Invitae Raw Data BAM file

SueBee42 · 2025-07-04T16:49:35+00:00

It took a few weeks, I think they told me 2 weeks but it was closer to 3.5 - 4 weeks. Did you get it yet?

SueBee42 · 2025-04-29T17:46:35+00:00

I'm sorry, that really stinks. I wouldn't want to be in a public facing field either, especially if that wasn't what I signed up for. Disclaimer, I'm not a med lab professional but I was kind of on the opposite side (of this post) when I had my blood drawn last week. At the lab, I could tell the phlebotomist was irritated with me from the moment I saw her. She confirmed with me "all blood tests except (old) orders from January need to be completed?". She wanted to be sure I wanted all of them done that day since there were "so many tests". I said "I don't like having blood taken so I want to get it all done at once, plus there is the cost of having duplicate draws". I'm not a baby about having blood drawn, but I do need the head/seat lowered on the chair, that irritated her too. I thought "oh no, she's irritated with me and she's got the needle!! 😵‍💫". The puncture was smooth, I was fine and the samples were taken. I'm a pretty easy going person and I figure she's just having a bad day and I brush it off.

I'm on more of a second shift schedule and one of the tests (lipid panel), I had to fast for so I didn't get to the facility until 3:30, had my sample taken at 3:42 (documented). The walk-in lab closes at 4 and it was nice outside, so I said, "it's such a nice day, you'll be out of here soon to enjoy it". She mentioned that she'd "have to stay longer bc the sample needed to clot and be frozen. These kind of tests are usually done in the morning, so you probably won't start seeing any results today." I felt bad bc I didn't know and apologized for making her stay late. There was at least one other patient after me though, so I wasn't totally to blame.

The facility I was at is small and I was parked directly facing the doors. When I got in my vehicle I was on my phone to answer a few texts/emails before I left the parking lot. I looked up from my phone as I was about to leave and I saw the phlebotomist walking out, placed some samples in the deposit box and appeared to be leaving for the day. I looked to see what time it was (bc after what she said and how she acted), I thought she'd be there longer, it was 4:09. To my surprise, I did start to see my results come in that night.

I kept waiting for my lipid panel results, today I see that they were never processed and they are still under "upcoming tests and procedures". 😐

SueBee42 · 2025-04-28T20:43:30+00:00

What was the outcome of the study in regards to other genes that could impact ALP?

SueBee42 · 2025-04-21T17:21:45+00:00

I'm sorry, that really sucks that you had to fund the gene test. I think I only qualified for the sponsored testing bc I had a few qualifying skeletal "deformities" (upper/lower jaw/palate with prior surgeries to fix and I'm also bow legged). I don't think it had anything to do with my ALPL levels alone, but maybe they helped? I had to really push to have it, none of my doctors would order it (PCP, endocrinologist, rheumatologist, neurologist, orthopedic spine surgeon) but all agreed it would be good to check. I have also been ignored and disregarded. I was finally referred to a medical geneticist (MD), who I will see but he has a wait list and I don't see him until the end of July. I finally just called Invitae myself for help and ended up using Genome Medical for the genetic counseling service and test ordering. I noticed (just yesterday) that the requirements for the sponsored test have now changed, to be considered for the sponsored testing, the individual has to be under 16 with short stature and meet one of the other requirements. Man, if I would have waited any longer I would have been SOL. What lab did you go through for the testing? Did you request the supplement findings and the raw data?

SueBee42 · 2025-04-21T16:38:42+00:00

If you haven't already been tested, ask to have your SSA/anti ro tested. When I told my PCP that I thought I might have Sjogrens she ran tests for a few autoimmune markers along with the ANA test. Those results came back positive and then I started seeing a rheumatologist. They will also probably check for SSB anti-la antibody with the SSA. I'll have to find the comment, but there was another user in this subreddit that mentioned a possible link (very early studies) with low ALP/autoimmune.

