Commit 84aedd9b authored by Daniel Teixeira's avatar Daniel Teixeira
Browse files

adding new implementation with doc in mk

parent 45443fb4
0000/0;not classified in icd-o 3 [e.g. non-neoplastic or benign]
8000/3;neoplasm, malignant
8010/0;epithelial tumor, benign
8010/2;carcinoma in situ, nos
8010/3;carcinoma, nos
8012/3;large cell carcinoma, nos
8013/3;large cell neuroendocrine carcinoma
8020/3;carcinoma, undifferentiated type, nos
8021/3;carcinoma, anaplastic type, nos
8022/3;pleomorphic carcinoma
8031/3;giant cell carcinoma
8032/3;spindle cell carcinoma
8033/3;sarcomatoid carcinoma
8041/3;small cell carcinoma, nos
8046/3;non-small cell carcinoma
8050/3;papillary carcinoma, nos
8052/0;squamous cell papilloma
8070/1;premalignant squamous epithelium, nos
8070/2;squamous cell carcinoma in situ, nos
8070/3;squamous cell carcinoma, nos
8071/0;squamous cell keratosis, nos
8075/3;squamous cell carcinoma, acantholytic
8077/2;squamous intraepithelial neoplasia, grade iii
8082/3;undifferentiated nasopharyngeal carcinoma
8090/3;basal cell carcinoma, nos
8120/2;transitional cell carcinoma in situ
8120/3;transitional cell carcinoma, nos
8130/1;urothelial papilloma, nos
8130/2;papillary transitional cell carcinoma, non-invasive
8130/3;papillary transitional cell carcinoma
8140/0;adenoma, nos
8140/1;atypical adenoma
8140/2;adenocarcinoma in situ
8140/3;adenocarcinoma, nos
8144/3;adenocarcinoma, intestinal type
8145/3;carcinoma, diffuse type
8148/2;glandular intraepithelial neoplasia, grade iii
8150/1;islet cell adenoma
8150/3;islet cell carcinoma
8151/1;insulinoma, nos
8151/3;insulinoma, malignant
8152/1;glucagonoma, nos
8152/3;glucagonoma, malignant
8153/1;gastrinoma, nos
8153/3;gastrinoma, malignant
8156/1;somatostatinoma, nos
8161/3;bile duct cystadenocarcinoma
8170/0;hepatocellular adenoma, nos
8170/3;hepatocellular carcinoma, nos
8171/3;hepatocellular carcinoma, fibrolamellar
8180/3;combined hepatocellular carcinoma and cholangiocarcinoma
8200/3;adenoid cystic carcinoma
8201/3;ductal carcinoma, cribriform type [c50._]
8210/3;adenocarcinoma in adenomatous polyp
8211/0;tubular adenoma, nos
8211/3;tubular adenocarcinoma
8215/3;adenocarcinoma of anal ducts [c21.1]
8220/3;adenocarcinoma in adenomatous polyposis coli
8240/3;carcinoid tumor, nos
8246/3;neuroendocrine carcinoma
8247/3;merkel cell carcinoma
8249/3;atypical carcinoid tumor
8250/3;bronchiolo-alveolar adenocarcinoma
8251/3;alveolar adenocarcinoma
8252/3;bronchiolo-alveolar carcinoma, non-mucinous
8254/3;bronchiolo-alveolar carcinoma, indeterminate type [c34._]
8260/0;papillary adenoma, nos
8260/3;papillary adenocarcinoma, nos
8263/0;tubullovillous adenoma, nos
8272/0;pituitary adenoma, typical
8272/3;pituitary carcinoma, nos
8290/3;follicular carcinoma, oxyphilic cell
8310/3;clear cell renal cell carcinoma
8312/3;renal cell carcinoma
8317/3;renal cell carcinoma, chromophobe
8318/3;renal cell carcinoma, spindle cell [c64.9]
8319/3;renal medullary carcinoma
8330/0;follicular adenoma, nos
8333/0;fetal adenoma
8333/3;fetal adenocarcinoma
8335/3;follicular carcinoma
