Skip to content

Commit

Permalink
Merge pull request #31 from monarch-initiative/textmining
Browse files Browse the repository at this point in the history
Textmining
  • Loading branch information
pnrobinson authored Jun 22, 2024
2 parents dbd3959 + f556d66 commit 8d966fa
Show file tree
Hide file tree
Showing 76 changed files with 2,537 additions and 269 deletions.
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -25,3 +25,4 @@ replay_pid*
/.idea/
/data/
/prompts/
/fenominal-mined.txt
15 changes: 15 additions & 0 deletions docs/cases/PMID_15673476.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
[source]
pmid = PMID:15673476
title = A novel heterozygous missense mutation in the UMOD gene responsible for Familial Juvenile Hyperuricemic Nephropathy
[diagnosis]
disease_id = OMIM:162000
disease_label = Tubulointerstitial kidney disease, autosomal dominant, 1
[text]
The proband is an affected female who was first evaluated at the age of 24, when she presented with a gout attack and hyperuricemia.
At age 27 she was told having renal failure. However, a renal biopsy was not performed.
At age 44, serum creatinine was 2.8 mg/dl and ultrasound imaging detected numerous renal cysts.
Renal disease slowly progressed and the patient reached ESRD when she was 49 years old.
Her father died at the age of 55 from ESRD and suffered from hyperuricemia and gout.
The proband's only son is also affected. At the age of 18 years he had a gout attack.
On the initial evaluation, serum uric acid was 15 mg/dl and serum creatinine 1.6 mg/dl.
Renal cysts were also detected on ultrasound examination.
11 changes: 11 additions & 0 deletions docs/cases/PMID_16962354.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
[source]
pmid = PMID:16962354
title = Functional analysis of mutations in TGIF associated with holoprosencephaly
[diagnosis]
disease_id = OMIM:142946
disease_label = Holoprosencephaly 4
[text]
A male proband presenting with lobar holoprosencephaly, atypical ventricles with small frontal horns,
hypothalamic and caudate fusion, diabetes insipidus, seizures,
premaxillary agenesis, microcephaly, absent nasal root and septum with a
depressed nasal tip (Fig. 1A and B).
43 changes: 43 additions & 0 deletions docs/cases/PMID_17661815.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,43 @@
[source]
pmid = PMID:17661815
title = Familial CHARGE syndrome because of CHD7 mutation: clinical intra- and interfamilial variability
[diagnosis]
disease_id = OMIM:214800
disease_label = CHARGE syndrome
[text]
Patient A III-2 is the second boy of non-consanguineous French parents, respectively, aged 30 and 29 years, at the time of conception.
The pregnancy was characterized by polyhydramnios from the 26th week of gestation.
Delivery took place after 38 weeks by caesarean section with normal birth weight (BW) (3025 g, 50th centile), birth length (BL)
(48 cm, 25th centile) and head circumference (OFC) (34.5 cm, 50th centile). MCA noted at birth included esophageal atresia with tracheoesophageal fistula,
bilateral cleft lip and palate, large ventricular septal defect, dextroposition of aorta, atresia of the brachiocephalic trunk,
malacia of the right main bronchus, costovertebral abnormalities (bifid fourth dorsal vertebrae, duplication of the fourth right rib,
and spina bifida occulta from the seventh to the ninth dorsal vertebrae) and left cryptorchidism.
Axial control acquisition was delayed as he sat at the age of 11 months, walked at 22 months.
Balance problems persisted for several years. Recurrent otitis media, responsible for conductive hearing loss,
required bilateral tympanostomy tubes. First words were delayed till 30 months. Learning disabilities and writing difficulties
were confirmed when he was 8 year. When referred to the genetic department at the age of 15 years,
he was 151 cm tall (−2 SD ), weighted 40 kg (−2 SD), and had an OFC of 52 cm (−2 SD).
At that time, he had a long face with prominent chin, small mouth, high nasal bridge and triangular shape of right concha
(Fig. 1). He had postural instability. Vestibular testing showed absence of response on canal function test with residual otolith
function and residual left vestibulospinal responses on vestibular evoked myogenic potential test.
