Genomic Pathology Clinical Laboratory

Methicillin-resistant Staphylococcus aureus (MRSA) are gram positive cocci that are resistant to a number of antibiotics.  MRSA can colonize the nares of asymptomatic patients.  Colonization with MRSA increases a patient’s risk for a staph infection following invasive medical or surgical procedures. Appropriate screening and subsequent contact precautions can decrease the rate of transmission from asymptomatic carriers to other patients in a hospital.  The MRSA screen uses PCR to detect DNA sequences specific to the MRSA genome.  This PCR test is helpful in screening for colonization, not for diagnosis of infection or guiding therapy.Individuals referred from residential institutions, such as nursing homes, have an increased incidence of colonization by MRSA.

The assay is performed on a nasal swab daily.  The turn-around time is ~ 24 hours.

There are numerous respiratory viruses that can cause acute local and systemic illnesses.  The symptoms range in severity, with the potential to cause severe disease, especially in the young and elderly. The respiratory virus panel will detect viral genomes in patients infected by Influenza A (H1 or H3), Influenza B, Respiratory Syncytial Virus, Parainfluenza (1, 2, or 3), Metapneumovirus, Rhinovirus, and Adenovirus. Negative results do not preclude respiratory virus infection. 

The assay is FDA approved for nasopharyngeal swabs.  Other respiratory samples, such as nasopharyngeal, bronchial, and tracheal washes and aspirates, bronchial lavages, sputum, throat gargles, and nasal and throat swabs were validated in house and these results will be appended with a comment stating that the specimen source is not FDA approved. During flu season, this test is performed five to six times a week. Non-flu season, it is performed two times a week.

Human immunodeficiency virus (HIV) is the etiologic agent of Acquired Immunodeficiency Syndrome (AIDS). HIV can be transmitted by sexual contact, exposure to infected blood or blood products, or by an infected mother to a fetus. There are two forms of HIV, HIV-1 and HIV-2. HIV-1 is the most commonly encountered form in the United States.  This assay quantifies the amount of HIV-1 particles present in the plasma. This test is helpful for monitoring viral load to guide therapy.  This assay is not intended for screening or diagnosis of HIV infection.

The assay is performed on 3 lavender top tubes of peripheral blood.  The linear range of the assay is 48 – 10,000,000 copies/mL.  The turn-around time is ~ 7 days.

HBV is a major etiological agent associated with the development of hepatitis, cirrhosis, and hepatocellular carcinoma.  Viral load testing helps monitor response to therapy. In addition, this HBV test can also be useful in the differential diagnosis of post-transfusion hepatitis, fulminant hepatitis, recurring hepatitis due to reactivation or superinfection, and cases of atypical hepatitis in which HBV is suspected.  It can be used to identify a potential viral etiology of cryptogenic cirrhosis and hepatocellular carcinoma in the absence of serological markers of HBV.  The assay will detect virus particles in patients lacking serological markers of HBV infection because of immunodeficiency or immunosuppression. Therefore, real time PCR-based HBV viral load testing is helpful in diagnosis, prognosis, and patient management.

The assay is performed on 3 lavender, red, or gold top tubes of peripheral blood.  The linear range of the assay is 29 – 110,000,000 IU/mL.  The turn-around time is ~ 7 days.

CV is a major etiological agent associated with the development of hepatitis, cirrhosis, and hepatocellular carcinoma. Viral load testing helps monitor response to therapy. In addition, this HCV test can also be useful in the differential diagnosis of post-transfusion hepatitis, recurring hepatitis due to reactivation or superinfection, and in other cases of atypical hepatitis or non-A/non-B hepatitis in which HCV is suspected.  It can be used to identify a potential viral etiology of cryptogenic cirrhosis and hepatocellular carcinoma in the absence of serological markers of HCV infection because of immunodeficiency or immunosuppression.  Therefore, real time PCR-based HCV viral load testing is helpful in diagnosis, prognosis, and patient management.

The assay is performed on 3 lavender, red, or gold top tubes of peripheral blood.  The linear range of the assay is 43 – 69,000,000 IU/mL. The turn-around time is ~ 7 days.

