The cobas® CT/NG Test is an automated, in vitro nucleic acid amplification test for the qualitative detection of Neisseria gonorrhoeae (NG or GC) DNA in urogenital specimens.
Infection with Neisseria gonorrhoeae (NG) is the causative agent of gonorrhea. Clinical manifestations of NG infections are numerous. In men; acute urethritis presents itself after a 1- 10 day incubation period with urethral discharge and dysuria. Only a small proportion of men remain asymptomatic without signs of urethritis. Acute epididymitis is the most common complication, especially in young men. In women, the primary site of infection is the endocervix. In symptomatic women increased discharge, dysuria, and intermenstrual bleeding may be observed. Pelvic inflammatory disease can occur in 10%-20% of women, combined with endometritis, salpingitis, tubo ovarian abscess, pelvic peritonitis, and perihepatitis. Other gonococcal infected sites in men and women are the rectum, pharynx, conjunctiva, and to a lesser degree the disease presents itself as disseminated gonococcal infection. Infants from infected mothers can develop conjunctivitis.
Urine (First catch, preferred), Vaginal/Endocervical Swab, ThinPrep, (See OB/GYN Specimen Collection Media)
A: Urine Collection for Male and Female (using Cobas PCR Kit)
B: Vaginal swab – Clinician collection
C: Endocervical swab
D: Endocervical ThinPrep using Plastic Spatula and Brush
E: Cervical ThinPrep using a Broom-like device
A: Urine Collection
Urine specimens with more than 24 hours of collected without transferred to cobas PCR media. Urine specimen with volume under or above the black lines, specimen contains excess of blood (has a dark red or brown color), Expired collection and transport vials, specimens contains excess of mucous, swab specimens without Dacron or Flock swab inside.
The cobas® CT/NG Test is an automated, in vitro nucleic acid amplification test for the qualitative detection of Chlamydia trachomatis (CT) DNA in urogenital specimens.
Infection with Chlamydia trachomatis (CT) is the most frequently reported bacterial sexually transmitted disease (STD) in the United States. CT can cause urethritis, cervicitis, proctitis, conjunctivitis, endometritis, and salpingitis; if left untreated, the infection may ascend to the uterus, fallopian tubes, and ovaries causing pelvic inflammatory syndrome, ectopic pregnancy, and tubal factor infertility. Reiter’s syndrome (urethritis, conjunctivitis, arthritis, and mucocutaneous lesions) has also been associated with genital CT infection. Many infections remain asymptomatic, and high numbers of infected patients may not seek care.
After a diagnosis of metastatic breast cancer has been made, Her-2/neu testing may be used as a prognostic marker to help determine how aggressive the breast cancer tumor is likely to be. It is usually ordered along with estrogen and progesterone hormone receptor status tests (ER and PR). The results of these three tests give the doctor information about the person’s likely prognosis and response to specific therapies such as hormone therapy and chemotherapy.
The serum Her2/neu test is sometimes used to monitor Her2/neu-positive breast cancer patients who are receiving cancer therapy including, for example, hormone therapy, chemotherapy, or Her-2/neu targeted therapy. If the level of serum Her-2/neu is initially elevated (greater than 15 ng/mL) then falls, it is likely that treatment is working; if it stays elevated, treatment is not working; and if the level falls then rises, the cancer may be recurring.
The Papanicolau test (also called Pap smear, Pap test, cervical smear, or smear test) is a screening test used in gynecology to detect premalignant and malignant (cancerous) processes in the ectocervix. Significant changes can be treated, thus preventing cervical cancer. An anal Pap smear is an adaptation of the procedure to screen and detect anal cancers.
The test aims to detect potentially pre-cancerous changes (called cervical intraepithelial neoplasia (CIN) or cervical dysplasia), which are usually caused by sexually transmitted human papillomaviruses (HPVs). The test remains an effective, widely used method for early detection of pre-cancer and cervical cancer. The test may also detect infections and abnormalities in the endocervix and endometrium.
In general, it is recommended that females who have had sex seek regular Pap smear testing. Guidelines on frequency are annually. If results are abnormal, and depending on the nature of the abnormality, the test may need to be repeated in three to twelve months. If the abnormality requires closer scrutiny, the patient may be referred for detailed inspection of the cervix by colposcopy. The patient may also be referred for HPV DNA testing, which can serve as an adjunct to Pap testing.
Transcription Mediated Amplification (TMA) and Dual Kinetic Assay (DKA).
The APTIMA Combo 2 Assay is an automated, target amplification nucleic acid probe test that utilizes target capture for the in vitro qualitative detection of ribosomal RNA (rRNA) of Neisseria Gonorrhoeae (NG or GC) in urogenital specimens.
A: Urine Collection for Male (using Aptima PCR Urine Kit)
B: Vaginal swab – Clinician collection (using Aptima Unisex Swab Kit)
Urine specimens with more than 24 hours of collected without transferred to Aptima Urine media. Urine specimen with volume under or above the black lines, specimen contains excess of blood (has a dark red or brown color), expired collection and transport vials, specimens contains excess of mucous, swab specimens without Dacron or Flock swab inside.
Chlamydia is the most frequently reported bacterial sexually transmitted disease. If untreated, chlamydial infections can progress to serious reproductive and other health problems with both short-term and long-term consequences. Like the disease itself, the damage that chlamydia causes is often “silent.”
The COBAS® TaqMan® CT Test, v2.0 is an in vitro nucleic acid amplification test for the qualitative detection of Chlamydia trachomatis DNA in female endocervical swab specimens or male and female urine, using the AMPLICOR® CT/NG Sample Preparation Kit for manual specimen preparation and the COBAS® TaqMan® 48 Analyzer for automated amplification and detection.