8340/3;papillary carcinoma, follicular variant
8361/0;juxtaglomerular tumor [c64.9]
8370/0;adrenal cortical adenoma
8370/3;adrenal cortical carcinoma
8380/1;endometrioid dysplasia
8380/3;endometrioid carcinoma, nos
8382/3;endometrioid adenocarcinoma, secretory variant
8384/3;adenocarcinoma, endocervical type
8401/2;apocrine dcis
8401/3;apocrine adenocarcinoma
8430/3;mucoepidermoid carcinoma
8440/3;cystadenocarcinoma, nos
8441/3;serous adenocarcinoma, nos
8442/1;serous cystadenoma, borderline malignancy
8450/3;papillary cystadenocarcinoma, nos
8453/0;intraductal papillary-mucinous adenoma [c25._]
8453/1;intraductal papillary-mucinous tumor with moderate dysplasia [c25._]
8453/2;intraductal papillary-mucinous carcinoma, non-invasive [c25._]
8453/3;intraductal papillary-mucinous carcinoma, invasive [c25._]
8460/3;micropapillary serous carcinoma [c56.9]
8461/3;serous surface papillary carcinoma
8462/1;serous papillary cystic tumor of borderline malignancy
8470/3;mucinous cystadenocarcinoma, nos
8472/1;mucinous cystic tumor of borderline malignancy
8480/3;mucinous adenocarcinoma
8481/3;mucin-producing adenocarcinoma
8490/3;signet ring cell carcinoma
8500/2;ductal carcinoma in situ, nos
8500/3;invasive carcinoma of no special type
8501/2;dcis, comedo type [c50._]
8501/3;comedocarcinoma, nos
8502/3;secretory carcinoma of breast
8503/2;ductal carcinoma in situ, papillary [c50._]
8503/3;intraductal papillary adenocarcinoma with invasion
8507/2;intraductal micropapillary carcinoma
8507/3;invasive micropapillary carcinoma
8510/3;medullary carcinoma, nos
8513/3;atypical medullary carcinoma
8520/2;lobular carcinoma in situ
8520/3;invasive lobular carcinoma
8522/3;infiltrating duct and lobular carcinoma
8523/3;infiltrating duct mixed with other types of carcinoma [c50._]
8524/3;infiltrating lobular mixed with other types of carcinoma
8530/3;inflammatory carcinoma
8541/3;paget disease and infiltrating duct carcinoma
8550/3;acinar cell carcinoma
8560/3;adenosquamous carcinoma
8562/3;myoepithelial carcinoma
8570/3;adenocarcinoma with squamous metaplasia
8575/3;metaplastic carcinoma, nos
8576/3;hepatoid adenocarcinoma
8581/3;thymoma, medullary [who a], malignant
8585/3;thymoma, atypical [who b3], malignant
8586/3;thymoma, type c [c37.9]
8589/3;carcinoma showing thymus-like differentiation
8620/3;granulosa cell tumor, malignant
8640/3;sertoli cell carcinoma
8680/1;paraganglioma, nos
8682/1;parasympathetic paraganglioma
8693/3;extra-adrenal paraganglioma, malignant
8700/0;pheochromocytoma, nos
8700/3;pheochromocytoma, malignant
8720/0;pigmented nevus, nos
8720/3;malignant melanoma, nos
8721/3;nodular melanoma
8730/3;amelanotic melanoma
8742/3;lentigo maligna melanoma
8743/3;superficial spreading melanoma
8744/3;acral lentiginous melanoma, malignant
8761/0;congenital melanocytic nevus
8770/0;spitz nevus
8770/3;mixed epithelial and spindle cell melanoma
8780/3;blue nevus, malignant
8800/3;sarcoma, nos
8802/3;giant cell sarcoma
8804/3;epithelioid sarcoma
8805/3;undifferentiated sarcoma
8810/0;fibroma, nos
8810/3;fibrosarcoma, nos
8811/0;fibromyxoid tumor, nos
