MOLECULAR GENETICS TESTS

1

Ordering recommendation

• Mutation of androgen receptor (AR) are the most frequent cause of 46,XY disorders of sex development (DSD) and associated with a variety of phenotypes, ranging from phenotypic women (complete androgen insensitivity syndrome (CAIS)) to milder degrees of undervirilization (partial form or PAIS) or men with only infertility (mild form or MAIS).

2

Accreditation status (MS ISO 15189)

• No

3

Submit with order

• Link to request form

4

Specimens required

Collection tube

• EDTA tube

Specimen preparation

• One tube of 2-3 mL (adult) or 1-2 mL (neonate) blood

Storage/Transport temperature

• Keep the sample in ice packing if delivery takes more than 24 hours to Human Genome Centre

5

Methodology

PCR & Sanger Sequencing

6

Turnaround time (TAT)

30 days

7

Shipping instruction

Sample should be sent to:

Human Genome Centre (HGC), School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, kelantan

1

Ordering recommendation

• BCR::ABL1 Mutation Analysis is an important element of clinical decision algorithms for chronic myeloid leukaemia (CML) patients who do not achieve an optimal response to tyrosine kinase inhibitor (TKI). Our laboratory recently participates EQA programme with UK-NEQAS for BCR::ABL1 kinase domain variant (mutation) status.

2

Accreditation status (MS ISO 15189)

• Yes

3

Submit with order

• Link to request form

4

Specimens required

Collection tube

• EDTA tube

Specimen preparation

• 2 tubes (2-3 mL (adult)) of blood

Storage/Transport temperature

• Keep the sample in ice packing immediately after sample collection

5

Methodology

• PCR & Sanger Sequencing

6

Turnaround time (TAT)

• 30 days

7

Shipping instruction

• Sample should be sent to: Human Genome Centre (HGC), School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan

1

Ordering recommendation

• Duchenne Muscular Atrophy (DMD) and Becker Muscular Atrophy (BMD) are X-linked recessive disorders caused by mutations in the DMD gene and characterized by the muscle enlargement and rapid progression of muscle degradation that occurs early in life.
• Multiplex Ligation-Dependent Probe Amplification (MLPA) is offered as an initial diagnostic test of choice and can diagnose 70% of DMD/BMD patients having deletions/duplications, meanwhile the remaining 30% of patients with small mutations require further analysis, such as DNA sequencing.

2

Accreditation status (MS ISO 15189)

• No

3

Submit with order

• Link to request form

4

Specimens required

         Collection tube

• EDTA tube

         Specimen preparation

• One tube of 2-3 mL (adult) or 1-2 mL (neonate) blood

         Storage/Transport temperature

• Keep the sample in ice packing if delivery takes more than 24 hours to Human Genome Centre

5

Methodology

• MLPA

6

Turnaround time (TAT)

• 30 days

7

Shipping instruction

• Sample should be sent to: Human Genome Centre (HGC), School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan

1

Ordering recommendation

• DNA sequencing (Sanger sequencing) is a laboratory method to determine the order of the bases within the DNA. This technique is used for a range of purposes including diagnosis and treatment of disease. Generally, DNA sequencing allows determination if a gene or the region of interest that regulates a gene contains changes, called variants or mutations, that are linked to a disorder.
•  Fragment analysis is an analysis method comprising a series of techniques in which DNA fragments are fluorescently labelled, separated by capillary electrophoresis (CE), and sized by comparison to an internal standard. In contrast to Sanger sequencing, fragment analysis can provide sizing, relative quantitation, and genotyping information using fluorescently labelled DNA fragments produced by PCR using primers designed for a specific DNA target.

2

Accreditation status (MS ISO 15189)

• No

3

Submit with order

• Link to request form

4

Specimens required

Collection tube

• Not applicable

Specimen preparation

• PCR product

Storage/Transport temperature

• Keep the sample in ice packing if delivery takes more than 24 hours to Human Genome Centre

5

Methodology

• Sanger Sequencing and Fragment Analysis

6

Turnaround time (TAT)

• 7 days

7

Shipping instruction

• Sample should be sent to: Human Genome Centre (HGC), School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan

1

Ordering recommendation

• Fragile X is a group of conditions associated with different mutation occurring in the unstable CGG repeat in the 5’ untranslated region of the FMR1 gene. The gene can be typical, or it can exhibit a “premutation” or a “full mutation”. When a premutation or full mutation is present, it can result in a Fragile X-associated disorders such as Fragile X syndrome (FXS), Fragile X-associated primary ovarian insufficiency (FXPOI), or Fragile X-associated tremor/ataxia syndrome (FXTAS).

