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Diagnostic Genomic Division – DGD lab Guide of 83

Lab Guide – 2019 Diagnostic Genomic Division (DGD)


Cytogenetics Section

Title ACUTE MYELOID LEUKEMIA PANEL BY FISH

ITEM Acute Myelogenous Leukemia (AML) is a disorder of

myeloid cells which were historically categorized by the

myeloid cell lineage involved, several of which showed recurrent balanced chromosomal rearrangements

resulting in the creation of novel fusion proteins. Recent

reclassification (groups the recurrent rearrangements into

a single category. This FISH panel is designed to detect

the most common, and/or prognostically-significant

abnormalities in AML with recurrent genetic abnormalities

and in therapy-related AML. Recurrent abnormalities are

observed in the majority of AML cases.

Specimen Specimen Type: Blood/Leukemic Blood

Container/Tube: Green top (sodium heparin)

Specimen Volume: 2-6 mL (Varies depending on the

WBC-Count).

(Adult - 3-6 mL ,Child - 2 mL, Infant - 2 mL)

Specimen Type: Bone marrow

Container/Tube: Bone Marrow Transport Media


WBC-Count).

Transport Ambient Temperature

Days test is Sunday-Wednesday 7:00am-3:00PM performed

Turnaround time 7 days

Method Interphase Fluorescence In situ Hybridization (iFISH)

study.

Reference Value Negative

Interpretation In addition to morphology, several recurrent chromosomal abnormalities have been linked to specific subtypes of AML. The most common chromosome abnormalities associated with AML include t(8;21), t(15;17), inv(16), +8, t(6;9), t(8;16), t(1;22), t(9;22), t(3;5), and abnormalities of

the MLL (KMT2A) gene at 11q23. The most common

genes juxtaposed with MLL through translocation events


in AML include AFF1- t(4;11), MLTT4- t(6;11),

MLLT3-

t(9;11), MLLT10- t(10;11), CREBBP- t(11;16),

ELL-

t(11;19p13.1), and MLLT1- t(11;19p13.3).

AML can also evolve from myelodysplasia (MDS). Thus,

the common chromosome abnormalities associated

with

MDS can also be identified in AML, which include:

inv(3), -

5/5q-, -7/7q-, +8, 13q-, 17p-, 20q-, t(1;3), and t(3;21). In

combination, the multiple recurrent chromosome

abnormalities identified in patients with AML are

observed

in approximately 60% of diagnostic AML cases.

Rejection Criteria Consistent with Diagnostic Genomic Division policies

Performing Lab Diagnostic Genomic Division, Dept Lab Med & Path, QRI

Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974-

40260376

Location


Title

ALK BY FISH

ITEM ALK gene rearrangement is observed in a small subset

(3–7%) of non-small cell lung cancer (NSCLC) patients.

The efficacy of crizotinib was shown in lung cancer

patients harboring ALK rearrangement. Anaplastic

lymphoma kinase (a receptor tyrosine kinase anaplastic

lymphoma, CD246), is a transmembrane protein – a

member of the insulin-like tyrosine kinase receptor

superfamily, encoded by the ALK gene on chromosome 2.

In non-small-cell lung cancer patients, the inversion [Inv

(2) (p21p23)] within the short arm of chromosome 2 is the

most frequently described abnormality of the ALK gene,

occurring in approximately 3–7% of lung adenocarcinoma

patients.

Specimen Specimen Type: Tissue Block/ Slide

Container/Tube: Slides from Tissue block

Specimen Volume: 1stained H&E slide - 4 unstained

slides





study.


Interpretation A positive result (ALK rearrangement identified) is detected when the percent of cells with an abnormality

exceeds the normal cutoff for the ALK probe set. A

positive result suggests rearrangement of the ALK locus

and a tumor that may be responsive to ALK inhibitor

therapy. A negative result suggests no rearrangement of

the ALK gene region at 2p23.


Performing Lab Diagnostic Genomic Division, Dept Lab Med & Path, QRI Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974- 40260376 Location


Title 1p/19q FISH Testing

ITEM The test is used to diagnose oligodendroglioma brain

tumors; indicated in both low-grade and high-grade (anaplastic) oligodendrogliomas. Predict response to therapy in oligodendrogliomas. May be useful in tumors with a complex "hybrid" morphology requiring differentiation from pure astrocytomas to support the presence of oligodendroglial differentiation/lineage. Strongly recommended when a diagnosis of mixed oligoastrocytomas is rendered.



Specimen Volume: 1stained H&E slide - 4 unstained slides

Transport Temperature

Ambient

Days test is performed

Sunday-Wednesday 7:00am-3:00PM


Method Interphase Fluorescence In situ Hybridization (iFISH) study.


Interpretation The presence of 1p deletion and combined 1p and 19q

deletion supports a diagnosis of oligodendroglioma may

indicate that the patient may respond to chemotherapy

and radiation therapy. The presence of gain of

chromosome 19 supports a diagnosis of high-grade

astrocytoma (glioblastoma multiforme).

A negative result does not exclude a diagnosis of

oligodendroglioma or high-grade astrocytoma.

Rejection Criteria Consistent with Diagnostic Genomic Division policies.

Performing Lab Location

Cytogenetics & Molecular Cytogenetics Laboratory, Diagnostic Genomic Division, QRI, 3rd floor, HBKMC, Doha, Qatar. Lab Secretary# 40260376


Title

B‐CELL ACUTE LYMPHOBLASTIC LEUKEMIA PANEL BY FISH

ITEM

B-Acute Lymphoblastic Leukemia (ALL) is a disorder of B

lymphoblast that accounts for the vast majority of children

with acute leukemia and a fraction of adults with acute

leukemia. B-ALL is broadly categorized as either having

recurrent genetic abnormalities or not; recurrent genetic

abnormalities include both balanced translocations and

aneuploidy (Swerdlow et al. 2008). This FISH panel is

designed to detect the most common, and/or prognosticaly

-significant abnormalities in B-ALL (Swerdlow et al. 2008).

FISH studies are useful adjuncts to complete chromosome

studies, particularly when following an abnormal clone,

assessing relapse and progression. As an adjunct to

conventional chromosome studies.




WBC-Count).





WBC-Count).





study.



Interpretation B-ALL is broadly categorized as either having recurrent genetic abnormalities or not; recurrent genetic

abnormalities include both balanced translocations and

aneuploidy (Swerdlow et al. 2008). This FISH panel is

designed to detect the most common, and/or

prognostically-significant abnormalities in B-ALL

(Swerdlow et al. 2008).




40260376

Location


Title BURKITT’S LYMPHOMA PANEL BY FISH

ITEM This small, multiprobe panel contributes to the distinction

of Burkitt’s from large B-cell lymphoma on problematic

specimens demonstrating borderline morphologic or

immunophenotypic features, limited sample volume, or

zero to low probability for successful karyotyping. Burkitt’s

lymphoma characteristically demonstrates a very high

Ki67 staining index, strong CD10, and positive bcl-6

staining with negative staining for bcl-2. Burkitt’s

lymphomas typically reveal MYC translocation partnered

to Ig heavy or light chain genes in the background of an

otherwise simple karyotype. Rarely, Burkitt’s lymphomas

may lack MYC translocation.




