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GENETICS

Biolab is a medical diagnostic laboratory that offers a full range of laboratory services in Jordan. Recognized for our innovation, quality, and convenience, biolab delivers timely, accurate results for improved patient care. Our mandate is to provide high quality, cost-effective laboratory operation through a consolidated service delivery model consisting of: one centralized laboratory and three specialty testing laboratories.

 

 

MOLECULAR GENETICS

 

Introduction

 

In recent years, the field of medical genetics has been expanding our knowledge in the involvement of genes and chromosomes with certain diseases and disorders. It is now well established that genetic aspects are responsible for a variety of birth defects, chronic diseases and a high percentage of mental retardation.

The Molecular Genetics Laboratory at Biolab provides comprehensive DNA-based diagnostic testing for a variety of genetic conditions and diseases, as well as prenatal diagnosis, presymptomatic, predictive and carrier testing.

A new test, the Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR), has been introduced to perform rapid prenatal diagnoses of common chromosome aneuploidies. The clinical utility of this assay has repeatedly been confirmed together with its high sensitivity and specificity in detecting major chromosome abnormalities. One of the advantages of QF-PCR is the automation of part of the procedure that allows high throughput of samples; this makes rapid prenatal diagnosis available to all pregnancies either as a tool to reduce parental anxiety while waiting for completion of fetal karyotype or to improve pregnancy management in case of abnormal result.

The Molecular Genetics Laboratory combines state-of-the art genetic testing run by a team of qualified consultants, skilled specialized scientists working in a professional environment dedicated to provide quality diagnostic services constantly aligned with the rapidly growing field of laboratory medicine.  


 

Indications for Molecular Genetics Testing

 

Common reasons for referral of molecular genetic tests

Thrombosis Screen

·       For the evaluation of inherited thrombotic risk within families.

·       Transient ischemic attack or premature stroke

·       Hyperhomocysteinemia, low plasma folate levels.

·       Prior to pregnancy, oral contraceptive prescription, estrogen therapy or major surgery if there is a family history of thrombosis

·       Recurrent abortion.

 

Single Gene Disorders

1.   Recessive Disorders

e.g. Cystic Fibrosis, Familial Mediterranean Fever, Hereditary Hemochromatosis, Spinal Muscular Atrophy

·       Carrier testing and risk assessment in families

 

2.   Dominant Disorders

            e.g. Osteogenesis Imperfecta

·       Confirmation or exclusion of a diagnosis

 

3.   X – Linked Disorders

e.g. Duchenne Muscular Dystrophy, Fragile X Syndrome

·       Carrier testing and risk assessment in families

 

Fertility Testing

e.g. Y- Chromosome Microdeletions, Cystic Fibrosis

·       Azoospermia

·       Confirmation or exclusion of a diagnosis

·       Carrier testing and risk assessment in families

             

Hemoglobinopathies

e.g. alpha-Thalassemia, beta-Thalassemia, Sickle Cell Anemia

·       Carrier testing and risk assessment in families

 

Tissue Typing and Rh Genotyping

·       Organ transplant

·       Maternal-fetal Rh incompatability which can cause Alloimmune Hemolytic Disease in the fetus or newborn.

 

Oncology

e.g. Breast Cancer Genes 1 and 2 (BRCA1 and BRCA 2),  Philadelphia Chromosome bcr/abl Translocation

·       Carrier testing and risk assessment in families

·       Presymptomatic testing in individuals at risk of late-onset genetic disorder (patient may present positive family history or positive preliminary testing).

Prenatal Testing

    Prenatal diagnosis is available for the following genetic disorders:

·       Cystic Fibrosis

·       α-Thalassemia

·       β-Thalassemia

·       Sickle Cell Anemia

·      Duchenne and Becker Muscular Dystrophies

·       Fragile X Syndrome

·       Spinal Muscular Atrophy

·       AmnioPCR by QF-PCR for aneuploidy screening of chromosomes 13,18, 21, X, and Y

 

AmnioPCR by QF-PCR (QUANTITATIVE FLUORESCENT POLYMERASE CHAIN REACTION)

·         AmnioPCR by QF-PCR is a rapid screening for the detection of aberrant copy numbers of human chromosomes 13, 18, 21, X and Y in small uncultured amniotic fluid samples. This is not equivalent to a full chromosome analysis and is always followed by a full karyotype.

