Molecular Genetics

Molecular genetics is the field of biology and genetics that studies the structure and function of genes at a molecular level. The study of chromosomes and gene expression of an organism can give insight into heredity, genetic variation, and mutations.


Achondroplasia is inherited as an autosomal dominant with complete penetrance, although the majority (80-90%) of cases are sporadic. Estimated disease frequency is between 1/15,000 and 1/40,000. Clinically achondroplasia is characterized by macrocephaly, craniofacial disproportion, midface hypoplasia and dysplasia of the metaphysis of the tubular bone. Short limbs with a normal trunk are remarkably consistent. Achondroplasia exhibits considerable genetic homogeneity, because specific mutations correlate strongly with the disease.

99% of Achondroplasia has been attributed to the G380R mutation. Most cases of this mutation were due to a G to A transition (98%), and the remainder to a G to C transversion (1%) at nucleotide 1138 in the transmembrane domain of the FGFR3 gene

Indication for testing

Diagnostic testing for individuals affected by Achondroplasia

Prenatal testing can also be offered.

Genetic testing

DNA testing for the G380R mutation

Alpha 1 – Antitrypsin (AAT)

Alpha 1 – Antitrypsin (AAT) deficiency due to mutations in the SERPINA1 gene is the most common genetic cause of liver disease in children and of chronic obstructive pulmonary disease. It is one of the most common fatal genetic disorders in people of European decent and has an estimated prevalence of 1 in 1600 newborns. The variants are classified according to Proteinase inhibitor (Pi) typing and the two most important abnormal variants are known as the S and Z alleles as opposed to the wild type M-allele. Patients with a PiMM genotype are normal. Those with a PiMS, PiSS and PiMZ genotype are mildly deficient. Patients with a PiSZ genotype are at increased and PiZZ genotype at high risk for the disease. The Pittsburg (combined PiSS and PiZZ) genotype is fatal

Indication for testing

Diagnostic testing for individuals affected by alpha 1-antitrypsin (AAT) deficiency.

Carrier screening for AAT deficiency.

Genetic testing

DNA testing for both mutations E342K (Allele PiZ) and E264V (Allele PiS).

Ankylosing Spondylitis (HLA-B27)

Human Leukocyte Antigen B27 (subtypes B*2701-2724) is a class I surface antigen encoded by the B locus in the major histocompatibility complex (MHC) on chromosome 6 and presents microbial antigens to T-cells. HLA-B27 is strongly associated with a certain set of autoimmune diseases referred to as the “seronegative spondyloarthropathies”.

One form is ankylosing spondylitis which is a chronic, inflammatory arthritis. It affects joints in the spine and the sacroilium in the pelvis, causing eventual fusion of the spine. Early onset occurs from 18-30 years of age and is more common in men.

The HLA-B27 test is not diagnostic, but the results add information, increasing or decreasing the likelihood that the person being evaluated has the suspected autoimmune disorder.

Indication for testing

When a person has acute or chronic pain and inflammation in the spine, neck, chest, eyes, and/or joints, and it is suspected the cause is an autoimmune disorder that is associated with the presence of HLA-B27.

It may also be ordered when someone has recurrent uveitis.

The HLA-B27 test result is also used when ankylosing spondylitis is suspected but the disease is in an early stage and the vertebrae in the spine have not yet undergone the characteristic changes that would be seen on X-ray.

Male preference with symptoms beginning in early 30’s.

Genetic testing

Ankylosing Spondylitis (HLA-B27) genotyping.

Apolipoprotein E (ApoE)

Apolipoprotein E (ApoE) is a class of proteins involved in the metabolism of fats in the body. It is important in Alzheimer’s disease (AD) and cardiovascular disease. ApoE is encoded by a polymorphic gene with three common isoforms (E2, E3 and E4). Apo E3 is the neutral form and codes for apolipoprotein E3 which has normal function. In the absence of function of the APOE gene, excessive beta-amyloid deposits occur in the brain, which is one of the finding in patients with late-onset AD. Individuals who develop AD are more likely to have an APO E4 allele. APO E4 is a risk-factor allele, however most individuals with Apo E4 will never develop AD and there are many AD patients who are ApoE4 negative.

The APOE gene is also known to be the major transporter of lipids, fats and cholesterol in the blood and central nervous system and is a risk factor for coronary heart disease. Apo E4 isoforms are associated with an increased risk of atherosclerosis. These patients are predisposed to elevation of LDLC with a diet high in saturated fat.

Indication for testing

This test is only used for the purpose of risk assessment for Alzheimer’s disease.

This test alone is not intended to be diagnostic or predictive of CHD.

Genetic testing

DNA for ApoE genotype analysis to assess the E2, E3 and E4 isoforms.


The BRAF protein is a member of the serine-threonine kinase RAF family and plays a role in the RAS-RAF-MEK-ERK pathway leading to enhanced survival of certain cells. BRAF mutant tumors represent a discrete subset of colorectal cancer (CRC) characterized by poor overall survival, unique patterns of metastatic spread, and limited response to current chemotherapy and targeted therapies. The BRAF V600E mutation at position 1799 on exon 15 occur in about half of melanomas and in 10-15% of colon cancers.

