FUKUYAMA CONGENITAL MUSCULAR DYSTROPHY # Colorectal cancer, hereditary nonpolyposis # Meckel syndrome, type 1 #249000

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1 Supplementary Table 1 A randomly selected subset of 100 record pairs crossreferenced by the curators. To be sure the 7,000 cross referenced records in fact were pairs of highly overlapping phenotypes, we manually cuated a random subset of 100 record pairs. This investigation shows that 94 of the record pairs had a high degree of phenotypic overlap. 94 our of 100 record pairs are true positives (TP) (i.e., record pairs cross-referenced because of a high degree of phenotypic overlap. 6 record pairs were false positives (FP) (i.e., record pairs that were cross-referenced for other reasons than a high degree of phenotypic overlap). Based on this investigation we concluded that the full set of 7,000 pairs could be used as a benchmarking reference for the phenotype similarity score. In the table we have included a comment stating why there is a phenotypic overlap. If the text regarding the overlap is very clear, or the overlap is obvious, we have not included a reference to Pubmed, but simply stated as the reference. If the overlap is not obvious, or the statements in were ambiguous, we referenced one or more articles describing the phenotypic overlap. Disease ( ID) Disease (OMIN ID) Comment Pubmed ID Walker-Warburg Muscular, congenital, mental retardation included # Muir-Torre # Bardet-Biedl # Achalasia-Addisonianism- Alacrima # Knobloch # Blood group, Froese # Granulomatous disease, cytochrome b-positive # Glaucoma 1, open angle, A # FUKUYAMA CONGENITAL MUSCULAR DYSTROPHY # Colorectal cancer, hereditary nonpolyposis # Meckel, type 1 # Addison disease and cerebral sclerosis # Knobloch, type II % Blood group, Diego system # Granulomatous disease, cytochrome b-negative # Glaucoma 1, open angle, C % and loci of Muscular and mental retardaion TP: Muir-Torre is a subtype of Colorectal cancer, hereditary nonpolyposis TP: cystic kidney dysplasia and polydactyly occurs in both s TP: The association of adrenal and neurologic disease in # is similar to that in # and loci of Knobloch TP: Blood group Froese is part of the Diego system. Same molecular basis. Antigen polymorphism is based on a change in the SLC4A1 gene and loci of Granulomatous disease Glaucoma Reis-Bucklers Corneal Thiel-Behnke Corneal

2 # % and loci of Corneal Hypophosphatemic rickets # Mullerian Aplasia # Situs invertus viscerum # Hypertension with brachydactyly % Primary lateral sclerosis # Cataract, nonnuclear congenital % Epidermolysis bullosa dystrophica # Rett # FG including partial agenesis of corpus callosum % Medullary cystic kidney disease 1 % Dent disease 1 (Nephrolithiasis, hypercalciuria) # Maturity-onset diabetes of the young 1 # Primary ciliary dyskinesia # Brachydactyly, type E # Spastic paralysis # Cataract, embryonic nuclear # Epidermolysis bullosa simplex # Incontinentia pigmenti # Corpus callosum, partial agenesis # Polycystic kidney disease # TP: Hypophosphatemic rickets is a form of hypercalciuric nephrolithiasis, Dent disease complex TP: Mullerian Aplasia like MODY1 is characterized by frequent complications of diabetic nature including effects on the kidneys. Both conditions caused by mutations in transcription factors influencing e.g. insulin transcription TP: Two associated diseases making up Kartagener # TP: Two forms and loci of brachydactyly and hypertension TP: lateral sclerosis and spastic paralysis are allelic disorders with overlapping phenotypes but associated with same loci and loci of Epidermolysis bullosa TP: Some times Rett co-occurs with incontinentia pigmenti TP: Phenotypically overlapping diseases TP: Two different form and loci of cystic kidney disease Nanophthalmos 1 Nanophthalmos 2 % # Nanophthalmos Spondyloepimetaphyseal Spondyloepimetaphyseal dysplasia with multiple dysplasia, sponastrime and loci of dislocations % type Spondyloepimetaphyseal % dysplasia Noncompaction of left Noncompaction of left