Magnetic resonance imaging (MRI) examination showed hypoplastic superior and lateral semicircular canals (SCC) in the right ear
and aplastic superior and hypoplastic lateral SCC in the left ear (Fig. 2). The vestibulae and the cochleae were normal.
Facial and vestibulo-cochlear nerves were present on both sides. Brain MRI revealed a hypoplastic internal left carotid artery.
There was no evidence for arhinencephaly. He had mild convergent strabismus, discrete myopia and posterior embryotoxon.
Funduscopic examination revealed hypoplastic papillae. Using WISC IV scale at age 15 years his verbal conceptual index (VCI) was 78,
perceptual reasoning index (PRI) 58, working memory index (WMI) 62 and processing speed index (PSI) 81.
[text]
Patient B III-1 is the first child from healthy unrelated Caucasian parents. Mother and father were both 26 years old at time of conception.
Cerebral ventricular dilatation was suspected on pre-natal ultrasound but not confirmed by fetal cerebral MRI.
Fetal karyotype was normal (46, XY). Premature labor occurred and delivery took place at a gestational age of 35 weeks.
BW was 2050 g (third centile); BL 46.5 cm (50th centile) and OFC 34 cm (90th centile). He had cup-shaped ears with missing earlobes,
right facial palsy, bifid uvula and mild retrognathism (Fig. 4) with associated cryptorchidism and global hypotonia.
Swallowing difficulties with poor feeding were noted. Laryngoscopy revealed left vocal cord palsy.
An atrial septal defect was diagnosed by echocardiography. Fundoscopy showed right retinal coloboma.
Brainstem electric response audiometry identified a sensorineural deafness, visual evoked potentials were in the normal range.
Metabolic work-up did not show any anomaly. This boy died on day 19 after refractory convulsive episodes starting on day 4.
Encephalopathy and hydrocephaly were subsequently noted, as post-natal cerebral MRI (day 7) showed quadriventricular enlargement
because of bloody effusion in occipital horns without any underlying vascular malformation. On autopsy,
brain external examination revealed the absence of olfactory bulbs with a thin corpus callosum.
On microscopic exam, cranial nerve roots were normal. Deep cerebellar heterotopia was present.
Complete macroscopic and microscopic examinations were otherwise normal except for the presence of testis in the inguinal canals.
39 changes: 39 additions & 0 deletions docs/cases/PMID_19208399.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
[source]
pmid = PMID:19208399
title = A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia
[diagnosis]
disease_id = OMIM:167320
disease_label = Inclusion body myopathy with early-onset Paget disease and frontotemporal dementia 1
[text]
Patient II-3. At the age of 41 years, the
male index patient developed slowly progressive symmetric muscle weakness, which started in the proximal upper limb muscles
but is now most pronounced in the proximal leg muscles. Three years
after onset he noticed increasing hearing impairment and bone pain. Elevated plasma levels of the
bone-specific alkaline phosphatase isoenzyme (168 g/L, normal 8 –17) in combination with typical
changes on a 99mTc total body bone scan suggested
a diagnosis of PDB. Biphosphonate treatment was
initiated and led to improvement of bone pain and a
marked reduction of alkaline phosphatase.
The muscle weakness, however, continued to increase, and
eventually the patient became unable to walk more
than 30 meters unaided. On examination, there was
proximal weakness and atrophy of the limb muscles
with bilateral scapular winging and a positive Trendelenburg sign. He had a waddling gait and required
the support of two crutches. The patient’s wife had
recently noticed an impaired capability of her husband to recognize faces of persons known to him. In
addition, he had become apathetic and had lost
interest in previous hobbies. Plasma creatine kinase
(CK) levels were mildly elevated. Nerve conduction
studies were normal, but electromyographic studies
showed moderate myopathic changes with fibrillation potentials and polyphasic small-amplitude,
short-duration motor unit potentials. Neuropsychological evaluation (DemTect, frontal assessment battery)
did not show significant cognitive impairment. Audiometry revealed moderate left-sided
perceptive deafness of 50 dB HL. Cranial magnetic
resonance imaging (MRI) showed bony changes typical of Paget disease, but no evidence of auditory
nerve compression due to Paget disease. Intracranial
findings were normal without signs of frontal lobe
atrophy. A muscle biopsy from the quadriceps muscle revealed moderate histopathological changes
consisting of angulated and atrophic fibers with a
few inclusion bodies, but no rimmed vacuoles. The
inclusions were ubiquitin-positive, but they were negative for beta-amyloid. Ubiquitin-positive inclusions
could also be demonstrated in the nucleus of myocytes, endothelial cells, and fibroblasts.