WBC-Count).





WBC-Count).



Turnaround time 7 Days


study.


Interpretation Burkitt’s lymphomas typically reveal MYC translocation partnered to Ig heavy or light chain genes in the background of an otherwise simple karyotype. Rarely,

Burkitt’s lymphomas may lack MYC translocation.


Among large B-cell lymphomas, MYC translocation is

demonstrated in a small but significant subset, almost

always in the background of a complex karyotype,

presumably representing secondarily acquired genetic

change. Frequently, these MYC+ large B-cell lymphomas

are also positive for BCL2 or BCL6 rearrangements.

Incomplete clinical evidence suggests that MYC+ large B-

cell lymphomas may benefit from Burkitt-like

chemotherapeutic regimens.


Performing Lab

Diagnostic Genomic Division, Dept Lab Med & Path, QRI Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974- 40260376

Location


Title CHROMOSOMAL MICROARRAY ANALYSIS

ITEM Chromosomal Microarray Analysis is useful for the detection of

DNA copy number gains and losses associated with unbalanced

chromosomal aberrations. The utility of this technology for the

detection of gains and losses in patients with intellectual

disabilities, autism/ASD, and/ or congenital anomalies has been

well documented and chromosomal microarray analysis is now

recommended as a first tier test for these indications.

Specimen 1. Specimen Type: Whole blood/ Cord blood

Container/Tube: EDTA- Lavender top

Specimen Volume: 3-5 mL preferred, minimum 1ml

2. Specimen Type: Amniotic Fluid

Container/Tube: 10-15 ml Sterile falcon tube/ container

Specimen Volume: 20 mL

3. Specimen Type: CVS, Skin Biopsy and POC

Container /Tube: Sterile Container containing normal saline/Sterile

transport media

Specimen Weight/Volume: 20-30mg of specimen

Note: Cord blood, Amniotic Fluid, CVS and POC should be

accompanied with maternal blood (3-5ml in lavender top

tube) to rule out maternal cell contamination

Transport Ambient

Temperature

Days test is

Sunday to Thursday 07:00 AM to 02:00 PM performed

Turnaround Postnatal aCGH: 4 weeks

time

Prenatal aCGH:

2 weeks

Postnatal NICU: 7 days

Products of conception/Fibroblasts: 6 weeks

Method Array Comparative Genomic Hybridization using Surescan High

Resolution Technology


Reference Negative

Value

Interpretation Copy number variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive

comments detailing their potential or known significance

Rejection Consistent with Diagnostic Genomic Division policies

Criteria Performing

Diagnostic Genomic Division, Dept Lab Med & Path, QRI Bldg,

Hamad Bin Khalifa Medical City, Doha. Tel: +974-40260376 Lab Location


Title

CHROMOSOME ANALYSIS‐ CONSTITUTIONAL

ITEM Chromosome analysis is the microscopic examination of

chromosomes in dividing cells. Such analysis can detect

changes in chromosomal number and structure. Deletions (eg,

partial monosomy), duplications (eg, partial trisomy), and

structural abnormalities such as translocations, inversions, and

rings can be detected. These chromosomal changes may be

associated with infertility, miscarriage, stillbirth, birth defects,

intellectual disability, developmental delay, or abnormalities of

sexual differentiation and development.

Specimen 1. Specimen Type: Whole blood/ Cord blood

Container/Tube: Sodium Heparin-

Green top





3. Specimen Type: CVS

Container /Tube: Sterile Container containing normal saline/Sterile

transport media


Note: Cord blood, Amniotic Fluid and CVS should be accompanied

with maternal blood (3-5ml in lavender top tube) to rule out

Maternal cell contamination.


Days test is Sunday to Thursday 07:00 AM to 02:00 PM

performed

Turnaround Amniotic fluid: 14 days

time

CVS:

14 days

Peripheral blood: 7-28 days

Method Cell Culture with Mitogens followed by Chromosome Analysis


Reference

Negative Value

Interpretation The numerical and structural abnormalities are reported as per

An International System for Human Cytogenomic Nomenclature

(ISCN). The report includes chromosomal findings, clinical

significance, and recommendations for additional studies (eg,

FISH and microarray) when indicated.

Rejection Consistent with Diagnostic Genomic Division policies Criteria Performing Lab

Diagnostic Genomic Division, Dept Lab Med & Path, QRI Bldg,

Hamad Bin Khalifa Medical City, Doha. Tel: +974-40260376 Location


Title

CHROMOSOME ANALYSIS‐ HEMATO‐ONCLOGY

ITEM Chromosome analysis is the microscopic examination of

chromosomes in dividing cells and can be used for

hemato-oncology specimens to determie and diagnose

the acquired chromosomal changes that are related to

multiple malignancy types. This study also assists in

classification of different malignant hematological

disorders, monitoring effect of treatment and knowing the

remission status of disorders.

Specimen 1. Specimen Type: Whole blood

Container/Tube: Sodium Heparin- Green top


2. Specimen Type: Bone Marrow

Container/Tube: 10-15 ml of Bone marrow transport media/

container


Transport Ambient

Temperature Days test is Sunday to Thursday 07:00 AM to 02:00 PM performed


Method Cell Culture without/ with Mitogens followed by

Chromosome Analysis


Interpretation The numerical and structural abnormalities are reported as per An International System for Human Cytogenomic

Nomenclature (ISCN). The report includes chromosomal

findings, clinical significance, and recommendations for

additional studies (eg, FISH and microarray) when

indicated.




40260376

Location


Title

CHRONIC LYMPHOCYTIC LEUKEMIA PANEL BY FISH

ITEM Used for detecting a neoplastic clone associated with the

common chromosome abnormalities seen in patients with

chronic lymphocytic leukemia (CLL). Identifying and

tracking known chromosome abnormalities in patients with

CLL and tracking response to therapy. Distinguishing

patients with 11;14 translocations who have leukemic

phase of mantle cell lymphoma from patients who have

CLL. Detecting patients with atypical CLL or other forms of

lymphoma associated translocation between IGH/CCND1

and ATM, TP53, D13S319 or other partner genes.

Specimen

Specimen Type: Blood/Leukemic Blood

Container/Tube: Green top (sodium heparin) Specimen Volume: 2-6 mL (Varies depending on the WBC-Count).

(Adult - 3-6 mL , Child - 2 mL, Infant - 2 mL)




WBC-Count).

Transport Ambient Temperature Days test is Sunday-Wednesday 7:00am-3:00PM performed



study.


Interpretation This FISH test detects an abnormal clone in approximately 70% of patients with indolent disease and >80% of patients who require treatment. At least 5% of patients

referred for CLL FISH testing have translocations involving

the IGH locus; approximately 66% of these patients have


Location

translocations that result in fusion of IGH/CCND1, Fusion

of IGH and CCND1 is associated with t(11;14)(q13;q32),

The prognostic associations for chromosome

abnormalities detected by this FISH assay are, from best

to worst: 13q-, normal, +12, 6q-, 11q-, and 17p-.



Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974- 40260376


Title

CHRONIC MYELOGENOUS LEUKEMIA PANEL BY FISH

ITEM Used for detecting a neoplastic clone associated with a

BCR/ABL1 rearrangement in patients with chronic myeloid

leukemia (CML). Tracking the percentage of nuclei with

BCR/ABL1 rearrangement and response to therapy in

patients with CML.