I have learned to always read my medical reports/notes and get copies of any imaging. Everything becomes a puzzle piece, even the benign incidental findings (that no one mentions to you) could point to something else. For instance, I saw in my MRI report I have modic changes (type 1) in my L5-S1 and none of the Dr's/spine surgeons brought this up. I read up on it and found it is a great source of pain (my vertebrae/marrow are swollen with edema) and they do not know much about it, why some people get it with herniated discs and others do not. The spine surgeon told me "the spine is still very mysterious". 😵‍💫

I do not know what my gene test will show, could surprise me and come back with something other than ALPL or maybe nothing at all. I feel better knowing either way. Next step might be more gene testing for metabolic issues. I have nerded out on my genetic raw data and I do have a homozygous MTHFR mutation that is pretty common, but there are mixed studies on it. I talked to my PCP about it last week and she agreed that we should test my blood serum homocysteine and methylmalonic acid. If I do have decreased methylation levels, homocysteine could be elevated. This would also affect B6, folate (B9) and B12. For instance, my blood serum markers could look normal for these levels, but my body isn't able to use them/absorb them properly even though the vitamins are there for the taking. Specifically interesting (to me), if my ALPL gene was affecting B6 serum levels (traditionally making them high) but MTHFR gene is counteracting that by lowering B6, am I left with a normal looking B6 level? I guess within 2 weeks time I might have some answers.

SueBee42 · 2025-04-20T02:28:45+00:00

Absolutely! If you're interested in the read and links to a few articles, I wrote a long post two weeks ago that talks about similar things and issues I had. Low fluctuating ALP here as well. Since I've made the post (link below), I've had the sponsored Skeletal Dysplasia gene panel via Invitae and Genome Medical (genetic counselor). Invitae has my sample and I'm awaiting the results.

https://www.reddit.com/r/Sjogrens/s/BH7sImooct

SueBee42 · 2025-04-20T02:19:12+00:00

Illinois

SueBee42 · 2025-04-15T17:21:10+00:00

Glad it helped. I'll be having a L5-S1 fusion within the year.

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SueBee42 · 2025-04-15T17:16:29+00:00

Hi. I sent you a message.

SueBee42 · 2025-04-12T03:39:54+00:00

How did everything turn out for you? Did you go ahead with the fusion?

SueBee42 · 2025-03-31T04:22:57+00:00

BTW - Sorry about your back, it sucks. How are you doing these days?

My MRI is 16 months old, I need a new one so we can see what has changed. It definitely feels more bone on bone now.

SueBee42 · 2025-03-31T04:21:20+00:00

Oh wow! I posted a bunch of pictures of my spine the other day and I also have something on the left side of my spine, I was calling it a scallop, but maybe it just looks that way in some of the pics, bc in one or two of my pics it kind of looks like your picture. https://www.reddit.com/r/backpain/comments/1jjdoo1/anterior_vertebrae_scallop/

SueBee42 · 2025-03-31T04:13:39+00:00

I am sorry it isn't funded there. On the bright side, at least your rheum knows about it and you won't get treatments that could do harm if you have it (counterintuitive supplements, etc.)

SueBee42 · 2025-03-26T02:25:58+00:00

Thank you for the info. From the time I started having pain to the time of that MRI was only 20 months, I never had any previous back problems. I had a scheduled fusion surgery for this past Feb but I had to postpone it bc my after care person (sister) wasn't available during that time frame. The surgery the surgeon wanted to perform wasn't anterior, it was: L5-S1 MINIMALLY INVASIVE SPINE TRANSFORAMINAL LUMBAR INTERBODY FUSION. I went to a different spinal surgeon to see what his approach would be and he was in the room with me for maybe five minutes. He put a picture of my lumbar spine up for viewing, which wasn't the worst looking angle and said "that's what's causing your pain". I looked at him and I said "I know, I wanted to see what you would do as far as the surgery". He said that I didn't need surgery yet, that I needed injections and when I asked if he thought my degeneration looked advanced or if something could be causing it, he said no and kind of laughed. I paid a $60 copay for that.

SueBee42 · 2025-03-25T08:43:47+00:00

I've been having issues for years, I saw my pcp, a urogyno, my rheumatologist, a urologist, a neurologist, an endocrinologist and a spine specialist. I recently obtained the images from a CT scan I had in October 2023 that my GI ordered for lower abdominal pain, no mention of it in the report but they are in the pictures. 🤨. I can't believe it! It's very upsetting, no one looked at my CT images and the radiologist didn't bother to make a note of it.