Chronic hepatitis C is an important risk factor for developing hepatic cirrhosis and hepatocellular carcinoma. Response to therapy depends on the genotype of the virus. Patients infected with genotype 1 need treatment for a significantly longer time in order to achieve a sustained response, whereas patients infected with genotypes other than 1 do not benefit from prolonged treatment.  PCR products from HCV viral load assay are used to perform the DNA sequencing.  For this reason HCV Genotype has to be ordered along with the viral load assay.  The sequencing result is compared to reference sequences in the database to identify the specific genotype. 

The assay is performed on 3 lavender top tubes of peripheral blood.  A viral load of 43 IU/ml plasma is necessary. The assay is reported as Genotype 1, 2, 3, 4, 5, 6 or combinations thereof in case of co-infection. The turn-around time is ~ 7 days.

K virus is a common infection in the population.  However, clinical manifestations typically only occur in immunocompromised patients, particularly in transplant recipients.  These findings include tubulinterstitial nephritis, ureteral stenosis, and hemorrhagic cystitis. A sustained viremia of at least two weeks duration in the setting of genitourinary dysfunction implies a diagnosis of BK viral nephropathy. Regular screening of transplant recipients for BK virus by PCR may allow for early detection of a systemic infection, thus limiting morbidity in this population. This assay detects viral genomes in the serum of both symptomatic and asymptomatic patients.

The assay is performed on 2 lavender top tubes of peripheral blood and urine.  The linear range of the assay is 100 – 1,000,000,000 copies/mL. The turn-around time for this assay is ~ 7 days.

CMV is a common infection, and in immunosuppressed or immunocompromised patients, infection or reactivation can result in severe pathology. The PCR-based assay establishes the diagnosis significantly faster than viral culture. Therefore it is very important for the early diagnosis of congenital CMV infections and CMV infections in immunocompromised patients, as well as of cases of possible virus reactivation.  In addition, viral load testing serves to monitor treatment.  Therefore, real time PCR-based CMV viral load testing is helpful in diagnosis, prognosis and in patient management.

The assay is performed on 3 lavender top tubes of peripheral blood. The linear range is 100 to 500,000 copies/ml plasma. The assay is performed on Tuesdays and Fridays and turn around time is 3 to 4 days.

The assay is performed on urine, bronchial lavage/wash, and throat gargle specimens by the same methodology as the Quantitative CMV assay.  It is not possible to report out the viral particles in a specific unit for these types of specimen, the results are reported as “not detected,” “low positive CMV viral load”for a range from 100 to 5000 cp/ml;   “mid positive CMV viral load”for a range from 5001 to 100,000 cp/ml, and “high positive CMV viral load” for numeric titer > 100,000 cp/ml.   The assay is performed on Tuesdays and Fridays and the turn around time is 3 to 4 days.

Chlamydia trachomatis and Neisseria gonorrhea are two of the most common sexually transmitted diseases in the United States.  Both bacteria can cause urethritis, cervicitis, and pelvic inflammatory disease (PID).  In addition, C. trachomatis can cause conjunctivitis and pneumonia in infants.  Female patients with C. trachomatis are often asymptomatic.  This leads to the risk of transmission of C. trachomatis from infected mothers to neonates.

The assay is performed on urethral, cervical, and endocervical swabs in M4 media, and male clean catch urines  The turn-around time is 2 to 3 days.

The key difference between this assay and the CCG (above) is the specimen type.  ThinPrep cytology specimens are FDA approved with Roche Cobas method but not the microwell method used for CCG.  Therefore, ThinPrep cytology specimens are handled separated from other urogenital samples at this time.  The turn-around time is ~ 7 days.

In some instances, the identification of bacteria, mycobacteria, and fungi from clinical specimens grown on culture media can be difficult and time consuming using biochemical and metabolic assays.  This assay uses PCR to amplify the conserved regions of ribosome rRNA genes of the infectious organism for nucleotide sequence analysis. This sequence, once proofread, is analyzed using SmartGene software to find matches in curated databases of reference sequences.  A perfect match or near perfect match will yield a positive identification.

