Database 2: One page profiles of current genetic tests (Continued)

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47. MLH1, MSH2, MSH6 mutations

Test name	MLH1, MSH2, MSH6 mutations
Other names	HNPCC mismatch repair gene
Description	About 90 percent of individuals with HNPCC have mutations in one of two mismatch repair (MMR) genes, MLH1 or MSH2. Mutations in MSH6, PMS1, and PMS2 have also been implicated in this malignancy. These genes are responsible for correcting nucleotide base mispairs and small insertions or deletions that occur during DNA replication. The lifetime risk of colorectal cancer in individuals with an MMR gene mutation is about 80 percent.
Purpose	Primary prevention
Availability	Commercial laboratories, academic hospitals
Specimen	Blood
Methodology	PCR
Cancers	Colorectal
Clinical use(s)   a) Routine:	Differentiate hereditary non-polyposis colorectal cancer (HNPCC) from non-HNPCC colorectal cancer Assess risk of HNPCC in family members of individuals with HNPCC
Source of information	Quest Diagnostics and UpToDate Web sites
Exploratory Medline search (8/2/05)	“MLH1” = 1,285 citations “MSH2” = 887 citations “MSH6” = 294 citations “colorectal neoplasm” = 37,826 citations (“MLH1” or “MSH2” or “MSH6”) and “colorectal neoplasms” = 792 citations

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48. Neuron specific enolase

Test name	Neuron specific enolase
Other names	NSE
Description	NSE is a glycolytic enzyme that catalyzes the conversion of phosphoglycerate to phosphoenol pyruvate. Elevated NSE concentrations are observed in patients with neuroblastoma, pancreatic islet cell carcinoma, medullary thyroid carcinoma, pheochromocytoma, and other neuroendocrine tumors. Additionally, NSE levels are frequently increased in patients with small cell lung cancer (SCLC) and infrequently in patients with non-SCLC.
Purpose	Monitoring
Availability	Commercial laboratories, academic hospitals
Specimen	Serum
Methodology	RIA
Cancers	Lung, pancreas
Other cancers	Neuroblastoma, carcinoma, medullary thyroid carcinoma, pheochromocytoma and other neuroendocrine tumors.
Clinical use(s)   a) Routine:	Monitor disease progression and therapy in individuals with small cell lung cancer Monitor effectiveness of therapy in various other cancers
Source of information	Specialty Laboratories, Quest Diagnostics Web sites
Exploratory Medline search (8/2/05)	“neuron specific enolase” = 1,577 citations “lung neoplasms” = 37,232 citations “neuron specific enolase” and “lung neoplasms” = 223 citations

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49. Nuclear matrix proteins

Test name	Nuclear matrix proteins
Other names	NMP 22
Description	Nuclear matrix proteins (NMPs) are associated with functions such as DNA replication and RNA synthesis. Identification of increased concentrations of NMP 22 can aid in the management of patients with transitional cell carcinoma of the urinary tract and also in the differential \ diagnosis of persons with symptoms or risk factors for transitional cell carcinoma of the bladder.
Purpose	Diagnostic, recurrence, monitoring
Availability	Commercial laboratories, academic hospitals
Specimen	Urine
Methodology	EIA
Cancers	Bladder
Clinical use(s)   a) Routine:	Diagnosis of bladder cancer Monitor patients for bladder cancer recurrence
Source of information	Quest Diagnostics, LabCorp Web sites
Exploratory Medline search (8/2/05)	“nuclear matrix-associated proteins”= 830 citations “NMP 22” = 25 citations “bladder neoplasms” = 9,483 citations “NMP 22” and “neoplasms, bladder” = 23 citations “nuclear matrix-associated proteins” and “bladder neoplasms” = 3 citations

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50. Oncotype DX™

Test name	Oncotype DX™
Other names	Breast cancer assay
Description	Oncotype DX is an assay that quantifies the likelihood of breast cancer recurrence in women with newly diagnosed, stage I or II, node negative, estrogen receptor positive breast cancer who will be treated with Tamoxifen. The assay analyzes the expression of a panel of 21 genes and the results are provided as a Recurrence Score™ (0-100). Using the Recurrence score, patients are classified into low, intermediate, and high risk categories for likelihood of disease recurrence.
Purpose	Prognostic
Availability	Limited commercial availability via Genomic Health (Redwood City, CA), academic institutions participating in clinical trials.
Specimen	Tumor tissue RNA
Methodology	PCR
Cancers	Breast
Clinical use(s)   b) Investigational	To assess risk of recurrence in certain breast cancer patients and thus aid in treatment planning
Source of information	Genomic Health Web site and promotional material
Exploratory Medline search (5/12/05)	“gene assay” = 599 citations “breast neoplasms” = 55,886 citations “gene assay” and “breast neoplasms” = 33 citations “oncotype dx” or “oncotype” = 4 citations company Web site = 11 citations: 2 publications, 9 abstracts