·         AmnioPCR by QF-PCR can be undertaken for rapid sexing on amniotic fluid. Useful when suspecting Turner syndrome, or where there is a risk of sex linked single gene disorders.

 

Limitations of Molecular Genetics Testing

·         Reliable results are dependent on adequate sample collection, transport, storage and processing procedures.

·         Prenatal diagnosis is affected by maternal cell contamination in amniotic fluid and may therefore complicate the interpretation of test results.

·         On rare instances, technical limitations associated with some of the technologies used may be present.

·         The diagnostic efficiency of the test can be impeded by drug interference.

·         Heparin inhibits the PCR reaction, therefore samples collected in heparin tubes will be rejected and a repeat assay requested.

 

 

 

Molecular Genetics Tests

Genetic Tests Specimen sample Turn Around Time
Amnio PCR for aneuploidy screening of chromosomes 13, 18, 21, X and Y, QF-PCR Amniotic fluid 2 – 3 days
Cardio Vascular Disease Risk Factors, 12 Mutations Profile, PCR EDTA whole blood 7 days
Cystic Fibrosis CFTR Gene Mutations (36 mutations), Amniotic fluid Amniotic fluid 17 days
Cystic Fibrosis CFTR Gene Mutations (36 mutations), Blood EDTA whole blood 7 days
Cystic Fibrosis CFTR Gene Mutations (36 mutations), CVS Chorionic Villus Sampling (CVS) 17 days
Duchenne and Becker Muscular Dystrophy (DMD,BMD), Genetic Analysis EDTA whole blood 18 – 20 days
Duchenne and Becker Muscular Dystrophy (DMD,BMD), Genetic Analysis Amniotic fluid 30 days
Duchenne and Becker Muscular Dystrophy (DMD,BMD), Genetic Analysis Chorionic Villus Sampling (CVS) 30 days
Factor II G20210A Prothrombin Gene Mutation (for CVD and Recurrent Abortion) EDTA whole blood 4 days
Factor V G1691A (Leiden) Gene Mutation ( for CVD and Recurrent Abortion) EDTA whole blood 4 days
Familial Mediterranean Fever (12 mutations) EDTA whole blood 4 days
Hereditary Hemochromatosis HFE Gene Mutations (H63D, S65C, C282Y), PCR EDTA whole blood 4 days
HLA ABC, Blood, PCR EDTA whole blood 7 days
HLA B27, Blood, PCR EDTA whole blood 4 days
HLA B5, Blood, PCR EDTA whole blood 4 days
HLA DR, Blood, PCR EDTA whole blood 4 days
Human Oncogenes, Breast Cancer genes (BRCA1, BRCA2), Gene Analysis, PCR EDTA whole blood 3 weeks
MTHFR C677T (for CVD and Recurrent Abortion) EDTA whole blood 4 days
Spinal Muscular Atrophy (SMA), Genetic Analysis EDTA whole blood 18 – 20 days
Spinal Muscular Atrophy (SMA), Genetic Analysis Amniotic fluid 30 days
Spinal Muscular Atrophy (SMA), Genetic Analysis Chorionic Villus Sampling (CVS) 30 days
Y Chromosome Microdeletions (6 deletions), PCR EDTA whole blood 7 days
α-Globin Gene, α-Thalassemia, (21 mutations), PCR, Amniotic Fluid Amniotic fluid 7 days
α-Globin Gene, α-Thalassemia, (21 mutations), PCR, Blood EDTA whole blood 7 days
α-Globin Gene, α-Thalassemia, (21 mutations), PCR, CVS Chorionic Villus Sampling (CVS) 7 days
β-Globin Gene, β-Thalassemia, (22 mutations), PCR, Amniotic Fluid Amniotic fluid 17 days
β-Globin Gene, β-Thalassemia, (22 mutations), PCR, Blood EDTA whole blood 7 days
β-Globin Gene, β-Thalassemia, (22 mutations), PCR, CVS Chorionic Villus Sampling (CVS) 17 days
 

MICROBIAL GENETICS

Introduction

 

Emerging infections are attracting greater attention from the public health and medical communities. Pathologists and other physicians are increasingly aware of the importance of the subspecialty of infectious disease pathology as a tool for diagnosis, monitoring therapy and prognosis as well as research of emerging infections.