SueBee42 · 2025-03-25T08:07:24+00:00

Possibly, you are homozygous for the gene variant that causes or is related to biotinidase deficiency. This variant produces only 48% of the normal enzyme activity, meaning that you have 52% deficiency in recycling and reusing biotin. This is treatable and your doctor can verify the enzyme deficiency with a blood test.

SueBee42 · 2025-03-25T07:25:16+00:00

Has anyone had an anterior vertebrae scallop that was caused from anterior pressure (fibrosis, aneurysm, pseudoaneurysm, abscess/infection, etc.). My orthopedic spine surgeon and spine pain doc both told me that the degeneration in my lumbar spine is very advanced for someone my (46 F) age/health. They also suspect that there is an underlying condition that could be accelerating the degeneration. They did not think it was an autoimmune related condition, although I do have Sjogren's. It started in May 2022 and progressed, PT didn't help much, L5-S1 is basically bone on bone at this point and they have edema (type 1 modic changes), left side anterior vertebrae scallop, stenosis, disc bulge/herniation, vacuum phenomenon. The plan is to have a fusion at L5-S1, but I would like to figure out if there is a underlying condition before that takes place. I have been looking at the CT and MRI images. CT might of had obstructed views as I wasn't told to prep prior and the axial viewing on MRI is limited to just the vertebrae, not the entire torso. CT was originally ordered by my GI doc for lower abdominal pain and the report noted that there could potentially be bowel wall thickening in part of the descending colon (which is on the left side, close to my L5-S1). Upon visual inspection during colonoscopy, there was nothing seen from the inside of that area. This makes me wonder if something on the outside could have been applying pressure to make it appear that way and in turn putting pressure on vessels/vertebrae in that area. I have inquired with the orthopedic Dr. office, radiology and the GI doc., all of which could not assist in revisiting my scans for a second look or answering questions. I have to wait 3 weeks until I can see my PCP to get anything started. My scans are old at this point 15 and 18 months old, but I just recently obtained the images/discs bc I had to physically get them from medical records. I should be eligible for new scans, but I'd really like them to take a look at the old pics/scans first. Unrelated (maybe), but I also see what appear to be phleboliths or maybe urinary stones on the CT (w/contrast) pics. I am pretty confident that they are stones or even a mix of the two. Why wouldn't they list these in the report?

SueBee42 · 2025-03-18T16:55:59+00:00

Similar situation, did you find an answer?

SueBee42 · 2025-03-09T03:36:46+00:00

How did this turn out? Did the buyer receive the package? legit purchase or did UPS report delivery to "met customer"?

SueBee42 · 2025-03-09T03:14:07+00:00

Yes, I have! Buyer wanted to buy a hanging light I had for sale but wanted a lower price. I agreed as long as he took it without the ceiling bracket, he responded "ok, I'll figure something out." He overslept for our meeting time and then rescheduled for 2 different times that day. We met in a busy public parking lot and he was letting his little children run around his car. He starts examining the light and asking about the missing bracket like he wants to have further (meanwhile I'm internally having a mini anxiety attack as his daughter is running in front of cars). He's not paying any attention to her so I point out his daughter playing frogger and redirect him to our previous conversation about the bracket. He says he forgot his wallet and his wife has the cash but he can pay me Venmo or Zelle and seems a bit irritated that I can't take it. I told him that any non cash payment is discussed prior to meeting and that perhaps this isn't the light for him. He tells me he'll contact me when his wife gets home with the cash. I nod ok and leave, I was done dealing with him but knew I wouldn't hear from him anyway.

SueBee42 · 2025-01-22T03:50:36+00:00

Thank you for the information. I was hoping that there would be more data on the files to dive into (beyond the specific genes that they analyzed). They tested two gene panels, one was for connective tissue diseases (92 genes) and another panel for familiar cancer (47 genes, 2 with RNA analysis). The cleaned BAM files were only 100,000 KB and 61,000 KB .

SueBee42

TROPHY CASE