WBC-Count).





WBC-Count).




study.


Interpretation Fusion of BCR/ABL1 is observed in all patients with chronic myeloid leukemia (CML), in approximately 25% of

adult patients with precursor B-cell acute lymphoblastic

leukemia (B-ALL) and in 1% of patients with pediatric B-

ALL. The chromosome mechanism resulting in BCR/ABL1

fusion is a t(9;22)(q34;q11.2) in approximately 85%, a

complex 9;22 translocation with 1 or more additional

chromosomes in approximately 15% and a chromosomally


"cryptic" or insertional translocation in fewer than 1% of

patients.


Performing Lab Diagnostic Genomic Division, Dept Lab Med & Path, QRI Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974- 40260376

Location


Title

Diffuse Large B‐Cell Lymphoma (DLBCL) PANEL BY FISH

ITEM

This probe panel detects specific structural chromosome

abnormalities commonly associated with Diffuse Large B-

cell Lymphoma. Routine chromosome analysis is

performed on all diagnostic samples and is recommended

on all bone marrow specimens to exclude abnormalities

not identified by the specified FISH probe(s).




WBC-Count).





WBC-Count).


Days test is Sunday-Wednesday 7:00am-3:00PM

performed



study.


Interpretation Diffuse Large B-Cell Lymphoma (DLBCL) is a lymphoid

neoplasm, particularly involving large (microscopically) B

cells. This FISH panel is designed to detect the most

common, and/or prognostically-significant abnormalities in


DLBCL, and may aid in discrimination between DLBCL

and other lymphomas (Swerdlow et al. 2008) as well as

uncovering ‘double hit’ lymphomas (Aukema et al.

2011). FISH studies are useful adjuncts to complete

chromosome studies, particularly when following an

abnormal clone, assessing relapse and progression, or

when material is inadequate for chromosomal analysis.




40260376 Location


Title

DUCHENNE MUSCULAR DYSTROPHY GENE ANALYSIS BY MICROARRAY

ITEM Chromosomal Microarray Analysis is useful for the detection

of Micro deletions and duplications in Duchenne Muscular

Dystrophy (DMD) and Beckers Muscular Dystrohy (BMD)

genes. DMD/BMD gene analysis by CMA can also help in

determining the carrier status in family members at the risk of

having DMD/BMD.

Specimen

1. Specimen Type: Whole blood/ Cord blood

Container/Tube: EDTA- Lavender top





3. Specimen Type: CVS, Skin Biopsy and POC

Container /Tube: Sterile Container containing normal saline/

Sterile transport media


Note: Cord blood, Amniotic Fluid, CVS and POC should be

accompanied with maternal blood (3-5ml in lavender top tube)

to rule out maternal cell contamination Transport Ambient Temperature

Days test is Sunday to Thursday 07:00 AM to 02:00 PM performed


Method Array Comparative Genomic Hybridization using Surescan

High Resolution Technology on OGT CytoSure Platform.


Interpretation DMD/BMD gene analysis by microarray is useful for studying exonic copy number variations. Deletions account for


approximately 65% of DMD mutations and 85% of BMD

mutations. Duplications occur in approximately 6–10% of

males with either DMD or BMD.




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Location

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Title EWING SARCOMA FISH TESTING

ITEM This Test is used to diagnose members of the Ewing

sarcoma family of tumors (ESFT). Does not identify the translocation partner. Ewing Sarcoma FISH Testing is useful for Supporting the diagnosis of Ewing sarcoma (EWS)/primitive neuroectodermal tumor (PNET), myxoid chondrosarcoma, desmoplastic small, round cell tumor, clear cell sarcoma, and myxoid liposarcoma when used in conjunction with an anatomic pathology consultation. This test is an aid in the diagnosis of EWS when reverse transcriptase-PCR results are equivocal or do not support the clinical picture.





Ambient






Interpretation A neoplastic clone is detected when the percent of cells

with an abnormality exceeds the normal cutoff for

the EWSR1 FISH probe set.

A positive result is consistent with a diagnosis of Ewing

sarcoma (EWS)/primitive neuroectodermal tumors

(PNET).

A negative result suggests that a EWSR1 rearrangement

is not present but does not exclude the diagnosis of

EWS/PNET.




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Title EXTRA‐NODAL MZL PANEL BY FISH

ITEM Marginal Zone Lymphoma (MZL) is comprised of two

lymphoid neoplasms: extranodal marginal zone

lymphoma of mucosa-associated lymphoid tissue (MALT

lymphoma) and nodal MZL; the former is more common

than the latter and affects the GI tract most commonly,

whereas MZL affects peripheral lymph nodes

predominately. The two may also be discriminated with

the translocation probes listed below. This FISH panel is


prognostically-significant abnormalities in MZL (Swerdlow

et al. 2008). FISH studies are useful adjuncts to complete







WBC-Count).

(Adult - 3-6 mL , Child - 2 mL, Infant - 2 mL)




WBC-Count).




study.


Interpretation Marginal zone lymphomas (MZL) are distinct B cell

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M

neoplasms with variable clinical presentations. The

clinicopathologic entities include extranodal marginal

zone

MALT lymphoma, nodal marginal zone lymphoma

(MZL), and splenic marginal zone lymphoma (MZL).

The Extra-nodal MZL FISH panel includes:

1)

MALT1 dual-fusion probe, to detect rearrangement

on

chromosome 18.

2) IGH break-apart probe, to detect disruption of IGH

(14q32).

3) BCL6 break-apart probe to detect disruption of BCL6

and/or trisomy 3.




40260376 Location

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Title FFPE LYMPHOMA PANEL BY FISH

ITEM Useful for detecting a neoplastic clone associated with the


various B-cell lymphomas. Tracking known chromosome

abnormalities and response to therapy in patients with B-

cell lymphomas. This targeted panel is appropriate when

clinical and morphologic evaluation is most suggestive of a

low-grade/small B-cell lymphoma, and high-grade

lymphomas (such as large cell anaplastic and Burkitt’s

lymphoma) are not a diagnostic consideration.



Specimen Volume: 1stained H&E slide - 6 unstained

slides





study.


Interpretation A neoplastic clone is detected when the percent of cells with an abnormality exceeds the normal reference range

for any given probe. Detection of an abnormal clone is

supportive of a diagnosis of a B-cell lymphoma. The

specific abnormality detected may help subtype the

neoplasm. The absence of an abnormal clone does not

rule out the presence of a neoplastic disorder.

Fixatives other than formalin (eg, Prefer, Bouin) may not

be successful for FISH assays.


Performing Lab Diagnostic Genomic Division, Dept Lab Med & Path, QRI Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974- 40260376

Location

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Title

FOLLICULAR LYMPHOMA PANEL BY FISH

ITEM This assay is useful to diagnose follicular lymphoma (>

75%) and diffuse large cell lymphomas (25%).

Translocation t (14; 18) (q32; Q21. 3) is assayed by FISH

with probes from the regions IgH (14q32) and BCL2

(18q21. 3).




WBC-Count).





WBC-Count).





study.


