Tuesday, September 18, 2007

List of inherited syndromes associated with neoplasms

I've been trying to assemble a list of inherited conditions that carry an heightened risk of developing one or more neoplasms. The following are syndromes collected from OMIM (Online Mendelian Inheritance in Man) and each item is preceded by the OMIM identifier number. If anyone thinks that any of these items should be omitted or knows of additional items that should be added, please post them as a comment to this blog.

Familial syndromes associated with neoplastic development.

-1010000 Acoustic schwannomas bilateral

-1026600 Adamantinoma of long bones

-1027000 Severe combined immunodeficiency due to ada deficiency

-1035800 Albright hereditary osteodystrophy

-1056000 Anemia with multinucleated erythroblasts erythroreticulosis hereditary benign included

-1060700 Angioma hereditary neurocutaneous spinal arterial venous malformations with cutaneous hemangiomas included

-1062000 Aniridia

-1064000 Ankylosing vertebral hyperostosis with tylosis diffuse idiopathic skeletal hyperostosis included

-1074000 Serpina1 alpha-1-antitrypsin deficiency autosomal recessive included

-1093500 Gastroesophageal reflux pediatric adenocarcinoma of esophagus included

-1093900 Basal cell carcinomas with milia and coarse sparse hair

-1094000 Basal cell nevus syndrome

-1122000 Blue rubber bleb nevus

-1122500 Diaphyseal medullary stenosis with malignant fibrous histiocytoma

-1137050 Brca1 breast cancer type 1 included

-1139700 Burkitt lymphoma

-1140300 Cafe-au-lait spots multiple

-1144000 Lynch cancer family syndrome ii

-1153100 Carotid body tumors and multiple extraadrenal pheochromocytomas

-1168600 Cerebral capillary malformations cerebral cavernous malformations 1 included

-1175500 Sotos syndrome

-1182000 Charcot-marie-tooth neuropathy type 1b

-1183500 Chemodectoma intraabdominal with cutaneous angiolipomas

-1184500 Alagille-watson syndrome

-1188650 Choroidal osteoma bilateral

-1204350 Colorectal cancer hereditary nonpolyposis type 1

-1240300 Debrisoquine 4-hydroxylase codeine ultrarapid metabolism of included

-1240800 Aldosterone deficiency due to deficiency of 18-hydroxysteroid dehydrogenase included

-1242000 Keratosis follicularis (darier disease)

-1263370 Dna damage-inducible transcript 3 (gadd153 myxoid liposarcoma and chop/fus fusion gene included)

-1306500 Wiedemann-beckwith syndrome

-1311000 Multiple endocrine neoplasia type i

-1314400 Myeloproliferative disorder chronic with eosinophilia

-1314450 Ependymoma familial

-1326000 Pilomatrixoma

-1327000 Cylindromatosis familial

-1328100 Diphenylhydantoin defect lymphoproliferative disorders susceptibility to included

-1331000 Polycythemia familial

-1331800 Erythroleukemia familial

-1334500 Ews gene neuroepithelioma peripheral included

-1335100 Xeroderma pigmentosum complementation group b

-1337000 Exostoses multiple type i

-1351500 Birt-hogg-dube syndrome fibrofolliculomas with trichodiscomas and acrochordons

-1353000 Fibromatosis gingival hereditary

-1373570 Genitourinary dysplasia component of wagr syndrome

-1373600 Genochondromatosis

-1375500 Giant pigmented hairy nevus

-1375750 Gigantiform cementoma familial

-1378000 Glioma of brain familial glioblastoma multiforme included

-1388000 Goiter nontoxic with intrathyroidal calcification

-1410000 Hemangioma-thrombocytopenia syndrome kasabach-merritt syndrome

-1429810 Homeobox d4 hoxd4 acute lymphoblastic susceptibility to included

-1447000 Renal carcinoma familial associated 1 included

-1465100 Pallister-hall syndrome hypothalamic hamartoblastoma hypopituitarism imperforate anus and postaxial polydactyly

-1480000 Kaposi sarcoma

-1485000 Tylosis with esophageal cancer

-1490000 Klippel-trenaunay-weber syndrome angioosteohypertrophy syndrome

-1506990 Leiomyoma uterine

-1508000 Leiomyoma hereditary multiple of skin

-1516230 Li-fraumeni syndrome 1

-1534800 Bannayan-zonana syndrome macrocephaly pseudopapilledema and multiple hemangiomata bannayan-riley-ruvalcaba syndrome included