The assay is performed on purified colonies provided by Microbiology.  The turn-around time is ~ 7 days after receiving the colonies on plates.

High risk Human Papilloma Virus (HPV) is causally involved in the vast majority of cervical cancers in the United States. The most common oncogenic types are 16 and 18. Other high -risk types 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68 are seen less frequently. HPV testing in cases of Atypical Squamous Cells on Cervical Cytology is important for clinical management, as patients with negative HPV results are unlikely to develop cervical cancer.  Currently we uses FDA approved Cervista assay for this testing.  However, a PCR based and FDA approved Roche HPV testing that can simultaneously genotype HPV16 and HPV18 is being validated in the lab and the new method will be in place in the near future.

This assay is performed on ThinPrep Liquid Cytology Samples. The results are reported as “high risk HPV not detected”, “high risk HPV detected” and “equivocal”. The turn around time for the assay is ~ 7 days after the reflex order for the HR HPV is issued.

Clonal rearrangements of the IgH gene are typically found in B-cell malignancies, but rarely can be detected in T-cell malignancies and AML. Monoclonal processes can be distinguished from the normal polyclonal pattern at a level of sensitivity of less than 5% of clonal cells in a polyclonal background. Identification of an IgH clone can support the diagnosis of a malignant process and the clone can be used as a sensitive marker for follow up after treatment. Synchronous and metachronous clones in different lesions in one patient can be compared based on the molecular sizes of the clonal peaks.  Approximately 80% of clonal IGH gene rearrangements can be detected using this approach.

Primers for frameworks 1, 2 and 3 are amplified and PCR products are separated by capillary electrophoresis to identify the presence of absence of clonal peak(s).

The test is performed on blood and bone marrow aspirates (lavender top tube), formalin-fixed and paraffin-embedded tissues, as well as fresh and frozen tissues. The result is reported as "positive" or "negative". The turn-around time for this assay is ~7 days.

Clonal rearrangements of TCRgamma are typically found in T-cell malignancies, but can also be detected in a number of other immunological processes and in B-cell malignancies, particularly in precursor B-ALL. Monoclonal processes can be distinguished from the normal polyclonal pattern at a sensitivity of less than 5% in a polyclonal background. Identification of a TCR gamma clone can support the diagnosis of a malignant process and the clone can be used as a sensitive marker for follow up after treatment. Synchronous and metachronous clones in different lesions in one patient can be compared based on their peak sizes.

The test currently is sent to a reference laboratory.  The test is performed on blood and bone marrow aspirates (lavender top tube), formalin-fixed and paraffin-embedded tissues. The result is reported as "positive" or "negative". The turn-around time for this assay is ~7 days.

The JAK2 V617F mutation is found with high frequency in patients with polycythemia, essential thrombocythemia, and chronic idiopathic myelofibrosis. The V617F mutation has not been found in healthy people and therefore helps to confirm any of the above diagnoses. The analytical sensitivity of this test is 2% for the V617F mutation allele in the wildtype background.

JAK2 MutaScreen Mini Kit is used to detect the point mutation at position c.1849 (G>T) in the JAK2 gene, which causes valine to be replaced by phenylalanine at amino acid position 617 in the JAK2 protein.

The test is performed on blood and bone marrow aspirates (lavender top tube). The result is reported as "positive" or "negative". The turn-around time for this assay is 7 days.

BRAF somatic mutations are found in multiple types of cancers, including colorectal carcinoma, malignant melanoma, papillary thyroid carcinoma, hairy cell leukemia and non-small cell lung carcinoma. The most common BRAF mutation is V600E.  Analysis of the BRAF V600E mutation on fine needle aspirate (FNA) specimens is mainly used to modify cytology results that are “indeterminant” or show atypia, but are not diagnostic of a malignancy.  BRAF mutations are present in ~50% of papillary thyroid cancer specimens. The presence of a BRAF mutation is an indication that the tumor is malignant. To be eligible for FDA approved Zelboraf (vemurafenib), the patient should be tested by a FDA-approved BRAF mutation assay.