Interpretation This FISH assay specifically detects the t(14;18)(q32;q21) involving the BCL2 and IGH chain genes. This

translocation is present in over 90% of follicular

lymphomas and in a significant minority (20-30%) of

diffuse large B cell lymphomas. It is characterized by the

aberrant juxtaposition of the BCL2 proto-oncogene on

chromosome 18 with the immunoglobulin heavy chain

gene on chromosome 14, resulting in constitutive

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overexpression of the BCL2 protein which ultimately leads

to alterations in programmed cell death (i.e., apoptosis)

and tumor cell proliferation. Evaluation for a

t(14;18)(q32;q21) is of use in the diagnostic evaluation for

follicular lymphoma as well as in the evaluation of

aggressive B cell lymphomas where Burkitt's lymphoma (BL), diffuse large B cell lymphoma (DLBCL), and the

intermediate category are diagnostic considerations. In

aggressive B cell lymphoma, the presence of a

t(14;18)(q32;q21) in addition to a MYC rearrangement

argues against the diagnosis of BL. The presence of a

t(14;18)(q32;q21) is seen more often in DLBCLs of

germinal center cell type and has been reported to be a

poor prognostic factor in some studies.




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Location

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Title HAIRY CELL LEUKEMIA PANEL BY FISH



Hairy cell leukemia (HCL). Identifying and tracking known

chromosome abnormalities in patients with HCL and

tracking response to therapy. Distinguishing patients with

11;14 translocations who have leukemic phase of HCL.

Detecting patients with atypical HCL/CLL or other forms of

lymphoma associated translocation between IGH/CCND1

and CEP12,TP53,deletion or other partner genes




WBC-Count).





WBC-Count).


Days test is Sunday-Wednesday 7:00am-3:00PM

performed



study.


Interpretation Hairy cell leukemia (HCL) is a low grade B-cell lymphoproliferative disorder that typically presents with

splenomegaly, cytopenias, and diffuse bone marrow

infiltration. There have been few cases in the literature of

HCL presenting as lymphomas in extra-nodal locations,

such as soft tissues and bones without circulating

leukemic cells, splenomegaly, or iliac crest bone marrow

involvement. Panel includes testing for the abnormalities

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using the probes listed:


Performing Lab

Location

Diagnostic Genomic Division, Dept Lab Med & Path, QRI


40260376

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Title HER2 GENE ANALYSIS BY FISH

ITEM Used as a prognostic indicator for patients with both node-

positive and node-negative primary and metastatic breast

cancer. Guiding therapy, as patients with HER2

amplification may be candidates for therapies that target

the human epidermal growth factor receptor 2 (HER2)

proteins (eg, trastuzumab [Herceptin], pertuzumab,

lapatinib). Confirming the presence of HER2 amplification

in cases with 2+ (low level) or 3+ (high level) HER2

overexpression by immunohistochemistry.

Specimen Specimen Type: Tissue


Specimen Volume: 1stained H&E slide - 2 unstained slide

Transport Ambient

Temperature Days test is Sunday-Wednesday 7:00am-3:00PM performed



study.


Interpretation An interpretive report is provided. Results are interpreted utilizing the 2013 American Society of Clinical Oncology

(ASCO)/College of American Pathologists (CAP)

guidelines.


Performing Lab

Diagnostic Genomic Division, Dept Lab Med & Path, QRI Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974-

40260376

Location

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Title

HYPEREOSINOPHILIC SYNDROME PANEL BY FISH

ITEM Useful in providing genetic information for patients with

hypereosinophilic syndrome (HES) and systemic mast cell

disease (SMCD) involving CHIC2 deletion. Identifying and

tracking chromosome abnormalities and response to

therapy.




WBC-Count).





WBC-Count).




study.


Interpretation Imatinib mesylate, a small molecule tyrosine kinase inhibitor from the 2-phenylaminopyrimidine class of compounds, has shown activity in the treatment of

malignancies that are associated with the constitutive

activation of a specific subgroup of tyrosine kinases. A

novel tyrosine kinase, generated from fusion of the Fip1-

like 1 (FIP1L1) gene to the PDGFRA gene, was identified

in 9 of 16 patients (56%) with hypereosinophilic syndrome

(HES). This fusion results from an approximate 800 kb

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interstitial chromosomal deletion that includes the

cysteine-rich hydrophobic domain 2 (CHIC2) loci at 4q12.

FIP1L1-PDGFRA is a constitutively activated tyrosine

kinase that transforms hematopoietic cells, and is a

therapeutic target for imatinib in a subset of HES patients.




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Location

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Title MDM2 FISH Testing

ITEM MDM2 FISH testing aid in the differential diagnosis between well-differentiated liposarcoma and benign lipoma in individuals diagnosed with or suspected of having well-differentiated liposarcoma based on tissue morphology. The histological discrimination of well-differentiated liposarcoma/atypical lipomatous tumor (WDL/ALT) from lipoma can be diagnostically challenging. However, standard cytogenetic identification of ring and giant rod chromosomes strongly support the diagnosis of WDL/ALT. These abnormal chromosomes are mainly composed of amplified sequences derived from chromosome bands 12q13-15, and contain several amplified genes including MDM2, CPM, CDK4, and TSPAN31. MDM2 is amplified in >99% of WDL, and up to 30% of other types of sarcomas.





Ambient






Interpretation A positive result is consistent with amplification of the MDM2 gene locus (12q15) and supports the diagnosis of well-differentiated liposarcoma/atypical lipomatous tumor (WDL/ALT).

A negative result is consistent with absence of amplification of the MDM2 gene locus (12q15). However, negative results do not exclude the diagnosis of WDL/ALT. Amplification varies in individual tumors and among different cells in the same tumor




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Title

MANTLE CELL LYMPHOMA PANEL BY FISH

ITEM The 11;14 translocation is frequently associated with

mantle cell lymphoma and may be found in other

hematologic tumors such as multiple myeloma, plasma

cell leukemia and chronic lymphocytic leukemia. This

translocation results in the fusion of the immunoglobulin

heavy chain gene (IGH), located at chromosome region

14q32, with the cyclin D1 (CCND1) gene, and located at

chromosome region 11q13. Fluorescence in situ

hybridization (FISH) in interphase nuclei and in metaphase

spreads will detect the translocation. Results of this FISH

assay should be considered in context of routine

chromosome analysis, when possible.




WBC-Count).





WBC-Count).


Days test is Sunday-Wednesday 7:00am- 3:00PM

performed



study.


Interpretation Mantle-cell lymphoma (MCL) has a poorer prognosis than

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other small B-cell lymphomas, thus a definitive diagnosis

is essential. The t(11;14)(q13;q32) associated with MCL

juxtaposes portions of CCND1 (11q13) and IGH (14q32),

resulting in over-expression of cyclin D1. Thus we

use

FISH with a highly sensitive two-colour fluorescence in situ

hybridization (FISH) method to detect t(11;14)(q13;q32) in

nuclei isolated from Bone marrow samples.




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Location

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Title

MARGINAL MALT LYMPHOMA PANEL BY FISH


















WBC-Count).





WBC-Count).




study.