 

In view of the progress in the science of molecular biology, the applications of diagnostic microbial genetics has taken a major role in the way clinicians manage their patients utilizing an array of technologies such as PCR, RT-PCR, and Gene sequencing.

 

The microbial genetics laboratory provides a list of essential molecular bacteriological and viral tests that can detect, quantify and genotype these pathogenic organisms.

 


Indications for Microbial Genetics Testing


Common reasons for referral of Microbial Genetic tests

 

·      Confirm or exclude a diagnosis of an infectious disease

·      Monitor viral load in established infected individuals and evaluate the efficacy of antiviral treatment

·      Assess reactivation of infection in transplant patients and evaluate potential disease transmission from prospective donors to tissue transplant recipients

·      Diagnosis of sexually transmitted diseases

 

Limitations of Microbial Genetics Testing

 

·      Reliable results are dependent on adequate sample collection, transport, storage and processing procedures.

·      Heparin inhibits the PCR reaction, therefore samples collected in heparin tubes will be rejected and a repeat assay requested.

·      Any diagnostic test has its limits with regards to sensitivity and detection limit.

·      In rare instances, the diagnostic efficiency of some tests can be impeded by drug interference.

 

 

 

Genetic Tests

Specimen sample

Turn Around Time

 

Qualitative Assays

H1N1 Influenza Virus RNA

Nasal swabs, nasopharyngeal swabs, serum, plasma

4 days

 

Mycobacterium tuberculosis

Body fluids

4 days

 

Herpes Simplex Virus I &II DNA

Body fluids, swabs

4 days

 

Human Papilloma Virus DNA Genotyping

Body fluids, swabs, warts

4 days

 

Chlamydia trachomatis

Body fluids, swabs

4 days

 

Neisseria gonorrhea

Body fluids, swabs

4 days

 

Quantitative Assays

Hepatitis C Virus RNA, Quantitative

Serum

4 days

 

Hepatitis C Virus RNA, Genotyping

Serum

4 days

 

Hepatitis B Virus DNA, Quantitative

Serum

4 days

 

         

 

 

 

 

 

 

 

 

CYTOGENETICS

 

Introduction

 

Cytogenetic techniques allow for the unambiguous identification of each human chromosome and the detection of aneuploidy and many large structural rearrangements that cause physical and / or mental retardation, congenital anomalies related to inherited conditions, abnormal sexual development, and other defects. New techniques allow for increased resolution of chromosome banding patterns, permitting differentiation of a greater number of abnormalities. Fluorescent in situ Hybridization (FISH) technique (using Chromosome- Gene- or Translocation- specific DNA probes) is used in the detection of genetically important trisomies, diagnosis and classification of various neoplasia and hematological malignancies as well as prenatal and pre-implantation diagnosis.

 

The Department's activities fall into three main sectors, namely prenatal diagnosis (amniotic fluid, fetal blood, chorionic villus samples, product of conception, fetal biopsies), constitutional cytogenetics (peripheral blood) and onco-hematological cytogenetics (bone marrow, lymph nodes, solid tumors, and pleural effusions).

 

 

 

Indications for Cytogenetics Testing

 

CHROMOSOMAL KARYOTYPING

Post-Natal Blood Cytogenetics Testing 

·      Dysmorphology/multiple congenital abnormalities suggestive of a chromosome abnormality

·      Ambiguous genitalia/indeterminate gender

·      Unexplained learning difficulties/developmental delay

·      Delayed puberty, gynecomastia or inappropriate secondary sexual development

·      Short stature, amenorrhea in females

·      Oligospermia or azoospermia in males

·      Parental karyotyping after two or more unexplained pregnancy loss.

·      Parental karyotyping after pregnancy loss of an unkaryotyped fetus with multiple congenital abnormalities or intrauterine growth restriction (IUGR)

·      Family history (first degree relatives) of a known chromosome abnormality other than simple aneuploidy due to non-disjunction

·      Suspected family history of chromosome abnormality where the karyotype of the affected individual is not known

·      Conditions such as growth failure, microcephaly, neurological abnormalities, immunodeficiency, and an increased incidence of malignancy

 

Postnatal Cytogenetic Testing on Skin Biopsies and Other Tissues

·      Karyotyping of skin biopsy or other types of tissues from a live patient is usually performed to investigate the possibility of tissue-specific chromosomal mosaicism. This is usually undertaken once a karyotyping has been obtained on a blood sample.

