MEDICAL RECORDS

Over 200 pages of medical records, including Previous genetic results, Blood work and Clinical labs.

The patient has made his data available under the MIT License. [Note: access to data is limited to invited participants].

  1. Gene DX Test Results.

  2. Smith Family Clinic - 1.

  3. Smith Family Clinic - 2.

  4. Baylor Genetics Workups.

  5. New York Presbyterian Chart.

  6. Columbia Undiagnosed Program.

  7. Hudson Alpha Lab Results.

INSTRUMENT DATA

1) Long Read Whole Genome - Provided by Invitae and PacBio.

  • Instrument: PacBio Sequel.

  • Data Types: FASTQ, (BAM/VCF TBD).

  • Data Details: TBD Sequel performance metrics. 

2) Short Read Whole Genome - Provided by Invitae.

  • Instrument: Illumina Novaseq.

  • Data Types: FASTQ, (BAM/VCF TBD).

  • Data Details: ~40x coverage; Paired End 150bp reads; PCR-free.

3) Exome - Provided by Invitae.

  • Instrument: Illumina Novaseq.

  • Data Types: FASTQ, BAM, VCF.

  • Data Details: Paired End 150bp reads; Insert size ~300bp; ~150x Median Coverage.

4) Targeted Panel - Provided by Invitae.

  • Instrument: Illumina Novaseq.

  • Data Types: FASTQ, BAM, VCF.

  • Data Details: Paired End 150bp reads; Insert size ~300bp; ~350x Median Coverage.

CASE BACKGROUND SUMMARY

As a baby, the patient, “JCM” reports a history of vomiting after breastfeeding and FTT. Since childhood, he has had significant issues gaining weight despite adequate caloric intake, though his height has always remained on the curve. As a child, he reports a history of nausea, stomach aches and an overall aversion to food. He remembers having minimal muscle mass and being easily fatigued.

His GI issues became more severe in his 20’s when he began to have daily lower abdominal pain characterized by burning and nausea. He also began to have abdominal distension with minimal food intake. He was diagnosed with visceral hypersensitvitiy. During his 20’s he also developed chronic vomiting daily and vomited as many as 5 times per day. He had extensive workup including multiple EGDs, small bowel xray series, CT enterography, capsule endoscopy, nuclear gastric emptying studies and antral duodenal motility study. Findings have been notable for delayed gastric emptying, question of gastroparesis based on antral duodenal motility study, duodenal ulcer, and mild increase in IELs on full thickness jejunal biopsy. He saw an ENT to address his vomiting was told that his uvula was causing the episodes and had it removed. JCM reports that since then he no longer experiences vomiting, though it has not resolved his other GI issues.

Currently his height is 5’10” and weight is 109lbs. The heaviest he has been is ~124lbs, which he reports was when he was frequently using cannabis and taking benzodiazepines. Due to his low weight he has very limited muscle mass and is easily fatigued. He reports pain and weakness in his knees and has had a couple disc herniations as well as shoulder dislocations. He has attempted to build muscle mass on occasion with lifting and protein, but this has not been successful due to GI issues and pain.

JCM has tried many medications including PPIs, H2 blocker, low dose E-Mycin, Baclofen, Cymbalta, Nortriptyline, Amitriptyline, Mirtazepine, Zofran, Remeron, Etopiride, Cinetopride, Lyrica, Gabapentin, Benzodiazepines, prednisone and IVIG. He reports that the benzodiazepines helped the most with his abdominal pain and burning, however, he did not like the other side effects and has not taken this medication for several years. He also tried adipose stem cells and had significant improvement in his muscle tone and mobility, but this wore off in a year. He also reports undergoing two fecal transplants that he administered to himself and were not overseen by a physician and he did not get any symptom relief.

He has also had extensive biochemical evaluations and genetic testing. Biochemical evaluations in the past were revealing for increased urinary lactate. Serum markers have been inconsistent, with high ethylmalonic acid and mild metabolic alkalosis. Whole exome sequencing was revealing for multiple variants of uncertain significance as summarized below. Based on the variants in his ALDOB gene he was told that he might have HFI and abided by a strict diet for over a month with no improvement in symptoms.

Review of systems is otherwise notable for frequent urination and constant pelvic discomfort. JCM does not report pain when urinating, and instead reports burning pain in his abdomen. He has never had a full urology evaluation. He reports a history of frequent fungal infections on his chest and multiple plantar warts. He had a normal cardiology workup including normal echo and stress test.