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Interpretation MALT lymphoma is the extra-nodal presentation of marginal zone B-cell lymphomas (MZBCL). The most

common anomalies in extra-nodal MZBCL of MALT type

include:

The t(11;18)(q21;q21) / API2-MLT fusion, having a 20- 50%

incidence. The translocation is associated with low-grade

MALT lymphoma of the stomach, and of the lung.

Importantly, this translocation was associated with

increased rates of persistent disease or recurrence after HP

eradication therapy.

The translocation t(14;18)(q32;q21)/IgH-MLT1 fusion,

leading to enhanced MLT1 expression may occur in 10-

20% of all MALT lymphomas. It is associated with MALT

lymphoma of the liver, skin, ocular adnexa, lung and

salivary gland. It was not found in MALT lymphomas of the

stomach, intestine, thyroid, or breast.




40260376 Location

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Title MARGINAL ZONE PANEL BY FISH


















WBC-Count).





WBC-Count).





study.


Interpretation Marginal zone lymphomas (MZL) are distinct B cell neoplasms with variable clinical presentations. The

clinicopathologic entities include extra nodal marginal

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zone MALT lymphoma, nodal marginal zone lymphoma

(MZL), and splenic marginal zone lymphoma (MZL).

The MZL FISH panel includes:

1) IGH/MALT1 dual-fusion probe, to detect t(14;18);

and for trisomy 18.

2) IGH break-apart probe, to detect disruption of

IGH (14q32).

3) BCL6 break-apart probe to detect disruption of

BCL6 and/or trisomy 3.

4) IGH/CCND1dual-fusion probe, to detect t(11;14);

and for trisomy 14.

5) BIRC3/MALT1 (aka API2/MALT1) dual-fusion

probe, to detect t(11;18).


Performing Lab

Location



40260376

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ITEM The MM-MGUS FISH panel is often used as an initial

diagnosis/pre-treatment panel for the detection of FISH

and chromosome aberrations useful in prognosis in

plasma cell myeloma. As malignant plasma cells often

have a low proliferation index, conventional cytogenetics

frequently yields normal results. When this happens,

interphase FISH studies can increase the abnormality

detection rate.




WBC-Count).





WBC-Count).

Transport

Temperature

Ambien t






Interpretation Multiple Myeloma (MM) belongs to a family of neoplasms involving clonal expansion of immunoglobulin secreting

B-

cells, often with bone marrow involvement, resulting in

anemia and leukopenia. Additionally, bone lesions are

often seen. This FISH panel is designed to detect the most common, and/or prognostically-

MULTIPLE MYELOMA PANEL BY FISH Title

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significant

abnormalities in Multiple Myeloma and related plasma

cell

neoplasms (Swerdlow et al. 2008). FISH studies are useful adjuncts to complete chromosome studies,

particularly when following an abnormal clone, assessing

relapse and progression, or when material is inadequate

for

chromosomal analysis. Fluorescence in situ hybridization

(FISH) for multiple myeloma (MM), targeting 13q14,

IGH,

TP53, on plasma enriched cells.


Performing Lab

Location



40260376

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TITLE

MYELODYSPLASTIC SYNDROME PANEL BY FISH

ITEM Myelodysplastic syndrome (MDS) describes a group of

clonal haematopoietic disorders resulting in ineffective

production of one or more of the myeloid cell lineages;

risk

for transformation to AML is increased. MDS may occur

de novo or may arise as a secondary malignancy

associated with treatment. This FISH panel is designed to

detect the most common, and/or prognostically-significant

abnormalities in MDS (Swerdlow et al. 2008). FISH

studies are useful adjuncts to complete chromosome


assessing relapse and progression, or when material is

inadequate for chromosomal analysis. Chromosome

analysis is recommended either as an initial test for MDS

or at least in conjunction with FISH.




WBC-Count).





WBC-Count).


Ambient






Interpretation FISH studies can provide confirmatory evidence of MDS and can be used to provide clinical prognostic or

Title

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diagnostic information. Clonal cytogenetic abnormalities

are more frequently observed in cases of secondary MDS

(80% of patients) than in primary MDS (40%-60% of

patients). The common chromosomal abnormalities

associated with MDS include: inv (3), -5/5q-, -7/7q-, +8,

13q-, and 20q-. These abnormalities can be observed

singly or in concert. In addition, MLL (KMT2A)

rearrangements, t(1;3) and t(3;21) are more frequently

associatedwithsecondaryMDS. Conventional

chromosome analysis is the gold standard for

identification

of the common, recurrent chromosome abnormalities

in

MDS.


Performing Lab

Location Diagnostic Genomic Division, Dept Lab Med & Path, QRI


40260376

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Title

MYELOPROLIFERATIVE NEOPLASMS PANEL BY FISH

ITEM Myeloproliferative neoplasm panel is useful for detection

of neoplastic clone that is associated with chromosome

abnormalities observed in patients with MPN, to evaluate

specimens in which standard cytogenetic analysis has

been unsuccessful, to identify and track chromosome

abnormalities for follow‐up of patients, and to evaluate

response to therapy.




WBC-Count).





WBC-Count).

Transport

Temperature

Ambient






Interpretation The classic, more common MPNs include chronic

myelogenous leukemia (CML), essential thrombocythemia

(ET), polycythemia vera (PV), and primary myelofibrosis (PMF). Chronic eosinophilic leukemia, not otherwise

specified (CEL, NOS), systemic mastocytosis (SM), chronic neutrophilic leukemia (CNL), and unclassifiable

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MPN are rare. MPNs typically occur in adults 50 to 70

years old and are uncommon in individuals <20 years old.

Frequently, the onset is insidious and the clinical course indolent. Patient complaints may include fatigue and

lethargy, weight loss, abdominal discomfort, easy bruising,

night sweats, and swollen, painful joints. Physical

examination may reveal pallor, enlargement of the spleen

or liver, and petechiae.

Distinguishing between the MPNs is often difficult because

of the overlap of clinical and laboratory findings. For

example, most MPNs result in increased numbers of

granulocytes, RBCs, and/or platelets. Each MPN begins

with effective hematopoiesis resulting in circulating mature

blood cells, but may result in marrow failure due to

myelofibrosis, ineffective hematopoiesis, or progression to

acute myeloid leukemia (AML).


Performing Lab



40260376

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ITEM Useful for detecting the chromosomal abnormalities

associated with acute promyelocytic Leukemia (APL),

t(15;17) fusion or PML/RARA gene fusion. Detection of

residual or recurrent APL. Monitoring the level of

promyelocytic leukemia/retinoic acid receptor alpha

(PML/RARA) in APL patients.

The disease is characterized by a chromosomal

translocation involving the retinoic acid receptor-alpha

gene on chromosome 17 (RARA). In 95% of cases of

APL, retinoic acid receptor-alpha (RARA) gene on

chromosome 17 is involved in a reciprocal translocation

with the promyelocytic leukemia gene (PML) on

chromosome 15, a translocation denoted as

t(15;17)(q22;q12). The RAR receptor is dependent on

retinoic acid for regulation of transcription.




WBC-Count).





WBC-Count).

