

There was a recommendation for BRCA screening with a "B" grade in individuals with family histories, but a recommendation against BRCA screening with a "D" grade for individuals that didn't already have an increased risk of getting breast cancer (which I think is shown most clearly on the US Preventive Services website).  While the context is different, I think this figure from Biesecker 2019 shows one example of how filtering for prior risk may help (although not specifically for BRCA1/2).

While the topic of treatment strategies is a little different, I did notice some different number on an NCI Prevention Tweet (going back to topic of the range of risk estimates).  For example, that number seemed noticeably different for BRCA2, and the total risk reduction (particularly if you focus on death from breast cancer) also seemed different that the text in that Tweet (compared to what I see in the BRCA Decision Tool).

I also think I had another interesting conversation on Twitter here, some of which was converted into notes as a blog post (in terms of the overall prevalence of cancers where variants in moderate-to-high risk genes could be found).

There are some NCCN guidelines, although I thought those were more clear for criteria for screening versus recommendation for surgery in a BRCA-positive individual (which supports use on a "case-by-case basis").  Nevertheless, there is a lot of information available if you register for an account in this document, where some details for the "Bilateral Total Mastectomy" are on page MS-24.  Nevertheless, if this implies that people who don't qualify for the NCCN screening criteria (but had a test result, for some reason) are less likely to benefit from surgery, then perhaps that is helpful for making decisions.

The CDC has guidelines to define "average," "moderate," and "high" hereditary breast cancer risk.  I think their guidelines for genetic testing are similar to the NCCN and USPSTF (but you might find that website easier to read, and this page mentions that the USPSTF recommendations may affect health care coverage).  They also have an additional link for mammogram screenings that I didn't previously know about (on this page).

While I think there are some specific things that can be improved (for communication with non-scientists and communicating ranges for estimates of risk for specific variants, for example), I believe free, publicly-available resources like BRCAExchange.org should play an important roles in helping patients learn more about their results.  ClinVar also provides some information, for variants in general.

For example, I believe these are the 3 BRCA1/BRCA2 variants covered by 23andMe: rs386833395, rs80357906, and rs80359550.

The mutation described by the author of "Resurrection Lily" was referred to as "BRCA1 #5385 insC" as well as "BRCA1 #5382".  The book includes some references to ClinVar, but I don't believe I saw the rsID.  However, I believe those names refer to this variant in BRCA Exchange and this variant in ClinVar (based upon this Hamel et al. 2011 paper, and the synonyms in the database listings).  That makes this is second of the 3 variants tested by 23andMe above.

I am not sure about other available estimates.  However, there are selected genes with high (or highest?) lifetime risk variants for 7 cancer types (including breast and ovarian cancer) on this page from JScreen.

You can listen to some personal perspectives from a patient advocate in this podcast from DNA Today.  One statistic that caught my attention was that 1 in 40 Ashkenazi Jewish women have a mutation in the BRCA1 or BRCA2 genes.  I would also find that statistic on this page from the CDC.  I believe that page is combining pathogenic variants from the BRCA1 and BRCA2 genes when reporting "About 50 out of 100 women with a BRCA gene mutation will get breast cancer by the time they turn 70 years old".

There are also various ways to see the influence of ENIGMA on BRCA1 and BRCA2 variant annotations.  For example, BRCA Exchange includes pathogenic variant annotations from ENIGMA and ClinVar.  This page provides information for ENIGMA annotations in ClinVar, and there is also an ENIGMA BRCA1/BRCA2 expert panel in ClinGen (related to "Variant Pathogenicity" for BRCA1 and BRCA2).