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51. p53 tumor suppressor gene

Test name	p53 tumor suppressor gene
Other names	p53
Description	p53 is a tumor suppressor gene and normally has an inhibitory influence on the cell cycle. Once this gene is deleted or its function reduced, normal control mechanisms are altered. Alterations of the p53 tumor suppressor gene have been shown to serve as a powerful prognostic marker in a wide variety of tumor types such as colorectal, breast, prostate, and bladder. Additionally, alterations of p53 are associated with tumor recurrence and shorter disease-free survival.
Purpose	Prognostic
Availability	Commercial laboratories, academic hospitals
Specimen	Tissue
Methodology	IHC
Cancers	Breast, prostate, colorectal
Other cancers	Bladder
Clinical use(s)   a) Routine:	Determine prognosis in patients with colorectal, breast, prostate, bladder cancers Predict disease recurrence Predict disease free survival
Source of information	Quest Diagnostics, LabCorp, and UpToDate Web sites
Exploratory Medline search (5/25/05)	“genes, P53” = 7,910 citations “colonic neoplasms” = 15,654 citations “genes, P53” and “colonic neoplasms” = 276 citations

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52. PML/RARA translocation

Test name	PML/RARA translocation
Other names	t(15;17)
Description	More than 99 percent of (acute promyelocytic leukemia) APL patients harbor a translocation between chromosomes 15 and 17, which fuses the retinoic acid receptor alpha (RARA) gene on chromosome 17 with the PML gene on chromosome 15. Historically one of the most lethal forms of acute myeloid leukemia, APL leads to disseminated intravascular coagulation and death when not diagnosed and treated. Treatment with all-trans-retinoic acid substantially improves survival in patients who have failed anthracycline chemotherapy or for whom anthracycline is contraindicated.
Purpose	Diagnostic, prognostic, monitoring
Availability	Commercial laboratories, academic hospitals
Specimen	Blood, marrow
Methodology	PCR
Cancers	Acute promeylocytic leukemia
Clinical use(s)   a) Routine:	Diagnosis of acute promyelocytic leukemia (APL) Predict response to all-trans-retinoic acid or arsenic trioxide therapy Assess effectiveness of therapy Detection of minimal residual disease (MRD) Predict early relapse
Source of information	Quest Diagnostics, UpToDate Web sites
Exploratory Medline search (8/2/05)	“translocation, genetic” = 7,693 citations “leukemia, promyelocytic, acute” = 1,954 citations “translocation, genetic” and “leukemia, promyelocytic, acute” = 274 citations

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53. PreGen-26

Test name	PreGen-26
Other names	MSI, BAT-26
Description	Isolates human DNA in stool and detects microsatellite instability usually associated with HNPCC and in a subset of sporadic colorectal cancers. PreGen-26 identifies alterations in the BAT-26 mononucleotide marker, believed to be the most frequent alteration found in tissue in HNPCC. BAT-26 microsatellite instability is present in as many as 90 percent of the colorectal cancers that occur in patients with HNPCC. PreGen-26 results can help to determine which patients are likely to have the presence of cancer with BAT-26 MSI.
Purpose	Primary and secondary prevention, monitoring
Availability	LabCorp
Specimen	Stool DNA
Methodology	PCR
Cancers	Colorectal
Clinical use(s)   a) Routine:	Adjunct to colonoscopy for monitoring patients with HNPCC and family members of patients with HNPCC May be used as an alternative method to monitor patients with known or suspected HNPCC syndrome who are non-compliant with current screening recommendations.
Source of information	Exact Sciences, LabCorp Web sites
Exploratory Medline search (8/2/05)	“microsatellite repeats” = 15,424 citations “colorectal neoplasms” = 37,826 citations “microsatellite repeats” and “colorectal neoplasms” = 1,265 citations

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54. PreGen-Plus™

Test name	PreGen-Plus™
Other names	DNA-based colorectal cancer test
Description	PreGen-Plus is a noninvasive screening test designed to detect clinically significant colorectal cancer. PreGen-Plus consists of a panel of 23 individual tests, each looking for the presence of mutations in human DNA isolated from stool. Three distinct technologies look for the presence of mutations in the k-ras oncogene, the APC and p53 tumor suppressor genes, shortened forms of BAT-26 (microsatellite instability), and a novel marker for disordered apoptosis.
Purpose	Secondary prevention, monitoring
Availability	Developed by EXACT Sciences, available commercially at LabCorp exclusively.
Specimen	Stool DNA
Methodology	PCR
Cancers	Colorectal
Clinical use(s)   b) Investigational	Detection of clinically significant colorectal neoplasia in asymptomatic, average-risk patients 50 years old and older An adjunctive test for those patients who receive an fecal occult blood test (FOBT), flexible sigmoidoscopy, or colonoscopy May enhance current methods for early detection of colorectal cancer
Source of information	Exact Sciences, LabCorp Web sites
Exploratory Medline search (5/12/05)	“genes, ras” or “genes, apc” or “genes, p53” or “microsatellite, repeats” = 26,861 citations “colorectal neoplasms” = 36,712 citations “feces” and “DNA” = 1,162 citations “feces” and “DNA” and “colorectal neoplasms” = 62 citations a) and d) = 25 citations