Transport

Temperature

Ambient

Days test is

performed





PML/RARA(DF)t(15;17)(q22;q21.1) BY FISH Title

TITLE

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Interpretation Acute promyelocytic leukemia (APL) accounts for 5% to 10% of acute myeloid leukemia, and generally has a good

prognosis with current treatment protocols. APL cells

contain a fusion gene comprised of the downstream

sequences of the retinoic acid receptor alpha gene

(RARA)

fused to the promoter region and upstream sequences of

one of several genes, the most common (>80%) being the

promyelocytic leukemia gene (PML). The fusion gene is

designated PML/RARA and may be seen in a karyotype as

t(15;17)(q22;q12). FISH analysis of nonproliferating

(interphase) cells can be used to detect the common

chromosome abnormalities observed in patients with

AML.

The abnormalities have diagnostic and prognostic

relevance and this testing can also be used to track

response to therapy.


Performing Lab

Location



40260376

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Title Synovial Sarcoma FISH Testing

ITEM This test aids in molecular diagnosis of synovial sarcoma. It Supports the diagnosis of synovial sarcoma when used in conjunction with an anatomic pathology consultation.





Ambient






Interpretation A neoplastic clone is detected when the percent of cells

with an abnormality exceeds the normal cutoff for

the SS18 (SYT) FISH probe.

A positive result suggests rearrangement of

the SS18 (SYT) gene region at 18q11.2 and supports the

diagnosis of synovial sarcoma.

A negative result suggests no rearrangement of

the SS18 (SYT) gene region at 18q11.2. However, this

result does not exclude the diagnosis of synovial sarcoma.




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T-cell acute lymphoblastic leukemia (T-ALL). This FISH

panel is designed to detect the most common, and/or

prognostically-significant abnormalities in T-ALL. FISH

studies are useful adjuncts to complete chromosome


assessing relapse and progression, as an adjunct to

conventional chromosome studies.




WBC-Count).





WBC-Count).


Ambient






Interpretation Specific genetic abnormalities are identified in the majority of cases of T-ALL, although many of the classic

abnormalities are "cryptic" by conventional chromosome

studies and must be identified by FISH studies. Each of

the genetic subgroups are important to detect and can be critical prognostic markers. One predictive marker,

T‐CELL ACUTE LYMPHOBLASTIC LEUKEMIA PANEL BY FISH Title

TITLE

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amplification of the ABL1 gene region, has been identified

in 5% of T-ALL, and these patients may be responsive to

targeted tyrosine kinase inhibitors.


Performing Lab

Location



40260376

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ITEM Useful for detecting a neoplastic clone associated with the


various T-cell lymphomas. Tracking known chromosome

abnormalities and response to therapy in patients with T-

cell lymphoma




WBC-Count).





WBC-Count).


Ambient






Interpretation T-cell neoplasms are relatively uncommon, accounting for approximately 12% of all non-Hodgkin lymphomas. There

are several subtypes of T-cell neoplasms: T-cell acute lymphoblastic leukemia (T-ALL), T-cell prolymphocytic leukemia (T-PLL), T-cell large granular lymphocytic leukemia (T-LGL), anaplastic large cell lymphoma (ALCL),

peripheral T-cell lymphoma, and various other cutaneous,

nodal, and extranodal lymphoma subtypes. The 2 most

prevalent lymphoma subtypes are unspecified peripheral

T-cell lymphoma (3.7%) and ALCL (2.4%). T-cell

T‐CELL LYMPHOMA PANEL BY FISH Title

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neoplasms are among the most aggressive of all hematologic and lymphoid neoplasms with the exception

of ALCL, which is usually responsive to chemotherapy.


Performing Lab



40260376

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ITEM FISH studies can be used to detect chimerism for XX and XY

cells to evaluate successful engraftment post-bone marrow

transplant. Serial FISH chimerism studies are useful in

monitoring these patients.


Container/Tube: Green top (sodium heparin) Specimen Volume: 2-6 mL (Varies depending on the WBC-Count).





WBC-Count).


Ambient

Days test is

performed





Interpretation In patients who underwent allogeneic hematopoietic stem cell transplantation, engraftment (chimerism) studies are

used to evaluate the level of donor versus recipient cells in

post-transplant peripheral blood or bone marrow

specimens (and/ or specific sorted cell populations). In

order to proceed with engraftment analysis, a pre-

transplant specimen is obtained from the recipient and

from the donor. DNA from each pre-transplant specimen

is extracted and stored for future comparison with post-

transplant specimens from the recipient. X and Y

chromosome status is used to quantify donor/recipient

cells in sex mismatch transplants, allowing assessment of

engraftment.

TRANSPLANTATION MONITORING BY FISH Title

Title

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Performing Lab

Location



40260376

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ITEM Waldenström’s macroglobulinemia (WM) is an indolent

and incurable B-cell neoplasm defined by the

accumulation of lymphoplasmacytic cells in the bone

marrow and characterized by the hypersecretion of

monoclonal immunoglobulin M (IgM) protein.1

Representing 1–2% of hematologic cancers.




WBC-Count).





WBC-Count).


Ambient






Interpretation Initial cytogenetic studies reported chromosomal abnormalities in around 10–20% of patients with WM,

spanning observations involving IGH (14q32) to trisomy

12

to deletion of 6q.FISH analyses has consistently indicated

that IGH of immunoglobulin heavy chain (IgH) are

infrequently detected in WM with IGH rearrangments.


WALDENSTROMS MACROGLOBULINEMIA BY FISH

TITLE

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Performing Lab

Location

Diagnostic Genomic Division, Dept Lab Med & Path, QRI Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974-

40260376

Molecular Genetics Section:

Acquired malignancies – Haemato-Oncology:

Quantitation BCR-ABL1 transcript levels Test

BCR-ABL1 Quantitation Specimen 3-5mls Blood or Marrow in EDTA within 24 hours of the

patient being bled.


Ambient (2-230c)

Days Test is Performed

Batched Weekly

Turnaround Time 10 working days

Method Real time PCR (ABI Quant Studio) quantitative analysis of

cDNA using Europe Against Cancer standardized primers and

Qiagen-Ipsogen quantitation standards (Qiagen, Germany).

Reference Value Control Gene Transcript levels

Interpretation Quantitative assessment of mutation burden in leukemia patients undergoing treatment with tyrosine kinase inhibitors.


Performing Lab location

Diagnostic Genomic Division, Dept Lab Med & Path, QRI Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974-40260513. Email: [email protected]

mailto:[email protected]

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BCR-ABL1 Characterisation Test

BCR-ABL1 Breakpoint Characterisation

Specimen 3-5mls Blood or Marrow in EDTA within 24 hours of the

patient being bled.


Ambient (2-230c)


Batched Weekly


Method RT-PCR analysis of cDNA following extraction of total

RNA from blood/marrow


Interpretation Diagnosis of Chronic Myeloid Leukemia



Diagnostic Genomic Division, Dept Lab Med & Path, QRI Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974- 40260513. Email: [email protected]


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CALR MUTATION TESTING Test

CALR MUTATION TESTING Specimen 3-5mls Blood or Marrow in EDTA within 24 hours of the

patient being bled.


Ambient (2-230c)


Batched Weekly


Method PCR analysis of genomic DNA followed by fragment

analysis for detection of size changes representative of

somatic insertion/deletion mutations within exon 9 of the

CALR gene.