 

Prenatal Cytogenetic Testing (Amniotic Fluid, Chorionic Villus Sampling)

·      High risk of carrying fetus with chromosomal abnormality that may have been detected as a result of a screening test (first or second trimester screen).

·      Intracytoplasmic sperm injection (ICSI) or other medical intervention that increases the probability of chromosome abnormalities.

·      Abnormal ultrasonographic findings indicative of chromosome abnormality.

·      History of chromosome abnormality indicative of increased risk for future pregnancies (Chromosome abnormalities in either parent, a previous pregnancy or the family history)

·      Augmented nuchal translucency

Cytogenetic Testing of Fetal/Placental Tissue after Pregnancy Loss 

·      Any fetus, stillbirth or neonatal death with congenital abnormality suggestive of a chromosome anomaly or with neural tube defect or with intrauterine growth restriction (IUGR).

·      Unexplained stillbirth or spontaneous abortion.

·      Determine recurrence risk for future pregnancy losses.

 

FLUORESCENT IN SITU HYBRIDISATION (FISH)

Rapid Neonatal Aneuploidy Screening by FISH

  • Rapid neonatal screening by FISH for trisomies 13, 18 and 21 and for sex. This is not equivalent to a full chromosome analysis and is always followed by a full karyotyping.

 

Cytogenetic Testing of Bone Marrow and Unstimulated Blood

  • Chronic Lymphocytic Leukemia (CLL)
  • Acute Lymphocytic Leukemia (ALL)
  • Acute Myeloid Leukemia (AML)
  • Myelodysplastic Disorder (MSD)
  • Multiple Myeloma (MM)
  • Lymphoma
  • Cytopenia 

 

Cytogenetic Testing of Solid Tumors

  • Ewing Sarcoma
  • Neuroblastoma
  • Lymphoma
  • Hepatoblastoma
  • Germ Cell Tumor
  • Rhabdomyosarcoma
  • Synovial Sarcoma
  • Breast Carcinoma

 


Limitations of Cytogenetics Testing

Small Subtle Chromosome Abnormalities

·       Cytogenetic analysis relies on G-band quality and resolution. In general, blood samples give the best quality chromosomes and therefore provide the best chance of detecting small subtle chromosome abnormalities. Chromosomes from other tissues (e.g. amniotic fluid, chorionic villus and products of conception) give poorer quality chromosomes; hence the risk of missing a subtle abnormality is increased.

·       It should be noted that on rare occasions a subtle abnormality may be missed at prenatal diagnosis, only to be diagnosed later on a postnatal blood sample.

·       It should also be understood that even a G-band blood karyotype can never exclude extremely subtle chromosome abnormalities that are at the limit of resolution of light microscopy.

 

Detection of Mosaicism

·       It is well established that although mosaicism may be detected by routine karyotyping it can never be 100% excluded. However, if there is an indication of suspected mosaicism, additional cells will be examined to exclude 10% mosaicism at a 95% confidence level.

 

Interpretation of Mosaicism in Prenatal Diagnosis

·       True mosaicism, when detected prenatally, can be difficult to interpret and a further invasive diagnostic test may be required. Mosaic cell lines may be unevenly distributed between the fetus and extra-fetal tissues leading to false positive and false negative results in the most extreme cases. ‘Confined placental mosaicism' (CPM) is observed in approximately 1-2% of CVS samples.

·       Pseudomosaicism can arise as an artifact of culture and is not representative of the fetal karyotype. This is normally present in only one of two or three independently established cultures and can therefore be interpreted accordingly. In most cases, no further invasive testing is required.

 

Maternal Cell Contamination in Prenatal Diagnosis

·       Maternal cell contamination of chorionic villus and amniotic fluid occurs in approximately 1/250 samples and may occasionally complicate the interpretation of results.

 

Normal Variation

·       Each chromosome pair has a specific and identical G-banding pattern in all individuals. However, variation may occur around the centromeric regions and short arms of some chromosomes that is of no clinical significance. These variations are known as ‘polymorphic variants’, ‘polymorphisms’ or ‘normal variants’.