2

Accreditation status (MS ISO 15189)

• No

3

Submit with order

• Link to request form

4

Specimens required

Collect

• EDTA tube

Specimen preparation

• One tube of 2-3 mL (adult) or 1-2 mL (neonate) blood into EDTA

Storage/Transport temperature

• Keep the sample in ice packing if delivery takes more than 24 hours to Human Genome Centre

5

Methodology

•  NA

6

Turnaround time (TAT)

• 30 days

7

Shipping instruction

• Sample should be sent to: Human Genome Centre (HGC), School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan

1

Ordering recommendation

• Genomic DNA extraction is the process of releasing chromosomal DNA from the cellular matrix in which it is contained. This laboratory technique usually requires a robust disruption method to separate DNA from cell membranes, proteins, and other cellular components. Our laboratory actively participates in EQA programme for DNA extraction service with Royal College of Pathologist Australasia (RCPA).

2

Accreditation status (MS ISO 15189)

• No

3

Submit with order

• Link to request form

4

Specimens required

Collection tube

• EDTA tube

Specimen preparation

• One tube of 2-3 mL (adult) or 1-2 mL (neonate) blood

Storage/Transport temperature

• Keep the sample in ice packing if delivery takes more than 24 hours to Human Genome Centre

5

Methodology

• DNA extraction kit (QIAamp DNA Blood Mini Kit)

6

Turnaround time (TAT)

• 2 days

7

Shipping instruction

• Sample should be sent to: Human Genome Centre (HGC), School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan

1

Ordering recommendation

• This HLA genotyping test detects the presence of either one of these HLA-B alleles: HLA-B*15:02; HLA-B*15:13, HLA-B*15:21. These alleles are previously associated with markedly increased risk for patients taking selected antiseizure medications (i.e. carbamazepine, phenytoin and lamotrigine) to develop severe cutaneous adverse drug reactions (SCAR). SCAR includes Stevens–Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN).
•  A positive result of either one of these alleles may suggest an alternative antiseizure medication to be prescribed to the patient to prevent the occurrence of life-threatening SCAR.

2

Accreditation status (MS ISO 15189)

• No

3

Submit with order

• Link to request form

4

Specimens required

Collection tube

• EDTA tube

Specimen preparation

• One tube of 2-3 mL (adult) or 1-2 mL (neonate) blood

Storage/Transport temperature

• Keep the sample in ice packing if delivery takes more than 24 hours to Human Genome Centre

5

Methodology

• Allele specific PCR

6

Turnaround time (TAT)

• 7 days

7

Shipping instruction

• Sample should be sent to: Human Genome Centre (HGC), School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan

1

Ordering recommendation

• Prader Willi Syndrome (PWS) and Angelman syndrome (AS) are usually caused by chromosomal deletions on chromosome 15q11 or by uniparental disomy (UPD). It results in an abnormal expression profile of gene loci that are subject to imprinting. Absence of a paternal allele of chromosome 15q11, due to chromosomal deletion or uniparental disomy, results in PWS while the absence of the maternal copy of the same region causes AS.

2

Accreditation status (MS ISO 15189)

• No

3

Submit with order

• Link to request form

4

Specimens required

Collect tube

• EDTA tube

Specimen preparation

• One tube of 2-3 mL (adult) or 1-2 mL (neonate) blood

Storage/Transport temperature

• Keep the sample in ice packing if delivery takes more than 24 hours to Human Genome Centre

5

Methodology

• Methylation Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA)

6

Turnaround time (TAT)

• 30 days

7

Shipping instruction

• Sample should be sent to: Human Genome Centre (HGC), School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan

1

Ordering recommendation

• SRY (which stands for sex-determining region Y gene) is found on the Y chromosome. This test can detect the presence or absence of the SRY gene in patients with ambiguous genitalia. This test usually ordered in conjunction with conventional cytogenetic analysis (karyotyping).