Reference Value Wild Type

Interpretation Diagnosis of Myeloproliferative Neoplasm





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FLT3-itd MUTATION TESTING Test

FLT3-itd MUTATION TESTING Specimen 3-5mls Blood or Marrow in EDTA within 24 hours of the

patient being bled.


Ambient (2-230c)


Batched Weekly




somatic duplications within exons 14 & 15 of the FLT3

gene.


Interpretation Diagnosis of Acute Myeloid Leukemia





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JAK2 V617F MUTATION TESTING Test

JAK2 V617F MUTATION TESTING Specimen 3-5mls Blood or Marrow in EDTA within 24 hours of

the patient being bled.


Ambient (2-230c)


Batched Weekly


Method Real time PCR (Lightcycler) semi quantitative analysis of

genomic DNA using the MutaSearch detection kit

(Qiagen, Germany).

Reference Value Wild Type Sequence

Interpretation Diagnosis of Myeloproliferative Disorder





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NPM1 MUTATION TESTING Test

NPM1 MUTATION TESTING Specimen 3-5mls Blood or Marrow in EDTA within 24 hours of the

patient being bled.


Ambient (2-230c)


Batched Weekly




somatic duplications within exons 12 of the NPM1 gene.


Interpretation Diagnosis of Acute Myeloid Leukemia





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Quantitation of PML-RARA transcript levels Test

PML-RARA Quantitation Specimen 3-5mls Blood or Marrow in EDTA within 24 hours of the

patient being bled.


Ambient (2-230c)


Batched Weekly


Method Real time PCR (ABI Quant Studio) quantitative analysis

of cDNA using Europe Against Cancer standardized

primers and Qiagen-Ipsogen quantitation standards

(Qiagen, Germany).

Reference Value Control Gene Transcript levels

Interpretation Quantitative assessment of mutation burden in Acute

Promyelocytic leukemia patients undergoing treatment with targeted therapies





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Immunoglobulin and T cell Receptor gene rearrangement

Clonality Assessment HAEMATO ONCOLOGY Immunoglobulin and T cell Receptor

gene rearrangement Clonality Assessment

Specimen 3-5mls Blood or Marrow in EDTA within 24 hours of the

patient being bled.


Ambient (2-230c)


Batched Weekly



analysis for detection of size changes representative of T

and /or B cell clonality.


Interpretation Diagnosis of Lymphoproliferative Disorders



Diagnostic Genomic Division

Department of Laboratory Medicine & Pathology

Third Floor -Qatar Rehabilitation Institute (QRI)

Hamad Bin Khalifa Medical City (HBKM)

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Acquired malignancies – Solid tumor testing:

Test

BRAF V600E/K/D mutation analysis. Specimen FFPE tissue:

Option 1: Tissue sections of 10X (5-7 µm) fixed on non-

charged slides with an H&E stained slide with marked tumor

area.

Option 2: Tissue curls of 6 sections (10 µm) collected in 2 mL

tube (e.g. Eppendorf).


Room Temperature (16 - 25° C).


Arranged by laboratory Rota.

Turnaround Time Single gene testing: 10 working days.

Reflex testing: 10 working days for the first test and an

additional week (5 working days) for every following test.

Method Real Time - PCR: real-time polymerase chain reaction (PCR)-

based assay that uses mutant-specific probes to identify the

presence of V600X mutations and/or Sanger sequencing.

Reference Value N/A

Interpretation Diagnostic or prognostic molecular biomarker for colorectal

cancer, melanoma, papillary thyroid cancer and hairy cell

leukemia.



Diagnostic Genomic Division, Dept Lab Med & Path, QRI Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974-40260513. Email: [email protected]


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Test

KRAS mutation analysis. Specimen FFPE tissue:


charged slides with an H&E stained slide with marked

tumor area.

Option 2: Tissue curls of 6 sections (10 µm) collected in 2

mL tube (e.g. Eppendorf).








Method Real Time - PCR: real-time polymerase chain reaction

(PCR)-based assay that uses mutant-specific probes to

identify the presence of KRAS mutations and/or Sanger

sequencing.

Reference Value N/A

Interpretation Predictive molecular biomarker for response in patients

with metastatic colorectal cancer (mCRC) treated with

anti-EGFR antibody.




Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974- 40260513. Email: [email protected]


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Test

NRAS mutation analysis. Specimen FFPE tissue:



tumor area.












identify the presence of NRAS mutations and/or Sanger

sequencing.

Reference Value N/A

Interpretation Predictive molecular biomarker in patients with metastatic

colorectal cancer (mCRC) and Melanoma.






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Test

EGFR mutation analysis. Specimen FFPE tissue:



tumor area.







Turnaround Time 10 working days.



identify the presence of EGFR mutations and/or Sanger

sequencing.

Reference Value N/A

Interpretation Predictive molecular biomarker in patients with Lung

cancer.





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Test

cKIT mutation analysis. Specimen FFPE tissue:



tumor area.








Method Sanger sequencing.

Reference Value N/A

Interpretation Predictive molecular biomarker in patients with

Melanoma and with GIST.





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Test

PDGFRA mutation analysis. Specimen FFPE tissue:



area.









Reference Value N/A

Interpretation Predictive molecular biomarker in patients with GIST.





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Test

IDH1 and IDH2 mutation analysis. Specimen FFPE tissue:



area.



Transport Temperature Room Temperature (16 - 25° C).

Days Test is Performed Arranged by laboratory Rota.





Reference Value N/A

Interpretation Diagnostic molecular biomarker in patients with Gliomas.


Performing Lab location Diagnostic Genomic Division, Dept Lab Med & Path, QRI Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974- 40260513. Email: [email protected]


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Inherited conditions:

R

TEST Alpha-thalassemia

MUTATION(S) TESTED 3.7kb deletion

SPECIMEN REQUIREMENT Venous blood in EDTA (lavender top) tube Adult (2-5ml), Child (0.5-2ml)

TRANSPORT TEMPERATURE 4oC to ambient. Do not Freeze

DAYS TEST PERFORMED Sundays to Thursdays

TURNAROUND TIME 3 weeks

METHOD GAP PCR

REJECTION CRITERIA - Inappropriate collection tube - Lack of clinical information - Inadequate specimen identification

PERFORMING LAB LOCATION



TEST Arterial Tortuosity Syndrome

MUTATION(S) TESTED c.243C>G (p.Ser81Arg) in SLC2A10





METHOD PCR


PERFORMING LAB LOCATION Diagnostic Genomic Division, Dept Lab Med & Path, QRI Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974- 40260513. Email: [email protected]

TEST Achondroplasia

MUTATION(S) TESTED c.1138G>A/C (p.Gly380Arg) in FGFR3





METHOD DNA sequencing


PERFORMING LAB LOCATION Diagnostic Genomic Division, Dept Lab Med & Path, Q Bldg, Hamad Bin Khalifa Medical City, Doha. Tel: +974- 40260513. Email: [email protected]




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MUTATION(S) TESTED Targeted and full HBB gene sequencing




TURNAROUND TIME 3 weeks for known mutations and 10 weeks for full HBB exon, intron and 5’ & 3’ UTR sequencing