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55. Prostate Specific Antigen

Test name	Prostate Specific Antigen
Other names	PSA: free, total, ultra-sensitive, with HAMA
Description	PSA is elevated in about 30 percent of all cases with nodular prostatic enlargement. Circulating PSA exists as two major forms: complexed and free. Bound PSA is found in higher concentrations in patients with prostate cancer and free-PSA concentrations are higher in patients with Benign prostatic hypertrophy (BPH). PSA can be used to aid in the management of patients following surgical or medical treatment for prostate cancer.
Purpose	Secondary prevention, prognostic, recurrence, monitoring
Availability	Commercial laboratories, academic hospitals
Specimen	Blood
Methodology	ICMA, IRMA, EIA, MEIA
Cancers	Prostate
Clinical use(s)   a) Routine:	Detection of early prostate cancer Improve accuracy of staging prior to surgery Monitor patient response to therapy Detect disease recurrence
Source of information	Quest Diagnostics, Specialty Labs, Abbott Diagnostics, UpToDate
Exploratory Medline search (8/2/05)	“prostate-specific antigen” = 7,096 citations prostatic neoplasms” = 25,690 citations “prostate-specific antigen” and “prostatic neoplasms” = 6,084 citations

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56. T-cell receptor gene rearrangement

Test name	T-cell receptor gene rearrangement
Description	Study intended to provide some evidence that can help to distinguish between benign lymphadenopathy and malignant lymphoma. Specifically used to detect clonal gene rearrangements in the T-cell receptor beta-chain constant region. The presence of a monoclonal gene rearrangement usually, but not always, reflects the presence of a T-lymphocytic neoplasm while polyclonal gene rearrangement patterns are found in benign reactive conditions.
Purpose	Diagnostic
Availability	Commercial laboratories, academic hospitals
Specimen	Blood, marrow, tissue
Methodology	Southern blot analysis
Cancers	T-cell malignancies, lymphomas and leukemias
Clinical use(s)   a) Routine:	Leukemia and lymphoma lineage determination for prognosis and treatment selection Detection of minimal residual disease or recurrent disease
Source of information	LabCorp and UpToDate Web sites
Exploratory Medline search (8/2/05)	“Gene Rearrangement, T-Lymphocyte” = 1,735 citations “Lymphoma, T-Cell” = 4,837 citations “Gene Rearrangement, T-Lymphocyte” and “Lymphoma, T-Cell” = 303 citations

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57. TEL/AML 1 gene fusion

Test name	TEL/AML 1 gene fusion
Other names	t(12;21)
Description	The TEL/AML1 is a gene fusion resulting from a t(12;21)(p13;q22) chromosomal translocation. Although it occurs in only about 3 percent of adult acute lymphoblastic leukemia (ALL) cases, it is the most common genetic rearrangement in B-lineage pediatric ALL (frequency ~25 percent). The TEL/AML1 gene fusion is associated with a more favorable prognosis as evidenced by a significantly lower relapse rate.
Purpose	Diagnostic, prognostic, monitoring
Availability	Commercial laboratories, academic hospitals
Specimen	Blood, marrow
Methodology	FISH
Cancers	Leukemia, acute lymphoblastic leukemia
Clinical use(s)   a) Routine:	Differential diagnosis of acute lymphoblastic leukemia (ALL) Determine prognosis of patients with ALL Monitor patients with ALL
Source of information	Quest Diagnostics, UpToDate Web sites
Exploratory Medline search (8/2/05)	“Oncogene Proteins, Fusion” = 3798 citations “Leukemia, Lymphocytic, Acute” = 7786 citations “Oncogene Proteins, Fusion” and “Leukemia, Lymphocytic, Acute” = 453 citations

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58. Thyroglobulin

Test name	Thyroglobulin
Description	Thyroglobulin is elevated in differential thyroid tumors. Thyroglobulin is a tumor marker useful to assess the presence of residual papillary-follicular carcinoma of thyroid following resection, including tumors that fail to concentrate radioiodine. Additionally, thyroglobulin assays are used to monitor postoperative thyroid carcinoma patients.
Purpose	Recurrence, monitoring
Availability	Commercial laboratories, academic hospitals
Specimen	Serum
Methodology	ICMA
Cancers	Thyroid carcinoma
Clinical use(s)   a) Routine:	Detection of residual disease following resection Monitor therapeutic response Detect disease recurrence
Source of information	LabCorp and UpToDate Web sites
Exploratory Medline search (8/2/05)	“Thyroglobulin” = 1,501 citations “Thyroid neoplasms” = 9,062 citations “Thyroglobulin” and “Thyroid neoplasms” = 578 citations