3 ventricular myocardium, 1 # Periodic paralysis, potassium-sensitive # Craniosynostosis, midfacial hypoplasia and foot abnormalies # Preeclampsia/eclampsia 3 % Gastric cancer # Colorectal cancer # Moyamoya disease 3 % disease 6 # Premature ovarian failure 1 % Pseudohypoaldosteronism, type 1 # Specific granule deficiency # Osteosarcoma # Ichthyosis, lamellar 1 # von Hippel-Lindau # Arthrogryposis, type 5 % Dementia with spastic ataxia # ventricular myocardium, 2 % Hypokalemic periodic paralysis # Apert # Preeclampsia/eclampsia 1 % Helicobacter pylori infection # Endometrial cancer # Moyamoya disease 1 % disease 1B # Addison disease % Pseudohypoaldosteronism, type II # Chediak-Higashi # Chondrosarcoma # Ichthyosis, lamellar 2 # Pheochromocytoma # Arthrogryposis, type 2B # Creutzfeldt-Jakob disease # Noncompaction of left ventricular myocardium and loci of periodic paralysis and loci of craniosynostosis and loci of Preeclampsia/eclampsia TP: Helicobacter pylori infection is an established risk factor of gastric cancer, however gastric cancer occurs in only a very small proportion of people infected with the organism TP: Endometrial cancer is often co-occurring with colorectal cancer Moyamoya disease and loci of Charcot-Marie- Tooth disease TP: Premature ovarian failure occasionally occur in patients with Addison disease and loci of Pseudohypoaldosteronism TP: Both disorders characterized by severe defensin deficiency and loci of sarcoma and loci of Ichthyosis TP: Pheochromocytomas most commonly occur as part of several s including von Hippel- Lindau and loci of Arthrogryposis TP: Overlapping phenotypes. Dementia and another form of ataxia

4 Coffin-Siris % Systemic lupus erythematosus 7 % Pancreatic carcinoma # Pseudovitamin D3 deficiency Rickets due to 25-hydroxylase deficiency # Ceroid lipofuscinosis, neuronal 6 # Thyrotoxic periodic paralysis # Pilomatrixoma # Myopathy, myofibrillar, desmin-related # Hyperthyroidism # disease dominant intermediate D # Glioma of brain # Congenital alopecia # Hypomagnesemia 2 # Biotinidase deficiency # Systemic lupus erythematosus # Peutz-Jeghers # Vitamin D-dependent Rickets type 1 Ceroid lipofuscinosis, neuronal 3 # Hashimoto thyroiditis % Rubinstein-Taybi # Myopathy, myofibrillar, myotilin-related # Hypothyroidism # disease dominant intermediate A % Cowden disease # Omenn # Hypomagnesemia with secondary hypocalcemia # is part of the clinical synopsis for Creutzfeldt- Jakob disease. TP: Case report identifying an association between the two diseases TP: Different loci of Systemic lupus erythematosus TP: Increased risk of pancreatic cancer in patients with Peutz- Jeghers and loci of Vitamin D- dependent Rickets and loci of Ceroid lipofuscinosis, neuronal TP: Two phenotypically overlapping diseases TP: Occurrence of pilomatrixomas in Rubinstein-Taybi and loci of Myopathy FP: Both conditions can be caused by mutations in TSHR, but clinical phenotypes have little overlap and loci of Charcot-Marie- Tooth disease FP: From abstract, the patient did not show any of the clinical signs of Cowden disease. TP: Two sisters with congenital alopecia # Alopecia is highly frequent in Omenn and loci of Hypomagnesemia Craniosynostosis, Type 1 Greig TP: Craniosynostosis is

5 % cephalopolysyndactyly # Chondrodysplasia punctata 2 # Pancreatic insufficiency and bone marrow dysfunction # Muscular, Type 1 F % Attention deficithyperactivity disorder 2 % Albright hereditary osteo # Major affective disorder 1 % Malignant hyperthermia 1 # Cataract, anterior polar 2 % Prostate cancer aggressiveness QTL % Parkinson disease 9 % Hypertension # Epilepsy, with mental retardation. % Asphyxiating thoracic % Muscular, Type 1 A # Attention deficithyperactivity disorder 1 % Major affective disorder % Major affective disorder 2 % Malignant hyperthermia 4 % Cataract, anterior polar 1 % Prostate cancer # Pallidopyramidal % Pseudohypoaldosteronism 1 # part of the clinical synopsis of Greig cephalopolysyndactyly, although craniosynostosis is described three times in the literature as NOT being part of Greig cephalopolysyndactyly , , TP: Several reports where Chondrodysplasia punctata and epilepsy/mental retardations are connected TP: Skeletal abnormalities part of both diseases and loci of Muscular Attention deficithyperactivity disorder FP: The link of the diseases are due to their mode of inheritance Major affective disorder Malignant hyperthermia anterior polar cataract Prostate cancer TP: clinical features similar to those of idiopathic Parkinson disease and Pallidopyramidal FP: Opposite clinical phenotypes. However, both conditions are caused by changed renal tubular Na+ absorption (hypertension: increased. PHA-1: decreased)