Change Log:

9/14/2019 - public post date
11/12/2019 - add link to BRCA decision tool paper; website not currently working, but I will add some screenshots later (to show substantial difference in risk at the gene level for BRCA1 versus BRCA2)
11/20/2019 - add screenshots for BRCA Decision Tool.
12/2/2019 - add prior risk venn diagram link

7/6/2020 - add "breast cancer" label

8/16/2020 - add additional Penn/Basser link for risk estimates

8/22/2020 - add BRCAExchange link

10/25/2020 - add Resurrection Lily link

2/23/2022 - correct typo

12/1/2023 - add JScreen link (after listening to this podcast)

1/21/2024 - add additional DNA Today link as well as CDC Link for BRCA variants in women with Ashkenazi Jewish ancestry.

1/22/2024 - after receiving helpful feedback from GenomeConnect / ClinGen staff, add links for various types of ENIGMA annotations.

Informal Notes: Collection of References Regarding the Frequency of Pathogenic Mutations in Moderate-to-High Cancer Risk Genes

While I typically prefer to keep Twitter responses less formal than blog posts (which in turn are less formal than pre-prints or peer-reviewed journal articles), I feel kind of bad continuing to add citations to an earlier discussion thread.

So, I thought I would copy the notes here, and provide information for those that are interested (without having all the notices go to the person with the original response):

BRCA Exchange tries to provide some variant information (for BRCA1 / BRCA2)

data.color.com also provides some information about specific variants (but counts are often low).  Color also has this page for Breast Cancer Awareness Month (October).

Ambry provides an Interactive Prevalence Tool (in collaboration with Mayo)

Stanford BRCA Decision Tool provides some statistics to guide discussions about risk prevention options (although that relates more to risk than total frequency; however, this with total numbers is essentially what I want to see)

MSKCC lists total inherited breast cancer rate at 5-10%

There is a link from the CDC website listing the BRCA1+BRCA2 rate for hereditary breast cancer as 3% for breast cancer and 10% for ovarian cancer.  If you sum the frequencies, that is somewhat close to LaDuca et al. 2019.

There is also a different source of information from the CDC, mentioning for all hereditary breast and ovarian cancer (which must be greater than the sum of BRCA1+BRCA2), which was 5-10% and 10-15% respectively.

Offit 2006 

• Editorial about BRCA mutation frequency and risk

Hu et al. 2018

• Table 2 shows some percentages per gene

LaDuca et al. 2019

• Learned about from @kristinclift
• GenomeWeb review mentions "13.8 percent of ovarian cancer patients carried germline pathogenic variants in at least one of the 32 genes tested"
• Supplemental Table S7 also shows a higher BRCA1/2 ovarian cancer percent (3-5%, OC) than breast cancer percent (1-2%, BC)
• There are all high-risk patients 
• Total numbers are fairly different: 66,954 BC, 9,106 OC, 1,087 BC+OV.
• Supplemental Table S6 has gnomAD control frequencies, but I think variant calls may need to be more specialized for targeted gene panels.
• In other words, those percentages look low compared to that matched control study, but they do provide those details.
• I also think they used results from the reports from different Ambry panels, rather than obtaining and re-analyzing raw data independently.  So, I wonder how much of an effect that had.

Unpublished (?) CARRIER Study Data

• In a CARRIERS plot (a PDF from a Clinical Cancer Genomics Conference presentation that I don't know if I have permission to post), getting control variants for BRCA1/2 below 0.4% puts BRCA1/2 case mutation rates at under 1.4%.
• I think that is for breast cancer.
• Plots for 14 individual studies (for a total of 10,000s of samples, with matched controls) were shown for 21 genes of with overall case rate of ~6% and control rate of ~2.5%, as well as 17 higher-risk genes with overall case rate of ~5% and control rate of ~2% (which I guess could up to a 30% “false positive” rate either way).