Fluorescent In situ Hybridization
The Abbott® PathVysion HER-2 DNA Probe Kit (PathVysion Kit) is designed to detect amplification of the HER-2/neu gene via fluorescence in situ hybridization (FISH) in formalin- fixed, paraffin-embedded human breast and gastric cancer tissue specimens. In situ hybridization is a technique that allows the visualization of specific nucleic acid sequences within a cellular preparation. Specifically, DNA fluorescence in situ hybridization (FISH) involves the precise annealing of a single stranded, fluorescently-labeled DNA probe to complementary target sequences. The hybridization of the probe with the cellular DNA site is visible by direct detection using fluorescence microscopy.
Aid in prediction of response to HER2-directed therapy in patients with breast or gastric cancer. For breast and gastric cancer indication, results from the PathVysion Kit are intended for use as an adjunct to existing clinical and pathologic information currently used as prognostic. The PathVysion Kit is indicated as an aid in the assessment of breast and gastric cancer patients for whom HERCEPTIN® (trastuzumab) treatment is being considered.
Breast and Gastric, Tumor Tissue
Specimens fixed/processed in alternative fixatives. Insufficient quantity of tumor tissue.
Yes (CPT: 88377)
The frozen section procedure is used to perform rapid microscopic analysis of a specimen. It is used most often in oncological surgery. The intraoperative consultation which includes not only frozen section but also the gross evaluation of the specimen, the examination of cytology preparations taken on the specimen (e.g. touch imprints), and aliquoting of the specimen for special studies. The report given by the pathologist is usually limited to a “benign” or “malignant” diagnosis, and communicated to the surgeon operating via telephone. When operating on a previously confirmed malignancy, the main purpose of the pathologist is to inform the surgeon if the surgical margin is clear of residual cancer, or if residual cancer is present at the surgical margin.
Biological tissue has little inherent contrast in either the light or electron microscope. Staining is employed to give both contrast to the tissue as well as highlighting particular features of interest. Hematoxylin and eosin (H&E) is the most commonly used light microscopical stain in histology and histopathology. Hematoxylin, a basic dye, stains nuclei blue due to an affinity to nucleic acids in the cell nucleus; eosin, an acidic dye, stains the cytoplasm pink. Uranyl acetate and lead citrate are commonly used to impart contrast to tissue in the electron microscope.
There are hundreds of various other techniques that have been used to selectively stain cells and cellular components. Other compounds used to color tissue sections include safranin, oil red o, Congo red, fast green FCF, silver salts, and numerous natural and artificial dyes.
Immunohistochemistry or IHC refers to the process of localizing antigens (eg. proteins) in cells of a tissue section exploiting the principle of antibodies binding specifically to antigens in biological tissues.  Immunohistochemical staining is widely used in the diagnosis of abnormal cells such as those found in cancerous tumors. Specific molecular markers are characteristic of particular cellular events such as proliferation or cell death (apoptosis). Visualising an antibody-antigen interaction can be accomplished in a number of ways. In the most common instance, an antibody is conjugated to an enzyme, such as peroxidase, that can catalyse a colour-producing reaction.
A biopsy is the medical removal of tissue from a living subject to determine the presence or extent of a disease. When the laboratory receives the biopsy sample, the tissue is processed and an extremely thin slice of tissue is removed from the sample and attached to a glass slide. Any remaining tissue is saved for use in later studies, if required. The slide with the tissue attached is treated with dyes that stain the tissue, which allows the individual cells in the tissue to be seen more clearly. The slide is then given to the pathologist who examines the tissue looking for any abnormal findings. Depending on the result, the pathologist might request additional studies such as Immunohistochemistry, ER/PR/HER2-Neu, FISH, etc.
The cobas® HPV high risk Test is an automated, in vitro nucleic acid amplification test for the qualitative detection of HPV in cervical, anal and oral specimens collected by a clinician. The test utilizes amplification of target DNA by the Polymerase Chain Reaction (PCR) and nucleic acid hybridization for the detection of 14 high-risk HPV types (31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68) in a single analysis and specifically identifies types HPV16 and HPV18.
The Human Papilloma Virus (HPV) is a small, non-enveloped, double-stranded DNA virus, with a genome of approximately 8000 nucleotides. There are more than 118 different types of HPV, and approximately 40 different HPVs that can infect the human anal-genital and oral cavity mucosa. Persistent infection with HPV is the principal cause of cervical cancer and its precursor cervical intraepithelial neoplasia (CIN). The presence of HPV has been implicated in greater than 99% of cervical cancers, worldwide. However, only a subset of approximately 14 of these types is considered high-risk for the development of cervical cancer and its precursor lesions.
ThinPrep, (See OB/GYN Specimen Collection Media)
A: Endocervical ThinPrep using Plastic Spatula and Brush
B: Cervical ThinPrep using a Broom-like device
C: Anal ThinPrep (using a Dacron/Floq Swab or Cytobrush)
D: Oral ThinPrep (using a Dacron/Floq Swab or Cytobrush)
Specimen contains excess of blood (has a dark red or brown color), Expired collection and transport vials, specimens contains excess of mucous. Less than 1mL of ThinPrep volume after the Pap test. Anal specimen grossly contaminated with feces.
In vitro Nucleic Acid Amplification Test
The assay measures the concentration of Prostate Gene Cancer3 (PCA3) and Prostate Specific Antigen (PSA) RNA molecules and calculates the ratio of PSA RNA molecules (PCA3 Score) in post -digital exam (DRE)fist catch male urine specimens.