-1535500 5q- syndrome macrocytic anemia refractory due to 5q deletion

-1552400 Thyroid carcinoma familial medullary

-1556000 Dysplastic nevus syndrome hereditary b-k mole syndrome

-1583200 Muir-torre syndrome cutaneous sebaceous neoplasms and keratoacanthomas multiple with gastrointestinal and other carcinomas

-1583500 Cowden syndrome multiple hamartoma syndrome lhermitte-duclos disease included

-1595500 Myelocerebellar disorder

-1595550 Myeloid/lymphoid or mixed lineage leukemia trithorax drosophila homolog of mll/fbp17 fusion gene included

-1609800 Carney myxoma-endocrine complex carney syndrome

-1615500 Nasopharyngeal carcinoma

-1620910 Neurilemmomatosis congenital cutaneous

-1622000 Neurofibromatosis type i

-1622200 Nf3b

-1622400 Neurofibromatosis-pheochromocytoma-duodenal carcinoid syndrome

-1623000 Neuromata mucosal with endocrine tumors

-1630000 Nevi flammei familial multiple

-1632000 Linear sebaceous nevus syndrome

-1643300 Odontoma-dysphagia syndrome

-1660000 Osteochondromatosis

-1669500 Ovarian teratoma

-1680000 Paragangliomas familial 1

-1695450 Pelvic lipomatosis with crossed renal ectopia

-1714000 Multiple endocrine neoplasia type ii pheochromocytoma and amyloid-producing medullary thyroid carcinoma

-1714200 Pheochromocytoma--islet cell tumor syndrome

-1748000 Albright syndrome polyostotic fibrous dysplasia

-1750500 Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome

-1751000 Adenomatous polyposis of the colon apc

-1752000 Peutz-jeghers syndrome

-1764500 Sacral agenesis hereditary with presacral mass anterior meningocele and/or teratoma and anorectal malformation included

-1802000 Retinoblastoma

-1802950 Rhabdomyosarcoma embryonal 2

-1845000 Steatocystoma multiplex

-1866000 Syringomas multiple

-1873000 Telangiectasia hereditary hemorrhagic of rendu osler and weber

-1884000 Digeorge syndrome

-1884700 Thyroid carcinoma follicular

-1885500 Familial nonmedullary thyroid cancer

-1903450 Trichoepitheliomas multiple desmoplastic

-1906850 Leukemia megakaryoblastic of down syndrome

-1911000 Tuberous sclerosis

-1933000 Von hippel-lindau syndrome
-1940700 Wilms tumor 1

-1940800 Denys-drash syndrome nephropathy wilms tumor and genital anomalies

-1944000 Xeroderma pigmentosum autosomal dominant mild

-2019100 Adrenal hyperplasia congenital due to 21-hydroxylase deficiency

-2065500 Angiolipomatosis familial

-2089000 Ataxia-telangiectasia

-2109000 Bloom syndrome

-2119800 Lung cancer alveolar cell carcinoma included

-2276500 Fanconi anemia

-2285500 Fibromatosis congenital generalized

-2311000 Hemochromatosis neonatal

-2352000 Hemochromatosis

-2464000 Histiocytosis x acute disseminated

-2464700 Leukemia acute myelocytic with polyposis coli and colon cancer

-2544500 Myelofibrosis familial

-2547000 Myeloproliferative disease autosomal recessive

-2567000 Neuroblastoma

-2595000 Osteogenic sarcoma

-2595500 Osteoid osteoma

-2605000 Choroid plexus papilloma

-2633000 Polycythemia vera

-2670000 Nephroblastomatosis fetal ascites macrosomia and wilms tumor

-2677000 Hemophagocytic reticulosis familial

-2699500 Sideroblastic anemia autosomal

-2731200 Teratoma pineal

-2733000 Testicular tumors teratoma testicular included

-2763000 Turcot syndrome malignant tumors of the central nervous system associated with familial polyposis of the colon

-2787000 Xeroderma pigmentosum i

-3001470 Prostate cancer hereditary x-linked

-3018450 Follicular atrophoderma and basal cell carcinomas

-3053500 Epidermodysplasia verruciformis x-linked

-3082400 Lymphoproliferative disease x-linked

-3083000 Incontinentia pigmenti familial male-lethal type

-3089400 Leiomyomatosis esophageal and vulval with nephropathy

-3128200 Sarcoma synovial x-chromosome-related 1

-3128700 Dysplasia gigantism syndrome x-linked

-6000480 Breast cancer 11-22 translocation associated

-6000800 Myelocytic leukemia-like syndrome familial chronic

-6001390 Subependymoma

-6001850 Brca2 breast cancer type 2 included

-6001950 Venous malformations multiple cutaneous and mucosal

-6002580 Mismatch repair gene pmsl1 colorectal cancer hereditary nonpolyposis type 3 included