8811/3;myxoinflammatory fibroblastic sarcoma
8815/0;solitary fibrous tumor
8815/3;solitary fibrous tumor, malignant
8821/1;desmoid-type fibromatosis
8823/0;desmoplastic fibroma
8825/0;myofibroblastic tumor, nos
8825/1;inflammatory myofibroblastic tumour
8830/0;fibrous histiocytoma, nos
8830/3;fibrous histiocytoma, malignant
8832/3;dermatofibrosarcoma, nos
8833/3;pigmented dermatofibrosarcoma protuberans
8850/0;lipoma, nos
8850/3;liposarcoma, nos
8851/3;lipoma-like liposarcoma
8852/3;liposarcoma, myxoid
8854/3;liposarcoma, pleomorphic
8855/3;mixed type liposarcoma
8858/3;liposarcoma, dedifferentiated
8890/0;leiomyoma, nos
8890/3;leiomyosarcoma, nos
8891/3;epithelioid leiomyosarcoma
8900/3;rhabdomyosarcoma, nos
8901/3;rhabdomyosarcoma, pleomorphic
8910/3;embryonal rhabdomyosarcoma
8920/3;alveolar rhabdomyosarcoma
8930/3;endometrial stromal sarcoma
8931/3;endometrial stromal sarcoma, low grade
8936/0;gastrointestinal stromal tumor, benign
8936/1;gastrointestinal stromal tumor, uncertain malignant potential
8936/3;gastrointestinal stromal tumor, malignant
8950/3;mullerian mixed tumor
8951/3;mesodermal mixed tumor
8960/3;nephroblastoma, nos
8963/3;rhabdoid tumor, nos
8964/3;clear cell sarcoma of kidney
8973/3;pleuropulmonary blastoma
8980/3;carcinosarcoma, nos
8982/3;malignant myoepithelioma
8990/3;mesenchymoma, malignant
8991/3;embryonal sarcoma
9010/0;fibroadenoma, nos
9020/0;phyllodes tumor, benign
9020/1;phyllodes tumor, borderline
9020/3;phyllodes tumor, malignant
9040/3;synovial sarcoma, nos
9041/3;synovial sarcoma, monophasic
9043/3;synovial sarcoma, biphasic
9050/3;mesothelioma, nos
9051/3;desmoplastic mesothelioma
9052/3;epithelioid mesothelioma, malignant
9053/3;mesothelioma, biphasic, malignant
9061/3;seminoma, nos
9063/3;spermatocytic seminoma
9064/2;intratubular germ cell neoplasia [c62._]
9065/3;germ cell tumor, nonseminomatous
9070/3;embryonal carcinoma, nos
9071/3;yolk sac tumor
9080/0;teratoma, benign
9080/3;teratoma, malignant, nos
9085/3;mixed germ cell tumor
9100/0;hydatidiform mole
9104/3;malignant placental site trophoblastic tumor
9110/3;mesonephroma, malignant
9120/0;hemangioma, nos
9130/3;hemangioendothelioma, malignant
9133/3;epithelioid hemangioendothelioma, malignant
9140/3;kaposi sarcoma
9150/1;hemangiopericytoma, nos
9160/0;angiofibroma, nos
9180/3;osteosarcoma, nos
9181/3;chondroblastic osteosarcoma
9182/3;fibroblastic osteosarcoma
9183/3;osteosarcoma, telangiectatic
9186/3;central osteosarcoma
9191/0;osteoid osteoma, nos
9200/0;osteoblastoma, nos
9220/0;chondroma, nos
9220/3;chondrosarcoma, nos
9230/0;chondroblastoma, nos
9241/0;chondromyxoid fibroma
9250/1;giant cell tumor of bone, nos
9260/3;ewing sarcoma
9270/3;odontogenic tumor, malignant
9310/3;ameloblastoma, malignant
9364/3;peripheral neuroectodermal tumor, nos
9370/3;chordoma, nos
9380/3;glioma, nos
9381/3;gliomatosis cerebri
9382/3;glioma, mixed
9390/1;choroid plexus papilloma, nos
9390/3;choroid plexus papilloma, malignant
9391/3;ependymoma, nos
9394/1;myxopapillary ependymoma
9395/3;papillary tumor of the pineal region
