BH5.json

{
	"_id": "obj.5001",
	"_type": "Dentatorubral-pallidoluysian atrophy",
	"name": "Human[tax:9606] CAG repeats[SO:0000726] detection for dentatorubral-pallidoluysian atrophy[DOID:0060162].",
	"version": "1.0",
	"verification": "manual",
	"creation_date": "Tue Oct 18 09:23:07 EDT 2016",
	"modification_date": "Tue Oct 18 09:23:55 EDT 2016",
	"publication_status": "draft",
	"keywords": [
		"disease",
		"human disease"
	],
	"xref": [
			"DOID:0060162",
			"GOID:GO0005737",
			"ICD:R27.0",
			"SO:0000291",
			"tax:9606"
			],
	"usability_domain": [
		"Determine CAG repeats[SO:0000291] in a sequence for the diagnosis of Dentatorubral-pallidoluysian atrophy [ICD:G10] for ATN1 gene[GOID:GO0005737]: normal: 6 - 35 CAG trinucleotide repeats, disease state: 48 - 93 CAG trinucleotide repeats"
	],
	"authors": [
		{
			"first_name": "James",
			"last_name": "Burke",
			"affiliation": "Duke"
		}
	],
	"pipeline": "obj.5001",
	"alignment": {
		"seed": 14,
		"minimum_match_len": 50,
		"divergence_threshold_percent": 10
	},
	"variant_calling": {
		"minimum_coverage": 20,
		"frequency_cutoff": 0.20
	},
	"verification_kit":{
		"reference_sequence":[
			{
				"source": "NCBI",
				"db": "genbank",
				"id": [
					" NM_001940.3",
					"rs7969685"
				]
			}
		],
		"sequence_reads": [
			{
				"source": "HIVE",
				"db": "Honeycomb",
				"id": ["obj.00001"]
			}
		],
		"snp_profile_file": {
			"format": [".csv"],
			"filename": "SNPProfile.csv"
		}
	}
}