-6003760 Osler-rendu-weber syndrome 2

-6005420 Chondrosarcoma myxoid extraskeletal fused to ews

-6006780 Gtbp colorectal cancer hereditary nonpolyposis type 5 included

-6012230 Nid2

-6012280 Polyposis syndrome mixed hereditary

-6013210 Noonan-neurofibromatosis syndrome

-6013470 Myelodysplasia immunodeficiency facial dysmorphism short stature and psychomotor delay

-6013590 Sebaceous nevus syndrome and hemimegalencephaly

-6013630 Familial wilms tumor 1

-6013990 Platelet disorder familial with associated myeloid malignancy

-6015180 Prostate cancer hereditary 1

-6015830 Wilms tumor 5

-6016060 Trichoepithelioma multiple familial

-6016500 Glomus tumors familial 2

-6018030 Pallister-killian syndrome

-6018590 Canale-smith syndrome autoimmune lymphoproliferative syndrome type i autosomal dominant autoimmune lymphoproliferative syndrome type ia included

-6020890 Hemangioma capillary infantile

-6024500 Severe combined immunodeficiency with sensitivity to ionizing radiation

-6025960 Pancreatic lymphoma familial

-6033720 Thyroid carcinoma with thyrotoxicosis included

-6034390 Expansile bone lesions

-6035540 Reticuloendotheliosis familial with eosinophilia

-6036410 Neuroendocrine carcinoma of salivary glands sensorineural hearing loss and enamel hypoplasia

-6036560 Exostosis dupuytren subungual

-6036690 Eccrine syringofibroadenomatosis with eyelid abnormalities

-6036700 Blue nevi familial multiple

-6036880 Prostate cancer/brain cancer susceptibility

-6037370 Ovarian germ cell cancer

-6037440 Papillary thyroid microcarcinoma

-6042870 Carney triad

-6042870 Gastric leiomyosarcoma pulmonary chondroma and extraadrenal paraganglioma

-6043700 Epithelial ovarian cancer

-6043730 Checkpoint kinase 2 s. pombe homolog of breast and colorectal cancer susceptibility to included