9400/3;astrocytoma, nos
9401/3;astrocytoma, anaplastic
9410/3;protoplasmic astrocytoma
9411/3;gemistocytic astrocytoma
9412/1;desmoplastic infantile astrocytoma-ganglioglioma
9413/0;dysembryoplastic neuroepithelial tumour
9420/3;fibrillary astrocytoma
9421/1;pilocytic astrocytoma
9424/3;pleomorphic xanthoastrocytoma
9440/3;glioblastoma, nos
9450/3;oligodendroglioma, nos
9451/3;oligodendroglioma, anaplastic
9470/3;medulloblastoma, nos
9471/3;medulloblastoma with extensive nodularity
9473/3;primitive neuroectodermal tumor, nos
9474/3;large cell medulloblastoma
9500/3;neuroblastoma, nos
9501/3;medulloepithelioma, nos
9503/3;neuroepithelioma, nos
9508/3;atypical teratoid/rhabdoid tumor
9509/1;papillary glioneural tumour
9510/3;retinoblastoma, nos
9522/3;olfactory neuroblastoma
9530/0;meningioma, nos
9530/3;meningioma, malignant
9532/3;fibrous meningioma, malignant
9535/3;hemangioblastic meningioma, malignant
9538/3;rhabdoid meningioma
9540/0;neurofibroma, nos
9540/3;malignant peripheral nerve sheath tumor
9560/0;schwannoma, nos
9581/3;alveolar soft part sarcoma
9582/0;granular cell tumor
9590/3;malignant lymphoma, nos
9591/3;malignant lymphoma, b-cell nos
9596/3;composite hodgkin and non-hodgkin lymphoma
9650/3;hodgkin lymphoma, nos
9651/3;classical hodgkin lymphoma, lymphocyte-rich
9652/3;classical hodgkin lymphoma, mixed cellularity, nos
9653/3;classical hodgkin lymphoma, lymphocyte depletion, nos
9659/3;hodgkin lymphoma, nodular lymphocyte predominance
9663/3;classical hodgkin lymphoma, nodular sclerosis, nos
9671/3;malignant lymphoma, lymphoplasmacytic
9673/3;mantle cell lymphoma
9678/3;primary effusion lymphoma
9679/3;mediastinal large b-cell lymphoma
9680/3;diffuse large b-cell lymphoma, nos
9684/3;ml, large b-cell, diffuse, immunoblastic, nos
9687/3;burkitt lymphoma, nos
9689/3;splenic marginal zone lymphoma, nos
9690/3;follicular lymphoma, nos
9691/3;follicular lymphoma, grade 2
9695/3;follicular lymphoma, grade 1
9698/3;follicular lymphoma, grade 3
9699/3;marginal zone lymphoma, nos
9700/3;mycosis fungoides
9701/3;sezary syndrome
9702/3;malignant lymphoma, t-cell nos
9705/3;peripheral t-cell lymphoma, nos
9709/3;primary cutaneous peripheral t-cell lymphoma, nos
9714/3;anaplastic large cell lymphoma, nos
9716/3;hepatosplenic gamma/delta t-cell lymphoma
9717/3;enteropathy type t-cell lymphoma
9718/3;anaplastic large cell lymphoma, cutaneous type
9719/3;nk/t-cell lymphoma
9727/3;blastic plasmacytoid dendritic cell neoplasm
9728/3;precursor b-cell lymphoblastic lymphoma
9729/3;precursor t-cell lymphoblastic lymphoma
9731/3;multiple myeloma
9732/3;plasma cell myeloma
9733/3;plasma cell leukemia
9734/3;plasmacytoma, extramedullary
9751/1;langerhans cell histiocytosis, nos
9757/3;dendritic cell sarcoma, nos
9761/3;waldenstrom macroglobulinemia
9765/1;monoclonal gammopathy
9800/3;leukemia, nos
9801/3;acute leukemia, nos
9805/3;acute biphenotypic leukemia
9823/3;b-cell chronic lymphocytic leukemia/small lymphocytic lymphoma
9826/3;acute lymphoblastic leukemia, mature b-cell type
9827/3;adult t-cell leukemia/lymphoma [htlv1 pos.]