18 changes: 18 additions & 0 deletions docs/cases/PMID_20149460.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
[source]
pmid = PMID:20149460
title = A novel mutation in the signal transducer and activator of transcription 3 (STAT3) gene, in hyper-IgE syndrome
[diagnosis]
disease_id = OMIM:147060
disease_label = Hyper-IgE syndrome 1, autosomal dominant, with recurrent infections
[text]
A 12-year-old Greek girl was admitted because of fever, and cough for a week. Her parents were not consanguineous.
She had no remarkable perinatal problems and had been vaccinated as scheduled. She had a history of atopic dermatitis since 6 months of age.
Past medical history also revealed recurrent infections, including multiple episodes of skin abscesses and pneumonia.
She had a history of two hospitalizations for pneumonia with cyst formation in the right lung and numerous visits at the
clinic for the treatment of skin abscesses caused by Staphyloccocus aureus. Family history revealed no members with relevant allergic or immunologic diseases.
On physical examination, her height was 118 cm (under the 5th percentile), and her weight was 25.8 kg (under the 5th percentile).
She had coarse facial features with facial asymmetry, and prominent forehead. She was also diagnosed with scoliosis with maximal curvature of 14°.
Complete blood cell counts demonstrated a high total eosinophil count (max 4000 cells/μl).
The serum IgE level was increased at 74.000 IU/ml. All other laboratory data examined, such as serum immunoglobulin level,
the oxidative burst of granulocytes and complement components, were normal with the exception of slightly increased IgD titer (300 mg/l).
Lymphocyte subset analyses revealed normal levels of both CD4+ and CD8+ T cells (883 and 850 cells/μl, respectively).
26 changes: 26 additions & 0 deletions docs/cases/PMID_20932317.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
[source]
pmid = PMID:20932317
title = Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature
[diagnosis]
disease_id = OMIM:182290
disease_label = Smith-Magenis syndrome
[text]
Case 1
SMS324 is an 18-year-old male who was delivered at 38 weeks gestation following premature labor and antepartum haemorrhage.
His birth weight was 2,750 g (10th-50th centile). While his neonatal period was complicated by gastroesophageal reflux
and failure to thrive, he was admitted to the hospital at 1 year of age for being considerably overweight, with fat folds
on his arms and legs. He spoke his first words at 6 months and walked at 12 months. His medical history includes two
episodes of severe asthma, petit mal seizures between the ages of 5-10 y and three spontaneous pneumothoraces (SP).
He had a square shaped face, upslanting palpebral fissures, down turned mouth, inverted upper lip, and synophrys (Fig. 1A).
Other physical anomalies included brachydactyly, bilateral fifth finger clinodactyly with
a small middle phalanx of his fifth fingers, and pes planus. At 16 years of age, height was 163 cm (< 3rd centile),
head circumference was 54 cm, and he presented with relative truncal obesity.
Behaviorally, SMS324 exhibited head-banging and rage attacks starting at age 3.
At age 16, he continues to have recurrent episodes of rage attacks, anxiety, and obsessional behavior.
He has never slept through the night, with recurrent 3 a.m. wakenings.
Apart from finger chewing, he exhibits no self-injurious behaviors, self hugging, onychotillomania or polyembolokomania.
He has had a persistent history of sleep disturbance.
A formal developmental assessment indicated a mild global developmental delay.
He was initially diagnosed with attention deficit disorder;
however, a later assessment indicated this diagnosis was incorrect.
He was initially mainstreamed in a regular classroom at school but at age 16 now functions in an OI classroom with supervision.
Loading

0 comments on commit 8d966fa

Please sign in to comment.