We use DNA Sanger sequencing method to identify mutations. Genomic DNA is extracted from FNA or tissue sections from formalin-fixed, paraffin-embedded specimens using microdissection to enrich the tumor content. Exon 15 is amplified and the PCR products are then sequenced bidirectionally.

FNA and FFPE are validated for this lab developed assay and require at least 25% tumor content in the specimen pool or an area that can be isolated.  When testing on FFPE specimen, please submit 6 unstained FFPE sections at 10 um thickness and 1 H&E slide.  The result is reported as "positive" or "negative". The turn-around time for this assay is 10 days.

RAS mutations are found in 40-50% of follicular thyroid carcinoma and 10% of papillary carcinomas, particularly the follicular variant. Mutations in codon 61 have been found to be the most common genetic alteration. Analysis of NRAS Q61 mutations in conjunction with BRAF V600E mutation analysis on fine needle aspiration is used to reduce the “indeterminate” cytology result in cases that have significant atypia.

NRAS Q61 mutations have also been reported in benign lesions with similar frequency as the carcinomas. The presence of this NRAS mutation alone is not sufficient to establish a diagnosis of malignancy. Correlation with clinical, pathologic and radiologic findings is recommended.

We use PCR to amplify exon 3 of NRAS gene and sequence the entire exon 3 bidirectionally.

The test is performed on fine needle aspirates. It is required to have minimally 25% tumor content in the specimen pool.  The result is reported as "positive" or "negative". The turn-around time for this assay is 10 days.

The KRAS mutations, particularly in codons 12 and 13 of exon 2, constitutively activate KRAS oncogene. These mutations occur commonly in many types of human cancers including colorectal cancers. Since KRAS is downstream of EGFR pathway signaling pathway, tumors carrying KRAS mutations are not responsive to EGFR antibody treatment, such as panitumumab or cetuximab. This KRAS mutation analysis is intended to stratify cancer patients before their treatment with EGFR antibodies. We use DNA Sanger sequencing method to identify mutations in exon 2 of the KRAS gene. Genomic DNA is extracted from formalin-fixed, paraffin-embedded pathology specimens using microdissection to enrich the tumor content. The exon is amplified and the PCR products are then sequenced bidirectionally.

The test is performed on FFPE tumor specimens. It is required to have at least 25% tumor content in the specimen pool or an area that can be isolated.  Please submit 6 unstained FFPE sections at 10 um thickness and 1 H&E slide. The result is reported as "positive" with the specific amino acid changes or "negative". The turn-around time for this assay is 10 days.

This test assesses DNA mismatch repair proficiency in tumors that are associated with hereditary non-polyposis colorectal carcinoma syndrome (HNPCC)/Lynch Syndrome. Genomic DNA from tumor and normal tissues are amplified for 5 selected short tandem repeat loci (STRs or microsatellites) and the amplification profiles from the tumor and normal tissues are compared to identify if they are similar or different.  Two or more of the 5 STR loci have different profiles is an indication of mismatch repair deficiencies. Mismatch repair deficiency can be due to germline mutations of mismatch repair genes in HNPCC or can be found in sporadic tumors, caused by promoter hypermethylation of the mismatch repair gene MLH1.

Paraffin sections of colorectal cancers or other HNPCC-related cancers are microdissected under microscopic control and DNA is extracted from normal and tumor tissue. A panel of 5 microsatellites that has been recommended by the NCI and the International Collaborative Group on HNPCC is analyzed.

If there is microsatellite instability in 2 or more of the 5 markers, the tumor has high microsatellite instability (MSI-H), which is indicative of a mismatch repair deficiency. If there is no instability, the tumor is classified as microsatellite stable (MSS). If there is instability in <40% of microsatellite loci, the tumor is considered as having low microsatellite instability (MSI-L). MSI-L is not typically associated with mismatch repair deficiency, but may be seen in early lesions. Patients whose tumors are found to have mismatch repair deficiencies should be referred for genetic counseling to determine whether they have HNPCC or whether the mismatch repair deficiency might be caused by epigenetic inactivation.

The assay is performed on paraffin sections of cancer and normal tissue. Please submit 6 unstained FFPE sections at 10 um thickness and 1 H&E slide. The turn-around time is ~ 7 days.