6 Spinocerebellar ataxia 2 # Amyloidosis corneal # Globoid cell leuko # Granunomatous disease, x-linked # Lymphedema-Distichiasis # Celiac disease susceptibility to 1 # GM2-gangliosidosis type II # Inflammatory bowel disease 2 % Episodic ataxia, type 1 # Brachydactyly, type A1 # Usher, type IIB % Craniofacial-deafnesshand # Major depressive disorder # Waardenburg type IIA # Spinocerebellar ataxia 6 # Amyloidosis V # Metachromatic leuko # Duchenne muscular # Lymphedema, hereditary II # Celiac disease susceptibility to 3 # Gaucher disease type 1 # Inflammatory bowel disease 1 # Episodic ataxia, type 2 # Brachydactyly, type A1, B % Usher, type IIA # Waardenburg, type 1 # Major depressive disorder 2 % Waardenburg type IIB % and loci of Spinocerebellar ataxia TP: Two forms and loci of amyloidosis TP: Two forms and loci of leuko FP: Case study. One patient had 3 x-linked disorders incl. Granunomatous disease and Duchenne muscular. Deletion of part of Xp21 TP: Allelic disorders with overlapping phenotypes include Lymphedema type II Celiac disease TP: Gaucher disease, a related disorder that involves glycosphingolipid storage in peripheral tissues but not in the central nervous system Inflammatory bowel disease and loci of Episodic ataxia Brachydactyly, type A1 and loci of Usher type II TP: Several overlapping clinical traits between the diseases. Major depressive disorder and loci of Waardenburg Orofacial cleft TP: Many phenotypically overlapping features Orofacial cleft 5 # Orofacial cleft 1 % Thanatophoric dysplasia Asphyxiating thoracic # % Night Blindness, congenital Aland Island eye disease TP: congenital stationary

7 type 1 # % night blindness and Aland Island eye disease could be considered as a single entity disease type 2A1 # Myopia 12 % Migraine, familial typical, 2 % Dyslexia, susceptibility to 1 # Chordoma % Granulomatous disease, cronic, x-linked # Ulcerative colitis # Velocardiofacial # Hair color 3 % Alopecia-mental retardation % Epilepsy, idiopathic generalized # Hereditary myopathy with early respiratory failure # Wolfram 1 # Pancreatic carcinoma # disease type 2A2 # Myopia 2 % Migraine with or without aura, 1 % Dyslexia, susceptibility to 8 % Tuberous sclerosis complex # Granulomatous disease, cronic, autosomal recessive # Inflammatory bowel disease 2 % Asperger 1 % Eye color 3 % Hair-brain # Epilepsy, grand mal seizures on awakening # Duchenne muscular # Wolfram 2 % Melanoma, cutaneous malignant % and loci of Charcot-Marie- Tooth disease and loci of Myopia and loci of Migraine and loci of Dyslexia TP: identified 3 reports of chordomas found in patients with tuberous sclerosis complex TP: Two forms and loci of Granulomatous disease and loci of inflammatory bowel disease TP: VCF is caused by mutation in TBX1. There is evidence for that TXB1 haploinsufficiens may cause psychiatric disorders like ASP-1, although based only on casuistic reports TP: Association study shows the two traits are significantly inherited together TP: Overlapping phenotypes; mental retardation and abnormal hair growth. and loci of epilepsy and loci of myopathy Wolfram TP: Several familial cancer s increase the risk of

8 Piebald trait # Glaucoma 1, open angle, A # Oral-facial-digital IX % Hydranencephaly, fowler type % Vitamin D-dependent rickets type II % Cholestasis, progressive familial intrahepatic 2 # Vohwinkel # Fanconi anemia # Glaucoma 1, open angle, J % Oral-facial-digital II % Fetal akinesia deformation sequence (FADS) % Vitamin D-dependent rickets type I # Cholestasis, progressive familial intrahepatic 1 # Vohwinkel with ichthyosis # pancreatic cancer TP: White forelock and patches leukoderma occur also in Fanconi anemia Glaucoma 1, open angle and loci of Oral-facialdigital TP: Case study, both diseases included and loci of Vitamin D- dependent rickets and loci of Cholestasis, progressive familial intrahepatic and loci of Vohwinkel