CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow specimens

Table 1 Quality Control Metrics from DNA Workbench

Specimen	Age of specimen¹	Test Fluorochrome	Pass/fail	DLRSpread²	Signal to Noise ³ Green	Signal to Noise ³ Red
bone marrow	1 day	CY3	Pass	0.206803	65.848474	63.860383
		CY5	Pass	0.199919	62.305342	52.162212
bone marrow	9 days	CY3	Pass	0.14503	98.418512	76.505274
		CY5	Pass	0.142963	87.635554	88.5432
bone marrow	15 days	CY3	Pass	0.209813	44.387109	34.835231
		CY5	Pass	0.205444	53.479156	41.008914
bone marrow	26 days	CY3	Pass	0.283387	38.740122	43.751865
		CY5	Pass	0.257136	39.285321	42.250693
bone marrow	27 days	CY3	Pass	0.158672	85.404253	76.821745
bone marrow	36 days	CY3	Pass	0.181903	71.365826	75.92553
		CY5	Pass	0.192083	59.676813	56.174289
cytogenetic specimen	52 days	CY3	Pass	0.174283	123.04883	104.706454
cytogenetic specimen	1 year	CY3	Pass	0.333462	40.65296	49.663864
		CY5	Pass	0.193984	56.378169	43.05297
cytogenetic specimen	8 years	CY3	Pass	0.218933	47.366763	47.266465
		CY5	Pass	0.198984	57.315046	56.775467

DNA Workbench quality classifications are given below the table. Quality measurements classified as "excellent" are in bold print and the single "poor" measurement is underlined; all other measurements were classified "good". Pairs of duplicate experiments are grouped together.
¹ length of time at 4°C for bone marrow or at -80°C for chromosome suspension in Carnoy's fixative.
² Excellent: < 0.2; Good: 0.2-0.3; Poor: > 0.3
³ Excellent: > 100; Good: 30-100; Poor: < 30

ISSN: 1755-8166