Prostate Cancer Gene 3 (PCA3) is strongly expressed in 95% of primary prostate cancer specimens. The PCA3 test is indicated for use in conjunction with other patient information to aid in the decision for repeat biopsy in men age 50 or older who have had one or more previous negative prostate biopsies and for whom a repeat biopsy would be recommended by an urologist based on current standard care. The PCA3 result provide a risk assessment of a positive biopsy. This assay should not be used for men with atypical small acinar proliferation (ASAP)on their most recent biopsy. Men with ASAP on their recent biopsy should be treated in accordance with current medical guidelines.
Collect first catch (aprox. 20 – 30 ml of the initial stream) urine sample in an urine cup after DRE has been performed. Invert sample five times to resuspend the cells. Transfer 2.5 ml of urine (fill until the fluid level is between the black lines) into the Gen-Probe Progensa urine specimen transport tube using the disposable pipette provided. Recap the urine specimen transport tube tightly and invert five times to mix.
Gen-Probe Urine Specimen Transport Tube. Refrigerated.
Important: Verify expiration date of the Gen Probe urine specimen transport tube before procedure. Samples taken in expired sample collection tubes are not accepted for processing. Samples should arrive at SPS in 48 hrs or less.
Before collection, patient must undergo an attentive digital rectal exam (three strokes per lobe).
Evaluate stone composition, metabolic factors affecting stone formation; work up nephrolithiasis.
The incidence of urinary tract calculi is common, with one person in 1000 requiring hospital care and treatment. A typical urinary calculus is composed of crystalline substances precipitated in the body. To ensure proper treatment and prevention of recurrences of urinary calculi, it is critical that crystalline constituents of the stone be identified.
Calculi must be submitted completely dry.
Fluorescent In-situ Hybridization (FISH)
The Abbott® UroVysion Bladder Cancer Kit is designed to detect aneuploidy for chromosomes 3, 7, 17, and the loss of the 9p21 locus via FISH in urine specimens from persons with hematuria suspected of having bladder cancer.
Results from the UroVysion Kit are intended for use, in conjunction with and not in lieu or current standard diagnostic procedures, as an aid for initial diagnosis of bladder carcinoma in patients with hematuria and subsequent monitoring for tumor recurrence in patients previously diagnosed with bladder cancer.
Voided urine specimen with PreservCyt 2:1 (v:v). Minimum 33mL.
To obtain the greatest yield of diagnostic material:
The patient should not be urinating at least in two hour from the first urine.
Specimens in inappropriate fixative. Specimens submitted in expired reagents. Insufficient quantity urine. Urine specimens with more than 72 hours of collection. Low cellularity.
Yes (CPT: 88120)
Liquid based preparation
TP Processor 2000
Leica Auto Stainer
Urine cytology is a simple, inexpensive and effective tool in the detection and follow-up of high grade primary and secondary malignancies involving the urinary bladder. Urine cytology is also valuable in the detection of carcinoma insitu (CIS), where cystoscopy may be negative. It is also useful to follow-up recurrence of urothelial carcinoma (low and high grade), including screening for upper urinary tract lesions in patients status post cystectomy.
The most common indication for urinary cytology is hematuria. Another indication is surveillance for recurrent Urothelial Carcinoma, because patients with a previously diagnosed and treated urothelial cancer are at risk for recurrence. Several variables affect the sensitivity of urine cytology. First, sensitivity is higher (37% to 89%) when suspicious diagnoses are included with positive diagnoses. Second, the sensitivity increases when more than one specimen is examined. For this reason, it has been recommended at least three specimens per patient be examined. Third, the sensitivity of urine cytology is highly dependent on the grade of the bladder tumor. Ancillary techniques such as FISH method may more sensitive than cytology.
Three samples of urine are to be collected on 3 consecutive days. Second voided urine provide better preserved cells. First morning voided urine should be avoided because cells are mostly degenerated. The minimum amount of urine necessary to ensure adequate cellularity may be as high 25 to 100 mL.
Collect the urine in container with PreservCyt solution to preserve cells. Store PreservCyt solution with non-gynecological sample between 4˚C (39˚F) and 37˚C (98˚F) for up to 3 weeks.
Collect second urine of the morning and the patient should not be urinate at least in two hour from the first urine. Repeat the process during three consecutive days.
Urine cytology is a simple, inexpensive and effective tool in the detection and follow-up of high grade primary and secondary malignancies involving the urinary bladder.
The most common indication for urinary cytology is hematuria. Another indication is surveillance for recurrent Urothelial Carcinoma, because patients with a previously diagnosed and treated urothelial cancer are at risk for recurrence.
Urine (Second collection of the day).
ThinPrep (Preserv Cyt) Storage and Transport at Room Temperature.
Collect second urine of the morning and the patient should not be urinate at least in two hour from the first urine.
Liquid based preparation
TP Processor 2000
Leica Auto Stainer
Sputum consist of a mixture of cellular and noncellular elements that are cleared by mucociliary apparatus. It was once the most common respiratory tract specimen because is relatively easy to obtain, with little discomfort to the patient. Sputum cytology is generally reserved for symptomatic individuals.
In order to have an adequate specimen, there must be alveolar macrophages present. That indicates a satisfactory deep cough specimen of the lower respiratory tract has been obtained. The sensitivity of sputum cytology for the diagnosis of malignancy increases with the number of specimens examined, from 42% with a single specimen to 91% with five specimens. Th sensitivity of sputum cytology depends also on the location of the malignant tumor: 46% to 77% from central lung cancers but only 31% to 47% from peripheral cancers.
Collecting multiple sputum samples over several days optimizes sensitivity. Early morning, deep cough specimens are preferred. If the patient is not able to expectorate adequately, expectoration can be induced by having the patient inhale nebulized water or saline. Sputum induction increases the detection of lung cancer.
