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Dec. 30th, 2015 11:57 am![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png){kind=small}
the_rckScott got a new alarm clock yesterday. His old one had been randomly deciding that it wouldn’t let him turn on the alarm or change the setting unless he powered it down and restarted it, so he ordered a new one. Unfortunately, this one isn’t going to work for us. The box of the alarm clock glows brightly in shifting colors. That can be turned off, but if we do, it’s no longer possible to read the time when the room is dark. That means that, when Scott woke at 3:00, he didn’t know if he should stay in bed for ten more minutes until the alarm or get up, use the bathroom, and come back to sleep some more. This morning, the clock lit up five minutes before the alarm was supposed to go off and woke Scott. If we’d known we were going to go to Target yesterday, he wouldn’t have ordered online.
My sister called yesterday to tell me that, although her genetic report had ’Negative’ in big letters across the top, her oncology nurse indicated to her that she actually wasn’t genetically negative. She has a variation of the PALB-2 gene that might actually be a problem. The report labels it as 'likely benign,' but she’s dubious. She says she searched the sequence online and found sources she trusted that seemed to indicate that it could be a big issue. From what she gathered, this gene sequence has to do with whether or not the breast tissue can repair pre-cancerous damage. She thinks this makes it more important that I get genetic testing done. I was considering it (I asked for a referral to a genetic councilor, but that hasn’t come through yet).
She sent me a scan of the pertinent bit of the genetic report. I need to get her to send me scans of her pathology reports, too. I don’t think my oncologist believed me when I told him that she had at least three completely different cancers going on in her left breast (and there was the start of a fourth in her other breast). My impression is that he heard 'DCIS' and assumed that equalled not a big deal.
I have no idea what’s going on with my parents. They’re in Michigan, about two and a half hours away, and they have said that they’re going to visit us some time this week. The week is rather rapidly vanishing, so I really don’t know that they’re actually going to carry through. It would be disappointing to have them this close and not see them, but they were adamant that we shouldn’t try to visit them (and I’m not sure that I could have done it last weekend which would have been the best time). I don’t know when they have to be back in Baton Rouge. I suppose I could look up the starting date for classes at my step-father’s university, but that seems like trouble I shouldn’t have to go to. If they do come, judging by past experience, they’ll call when they’re about fifteen minutes from our house and consider that adequate notice. Which— Well, it won’t be like they didn’t know before that that they were coming our way.
Cordelia’s at the age where she wants to know why her grandparents are like that and expects sensible answers as opposed to 'that’s just how they are.' Of course, I’d like answers about why they’re like that. I’m just afraid that the real answers would make me sad. I know Scott thinks they’re flaky and selfish and has thought that for almost the whole time we’ve been married (and quite possibly longer). My mother and step-father are both very intelligent and very good at their chosen professions. They’re just terrible with family. My mother’s not so bad if she has something very, very clearly defined that needs to be done (she did a very good job making sure her father was taken care of for the last decade of his life). She’s just horrible if you need a hug and reassurance.
My sister called yesterday to tell me that, although her genetic report had ’Negative’ in big letters across the top, her oncology nurse indicated to her that she actually wasn’t genetically negative. She has a variation of the PALB-2 gene that might actually be a problem. The report labels it as 'likely benign,' but she’s dubious. She says she searched the sequence online and found sources she trusted that seemed to indicate that it could be a big issue. From what she gathered, this gene sequence has to do with whether or not the breast tissue can repair pre-cancerous damage. She thinks this makes it more important that I get genetic testing done. I was considering it (I asked for a referral to a genetic councilor, but that hasn’t come through yet).
She sent me a scan of the pertinent bit of the genetic report. I need to get her to send me scans of her pathology reports, too. I don’t think my oncologist believed me when I told him that she had at least three completely different cancers going on in her left breast (and there was the start of a fourth in her other breast). My impression is that he heard 'DCIS' and assumed that equalled not a big deal.