2

Accreditation status (MS ISO 15189)

• Yes

3

Submit with order

• Link to request form

 4

Specimens required

Collection tube

• EDTA tube

Specimen preparation

• One tube of 2-3 mL (adult) or 1-2 mL (neonate) blood

Storage/Transport temperature

• Keep the sample in ice packing if delivery takes more than 24 hours to Human Genome Centre

5

Methodology

• Conventional PCR

6

Turnaround time (TAT)

• 7 days

7

Shipping instruction

• Sample should be sent to: Human Genome Centre (HGC), School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan

1

Ordering recommendation

• SMA is a childhood neuromuscular disorder that is characterized by degeneration of anterior horn cells of the spinal cord. This disease is inherited and transmitted in an autosomal recessive pattern. The test is conducted to detect the deletion of exons 7 & 8 of the Survival Motor Neuron 1 (SMN 1) gene that is the responsible gene for this disease. Normal healthy individuals have both SMN1 and SMN2 but 90% of SMA patients have no SMN1 gene. This test detects over 90% of the SMA patients while the other 10% of patients will have other types of mutations.

2

Accreditation status (MS ISO 15189)

• No

3

Submit with order

• Link to request form

4

Specimens required

         Collection tube

• EDTA tube

         Specimen preparation

• One tube of 2-3 mL (adult) or 1-2 mL (neonate) blood

         Storage/Transport temperature

• Keep the sample in ice packing if delivery takes more than 24 hours to Human Genome Centre

5

Methodology

• PCR-RFLP

6

Turnaround time (TAT)

• 15 days

7

Shipping instruction

• Sample should be sent to: Human Genome Centre (HGC), School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan

1

Ordering recommendation

• The molecular diagnosis of Y-chromosomal microdeletions is a common routine genetic test which is a part of the diagnostic workup of azoospermic and severe oligozoospermic men. These microdeletions are distinguished by which segment of the Y chromosome is absent, identified as AZFa (the most proximal segment), AZFb (middle), and AZFc(distal). This test is carried out according to the EAA/EMQN best practice guidelines.
•  In basic analysis, PCR analysis of 2 markers from each of the three AZF regions plus appropriate controls in a two multiplex format will be carried out:

• • AZFa: sY84 and sY86
  • AZFb: sY127 and sY134
  • AZFc: sY254 and sY255

• It may be appropriate to request karyotyping simultaneously to exclude a chromosomal abnormality.

2

Accreditation status (MS ISO 15189)

• No

3

Submit with order

• Link to request form

4

Specimens required

Collection tube

• EDTA tube

Specimen preparation

• One tube of 2-3 mL (adult) or 1-2 mL (neonate) blood

Storage/Transport temperature

• Keep the sample in ice packing if delivery takes more than 24 hours to Human Genome Centre

5

Methodology

• Conventional PCR

6

Turnaround time (TAT)

• 15 days

7

Shipping instruction

• Sample should be sent to: Human Genome Centre (HGC), School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan

1

Ordering recommendation

• The molecular diagnosis of Y-chromosomal microdeletions is a common routine genetic test which is a part of the diagnostic workup of azoospermic and severe oligozoospermic men. These microdeletions are distinguished by which segment of the Y chromosome is absent, identified as AZFa (the most proximal segment), AZFb (middle), and AZFc(distal). This test is carried out according to the EAA/EMQN best practice guidelines.
•  For extension analysis, if a Y microdeletion is detected from the basic analysis, further analysis is carried out to confirm deletion of the markers from the basic analysis and analysis of appropriate markers at the borders of the AZF region(s) involved. It may be appropriate to request karyotyping simultaneously to exclude a chromosomal abnormality.

2

Accreditation status (MS ISO 15189)

• No

3

Submit with order

• Link to request form

4

Specimens required

Collection tube

• EDTA tube

Specimen preparation

• One tube of 2-3 mL (adult) or 1-2 mL (neonate) blood

Storage/Transport temperature

• Keep the sample in ice packing if delivery takes more than 24 hours to Human Genome Centre

5

Methodology

• Conventional PCR

6

Turnaround time (TAT)

• 7 days

7

Shipping instruction

• Sample should be sent to: Human Genome Centre (HGC), School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan