Example. Variable Number of Tandem Repeats

Content

This example shows findings from an assessment of the HTT gene sequence with the purpose of determining the number of CAG repeats in subjects with Huntington's Disease. In this example, findings generated from the assessment of variable number tandem repeats are generated using two methodologies, one of which provides a more accurate and direct counting of CAG repeat numbers. The arbitrary allele identifier is shown in GFCOPYID. The published symbol for the gene of interest is shown in GFSYM. The description of the type of genomic entity that is represented by the published symbol in GFSYM is shown in GFSYMTYP as GENE WITH PROTEIN PRODUCT. The location within a sequence for the observed value in GFORRES is shown in GFGENLOC. The unique identifier for the sequence used as the reference to identify the genetic variation in the result is shown in GFSEQID. The test method by which the examination was performed is shown in GFMETHOD.

gf.xpt

Row 1:	Shows the predicted number of CAG repeats for one allele of the HTT gene in the subject.
Row 2:	Shows the predicted number of CAG repeats for the other allele of the HTT gene in the subject.
Row 3:	Shows the number of CAG repeats one allele of the HTT gene in the subject.
Row 4:	Shows the number of CAG repeats for the other allele of the HTT gene in the subject.
Row 5:	Shows the nucleotide sequence for one allele of the HTT gene in the subject.
Row 6:	Shows the nucleotide sequence for the other allele of the HTT gene in the subject.

gf.xpt

Row	STUDYID	DOMAIN	USUBJID	GFSEQ	GFREFID	GFTESTCD	GFTEST	GFTSTDTL	GFORRES	GFSTRESC	GFSTRESN	GFSYM	GFSYMTYP	GFGENLOC	GFSEQID	GFCOPYID	GFSPEC	GFMETHOD	VISITNUM	GFDTC
1	ABC123	GF	HD01-101	1	789879	VNTR	Variable Number Tandem Repeats	PREDICTED NUMBER OF CAG REPEATS	43	43	43	HTT	GENE WITH PROTEIN PRODUCT	c.52_54	LRG_763t1	1	gDNA	CAPILLARY ELECTROPHORESIS	1	2017-05-22
2	ABC123	GF	HD01-101	2	789879	VNTR	Variable Number Tandem Repeats	PREDICTED NUMBER OF CAG REPEATS	25	25	25	HTT	GENE WITH PROTEIN PRODUCT	c.52_54	LRG_763t1	2	gDNA	CAPILLARY ELECTROPHORESIS	1	2017-05-22
3	ABC123	GF	HD01-101	3	679898	VNTR	Variable Number Tandem Repeats	NUMBER OF CAG REPEATS	44	44	44	HTT	GENE WITH PROTEIN PRODUCT	c.52_54	LRG_763t1	1	gDNA	SEQUENCING	1	2017-05-22
4	ABC123	GF	HD01-101	4	679898	VNTR	Variable Number Tandem Repeats	NUMBER OF CAG REPEATS	23	23	23	HTT	GENE WITH PROTEIN PRODUCT	c.52_54	LRG_763t1	2	gDNA	SEQUENCING	1	2017-05-22
5	ABC123	GF	HD01-101	5	679898	VNTR	Variable Number Tandem Repeats	NUCLEOTIDE SEQUENCE	CAG[44]CAACAG[2]CCGCCA[1]CCG[7]CCT[2]	CAG[44]CAACAG[2]CCGCCA[1]CCG[7]CCT[2]		HTT	GENE WITH PROTEIN PRODUCT	c.52_153	LRG_763t1	1	gDNA	SEQUENCING	1	2017-05-22
6	ABC123	GF	HD01-101	6	679898	VNTR	Variable Number Tandem Repeats	NUCLEOTIDE SEQUENCE	CAG[23]CAACAG[2]CCGCCA[1]CCG[7]CCT[2]	CAG[23]CAACAG[2]CCGCCA[1]CCG[7]CCT[2]		HTT	GENE WITH PROTEIN PRODUCT	c.52_153	LRG_763t1	2	gDNA	SEQUENCING	1	2017-05-22