Variability in Variant Calling

• May need more specialized variant calling for targeted gene panels - Warden et al. 2014
• For example, notice the difference in scale for the y-axis in Figure 9, where the relative “novel” variants in controls is a proxy for false positives:
• You may get better concordance between variants with reprocessing (in this case, using a more typical processing strategy for WGS and Exome Data) - blog post on custom scripts and precisionFDA comparisons.
• In addition to data.color.com, I think cBioPortal can be a useful research to look at mutation information across different cancer types and studies
• cBioPortal has some tutorials that can be viewed here
• For example, I think I could see results more similar to what I read elsewhere (with BRCA2 being found at higher frequencies) if I removed variants of unknown significance
• I think 47:45 - 51:55 of this webinar also gives some useful caveats to mutation and copy number calling that might be worth taking into consideration (where a region that is supposed to have a homozygous deletion has a variant with an allele frequency that you would normally consider a match for a heterozgyous variant, when a true homozygous deletion call shouldn't have any variants)

Polygenic Risk Scores

These are arguably more for risk assessment rather than frequency (although the risk estimate vary across the population).

Nevertheless, I would also be interested in seeing more results from Myriad myRisk and AmbryScore-Breast Polygenic Risk Scores (PRS).  This is in part because I haven't been highly satisfied with the polygenic scores that I was able to apply to myself, but I should note that clinical features are included in the calculation for these scores (beyond just the genetic information).

For example, I noticed that some more information Myriad myRisk was provided in these slides, which I believe reference this announcement.  I believe that is a reference to the Hughes et al. 2020 and Gallagher et al. 2020 papers.  However, what caught my eye was this figure, which I don't think it is directly from those publications?

I am not sure if I am correctly understanding that both Myriad myRisk and AmbryScore-Breast use "clinical history" information?

As a possibly separate point, I thought Figure 2 of Fahed et al. 2020 was interesting because of the difference in the range of risk estimates by PRS with versus without a BRCA1 or BRCA2 mutation.  The stratification without being a BRCA1/2 carrier was more limited.  However, I would be interested to get a better sense of how PRS stratification compares to variants in or near the BRCA1 or BRCA2 genomic footprint.  I think the later more along the goals of resources like BRCA Exchange.

Those interested in these notes may also be interested in this post with notes on the range of risk estimates.

Change Log:

9/9/2019 - public post date
9/10/2019 - add "informal note" category, along with link to original response
9/13/2019 - add CDC links, as well as some extra information not previously copied over from earlier Twitter discussion
10/10/2019 - add Color link for BRCA1/2 mutation frequencies
11/12/2019 - add link to other blog post
5/8/2020 - add cBioPortal notes

7/6/2020 - add "breast cancer" label
7/7/2020 - add note about interest in hearing about a range of PRS experiences.

8/14/2020 - add additional PRS links

8/16/2020 - minor change

3/9/2021 - add link for Ambry Prevalence Table

4/23/2021 - move link from earlier blog post to this blog post

6/26/2022 - add link to PRS within BRCA1/2 carriers

My Take on the FDA Warning to 23andMe

NOTE (8/5/2020): As I gained more experience finding problems that were not clear until after 5-10 years of research, I looked back at this and I would not have completely agreed with earlier responses.  So, I have separated my first response (Response #1) and additional responses (Response #2).  I have also started to keep a change log, for updates after this point.

NOTE: Getting Advice About Genetic Testing

I have recently participated in a forum discussion on Biostar about the newest warning to 23andMe from the FDA.  I think my responses will be of interest to a broader audience, so I have copied them here.  If I end up contributing more to the Biostar discussion, I will update my blog post as well.

Comment: The majority of published reactions seem to miss what the FDA's major issue is: about marketing and describing the service.

Response #1: Yeah, I agree that the wording in this warning focuses mostly on marketing.

However, the FDA has previously tried to shut down DTC genomics companies (including 23andMe) and the 3rd paragraph seems to mostly focus on the accuracy of the test. The carrier status report should really be OK for diagnosis (and I think many of the specific associations mentioned in that warning are also pretty well established). Now, there are some caveats to some results like deciding how to combine independent SNP risks and explaining the difference between a mutations that guarantee onset of a disease versus modulate risk (which may only have a modest impact on risk in many cases). I personally think 23andMe does a decent job of this already, but I'm sure there can always be room for improvement.

