User:GMPD/sandbox

GMPD (talk) 11:14, 19 December 2011 (UTC)

3.3.1	TEST CATEGORY
The report should explicitly state the clinical question being addressed by the

investigation, especially if the request or clinical details are ambiguous. This is essential to reduce the potential for misinterpretation of the test result. The categorisation of tests could reflect the classification of human genetic testing utilised by NPAAC [NPAAC 2007b].

3.3.1.1	Possible field values
3.3.2	CLINICAL DETAILS & REQUEST The clinical details as provided by the requesting practitioner should be stated verbatim. If the clinical details are illegible or absent, this should be stated.
 * 1) Genetic test of breast cancer tissue to identify somatic variant/s as a guide to prognosis and therapy.
 * 2) * Genetic test to identify variants associated with altered warfarin mtabolism.
 * 3) * Genetic test of an affected person for common inherited mutations which cause ha	emochromatosis.
 * 4) * Genetic testing of an unaffected child for inherited mutations which cause myotonic dystrophy (wri	tten consent provided)
 * 5) * Testing of an unaffected fetus for inherited mutations which cause spinal muscular atroph	y (written consent provided)
 * 6) * Testing of an unaffected adult for an inherited mutation which increases the risk of breast and ovarian cancer (written consent provided)
 * 1) * Testing of an unaffected adult for an inherited mutation which increases the risk of breast and ovarian cancer (written consent provided)

3.4	The sample 3.4.1	SAMPLE TYPE Specify the type and tissue source of the sample.

In some situations, it may be appropriate to collect two independent samples for genetic testing to reduce the risk of an erroneous result due to a sample collection error [RCPA 2007]. The report should indicate if such precautions were taken.

The state of the sample should be specified i.e. whether it is a fresh, frozen, fixed, etc. It is important to note whether the quality of the received sample is suboptimal as this may have a bearing on the interpretation of the test result. 3.4.1.1	Possible field values 	Two independent fresh blood samples 	Single fresh blood sample (tube signed by patient) 	Fixed normal and malignant tissue from descending colon 	Single fresh blood sample & fresh buccal swab 	Frozen sample from left breast cancer 	Amniotic fluid (tube signed by parent) 	Genomic DNA sample/s (extracted by referring lab). 3.4.2	DATE/TIME SAMPLE COLLECTED 3.4.3	[DATE/TIME SAMPLE RECEIVED] When testing fresh samples, it is essential that the delay between collection and receipt be specified on the report. A prolonged delay may indicate that the sample quality has been compromised. 3.4.4	[SAMPLE ID/LAB ACCESSION NUMBER] If the DNA had been extracted by another laboratory, the sample ID of that laboratory should be recorded, either at this point or as one of the patient identifiers (Section 3.2.2). 3.5	The test 3.5.1	GENE/S sort of tested The report must unambiguously identify the gene or genetic locus being assayed. The standard gene nomenclature as described by the Human Genome Organisation Gene Nomenclature Committee should be used. It is recognised that synonyms are in common use, but they are not specific and there is great potential for confusion to both current and future readers of the report. It is strongly recommended that standard gene names be used, with synonyms or alternative names shown in brackets until referrers become familiar with the correct terminology. Fusion genes should be shown as GENE1/GENE2, preferably in mechanistic order i.e. 5’ to 3’ in the fusion gene [Gulley et al 2007]

It is essential that the reference sequence used by the laboratory for the analysis is specified. The Human Genome Variation Society recommends that the genomic or gene sequence (cDNA), rather than the protein sequence, be used as the basis for reporting all genetic tests. NCBI Reference Sequences, if available, are recommended. The Human Genome Organisation Gene Nomenclature Committee nominates a recommended NCBI Reference Sequence for each gene or locus with an approved name.