The patient can expectorate into a sterile container. The specimen can be fixed with Saccomanno or Cytolyt solution. Also smears can be directly prepared and immediately fixed in 95% alcohol. Identify specimen container with patient’s name, date of birth, specimen type and collection date.
BAL specimens are obtained by infusion and reaspiration of sterile saline into distal areas of the lung.
BAL is particularly useful for the diagnosis of opportunistic infections in immunocompromised patients. Sensitivity: 82% (comparable to transbronchial biopsy sensitivity of 86%), when done with biopsy, the sensitivity increases to 98%. BAL can occasionally be used in the diagnosis of malignancy. Sensitivity: 35 – 70% (higher for multifocal tumors like bronchoalvelar carcinoma. BAL can be done as a part of therapy for diseases like protein alveolar proteinosis, cystic fibrosis, pulmonary alveolar microlithiasis and asthma.
With BAL, the bronchoscope is wedged into position as far as it will go in order to sample distal airways, which is flushed with sterile saline.
BAL should be collected in sterile container and fixed in 95% alcohol or Cytolyt solution. Label the container with patient name, date of birth, collection date and specimen type.
These specimens are from the lower respiratory tract and obtained using bronchoscopy. Brushings will usually be performed if there is a lesion that can be visualized on bronchoscopy, whereas a washing is typically done if there is no discrete endobronchial lesion seen.
For diagnosis of endobronchial lesion or masses. The diagnostic accuracy of bronchial washing / brushing cytology is comparable to that of bronchial biopsy. Accuracy improves when clinical history is provided with the specimen. The diagnostic yield also improves when several different sampling methods are used in concert.
Bronchial secretions can be aspirated directly from the lower respiratory tract through the bronchoscope, but an alternative (and more common)method is to wash the mucosa by instilling 3 to 10 mL of saline and suctioning the washings. Fiberoptic bronchoscopy allows direct visualization of the tracheobronchial tree. A brush is applied to the surface of an endobronchial lesion to collect the cells.
Bronchial washings should be collected in sterile container and fixed in 95% alcohol or Cytolyt solution. For bronchial brushings the entrapped cells are either smeared onto a glass slide or rinsed in a collection medium for thinlayer or in saline solution. If smeras are made immediate fixation into 95% alcohol or by spray is essential to preserve morphology details.
Liquid based preparation
An effusion is the accumulation of fluid in a serous body cavity (pleural, peritoneal and pericardial space). The primary purpose of cytology examination of serous fluid specimen is to detect malignancy. However. it is also possible to diagnose a variety of benign and infectious entities.
Diagnostic accuracy of effusion cytology depends on the volume of the liquid specimen examined (minimum of 20 – 50 mL is required), the type preparation and staining, the experience / training of the examiner, and the number of specimens examined. The sensitivity of one specimen is 53%, and this increases to 67% with 2 specimens and 73% with 3 specimens. Cell block preparation increases the sensitivity of detecting malignancy by 5 -10%. It is also useful for performing ancillary testing, if needed.
Serous fluid should be collected in a clean container without fixative, and sent directly to the laboratory. If the specimen cannot be directly sent, it can be refrigerated at 4˚C or adding a fixative, (50% alcohol or Cytolyt Solution).
Large quantities, ususally received in plastic bags shold be keep it refrigerated at 4˚C until transport. Label all containers with complete patient name, date of birth, collection date and specimen type.
The ASI RPR Test is a qualitative and semi quantitative nontreponemal flocculation test to be used for the macroscopic detection of regain antibodies in human serum as a screening test in syphilis serology. The micro particulate carbon RPR antigen enhances the visual discrimination between reactive and nonreactive results. The reagin-type antibody binds with the antigen that is composed of a complex of cardiolipin, lecithin and cholesterol particles with activated charcoal.
Treponema pallidum subspecies pallidum is the etiological agent of venereal syphilis, a sexually transmitted infection (STI). Treponema pallidum induces the production of anti-nontreponemal antibodies (regain) in human infection. If left untreated, syphilis can result in multisystem involvement with significant morbidity. Of note, mothers infected with syphilis can pass the infection to their children in utero (congenital syphilis).
Serum (Red Top Blood Collection Tube)
Strongly Hemolyzed specimens. Strongly lipemic specimens. Expired collection tube.
The cobas® HSV 1 and 2 Test is an automated, in vitro nucleic acid amplification test for the qualitative direct detection and differentiation of Herpes simplex virus 1 (HSV-1) and 2 (HSV-2) DNA in clinician-collected, external anogenital lesion specimens from symptomatic male and female patients.
Genital herpes is a sexually transmitted disease (STD) caused by Herpes simplex virus (HSV-1 and HSV-2), ubiquitous double-stranded neurotropic DNA viruses of the Herpesviridae family. Following primary infection via secretions the virus persists lifelong. The virus may remain latent for a prolonged time or cause recurrent episodes of reactivated symptomatic disease; the number of recurrences tends to decrease over a period of years. Most genital herpes infections are caused by HSV-2. HSV-1 can cause genital herpes, but it more commonly causes infections of the mouth and lips. Transmission of genital herpes is commonly caused by individuals that are unaware of their infections, or those with asymptomatic infections. Pre- or perinatal transmission of HSV to the neonate may result in severe disease or even death.
Anogenital Lesion Swab, (See OB/GYN Specimen Collection Media)
A: Anogenital Lesion with vesicles present (clear fluid-filled blister)
B: Anogenital Lesion with vesicles absent (ruptured and or weeping vesicle)
C: Anogenital Lesion with vesicles absent (crusted ulcer)
For optimal results, specimens should be collected in the acute stage of the disease whenever possible, preferably within 3 days and less than 7 days after onset of illness (eruption of lesions).