In other words, my understanding is that the problem was primarily with direct communication with the FDA regarding technical benchmarks that would justify marketing claims (and I think the FDA is supposed to provide permission based upon this data prior to advertising). This certainly relates to communication with customers, but I think delays in formal responses to the FDA from 23andMe were the primary problem.

Response #2: In retrospect, I don't think I should have used the phrase "shut down".

I might add additional thoughts, but this was the main thing that jumped out when I re-read the blog post.

Concern: There is at least one report of an individual with an inaccurate 23andMe report (click here to view).

Response #1: Make sure to read the entire article.  Once the bug was reported, it was fixed and the report was updated.

Response #2: Errors need to be made clear to customers.  You can see some notes like this among this collection of blog posts (which includes submission of multiple FDA MedWatch reports), but I don't believe any of this was made clear to other customers.

While a lack of confidence is sometimes necessary to communicate, it does need to be communicated.

There can also be negative consequences.  For example, if the trace for the automated Sanger sequence was not checked, then sequencing error could be a false positive for a pathogenic mutation.  If this was not caught before action was taken (which could be something like an unnecessary mastectomy), then permanent damage could be caused from providing a result prematurely and/or inaccurately.

That said, I don't want to over-emphasize the potential harm, and I think helping citizens become engaged in problem solving and critical assessment would be valuable (if genomics data / hypotheses were used for that purpose).

Concern: The issue isn't the bug. The issue is that 23andMe is offering a product while making claims about how customers can use results for improved medical care. Medical professionals and should be in charge of offering medical services.

Response: I agree that communication with customers is important and some customers may not have a good sense of what it is like to be part of a research project. It is possible that this is something 23andMe needs to work on.

However, I think the best solution is not to get rid of 23andMe, but rather help improve communication regarding the confidence of results. For example, I wrote a blog post about one possible solution after a previous FDA warning was issued:

http://cdwscience.blogspot.com/2010/08/benefits-to-3-tier-system-for-dtc.html

Also, I don't think this is a typical result. For example, here is a link to my results as well an article from Lifehacker (from someone with much less experience with genomics research). I'm sure I've seen more, but these are what I could think of off the top of my head.

http://cdwscience.blogspot.com/2011/02/thoughts-on-my-23andme-results.html

http://lifehacker.com/5802559/how-to-decode-your-dna-with-personal-genomics-service-23andme

Plus, I think an unfortunate reality is that this sort of thing will happen from time to time. I think pretty much all diagnostics will suffer from some degree of false positives, false negatives, and/or human error. I know I constantly have to update the bioinformatic programs that I design (for what I would call "research grade" analysis) - especially when hunting down bugs that are only apparent when analyzing a small number of data sets.

Concern: The fact that it turned out to just be a bug is one thing, it's pretty bad but they fixed it, but even if it had turned out to be true, it's still horrific. Imagine being sent an email saying, "Hey, you're going to get progressively disabled then die young," and no further information about what the condition is and how it's going to affect you, no kind sympathetic face offering you tissues and advice and options. This guy did his research and turned out to be fine, and that's great, but how many people fall into deep depression on getting this news? How many people kill themselves? You can't give out this kind of potentially devastating life-altering news in an email.