Epidermal growth factor receptor (EGFR) mutation analysis detects EGFR gene mutations in tumor specimens of patients with non-small cell lung cancer (NSCLC). EGFR, when activated, plays a role in cellular tumor growth and proliferation and is the target of tyrosine kinase inhibitors (TKI) such as Gefitinib. Clinical studies have found that up to 20% of NSCLC tumors harbor the EGFR mutation, and that ~85% of patients with these mutations respond to TKI treatment. Recurrent mutations in exons 18 to 21 of EGFR have been identified in these responsive tumors. Microdeletions in exon 19 and L858R are the most frequent, ~ 85 to 90% of the total, among the activating mutations associated with drug sensitivity. The T790M mutation has been associated with resistance to tyrosine kinase inhibitors.

We use DNA Sanger sequencing method to identify mutations in exons 18, 19, 20, and 21 of the EGFR gene. Genomic DNA is extracted from FFPE using microdissection to enrich the tumor content. The exons are amplified by 4 sets of primers in a multiplex fashion. The PCR products are then sequenced bidirectionally.

The test is performed on paraffin-embedded tissues. It is required to have at least 25% tumor content in the specimen pool or an area that can be isolated.  Please submit 6 unstained FFPE sections at 10 um thickness and 1 H&E slide. The result is reported as "positive" or "negative". The turn-around time for this assay is 10 days.

STR (short tandem repeat) loci consist of short, repetitive sequence elements of 3-7 base pairs in length. These repeats are well distributed throughout the human genome and are a rich source of highly polymorphic markers that may be detected using PCR. The discriminatory power of STRs to distinguish between different individuals and the sensitivity of quantitating PCR products by capillary electrophoresis is utilized for bone marrow engraftment studies.

Before the stem cell transplant (SCT), 16 STR loci are analyzed for both the recipient and the donor and the most suitable informative loci for detecting the recipient alleles in the donor’s STR pattern are selected. A formula is developed that can be used after the transplant to quantitate the relative content (%) of recipient alleles in hematopoietic cells in the post-transplant blood or bone marrow.

Pre-bone marrow transplant analysis is performed on peripheral blood (lavender top tube) and buccal cells from recipient and peripheral blood from the donor. Post-SCT analysis is performed on peripheral blood or bone marrow aspirate (lavender top tube) from the recipient.

The percentage of recipient alleles should be <1% in a fully engrafted marrow.  An increase of the recipient percentage may indicate hematopoietic chimerism, which can be associated with a relapse of disease or a graft failure. The turn-around time for this assay is 7 days.

The BCR-ABL fusion gene is the result of the formation of the Philadelphia translocation (Ph). The Ph chromosome is defining for the diagnosis of CML and can be found by RT-PCR in more than 95% of CML cases. In ALL, Ph is detected in 25-30% of adult and 2-5% of childhood cases, which is associated with poor prognosis. The sensitivity is 10-4, one fusion RNA in 10,000 normal RNA molecules.

Total RNA is reverse transcribed and the cDNA generated is amplified with specific primers in a two-step RT-PCR approach. Three sets of specific primers amplify BCR-ABL m-bcr, BCR-ABL M-Bcr and ABL (as internal control) in two separate reaction tubes. The PCR products are detected and distinguished by three specific TaqMan probes.

The test is performed on blood and bone marrow aspirates (lavender top tube). The specimen should be delivered STAT. The result is reported as "positive" or "negative". The turn-around time for this assay is 7 days.

This quantitative BCR-ABL assay is useful to monitor treatment efficiency and minimal residual disease.  Currently, the test is a sendout test. The test is performed on blood and bone marrow aspirates (lavender top tube). The specimen should be delivered STAT.

A positive result indicates the presence of Philadelphia chromosome. Increasing levels of BCR/ABL transcripts are associated with clinical progression. To monitor MRD, we recommend evaluating changes with time (trend) and in log10 scale rather than the absolute ratio from a single time point.  Use the same specimen type for direct comparison.  Results from bone marrow and blood will have different values.