Specimen contains excess of blood (has a dark red or brown color), expired collection and transport vials, specimens without Flock swab inside, specimens collected by the patient.
Real Time PCR
The cobas® MRSA/SA Test is a qualitative in vitro diagnostic real-time PCR assay, for the direct detection of methicillin-resistant Staphylococcus aureus (MRSA) and S. aureus (SA) DNA from nasal swabs to aid in the prevention and control of MRSA and SA infections in healthcare settings.
Staphylococcus Aureus (SA) is an opportunistic pathogen carried as a commensal organism on the skin and nares of approximately 30% of the normal population. It has the potential to cause a broad spectrum of diseases. SA can rapidly adapt to the selective pressure of antibiotics, which has resulted in the emergence and spread of Methicillin Resistant Staphylococcus aureus (MRSA) strains.SA and MRSA strains are a major source of healthcare-acquired infections and have been responsible for bacterial outbreaks in healthcare settings worldwide for many years. SA and MRSA infections are a tremendous burden for healthcare systems, for single hospitals, and are associated with significant healthcare costs. Guidelines and recommendations as well as hospital standard procedures recommend active screening and isolation and/or decolonization of patients as measures to control the spread of MRSA and SA.
Nasal Swab (using the MSwab Kit)
Specimen contains excess of blood (has a dark red or brown color), Expired collection vial, specimens contains excess of mucous, swab specimens with more than one Flock swab or without Flock swab inside.
Beckman Coulter FC-500
Immunophenotyping of White Blood Cells (WBC) from specimens with known or suspected hematopoietic neoplasms or other hematological disorders.
Hematopoietic neoplasms and other hematological disorders may be identified.
Bone Marrow, Peripheral Blood, Cerebrospinal Fluid, Fresh Tissue, others.
Bone Marrow and Peripheral Blood must be collected in Heparin. Cerebrospinal fluid and fresh tissue must be collected in saline (i.e. PBS 1x) or RPMI solution. Sample must be transported at room temperature.
Immunophenotyping of T-lymphocytes with monoclonal antibodies against CD3, CD4 and CD8 molecules expressed in the surface of cells. Specific cell staining is accomplished by incubating whole blood with the monoclonal antibody reagent
Identification of abnormal levels of CD4+ immunodeficiency, and corresponding CD4+/CD8+ ratios, might also aid in the diagnosis and/or prognosis of immunodeficiency disease. For example, infection with human immunodeficiency virus (HIV), the etiologic agent of acquired immunodeficiency syndrome (AIDS), results in profound immunosuppression due predominantly to a selective depletion of the CD4+ lymphocytes that express the receptor for the virus. Progressive clinical and immunologic deterioration generally correlates with a decreasing CD4+ lymphocyte count.
Peripheral Blood in EDTA. Transport at room temperature. Sample must be processed in 24 hours from the collection time.
PCR by Reference Laboratory
Varies by Reference Laboratory
NRAS mutation is recommended in colorectal cancer to identify mutations associated to resistance to anti EGFR therapies. NRAS mutations have been described in a variety of cancers including 3-5% of colorectal carcinomas, 10-20% of melanomas and 10% of acute myeloid leukemia’s. Mutations leading to an amino acid substitution at positions 12, 13, 61 and 146 of NRAS are the most common in naturally occurring neoplasms.
Colon, Tumor Tissue
4. Fix tissue in 10% neutral buffered formalin immediately after collection to avoid tissue degradation. Formalin Fixed Paraffin Embedded (FFPE) tissues are also acceptable.
5. Label the specimen vial with Patient Name, Date of Birth (DOB), Sample Type, Date and Time of Collection.
6. Store and transport at room temperature in 24 hours after collection.
Yes (CPT: 81311)
Real Time-PCR or Sequencing
The cobas® KRAS Mutation Test is a real-time PCR test for the detection of somatic mutations in codons 12, 13 (exon 2) and 61 (exon 3) of the KRAS gene in DNA derived from formalin-fixed paraffin-embedded human colorectal cancer (CRC) tumor tissue. Types of specimens other than Colon for KRAS by RT-PCR or Sequencing are sent to reference laboratory.
The test is intended to be used as an aid in the identification of CRC patients who should not be treated with Erbitux® (cetuximab) or with Vectibix® (panitumumab) when KRAS Codon 12 or 13 mutations is detected. Safety and efficacy of Erbitux® (cetuximab) or Vectibix® (panitumumab) have not been established in patients whose tumors have Codon 61 mutation. KRAS mutation is also recommended in non-small cell lung cancer (NSCLC) to predict EGFR response and patient’s prognosis.
Colon and Lung, Tumor Tissue
Yes (CPT: 81275, 81276)
The cobas® EGFR Mutation Test v2 is a real-time PCR test for the qualitative detection of defined mutations of the epidermal growth factor receptor (EGFR) gene in non-small cell lung cancer (NSCLC) patients. The cobas® EGFR Test is designed to detect the following mutations:
Exon 18: G719X (G719A, G719C, and G719S),
Exon 19: deletions and complex mutations (defined as the combination of a deletion and an insertion),
Exon 20: S768I, T790M, and insertions,
Exon 21: L858R and L861Q.
Types of specimens other than lung for EGFR by RT-PCR or Sequencing are sent to reference laboratory.
The test is indicated as a companion diagnostic to aid in selecting NSCLC patients for treatment with the targeted therapies in accordance with the approved therapeutic product labeling. EGFR mutation analysis is recommended in non-small cell lung carcinoma (NSCLC) to detect mutations associated with increased sensitivity to EGFR tyrosine kinase inhibitors.