-6044420 Nonpapillary renal carcinoma 1

-6044510 Basal cell carcinoma with follicular differentiation

-6048560 Langerhans cell histiocytosis

-6049190 Becker nevus syndrome

-6050270 Lymphoma non-hodgkin familial

-6050410 Spiegler-brooke syndrome

-6050740 Renal cell carcinoma papillary

-6050750 Renal cell carcinoma papillary 3

-6052330 Autoimmune lymphoproliferative disease without fas mutations

-6052440 Carney myxoma-endocrine complex type ii

-6052880 Primordial germ cell tumor susceptibility locus 1

-6053650 Breast cancer 3 brca3

-6053730 Paragangliomas 3

-6053730 Glomus tumors familial 3

-6054620 Basal cell carcinoma multiple

-6056420 Thyroid carcinoma papillary with papillary renal neoplasia

-6058270 Basaloid follicular hamartoma syndrome generalized autosomal dominant

-6058390 Leiomyomatosis and renal cell cancer hereditary

-6059820 Familial wilms tumor 2

-6061790 Aneurysmal bone cysts

-6061900 Meningioma radiation-induced

-6062400 Thyroid carcinoma nonmedullary 1

-6062430 Alveolar soft-part sarcoma

-6064450 Persistent polyclonal b-cell lymphocytosis

-6065190 Phace association

-6066600 Melanoma uveal susceptibility to 1

-6066900 Lymphangioleiomyomatosis

-6066900 Lymphangiomyomatosis lymphangioleiomyomatosis somatic included

-6067190 Familial atypical multiple mole melanoma-pancreatic carcinoma syndrome

-6067640 Gastrointestinal stromal tumor gist

-6068640 Paraganglioma and gastric stromal sarcoma

-6068930 Hemangioma intraosseous

-6071740 Meningioma familial meningioma caused by somatic mutation included

-6072480 Glioma familial 1

-6072780 Osteofibrous dysplasia

-6074640 Thyroid carcinoma hurthle cell

-6076850 Hypereosinophilic syndrome idiopathic

-6077850 Juvenile myelomonocytic leukemia

-6078590 Tufted angioma

-6078930 Ovarian cancer epithelial susceptibility to

-6079070 Dermatofibrosarcoma protuberans

-6080350 Melanoma cutaneous malignant 4

-6082320 Leukemia chronic myeloid

-6082660 Parathyroid carcinoma

-6083540 Capillary malformation-arteriovenous malformation

-6084560 Colorectal adenomatous polyposis autosomal recessive

-6086150 Oligodontia-colorectal cancer syndrome

-6086230 Neuroectodermal tumors supratentorial primitive with cafe-au-lait spots

-6086560 Prostate cancer hereditary 20

-6086580 Prostate cancer hereditary 7

-6088120 Colorectal cancer susceptibility to on chromosome 9

-6088370 Carney complex variant

-6089350 Lung cancer 1

-6090480 Melanoma cutaneous malignant 3

-6092990 Prostate cancer hereditary 3

-6093100 Colorectal cancer hereditary nonpolyposis type 2

-6093220 Rhabdoid tumor

-6093630 Colloid cysts of third ventricle

-Jules J. Berman
In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases.



I urge you to read more about my book. There's a generous preview of the book at the Google Books site.

- Jules J. Berman, Ph.D., M.D. tags: common disease, orphan disease, orphan drugs, genetics of disease, disease genetics, rules of disease biology, rare disease, pathology, cancer, genetics, neoplasia, neoplasms, tumor, tumour

Sunday, September 16, 2007

Latest update of Neoplasm Classification available

The latest version of the Developmental Lineage Classification and Taxonomy of Neoplasms is now available as a gzipped file at:

http://www.julesberman.info/neoclxml.gz

This Neoplasm Classification has been described at:

http://www.biomedcentral.com/1471-2407/4/10

It contains 5,827 neoplasm classified concepts and 130,283 different terms (codes beginning with "C"). It is more than ten times larger than any other neoplasm classification.

In addition to specific neoplasm concepts, it also contains general neoplastic terms (coded as C0000000), inherited conditions associated with neoplasms (codes beginning with "S") and terms related to the stage or anatomic location of neoplasms (codes beginning with "ST").


In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases.



I urge you to read more about my book. There's a generous preview of the book at the Google Books site. If you like the book, please request your librarian to purchase a copy of this book for your library or reading room.

- Jules J. Berman, Ph.D., M.D.

Friday, September 14, 2007

LUA programming language gaining popularity

In the previous log, I mentioned the programming language, Lua.

Lua came to my attention because its rank on the TIOBE Programming Community Index
for September 2007 is 18th (up from rank 50 this time last year!!!).

Lua is a no-cost programming language distritubed under the very liberal MIT license.

It is a small, no-frills procedural scripting language that boasts a fast speed.

It is designed with great flexibility, and a programmer can add functionality (such as object orientation) with only a little extra effort. According to a Lua tutorial, objects (data and code encapsulated together) can be created with Lua tables, and inheritance can be achieved with metatables.

I downloaded a Lua binary for Windows at:

http://luabinaries.luaforge.net/download.html

I got a small, 142,512 byte file, lua5_1_2_Win32_bin.zip

De-archived, this file produced:

36,864 bin2c5.1.exe
114,688 lua5.1.dll
20,480 lua5.1.exe
122,880 luac5.1.exe

I modified a few lines of code from the wikipedia entry for Lua and put it in a script file named, "hello.lua"
-------------------------------------------
print "Hello, World"

function factorial(n)
if n == 0 then
return 1
end
return n * factorial(n - 1)
end

print(factorial(4))
------------------------------------------

I ran it from the directory containing the Lua exe:

C:\ftp\lua5_1_2_Win32_bin>lua5.1.exe hello.lua
Hello, World
24

It worked!

I don't know enough about Lua to recommend or reject it, but it seems to be a neat little scripting language.

A Google search (Lua tutorial) will retrieve many resources.

-Jules J. Berman
Science is not a collection of facts. Science is what facts teach us; what we can learn about our universe, and ourselves, by deductive thinking. From observations of the night sky, made without the aid of telescopes, we can deduce that the universe is expanding, that the universe is not infinitely old, and why black holes exist. Without resorting to experimentation or mathematical analysis, we can deduce that gravity is a curvature in space-time, that the particles that compose light have no mass, that there is a theoretical limit to the number of different elements in the universe, and that the earth is billions of years old. Likewise, simple observations on animals tell us much about the migration of continents, the evolutionary relationships among classes of animals, why the nuclei of cells contain our genetic material, why certain animals are long-lived, why the gestation period of humans is 9 months, and why some diseases are rare and other diseases are common. In “Armchair Science”, the reader is confronted with 129 scientific mysteries, in cosmology, particle physics, chemistry, biology, and medicine. Beginning with simple observations, step-by-step analyses guide the reader toward solutions that are sometimes startling, and always entertaining. “Armchair Science” is written for general readers who are curious about science, and who want to sharpen their deductive skills.