Response #1: For some people, I agree this may not be the best way to communicate results. This is probably why 23andMe adds an additional step for viewing results like this that are not present for non-medical and non-predictive results. If you aren't prepared to view results on-line, then I would probably recommend either not getting a 23andMe profile, not viewing that portion of the results, and/or contacting a genetic counselor to review the results with you. For example, my 23andMe report indicates that I am a carrier for cystic fibrosis and they provide a link on how to talk to a genetic counselor on that page:

https://www.23andme.com/you/genetic_counseling/

That said, I think the concern overall is an over-reaction for the following reasons:

1) There have been several publications showing that most people have no problem responding to DTC genetic testing. I can't list all the publications off the top of my head, but here is a summary of one such article:

http://www.nature.com/news/2011/110112/full/news.2011.12.html

2) In general, the accuracy for the DNA sequencing portion of the tests (currently via an Illumina SNP array) is pretty good. For example, the FDA has recently approved Illumina sequencing for clinical application. I'm also pretty sure 23andMe has checked the accuracy of the array by comparing normal 23andMe clients to the results from people who participated in the exome sequencing pilot. That said, there is a difference between the interpretation for the carrier status results (which is relatively straightforward) and all of the other results, and my understanding is that failure to communicate these results to the FDA is one of the legitimate complaints from the FDA letter.

3) I think people need to be careful and critical in all cases. For example, let's say I had a wife who was also a cystic fibrosis carrier (identified via 23andMe) and we were thinking about kids. The first thing I would do is verify the result. For example, I could order a Counsyl test from a doctor (which might be a good alternative for some people instead of 23andMe, although I think you might still be viewing your results on-line) to verify that we were in fact both carriers. I wouldn't immediately run to an in vitro fertilization clinic. Plus, medical professionals can make wrong calls too. Also, to be clear: I have family members who are confirmed cystic fibrosis carriers, as determined by standard testing.  So, I think the probability of this being a false positive is very low, but I would always want to tread carefully.  This has certainly happened to me, which at least one time delayed hospitalization for a very serious infection. This is not an attack on the medical establishment: there is a reason I went to see the doctors in the first place. However, I think the actions made by this individual were spot on, regardless of whether something is FDA-approved and regardless of whether a result comes from a person or a computer: if something doesn't sound right, you should look into a second opinion, independent research, etc.

Response #3: As an update to 3), I later submitted my samples to multiple companies.  With the raw data, I would confirm that I am cystic fibrosis carrier.  However, multiple companies said that I wasn't a carrier.  So, I think having raw data and taking time to evaluate results is important.

Comment: There is now a class action lawsuit against 23andMe: http://gigaom.com/2013/12/02/23andme-hit-with-class-action-over-misleading-genetic-ads/

Response #1: That is unfortunate.

Response #2: While I hope issues can be resolved outside of court, I now agree that 23andMe (and AncestryDNA) ads can be misleading.  As one example, I had/have serious concerns of advertising Airbnb destinations (as mentioned in this blog post).

While I usually kept the previous responses, I thought this paragraph should be changed (hence the different font color).  Essentially, I think the link below is worth reading, but my impression is different.  I still think it was important to change the title (to avoid exaggerating the problem).  However, I think important points were also raised and I apologize for not sufficiently appreciating that before:

http://liorpachter.wordpress.com/2013/11/30/23andme-genotypes-are-all-wrong/ 

I'm still hoping that most conflicts can be settled out of court (if that is still possible at this point). At least this provides a list of specific claims that I hope 23andMe will directly address to customers in an official statement - at least they can reference a plethora of 3rd party experts who can generally back them up. I certainly think they made bad choices with the timing of advertising and providing terse official responses, but I don't think that should be a $5 million mistake (especially for a service that I assume is being provided below cost)

Update: I also have put together a survey on this topic. If you can fill out and/or distribute the survey, I would appreciate it!

http://cdwscience.blogspot.com/2013/12/survey-of-opinions-on-23andme-fda.html 

Change Log:

11/26/2013 - public post date

8/5/2020 - start keeping change log with updated responses

8/6/2020 - continue to add revised responses

Gene Patents and Genetic Testing

NOTE: Getting Advice About Genetic Testing

This week, Angelina Jolie wrote an editorial for the New York Times describing how she underwent a double mastectomy after testing positive for a deleterious BRCA1 mutation.