Lung, Tumor Tissue
Yes (CPT: 81235)
The cobas® 4800 BRAF V600 Mutation Test is an in vitro diagnostic real-time PCR test intended for the qualitative detection of BRAF V600E mutation in DNA extracted from formalin-fixed, paraffin-embedded human colorectal tissue. Melanoma, Lung and other specimen types for BRAF by RT-PCR or Sequencing are sent to reference laboratory.
The tests is intended to be used as an aid in selecting patients whose tumors carry the BRAF V600E mutation for treatment with BRAF inhibitor therapy (ex. vemurafenib). Detection of BRAF V600 mutation in colorectal cancer provides information about patient’s prognosis, response to therapy and may be used as an aid in the diagnosis of Lynch Syndrome. Information obtained from BRAF mutation analysis is used for selection of melanoma patients for vemurafenib therapy and for determination of prognosis and predicting response to anti-EGFR therapy in colon cancer.
Colon, Melanoma and Lung, Tumor Tissue
Yes (CPT: 81210)
MSI analysis and/or MMR IHC may be considered for all new colorectal cancer diagnoses to detect patients at increased risk of carrying germline mutations associated with Lynch Syndrome (HNPCC). Testing is recommended for tumors of patients meeting the Bethesda Guidelines. Recently, Keytruda (pembrolizumab) is indicated for the treatment of adult and pediatric patients with unresectable or metastatic solid tumors that have been identified as having a biomarker referred to as microsatellite instability-high (MSI-H) or mismatch repair deficient (dMMR). MSI is also detected in sporadic colorectal cancer and its presence may imply better prognosis.
Tumor and additional patient sample from normal, non-tumor tissue is required for comparison testing in MSI Analysis. Specimens for normal tissue are: 5 mL peripheral blood in EDTA tube OR FFPE tissue slides or block containing only non-tumor tissue. Please label these as “normal tissue”. OR in cases where no alternative tissue is available, we can attempt to isolate non- tumor tissue from the tumor specimen submitted.
1. Fix Tumor and Normal tissue in 10% neutral buffered formalin immediately after collection to avoid tissue degradation. Formalin Fixed Paraffin Embedded (FFPE) tissues are also acceptable. Specimens for normal tissue are: 5 mL peripheral blood in EDTA tube OR FFPE tissue slides or block containing only non-tumor tissue. Please label these as “normal tissue”.
2. Label the specimen vial with Patient Name, Date of Birth (DOB), Sample Type, Date and Time of Collection.
3. Store and transport at room temperature in 24 hours after collection.
Yes (CPT: 81301)
Cerebrospinal fluid is an ultrafiltrate of plasma produced by the chroroid plexus that flows the ventricles to the subarachnoid space and is a reabsorbed through the arachnoid villi into venous sinuses.
CSF cytologic examination is not a screening test, but a crucial diagnostic test for evaluating a wide variety of treatable yet potentially fatal diseases and conditions affecting the CNS. Conditions that can be diagnosed by cytologic examination includes: Primary tumors of the CNS or metastatic cancer, Infectious disease (meningitis and encephalitis), Inflammatory disease and Hemorrhage. Other noncytologic tests can be done on CSF including cell counts, chemical analysis, immunologic and serologic testing, flow cytometry, molecular testing and microbiologic culture. The sensitivity of CSF cytology for detecting malignant cells is about 60%, but sensitivity depends on several factors. The sensitivity of a single cytologic examination is 54% but increases to 84% with a second sample.
CSF specimens are most commonly obtained by passing a needle through the intervertebral space of the lumbar portion of the spinal column with the patient on his or her side (lumbar puncture). A minimum of 1 mL should be collected for cytologic evaluation, but 3 mL or more is preferable.
CSF should be collected fresh and delivered to the laboratory as quickly as possible to prevent cellular degeneration. If specimen cannot be prepared immediately, it should be refrigerated at 4˚C. If a delay of more than 48 hours is anticipated, cytomorphology can be preserved by adding an equal volume of 50% ethanol or RPMI.
Fluorescent In situ Hybridization
Liquid based preparation
Abbott Her2 DNA Probe Kit
In situ hybridization is a technique that allows the visualization of specific nucleic acid sequences within a cellular preparation. Specifically, DNA fluorescence in situ hybridization (FISH) involves the precise annealing of a single stranded, fluorescently-labeled DNA probe to complementary target sequences. The hybridization of the probe with the cellular DNA site is visible by direct detection using fluorescence microscopy.HER-2 DNA FISH detect amplification of the HER-2/neu gene via fluorescence in situ hybridization (FISH) in formalin-fixed, paraffin-embedded human gastric cancer tissue specimens.
Results from the HER-2 FISH are intended for use as an adjunct to existing clinical and pathologic information currently used as prognostic. The HER-2 FISH assay is indicated as an aid in the assessment of gastric cancer patients for whom HERCEPTIN® (trastuzumab) treatment is being considered.
In situ hybridization is a technique that allows the visualization of specific nucleic acid sequences within a cellular preparation. Specifically, DNA fluorescence in situ hybridization (FISH) involves the precise annealing of a single stranded, fluorescently-labeled DNA probe to complementary target sequences. The hybridization of the probe with the cellular DNA site is visible by direct detection using fluorescence microscopy.HER-2 DNA FISH detect amplification of the HER-2/neu gene via fluorescence in situ hybridization (FISH) in formalin-fixed, paraffin-embedded human breast cancer tissue specimens.
Results from the HER-2 FISH are intended for use as an adjunct to existing clinical and pathologic information currently used as prognostic. The HER-2 FISH assay is indicated as an aid in the assessment of breast cancer patients for whom HERCEPTIN® (trastuzumab) treatment is being considered.