Acute promyelocytic leukemia (APL or AML-M3) is a subtype of acute myeloid leukemia with distinct clinical and histopathologic features. Detection of the PML/RARA t(15;17) translocation is diagnostic for APL. The short isoform may be associated with shorter disease-free and overall survival. The presence of this translocation is necessary for response to all-trans-retinoic acid and arsenic trioxide. Thus, the PML/RARA t(15;17) assay is useful for diagnosis and predicting treatment response. It is also helpful for monitoring therapeutic response and MRD and for detecting early relapse.

The test is a sendout test. The test is performed on blood and bone marrow aspirates (lavender top tube). The specimen should be delivered STAT.

Positive results indicate that the cells carry the PML/RARA t(15;17) translocation and are diagnostic for APL. If the PML/RARA t(15;17) translocation is detected, the ratio of amplified PML/RARA fusion transcript to the control ABL transcript is reported. If there is no PML/RARA amplification (ratio = 0), the result is reported as negative. To monitor MRD, we recommend evaluating changes with time (trend) and with log 10 value rather than the absolute ratio from one measurement.

Test Indication
Chromosome analysis on the bone marrow helps in diagnosis and prognosis of the certain malignant hematological disorders, monitoring effects of treatment and monitoring bone marrow transplant patients

Methodology
Stimulated and unstimulated cultures are performed based on the diagnosis followed by 20 cell analysis and 2 karyotypes in normal result; the number of karyotypes may vary based on the complexity of the case.
 
Specimen Requirement
Bone marrow, Peripheral blood, bone core (0.5-1 cm³), lymph node
Please complete the requisition form completely, the specimen is not rejected but the quality and TAT may be compromised on a delayed set up.

Volume
2-3 ml of bone marrow

Container or anticoagulant
Green-top (sodium heparin) tube(s) (Make sure to read the label.  Green top can be lithium heparin)

Caution: Other anticoagulants like Lithium heparin is harmful to the cells and affects the viability of the cells and especially delayed transport of the specimen in wrong anticoagulant will destroy the cells before they are cultured.

Special Instruction
Please mention alternative tentative diagnosis if not sure to prevent wrong culturing and delayed results

Collection
Specimens should arrive in the laboratory within 48 hours of collection. Indicate date and time of collection on the request form.

Storage instruction
Ambient, Refrigerated OK
Frozen NO

Cause for rejection
Hemolysis; no immature cells; clotted specimen; frozen specimen; fixed specimen; wrong anticoagulant

Use

Chromosome analysis helps in identification of specific signature anomalies associated with hematological disorders in myeloid and lymphoid disorders as well as helps in determining how advanced the disease is with respect to the presence of the complexity of the karyotype; for example in case of chronic myeloid leukemia, you can see t(9;22) in the chronic phase and additional abnormalities in the acute or blast crisis of the disease.

Limitation

The test is limited with respect to the presence of blast cells present in the specimen and also with the presence of some types of cells that don’t grow well in culture for example Multiple myeloma where plasma cells don’t grow well in culture so it is sometimes difficult to catch the abnormality. For these cases FISH is the best adjunct diagnostic test.

Chromosome abnormalities cause a wide range of disorders associated with birth defects and congenital diseases. Congenital chromosome studies are done on blood for a wide variety of indications including mental retardation, failure to thrive, possible Down syndrome, delayed puberty or primary amenorrhea (Turner syndrome), frequent miscarriages, infertility, multiple congenital anomalies, sex determination, and many others.

Test Indication
Diagnosis of a wide variety of congenital conditions
Identification of congenital chromosome abnormalities, including aneuploidy (ie, trisomy or monosomy) and structural abnormalities

Methodology
Two stimulated cultures are performed for all constitutional analysis except in new born cases where an additional 48 hour culture is also set up followed by 5 cell analysis and 2 karyotypes in normal result; the number of karyotypes may vary based on the complexity of the case.

Specimen Requirement
Whole  blood

Volume
5 ml adult; 1-2 ml neonate

Container
Green-top (sodium heparin) tube(s)

Other anticoagulants like Lithium heparin is harmful to the cells and affects the viability of the cells and especially delayed transport of the specimen in wrong anticoagulant will destroy the cells before they are cultured.