9833/3;prolymphocytic leukemia, b-cell type
9834/3;prolymphocytic leukemia, t-cell type
9835/3;acute lymphoblastic leukemia, nos
9836/3;precursor b-cell lymphoblastic leukemia
9837/3;precursor t-cell lymphoblastic leukemia
9840/3;acute erythroid leukemia [fab m6]
9860/3;myeloid leukemia, nos
9861/3;acute myeloid leukemia, nos
9863/3;chronic myeloid leukemia, nos
9866/3;acute promyelocytic leukemia [fab type m3]
9867/3;acute myelomonocytic leukemia [fab type m4]
9872/3;acute myeloblastic leukemia with minimal differentiation [fab type m0]
9873/3;acute myeloblastic leukemia without maturation [fab type m1]
9874/3;acute myeloblastic leukemia with maturation [fab m2]
9875/3;chronic myelogenous leukemia
9876/3;atypical chronic myeloid leukemia, bcr/abl negative
9891/3;acute monoblastic leukemia with differentiation [fab m5b]
9895/3;acute myeloid leukemia with prior myelodysplastic syndrome
9910/3;acute megakaryoblastic leukemia [fab m7]
9920/3;therapy-related acute myeloid leukemia, nos
9931/3;acute myelofibrosis
9940/3;hairy cell leukemia
9945/3;chronic myelomonocytic leukemia, nos
9946/3;juvenile myelomonocytic leukemia
9948/3;aggressive nk-cell leukemia
9950/3;polycythemia vera
9960/3;chronic myeloproliferative disease, nos
9961/3;chronic idiopathic myelofibrosis
9962/3;essential thrombocythemia
9964/3;hypereosinophilic syndrome
9980/3;refractory anemia, nos
9982/3;refractory anemia with ringed sideroblasts [rars]
9983/3;refractory anemia with excess blasts [raeb]
9984/3;refractory anemia with excess blasts in transformation [raebt]
9985/3;refractory cytopenia with multilineage dysplasia
9986/3;myelodysplastic syndrome with 5q- syndrome
9987/3;therapy-related myelodysplastic syndrome, nos
9989/3;myelodysplastic syndrome, nos
......@@ -7,72 +7,22 @@
<title>Beacon ArrayMap</title>
<link rel="stylesheet" href="" integrity="sha384-1q8mTJOASx8j1Au+a5WDVnPi2lkFfwwEAa8hDDdjZlpLegxhjVME1fgjWPGmkzs7" crossorigin="anonymous">
<link rel="stylesheet" href="" integrity="sha384-fLW2N01lMqjakBkx3l/M9EahuwpSfeNvV63J5ezn3uZzapT0u7EYsXMjQV+0En5r" crossorigin="anonymous">
<script src="vendor/jquery.min.js"></script>
<script src="vendor/angular.min.js"></script>
<script src="vendor/angular-route.min.js"></script>
<script src="vendor/showdown.min.js"></script>
<script src="vendor/angular-sanitize.min.js"></script>
<script src="vendor/ng-showdown.js"></script>
<script src="js/index.js"></script>
<script src="" integrity="sha384-0mSbJDEHialfmuBBQP6A4Qrprq5OVfW37PRR3j5ELqxss1yVqOtnepnHVP9aJ7xS" crossorigin="anonymous"></script>
<base href="/">
<div ng-controller="BeaconController" ng-cloak class="container">
<div class="jumbotron">
<h1>Beacon ArrayMap</h1>
<p>First Prototype of a <a target="_blank" href="">Beacon</a>
<a target="_blank" href=""> v0.2</a> implementation for <a target="_blank" href="">ArrayMap</a>.</p>
<p>See <a href="documentation">documentation and open questions</a>.</p>
<form class="form-horizontal">
<div class="form-group">
<label for="chromosome" class="col-sm-2 control-label">Chromosome</label>
<div class="col-sm-4">
<input type="text" class="form-control" id="chromosome" ng-model="config.chromosome" placeholder="Chromosome">
<div class="form-group">
<label for="position" class="col-sm-2 control-label">Position</label>
<div class="col-sm-4">
<input type="text" class="form-control" id="position" ng-model="config.position" placeholder="Position">
<div class="form-group">
<label for="datasetSelect" class="col-sm-2 control-label">Dataset</label>
<div class="col-sm-4">
<select id="datasetSelect" ng-model="config.dataset" class="form-control">
<option ng-repeat="ds in datasets" value="{{ds.code}}" >({{ds.code}}) {{ds.description}}</option>
<div class="form-group">