·       In a few cases, it is necessary to distinguish between such variation and a true abnormality. It may therefore be necessary to karyotype the parents or to carry out further tests on a repeat sample.

 

 

On rare instances, technical limitations associated with some of the technologies used may be present.

 

 

 

 

Cytogenetics Tests

 

Karyotyping  Requirements

Specimen

 

Quantity

 

Container

 

 

Maximum Transit Time

 

Turnaround Time

Peripheral blood

2 – 4 ml

Li-Heparin bottle (sterile, vacutainer, plastic)

48 hours

7 days

Fetal blood/Cord

0.5 – 1 ml

Li-Heparin bottle (sterile, plastic)

48 hours

7 days

Bone marrow and unstimulated blood

2 - 5 ml

Li-Heparin bottle (sterile, plastic)

24 hours

5 days

Amniotic Fluid

15 – 20 ml

Universal container or 16 ml conical tube (sterile, plastic)

24 hours

14 days

Chorionic Villus Sampling

2 - 25 mg

Universal container (sterile, plastic). In sterile media.

24 hours

14 days

Products Of Conception

Variable

Universal container (sterile, plastic). In sterile saline.

24 hours

14 days

Fetal  tissue/skin

1 cm3

Universal container (sterile, plastic). In sterile saline

48 hours

14 days

Fragile X

2 - 4 ml

Li-Heparin bottle (sterile, vacutainer, plastic)

48 hours

7 days

Chromosomal Breakage

(Fanconi's anemia)

2 - 4 ml

Li-Heparin bottle (sterile, vacutainer, plastic)

48 hours

7 days

 

FISH Requirements

Tests

Quantity

Container

Maximum Transit Time

Average Turnaround Time

Amniotic Fluid,  Blood,  Chorionic Villus Sampling (CVS)

Trisomy 13 [Patau Syndrome]

3 ml

Amniotic Fluid in Universal container or conical tube, (sterile, plastic)

 

Li-Heparin bottle / EDTA whole blood (sterile, plastic)

 

CVS in media (sterile, plastic)

Within

24 hours

1 - 2 working days

 

Trisomy 18 [Edward’s Syndrome]

 

Trisomy 21 [Down’s Syndrome]

 

Rapid sexing ( X and Y )

 

Prader Willi

 

Digeorge

 

Miller Dieker

 

Trisomy 21, XY

 

Trisomy 13, 18 and 21 

 

Trisomy 13, 18, 21 and XY

 

Preimplantation Genetic Diagnosis (PGD)

 

PGD

Fixated Blastomere

Salinated Slide

N/A

Within 24 hours

 

Bone Marrow and Unstimulated Blood

 

BCR/ABL: t(9;22) [CML/ALL]

1 - 2 ml

Li-Heparin bottle (sterile, plastic)

 

24 hours

 

2 - 3 days

 

GLI: (12q13) [CLL]

 

ATM: (11q22) [CLL]

 

p53: (17p13) [CLL]

 

DLEU: 13q14 [CLL]

 

ETO/AML: t(8;21) [AML/M2]

 

CBFB: inv(16) [AML/M4]

 

PML/RARA: t(15;17) [AML/M3]

 

TEL/AML: t(12;21) [ALL]

 

MLL: 11q23 [ALL/AML]

 

Deleted q5: [MDS]/[AML]

 

Deleted q7: [MDS]/ [AML]

 

LSI/MYC: t(8q24) [Burkitt lymphoma] (screening)

 

MYC/IGH: t(8;14) [Burkitt lymphoma]

 

BCL1/IGH: t(11;14) [Mantle cell lymphoma]

 

IGH/BCL2: t(14;18) [Follicular lymphoma]

 

LSI/ALK: t(2p23) [Anaplastic large cell lymphoma]

 

Solid Tumors

 

HER-2: [Breast carcinoma]

N/A

Paraffin embedded block

N/A

3 – 5 days

 

EWSR: [Ewing sarcoma]

 

N-MYC: [Neuroblastoma]

 

FKHR: 13q14 [Alveolar rhabdomyosarcoma]

 

SYT: 18q11.2 [Synovial sarcoma]

 

                 

 

 

 

 

 

 

 



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