TP Processor 2000
Leica Auto Stainer
Synovial fluid, which lubricates the joints, is secreted by synovium, a membrane lining the joint capsules, provided with a highly specialized epithelium. Under normal circumstances, the fluid forms a thinlayer moistening the surface of the joints. The volume of synovial fluid may increase after trauma or inflammation and can then be aspirated for cytologic analysis.
As in other body cavities, there is normally only a small amount of fluid in the joint space; increased fluid or an effusion, indicates a pathologic process. Microscopic examination of synovial fluid can detect infections, crystals and tumors, as well as suggest diseases such as lupus erythematosus.
Synovial fluid should be anticoagulated (heparin or liquid EDTA) for cytologic examination to prevent clotting.
The fluid should be examined fresh, preferably within 24 – 48 hours after collection.
Liquid based preparation
Fine needle aspiration is a non-invasive diagnostic procedure that can be performed in different tissue; the most common targets are breast, salivary gland, thyroid and lymph nodes. FNA can be performed by palpation or with the use of image-guidance.
FNA provides a minimally invasive, quick, accurate, cost-effective way to obtain diagnostic material that can provide clinical answers to guide treatment decisions. Most complications associated with FNA includes: minor pain, bleeding and bruising. A hematoma develops occasionally. The reported sensitivity of this procedure for salivary gland neoplasm is greater than 90% and for thyroid 83 – 99%. Use of ancillary techniques including immunocytochemistry, flow cytometry and molecular test to diagnose malignancy increase sensitivity and accuracy of FNA.
Label the slides with patient’s name, date of birth and location of the mass. Smears can be prepared by spreading material into a thin, even layer on a glass slide. Also the aspirated material can be rinsed into a liquid based cytology solution to minimize obscuring blood or debris.
The slide should be immediately placed in 95% alcohol or spray fixed to avoid air-drying artifact. Place the slide on a plastic holder for transportation. Store PreservCyt solution with non-gynecological sample between 4˚C (39˚F) and 37˚C (98˚F) for up to 3 weeks.
Patient under anticoagulant therapy cannot be evaluated until this treatment is temporarily discontinued. Order to discontinue any medication should be given by referring or primary care physician only.
Liquid based preparation
TP Processor 2000
Oral Cytology is an effective tool in screening for oral cancer, pre cancer and other specific viral diseases. Oral brush cytology is a simple and rapid, non-aggressive and relatively painless collection method.
Oral cytology has potential application for screening programs and for the surveillance of patients with confirmed cancerous and precancerous lesions.
Oral Cytology can be obtained by brushing visible lesions, border of the tongue and oral mucosa, rotating the brush 10 times. Then rinse cytobrush in to PreservCyt vial.
Store PreservCyt solution with non-gynecological sample between 4˚C (39˚F) and 37˚C (98˚F) for up to 3 weeks.
Anal cytology is used as a screening test for ASIL. An essential component of anal examination is the digital anorectal exam (DARE). This is the primary anal cancer screening test. When screening is directed to the populations at high risk for anal cancer, cytologic abnormalities are common.
The most important risk factor for anal neoplasia is infection by human papilloma virus (HPV). Other risk factors include receptive anal intercourse, number of life-time sexual partners, history of cervical, vaginal and or vulvar cancer, HIV infection and smoking. Sensitivity of anal cytology for HSIL were comparable to that of Pap test ranging from 69% to 93%.
Anal cytology specimens should be sample the entire anal canal including anorectal transformation zone. The sample is collected with the patient in the lateral recumbent or dorsal lithotomy position. A Dacron swab moistened with tap water or cytobrush is inserted about 5 to 6 cm into anal canal. The swab is rotated with firm lateral pressure and slowly withdrawn. Rinse the Dacron swab or cytobrush in to PreservCyt vial.
Liquid based preparation
Nipple discharge cytology is a simple, noninvasive method that complements patient assessment. The most common cause of nipple discharge is hormonal influences. However, pathologic conditions may lead to nipple discharge in the absence of pregnancy and lactation.
Pathologic nipple discharge is associated with papilloma; fibrocystic disease (most common) and rarely by carcinoma. The sensitivity of nipple discharge cytology ranges from 41% to 60%.
Nipple discharge specimens are prepared by gently massaging the breast in the direction of the nipple. A glass slide is then touched by secreted drops; the discharge need not be smeared unless it is abundant.
The slides are fixed by spray fixation or by immersion in 95% ethyl alcohol. Label the end frosted with patient’s name, date of birth, location site and collection date. Place the slide on a cardboard holder for transportation
Fine needle aspiration can be used to evaluate palpable and nonpalpable, mammographically evident breast lesions. Breast FNA can occasionally be therapeutic as well as diagnostic in cases of abscess and benign breast cyst.
The advantages of breast FNA include the fact that is a rapid, simple cost effective procedure with rare complications. Breast FNA also has high diagnostic accuracy and is useful in the management of a palpable breast mass. Sensitivity for malignancy ranges from 65% to 98%. Obtaining a good clinical history prior to breast FNA is essential to determine if there is a family or personal history of malignancy. A strong family history of breast carcinoma requires adequate sampling and material for cell block for potential ancillary testing.
Collect the aspiration in a sterile container, PreservCyt vial or in directly smear slide. Immediately fix the slide in 95% alcohol . Identify the the container and slides with patient’s name, location site and collection date.
Place the slide on a carboard holder. Store PreservCyt solution with non-gynecological sample between 4˚C (39˚F) and 37˚C (98˚F) for up to 3 weeks.
Liquid based technology has revolutionized the Pap test and now accounts for as much as 80% of all collection methods. The benefits includes a better slide quality by reducing obscuring blood and inflammatory exudate. Also increase the sensitivity in detection of squamous lesions.