<label style="color:green" for="variantClass" class="col-sm-2 control-label">Variant Class</label>
<div class="col-sm-4">
<select id="variantClass" ng-model="config.variantClass" class="form-control">
<option value="">Substitution (For precise variants)</option>
<option value="DEL">DEL (Deletion)</option>
<option value="INS">INS (Insertion)</option>
<option value="DUP">DUP (Duplication)</option>
<option value="INV">INV (Inversion)</option>
<option value="CNV">CNV (Copy Number Variation)</option>
<option value="BND">BND (Breakend???)</option>
<div class="form-group">
<div class="col-sm-offset-2 col-sm-8">
<a target="beacon" ng-href="{{getApiUrl()}}">{{getApiUrl()}}</a>
<div class="col-sm-2">
<a target="beacon" ng-href="{{getApiUrl()}}" class="btn btn-info">Beacon Query</a>
<div class="form-group">
<div class="col-sm-offset-2 col-sm-8">
<a target="beacon" ng-href="{{getInfoUrl()}}">{{getInfoUrl()}}</a>
<div class="col-sm-2">
<a target="beacon" ng-href="{{getInfoUrl()}}" class="btn btn-info">Beacon Info</a>
<script src="js/index.js"></script>
<body ng-app="beaconArrayApp">
<div ng-view />
\ No newline at end of file
This diff is collapsed.
## Current implementation
<img src="/img/current_implementation.jpg" class="img-thumbnail img-responsive">
* reference genome: In [In Beacon 0.2 specifications](, the values expected for human data is of GRCh? format, whereas arrayMap uses hg?? nomenclature.
* allele: [In Beacon 0.2 specifications](, the parameter is required. However, it does not make sense at all for arrayMap (in which no sequence related data exists).
* variantClass: This is a new parameter. The value equals DUP corresponds to SEGTYPE=1 (gain) in arrayMap, while DEL is for SEGTYPE=-1 (loss). The parameter is mandatory.
* sampleuid: This is DEBUG info.
* matchedSegment: This is DEBUG info.
Query chromosome 11 at position 34439881 for the dataset 8070/3, showing a deletion: [query?chromosome=11&position=34439881&dataset=8070/3&variantClass=DEL](
**Outcome from the meeting with Jordi (Feb, 10, 2016):**
It chould be ok to have the variantClass in Beacon v0.3. As for ranges, this is more complicated and requires lots of discussions. We will probably go in 2 steps:
* add P (duPlication) to the list of allowed values for the allele parameter.
* modify I (insertion) slightly by making the "sequence" string optional, i.e. be fuzzy about what was inserted.
and then
* proper variantClass
* ranges (defined as start/stop position, e.g. [200000,30000] **or** start and length, e.g. 20000:100000)
## API description
<table class="table table-responsive table-striped">
<th style="width: 25%">Parameter name</th>
<th style="width: 25%">Required in Beacon</th>
<th style="width: 25%">Required in Beacon-arrayMap</th>
<th style="width: 25%">Comment</th>
<td>no control for now (dropdown list?)</td>
<tr class="text-danger">
<td>no control for now (&gt;0)</td>
<td>Genome ID. Should be added</td>
<tr class="text-danger">
<td>Not applicable to arrayMap (no sequence info).</td>
<table class="table table-responsive table-striped">
<th style="width: 25%">Parameter name</th>
<th style="width: 25%">Required in Beacon</th>
<th style="width: 25%">Required in Beacon-arrayMap</th>
<th style="width: 25%">Comment</th>
## Forthcoming implementation: Open questions
**Imprecise structural variants:**
Exact positions are definitely not suitable for arrayMap. We should be able to request for ranges rather than positions. However, the issue with using ranges is that the start and end positions are imprecise in arrayMap.
<div class="alert alert-info">
In the VCF, there is a field for the symbolic alternate alleles for imprecise structural variants in the meta-information lines.
<br>See <a target="_blank" href="">the VCF 4.2 specifications</a> for more details.
<table class="table">