I have no idea what’s going on with my parents. They’re in Michigan, about two and a half hours away, and they have said that they’re going to visit us some time this week. The week is rather rapidly vanishing, so I really don’t know that they’re actually going to carry through. It would be disappointing to have them this close and not see them, but they were adamant that we shouldn’t try to visit them (and I’m not sure that I could have done it last weekend which would have been the best time). I don’t know when they have to be back in Baton Rouge. I suppose I could look up the starting date for classes at my step-father’s university, but that seems like trouble I shouldn’t have to go to. If they do come, judging by past experience, they’ll call when they’re about fifteen minutes from our house and consider that adequate notice. Which— Well, it won’t be like they didn’t know before that that they were coming our way.
Cordelia’s at the age where she wants to know why her grandparents are like that and expects sensible answers as opposed to 'that’s just how they are.' Of course, I’d like answers about why they’re like that. I’m just afraid that the real answers would make me sad. I know Scott thinks they’re flaky and selfish and has thought that for almost the whole time we’ve been married (and quite possibly longer). My mother and step-father are both very intelligent and very good at their chosen professions. They’re just terrible with family. My mother’s not so bad if she has something very, very clearly defined that needs to be done (she did a very good job making sure her father was taken care of for the last decade of his life). She’s just horrible if you need a hug and reassurance.
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no subject
Date: 2015-12-30 05:11 pm (UTC)If this happened to me, I'd have to start making jokes that my real name was Dana Scully and I'd been abducted by aliens. That's just WILD. Also, terrifying.
ETA: Went and looked at my most trusted source of genetic overview information and OH HOLY WOW yes, I can see that PALB2 mutations could be an issue. If your sister is interested, Online Mendelian Inheritance in Man (OMIM) has been a reference for geneticists for years (since it was an annual book pub); it's an excellent and frequently updated site that collects references and functions as a speedy review of the literature. The link for PALB2 is: http://www.omim.org/entry/610355
no subject
Date: 2015-12-30 06:32 pm (UTC)I've transcribed the bit from the report below. I was very, very careful about getting the numbers right, and I checked for other typos, but... transcription.
____________________
PALB2 Exon 8 c.2816T>G (p.Leu939Trp), heterozygous. Likely Benign
This sequence change replaces leucine with tryptophan at codon 939 of the PALB2 protein (p.Leu939Trp). The leucine residue is highly conserved and there is a small phytochemical difference between leucine and tryptophan.
Because the frequency of this variant is 0.2% (rs45478192) in at least one subset of the population, it has been classified as Likely Benign.
_______________
I don't have the background in genetics or biochemistry to have much of an idea about what that means or what the actual certainty is that the variant is benign. 'Likely' is not the same as 'definitely.' And what subset of the population? I would like some idea of the size of that subset. 0.2% of a group of 1000 is a lot different than 0.2% of a group of 1000000.
The bit of the report she sent me (I think it's a photo she took with her phone rather than a scan even though she said scan) doesn't show the company that did the testing. I'd be interested to know that, too. It does say that they aren't going to bother listing variants that are known to be benign.
Thank you for the link. I will pass it on to my sister.
no subject
Date: 2016-01-02 05:37 am (UTC)On the up side, the effects of a missense mutation (swapping out one amino acid for another) is less likely to have profound effects on the function of the protein than other types of mutations (which can radically alter the length of the protein or the sequence).
I did a little hunting for that particular mutation. The population is probably a population of individuals with either breast or pancreatic cancer (PALB2 is associated with both), but I can't find a direct reference for the number. It appears to be little examined, though one study I found bioinformatically tests the probability of the mutation affecting PALB2 function, and the result was "predicted to likely affect PALB2 protein function by all the tested algorithms." But they don't know much of anything.
And it's not one of the molecular genetics items listed in OMIM yet, because it is so little studied. The breast cancer mutations in PALB2 are apparently mostly autosomal dominant -- 50/50 chance of inheriting it from the carrying parent and having it affect one, but see above about cancer genetics and people not knowing much. So who knows? In any case, I admire the nurse who told her about it, because it indicates that the nurse actually reads papers!
no subject
Date: 2015-12-30 05:22 pm (UTC)Since I'm a current customer of theirs, I can send you a signup link that will cause them to send me an Amazon gift card if you sign up. I'd be happy to pass the gift card back to you.
Let me know if you want the link?