This article stirred up a lot of discussion because she mentions how "[the] cost of testing for BRCA1 and BRCA2, at more than $3,000 in the United States, remains an obstacle for many women".

Although there have been responses pointing out that insurance can significantly decrease the out-of-pocket costs to the patient (under the right circumstances), the question remains "Why is the test so expensive?".  After all, the true cost to perform the test is much less than $3,000.

The genetic test in question is Myriad's BRACAnalysis test.  This company should sound familar because the Supreme Court recently heard a case from Myriad to decide if human genes can be patented (the BRCA1/2 gene patents are the reason why the Myriad test costs so much).

There are lots of resources to learn more about the court case and BRCA testing.  For example, Chris Mason recently wrote good summary on the topic.  However, I want to re-emphasize a couple important points here:

1) It is possible to provide a genetic test covering a panel of diseases at ~1/10th of the cost.  For example, 23andMe provides carrier status for a variety of diseases (including some BRCA1/2 mutations) for $99.  Likewise, Counsyl offers genetic testing that is less than $100 with insurance or less than $1000 without insurance.  There are also various options for discovering mutations in raw sequencing data, whose cost is continually decreasing.

2) The basis of Myriad's claims to retain its patents is the high development costs to develop the test.  Regardless of the ethical arguements against gene patients (and the high likelihood that genetic tests will be based upon findings from government-funded research), this is no longer a technical concern now that the human genome has been sequenced.  There a multitude of freely available tools to help clone any region of the human genome.  There are certainly still novel discoveries out there (like novel non-coding genes, fusion genes, etc.), but I would argue the tricky part is asking the right question - the production of the cDNA is then trivial.  I see no reason why individuals should have to pay for the costs of a patent for the interpretion of a medical discovery reported in the scientific literature.

Who should be responsible for genetic counseling?

Today, I read a GenomeWeb article regarding a debate on whether Myriad Genetics’ BRCA test (BRACAnalysis) should be interpreted by primary care physicians or genetic counselors. Myriad claims that primary care physicians can and should interpret the test results, but critics claim this can result in inaccurate interpretation of test results.

Certain mutations in BRCA1 or BRCA2 genes can lead to an increased risk of developing breast and/or ovarian cancer. I am trying to keep track of notes about BRCA risk here, and prevalence of high risk cancer genes here.  So, I welcome input from others, and I have modified some of the content in this paragraph since the original post.

At least one survey from Medco indicates “most [doctors] believe that personal genomic information can be useful in their care for patients and help them make treatment decisions [but] the majority said they do not know enough about such tests.” In contrast, a different survey reports that “community-based physicians appeared to be successful incorporating BRCA1/2 testing into their practices.” However, a majority of these doctors utilized the assistance of some sort of genetics expert when making decisions about patient care. Myriad also emphasizes the paucity of genetic counselors, but critics have pointed out that Myriad fails to inform doctors that telephone-based genetic counseling is available and, in fact, required by certain insurance companies such as United Healthcare and Aetna.

I do think patients should be given the option of talking to a genetic counselor, and I think most physicians would benefit from at least informally discussing the details of a specific genetic test with a genetics expert. In general, patients should always seek out second opinions if they do not feel comfortable with their physician’s advice, and I would also advocate that patients conduct some independent research. For example, the National Cancer Institute provides a lot of useful information on BRCA1/2.

More than 10 years after the original post, I think some of my impressions have changed.  However, I still believe that changes in medical training and public education about the role that genetic counselors can play in making medical decisions is important. I also still hope that legal intervention may not be necessary to improve the interpretation of medical diagnostics.

Change Log:

[post not created with change log]

4/23/2021 - add links to newer posts with notes about estimating BRCA risk / prevalence (since I think the numbers in the original post might have given the wrong impression).

Also, change concluding paragraph, which originally included this link, where I think I down-played the importance of oversight (and I myself have certainly been submitting FDA MedWatch reports for multiple more recent genomic results).