TEST Connexin 26

MUTATION(S) TESTED c.35delG (p.Gly12ValfsTer1) and full GJB2 exon screening








TEST Cystic Fibrosis and CFTR related disorders

MUTATION(S) TESTED p.Ile1234Val, CF29 panel, PolyT, other known mutations, full CFTR exon screening




TURNAROUND TIME 3 weeks for known mutations and 10 weeks for full CFTR exon sequencing

METHOD Real-time PCR, ARMS, DNA sequencing



TEST Beta-thalassemia




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MUTATION(S) TESTED G1691A, R506Q [standard nomenclature: c.1601G>A, p.Arg534Gln]

SPECIMEN REQUIREMENT Venous blood in EDTA (lavender top) tube. Adult (2-5ml), Child (0.5-2ml)




METHOD Real-time PCR



TEST Factor II (Prothrombin)

MUTATION(S) TESTED G20210GA or 20210G>A [standard nomenclature: c.*97G>A]








TEST Fragile X

MUTATION(S) TESTED CGG repeats 5 prime of FMR1





METHOD Fluorescent fragment analysis for CGG trinucleotide repeats



TEST Factor V Leiden




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and full exon sequencing of the cystathionine beta synthase (CBS) except for exons 15 & 17




TURNAROUND TIME 3 weeks for known mutations and 10 weeks for full CBS exon sequencing

METHOD Real-time PCR, DNA sequencing


PERFORMING LAB LOCATION Diagnostic Genomic Division, Dept Lab Med & Path, QRI


TEST Hypochondroplasia

MUTATION(S) TESTED c.1620C>A/G (p.Asn540Lys) of FGFR3








TEST IL28B genotyping

MUTATION(S) TESTED rs12979860 (C/C, C/T, T/T) variants





METHOD PCR



TEST Long QT syndrome (associated with KCNQ1)

MUTATION(S) TESTED Targeted and full exon sequencing of the KCNQ1 gene except for exons 1 and 16

TEST Homocystinuria

MUTATION(S) TESTED c.1006C>T (p.Arg336Cys), c.700G>A (p.Asp234Asn),




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TURNAROUND TIME 3 weeks for known mutations and 10 weeks for full KCNQ1 exon sequencing





TEST MTHFR (5,10-methylenetetrahydrofolate reductase)

MUTATION(S) TESTED c.665C>T; p.Ala222Val and c.1286A>C; p.Glu429Ala (legacy names: c.677C>T and c.1298A>C, respectively)








TEST Neonatal Sickle Cell Anemia Screening Program

Disorder Sickle cell anemia

SPECIMEN REQUIREMENT Dry blood spots on Guthrie cards

TRANSPORT TEMPERATURE Ambient

DAYS TEST PERFORMED Sundays and Wednesdays



REJECTION CRITERIA Samples are accepted from the Metabolic Laboratory.



TEST Prader-Willi / Angelman syndromes

MUTATION(S) TESTED Absence of paternal or maternal alleles at 15q11-q13








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METHOD Methylation analysis



TEST Premarital Screening Program

Disorder Cystic fibrosis, homocystinuria, spinal muscular atrophy

SPECIMEN REQUIREMENT 5ml venous blood in EDTA (lavender top) tube


DAYS TEST PERFORMED Sundays and Wednesdays

TURNAROUND TIME 1 week for CF & HCU, 3 weeks for SMA

METHOD Real-time PCR, Methylation analysis

REJECTION CRITERIA Samples are accepted from the authorized Primary Health Centers, only



TEST Prenatal services

Disorder Spinal muscular atrophy, beta-thalassemia, achondroplasia, sickle cell disease (HbS, HbSC)

SPECIMEN REQUIREMENT All prenatal samples must be provided with maternal venous blood (5ml in EDTA tube – lavender top) - Chorionic villus samples (CVS): >50mg in sterile

tissue culture solution - Amniotic fluid: >10ml

TRANSPORT TEMPERATURE 4oC or frozen for CVS. 4oC to ambient for amniotic fluid. Do not Freeze 4oC to ambient for maternal venous blood. Do not freeze


TURNAROUND TIME Up to 10 days

METHOD MLPA, DNA sequencing

REJECTION CRITERIA - Significant contamination with maternal blood / tissue - Inadequate specimen quantity


TEST RhD genotyping

MUTATION(S) TESTED RHD deletion





METHOD PCR




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TEST Sickle Cell Disease

MUTATION(S) TESTED Glu6Val for hemoglobin S [standard nomenclature: c.20A>T, p.Glu7Val] Glu6Lys for hemoglobin C [standard nomenclature: c.19G>A, p.Glu7Lys]

SPECIMEN REQUIREMENT Venous blood in EDTA (lavender top) tube. Adult (2-5ml), Child (0.5-2ml)




METHOD DNA sequencing, RFLP



TEST Spinal Muscular Atrophy

MUTATION(S) TESTED SMA1 and SMA2 deletions





METHOD MLPA



TEST SRY genotyping

MUTATION(S) TESTED SRY deletion





METHOD PCR

REJECTION CRITERIA - Inappropriate collection tube




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- Lack of clinical information - Inadequate specimen identification



TEST Wilson Disease

MUTATION(S) TESTED Targeted and full exon sequencing of the ATP7B gene




TURNAROUND TIME 3 weeks for known mutations and 10 weeks for full ATP7B exon, 5’UTR and promoter regions sequencing




TEST Y-chromosome microdeletions

MUTATION(S) TESTED AZFa, AZFb and AZFc deletions





METHOD PCR



TEST DNA storage

SPECIMEN REQUIREMENT Venous blood in EDTA (lavender top) tube Adult (2-5ml), Child (0.5-2ml) Chorionic villus samples (CVS): minimum 50mg in sterile tissue culture or buffered (pH7) saline solution Amniotic fluid: minimum 10ml For all other samples, please contact the laboratory



TURNAROUND TIME 1 week

METHOD PCR

REJECTION CRITERIA - Inappropriate collection tube




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- Lack of clinical information - Inadequate specimen identification




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Test Name BRCA1 & BRCA2 mutation analysis

Specimen 3-5mls venous blood in EDTA (lavender top) tube


4-230c. Do not freeze


Once a week

Turnaround Time 12 weeks

Method The entire coding exons and splice sites of the BRCA1

and BRCA2 genes are screened by Next Generation

Sequencing, using the Ion Torrent platform.

Reference Value N/A

Interpretation For affected patients:

1- Positive results: The variant is likely to be the

cause of breast and/or ovarian cancer in the

patient.

2- Negative results: Reduce the likelihood that the

breast and/or ovarian cancer in the patient is

associated with BRCA1 or BRCA2 germline

variants but do not entirely rule it out.

3- Inconclusive results: In some instances, the test

may identify a variant in BRCA1or BRCA2 which

cannot be conclusively classified as pathogenic

For unaffected individuals with a family history of

breast and/or ovarian cancers:

1- Positive results: Will predispose the individual to

BRCA1 or BRCA2-related cancers, depending on

the gene in which the mutation is located

2- Negative results: the patient´s individual risk of

developing breast and/or ovarian cancers is low

3- Inconclusive results: In some instances, the test

may identify a variant in BRCA1 or BRCA2

which cannot be classified as benign or

pathogenic.

Rejection Criteria Samples are accepted from the Breast Cancer High Risk

Clinic, only




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