The sensitivity in detection of SIL increase as high as 95% using liquid based cytology. The advantage of LBC is that specimens can undergo automated screening and the residual vial material can be used to make additional slides and perform ancillary testing including HPV, Chlamydia/Gonorrhea and Trichomonas.
Collect the ThinPrep Pap sample with either a broom-type device or a plastic spatula/endocervical brush combination. The sampling device is rinsed in a methanol based preservative solution (PresevCyt) for transport to the laboratory.
Thin Prep Ectocervix sample with a plastic spatula:
Endocervix sample with brush device:
Store PreservCyt Solution with cytologic sample intended for ThinPrep Pap testing between 15˚C (59˚F) and 30˚C (86˚F) for up to 6 weeks.
A Pap test should be avoided during menstrual bleeding. Blood may obscure important findings and result in unsatisfactory preparations.
Leica Autostainer XL
The Pap test has proven to be extremely cost-effective cancer screening tool. By detecting cervical abnormalities that can be treated before they develop into invasive cancer, Pap smear has correlated with remarkable reduction in the morbidity and mortality of this disease. Pap test can be useful identifying inflammatory conditions and specific infectious agents.
The sensitivity of the conventional Pap smear may be as low as 50%. Limitations of Pap test include problems with sampling , interpretation and clinical follow-up.
A Pap test should be performed at least 2 weeks after the 1st day of the last menstrual period (LMP). Use of a lubricant gel applied to facilitate insertion of the speculum should be avoided if possible. However, many clinicians use water-soluble gel lubricants. The frosted end of the glass slide should be labeled with patient’s name and the requisition form should be completed. Lab requisitions for Pap test should include the last menstrual period as well of any history of a prior abnormal Pap, treatment or biopsy.
The slide is placed on the cardboard holder and then placed in a biohazard bag with the requisition form. Slide. Storage and Transpor at Room Temperature.
Woman should ideally refrain from intercourse, douching, using tampons, using intravaginal medication or contraceptives for at least 48 hours before Pap test.
RT-PCR on Roche Cobas 4800 System
Roche Cobas 4800 System
The cobas® HSV 1 and 2 Test is an automated, qualitative in vitro diagnostic test, that utilizes real-time polymerase chain reaction (PCR), for the direct detection and differentiation of Herpes simplex virus 1 and 2 (HSV-1 and HSV-2) DNA in clinician-collected, external anogenital lesion specimens from symptomatic male and female patients. The cobas® HSV 1 and 2 Test is intended for use as an aid in diagnosis of anogenital HSV-1 and HSV-2 infections in symptomatic patients.
See OB/GYN Specimen Collection Media Information Below. Storage and Transport at Room Temperature.
Transcription Mediated Amplification (TMA) and Hybridization Protection Assay (HPA)
The APTIMA Trichomonas vaginalis Assay is an automated, target amplification nucleic acid probe test that utilizes target capture for the in vitro qualitative detection of ribosomal RNA (rRNA) of Trichomonas vaginalis (TV) in urogenital specimens.
Trichomonas vaginalis (TV) is the most common curable sexually transmitted disease (STD) agent in the United States, with an estimated 7.4 million new cases occurring annually. Infections in women cause vaginitis, urethritis, and cervicitis. Discharge and small hemorrhagic lesions may be present in the genitourinary tract. Complications can include premature labor, low-birth-weight offspring, premature rupture of membranes, and post-abortion or post- hysterectomy infection. An association with pelvic inflammatory disease, tubal infertility, and cervical cancer with previous episodes of trichomoniasis has been reported. Symptomatic women with trichomoniasis usually complain of vaginal discharge, vulvovaginal soreness, and/or irritation. Dysuria is also common. However, it has been estimated that 10 to 50% of T. vaginalis infections in women are asymptomatic, and in men the proportion may even be higher.
Vaginal/Endocervical Swab, ThinPrep, (See OB/GYN Specimen Collection Media)
A: Vaginal swab – Clinician collection (using Aptima Unisex Swab Kit)
B: Endocervical swab – Clinician collection (using Aptima Unisex Swab Kit)
C: Endocervical ThinPrep using Plastic Spatula and Brush
D: Cervical ThinPrep using a Broom-like device
Specimen contains excess of blood (has a dark red or brown color), expired collection and transport vials, specimens contains excess of mucous, swab specimens without Dacron or Flock swab inside.
Transcription Mediated Amplification (TMA) and Hybridization Protection Assay (HPA).
The Aptima HPV high risk assay is an in vitro nucleic acid amplification test for the qualitative detection of E6/E7 viral messenger RNA (mRNA) from 14 high-risk types (31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68) of HPV in cervical specimens. The Aptima HPV 16 18/45 genotype assay can differentiate HPV 16 from HPV 18 and 45, but does not differentiate between HPV 18 and HPV 45.
Specimen contains excess of blood (has a dark red or brown color), expired collection and transport vials, specimens contains excess of mucous. Less than 1mL of ThinPrep volume after the Pap test.
Specimen contains excess of blood (has a dark red or brown color), expired collection and transport vials, specimens contains excess of mucous less than 1mL of ThinPrep volume after the Pap test. Anal specimen grossly contaminated with feces.
The APTIMA Combo 2 Assay is an automated, target amplification nucleic acid probe test that utilizes target capture for the in vitro qualitative detection of ribosomal RNA (rRNA) of Chlamydia trachomatis (CT) in urogenital specimens.
C: Endocervical swab – Clinician collection (using Aptima Unisex Swab Kit)
Urine specimens with more than 24 hours of collected without transferred to cobas PCR media. Urine specimen with volume under or above the black lines, specimen contains excess of blood (has a dark red or brown color), expired collection and transport vials, specimens contains excess of mucous, swab specimens without Dacron or Flock swab inside.