Ruby moves up on TIOBE Programming Index

Yesterday marked the publication date for my new book, Ruby Programming for Medicine and Biology!




As a reality check, I checked Ruby's ranking on the TIOBE Programming Language Index for September 2007.

Ruby is now ranked 10th (up from rank 13 last year at this time).

Perl is now ranked 6th (same rank as this time last year).

Python is now ranked 8th (down from rank 7 this time last year).

Remarkably, Lua, a programming language that I had never heard of, is ranked 18th (up from rank 50 this time last year!!!).

More on Lua on my next blog.

- Jules

Wednesday, September 12, 2007

Tutorial document on image annotation

I just returned from the APIII2007 meeting in Pittsburgh, PA, where I gave a workshop on image annotation with RDF (concentrating on pathology images).

Bill Moore and I prepared a detailed white paper on the subject, which is available now at:

http://www.julesberman.info/spec2img.htm

The white paper is distibuted under the GNU Free Documentation License and can be copied, distributed, and cross-posted.

Table of Contents



Implementing an RDF Schema for Pathology Images

* Title
* How to read this document
* Conveying textual information with photomicrographs
* The Laboratory Digital Imaging Project (2004-2007)
* Increasing levels of complexity
o Level 1 - Free-text description inserted into image header
o Level 2 - Dublin Core descriptors inserted into image header
o Level 3 - Insert RDF document into image file
o Level 4 - Insert your image into RDF document
o Level 5 - Point to your image file from an RDF document.
o Level 6 - Combining of 1 through 5, with multiple images/annotations

How to do it
* How to acquire Perl and/or Ruby
* How to view a jpeg image
o How to view a jpeg image in Perl
o How to view a jpeg image in Ruby
+ Preliminaries
+ Displaying a JPEG image in Ruby
+ Manipulating an image in Ruby
* How to do Level 1 - Free-text description inserted into image header
o Perl
+ Preliminaries
+ Perl example
o Ruby
+ Ruby examples
# Inserting character strings into a JPEG header
# Inserting a text file into a JPEG header
* How to do Level 2 - Dublin Core descriptors inserted into image header
o Dublin core metadata is a special kind of text.
* How to do Level 3 - Insert RDF document into image file
o Introduction to RDF
+ Background
+ The definition of Meaning
+ Introduction to RDF syntax: RDF triples
* How to do Level 4 - Insert your image into an RDF document
o Example in Perl
o Base64 in Ruby
o Nota bene
* How to do Level 5 - Point to your image file from an RDF document.
* How to do Level 6 - Combining of 1 through 5, with multiple images/annotations
o Multiple RDF documents pointing to image file
o Multiple RDF files pointing to multiple image files

Dealing with DICOM

* What is DICOM?
* Standards are inter-convertible
* The DICOM header
* Manipulating DICOM with Ruby
o DICOM To JPEG Conversion - ezDicom And DCM2JPG And JPEG2DCM.
o Ruby scripts for converting DICOM to JPEG
o Extracting And Inserting Jpeg And Dicom Image Headers.
* RDF image specification contrasted with DICOM
* Porting between an RDF specification and a data standard

Advanced RDF tutorial (Can be skipped unless you have a special interest in subject)

* Common Data Elements (CDEs)
o ISO-11179 Specification for CDEs
* RDF Schemas
* A template for CDEs that can be transformed to RDF Schema elements
* Classes and Properties
* Creating Properties
* Specifying a datatype from within an RDF Schema Property Element
o Creating the external XSD document to datatype our property ranges
* The differences between Classes and Properties
* Creating instances of classes
* Preserving namespaces for Classes and Properties
* Unique subject identifiers
* LSID Examples:
* The RDF Schema for pathology images
* Data Specifications contrasted with Data Standards
* Creating your own RDF Schema
* Using an RDF Schema in your RDF documents
* A few publicly available RDF schemas
* Validating a specification
* Owl and DAML
* Problems with RDF
* Summary of advanced RDF section

-Jules Berman
My book, Principles of Big Data: Preparing, Sharing, and Analyzing Complex Information was published in 2013 by Morgan Kaufmann.



I urge you to explore my book. Google books has prepared a generous preview of the book contents. If you like the book, please request your librarian to purchase a copy of this book for your library or reading room.

tags: big data, metadata, data preparation, data analytics, data repurposing, datamining, data mining