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59. Tumor antigen 90 immune complex

Test name	Tumor antigen 90 immune complex
Other names	TA90-IC
Description	TA90 is a 90-kd tumor-associated antigen that is expressed by > 70 percent of melanomas. After curative resection of malignant melanoma, patients with occult metastasis may exhibit elevated levels of a TA90-IgG immune complex. TA90-IC is a sensitive and specific marker of recurrence in patients with malignant melanoma and is associated with shortened survival.
Purpose	Prognostic, recurrence, monitoring
Availability	Commercial laboratories, academic hospitals
Specimen	Serum
Methodology	EIA
Cancers	Melanoma
Clinical use(s)   a) Routine:	Assess prognosis after curative resection of malignant melanoma Monitor patients for melanoma recurrence after curative resection
Source of information	Quest Diagostics and UpToDate Web sites
Exploratory Medline search (8/2/05)	“Melanoma” = 17,770 citations “Antigens, Neoplasm” = 25,465 citations “Melanoma” and “Antigens, Neoplasm” = 1,128 citations

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60. Urokinase plasminogen activator

Test name	Urokinase plasminogen activator
Other names	uPA, PAI-1 (plasminogen activator inhibitor)
Description	The serine protease urokinase-type plasminogen activator (uPA) and its primary inhibitor, plasminogen activator inhibitor-1 (PAI-1), have shown promise for risk assessment and prediction of therapeutic response in primary breast cancer. High levels of uPA or PAI-1 in primary tumor tissue are associated with an aggressive disease course and poor prognosis in both node-positive and node-negative breast cancer.
Purpose	Prognostic
Availability	Commercial laboratories, academic hospitals
Specimen	Tissue
Methodology	EIA
Cancers	Breast
Clinical use(s)   a) Routine:	Assess risk of breast cancer recurrence after primary treatment Assess need for adjuvant therapy in women with lymph node-negative breast cancer Predict therapeutic response to adjuvant chemotherapy
Source of information	Quest diagnostics
Exploratory Medline search (8/2/05)	“Plasminogen Activator Inhibitor 1” = 3,320 citations “Urinary Plasminogen Activator” = 3,442 citations “Breast Neoplasms” = 57,603 citations “Plasminogen Activator Inhibitor 1” and “Breast Neoplasms” = 142 citations

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61. Urovysion

Test name	Urovysion
Other names	Vysis Urovision
Description	Detects chromosomal abnormalities associated with the development and progression of bladder cancer. Specifically, this test detects aneuploidy of chromosomes 3, 7, 17, and loss of the 9p21 locus. It detects high grade pT1 and pTis tumors that can be overlooked with traditional diagnostic methods and have high progression rates to muscle-invasive cancer
Purpose	Recurrence
Availability	Commercial laboratories, academic hospitals
Specimen	Urine
Methodology	FISH
Cancers	Bladder
Clinical use(s)   a) Routine:	Detection of bladder cancer recurrence
Source of information	Quest Diagnostics, Urovision, and UpToDate Web sites
Exploratory Medline search (8/2/05)	“Urovysion” = 17 citations “Bladder Neoplasms” = 9,483 citations “Urovysion” and “Bladder Neoplasms” = 16 citations

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62. ZAP-70

Test name	ZAP-70
Description	ZAP-70 is a 70-kD member of the Syk family of protein tyrosine kinases. It is expressed primarily in T-cells and natural killer (NK) cells and is critical for signal transduction following T-cell receptor engagement. In CLL B-cells, elevated ZAP-70 expression appears to predict the need for therapy as effectively as IgVH mutation status. Although ZAP-70 expression is strongly correlated with IgVH mutation status, the combination of the two markers may provide greater prognostic value than either marker alone. Positive ZAP-70 results predict an aggressive disease course.
Purpose	Prognostic
Availability	Commercial laboratories, academic hospitals
Specimen	Blood, marrow
Methodology	Flow cytometry
Cancers	CLL
Clinical use(s)   a) Routine:	Assess prognosis and need for aggressive therapy in patients with chronic lymphocytic leukemia (CLL)
Source of information	Quest Diagnostics and UpToDate Web sites
Exploratory Medline search (8/2/05)	“Protein-Tyrosine Kinase” = 45,983 citations “Leukemia, Lymphocytic, Chronic” = 3,422 citations “Protein-Tyrosine Kinase” and “Leukemia, Lymphocytic, Chronic” = 62 citations

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