The BRAF V600E mutation is associated with resistance to antibody therapy against the EGF receptor. The mutation status is evaluated to:

  • identify cutaneous or non-cutaneous melanomas that may benefit from anti-RAF treatment (drugs that target BRAF)
  • rule out Lynch syndrome (HNPCC) in patients with microsatellite unstable cancer
  • differentiate classical HCL (Hairy Cell leukemia) from HCL-like disorders.
Indication for testing

Patients with colorectal cancer or melanoma.

Genetic testing

DNA analysis of the V600E BRAF mutation.

Breast Cancer

Between 5-10% of female breast and ovarian cancer is due to a mutated copy of the BRCA1 or BRCA2 genes. BRCA mutations cause breast cancer in ~52% of families with multiple affected cases. The prevalence of BRCAmutations varies depending on ethnicity. Mutations in the BRCA1 and BRCA2 genes are also associated with other forms of cancer. Prostate cancer is more strongly associated with BRCA2 mutations.

If a mutation is identified in one of these genes then other family members can be tested. The pattern of inheritance is autosomal dominant; therefore there is a 50% chance of an affected adult passing the mutated allele onto his/her offspring.

Indication for testing

Predictive and diagnostic testing of individuals with a strong family history of breast and ovarian cancer.

Genetic testing

First option: Common mutation analysis testing for three common Afrikaner mutations (1493delC and E881X in BRCA1; and 8162delG in BRCA2), three common Ashkenazi Jewish mutations (185delAG and 5382insC in BRCA1; and 6174delT in BRCA2) and one common mutation (5999delTTCA in BRCA2) in the Xhosa and Coloured population group.

Second option: Full screen mutation analysis by sequencing and MLPA dosage analysis of the entire coding regions of the BRCA1 and BRCA2 genes.

Third option: Family follow-up testing for known familial mutations identified in the BRCA1 and BRCA2 genes.

Calreticulin (CALR)

Calreticulin (CALR) mutations have been found to be present in 67-88% of JAK2 and the thrombopoietin receptor gene (MPL) unmutated essential thrombocythaemia (ET) and primary myelofibrosis (PMF) cases. CALR mutations may be present in a very low frequency in other myeloid malignancie (MDS, atypical CML or CMML). A positive result may not distinguish between ET and PMF or other myeloid neoplasms. Very rarely, CALR mutations have been found with a concurrent JAK2 mutation.

Indication for testing

Diagnosis of myeloproliferative neoplasms (MPN), in particular essential thrombocythaemia (ET) and primary myelofibrosis (PMF) in JAK2 negative cases.

Genetic testing

Screening for somatic insertion/deletion-type mutations in exon 9 of the CALR gene.

Chimerism Testing

Chimerism testing (engraftment analysis) is performed for patients who have received a hematopoietic stem cell transplant. The test involves identifying the genetic profiles of the recipient and of the donor and then evaluating the extent of mixture in the recipient’s blood or bone marrow after the transplant. DNA is isolated from the recipient and potential donor before the transplant and analysed to determine whether the genetic markers unique to the donor and the recipient are sufficient to distinguish the donor from the recipient. After the transplant takes place, the performance of the transplant engraftment is assessed by evaluating the donor versus recipient. When a mixed profile occurs in the post-transplant sample of the recipient, the peak area from the informative alleles are used to calculate the percentage of the recipient DNA present in the sample. This data is reported together with successive historical data to monitor the patient’s progress.

Indication for testing

Individuals about to receive a bone marrow transplant or patients who had received a transplant and are being monitored as well as their donor’s.

Genetic testing

A subset of 21 STR markers are used for profile establishment of the recipient and donor before and after transplant and this can be used to monitor the recipient’s progress.

Connexin 26 and 30

Congenital deafness is a common form of hearing impairment, which occurs in about one in 1000 live births. Approximately 80% of the hereditary cases are non-syndromic hearing impairment (NSHI) and are inherited in an autosomal-recessive mode.

The GJB2 gene defects are the most frequent cause of autosomal recessive non-syndromic hearing loss (DFNB1). GJB2 has a single coding exon encoding for the gap-junction protein, connexion-26.

The second gap-junction protein, connexin 30, is expressed in the same manner as connexin 26. The 309 kb deletion implicating the GJB6 gene, del(GJB6-D13S1830), may coexist with GJB2 gene mutations. This deletion is also in the DFNB1 locus outside GJB2, but truncating the neighbouring GJB6 gene. The deletion represent the most common mutation reported in the GJB6 gene.

Indication for testing

Diagnostic testing for individuals affected by congenital deafness

Carrier testing can also be offered.

Genetic testing

GJB2 gene sequence and GJB6 targeted deletion testing.

Cystic Fibrosis (CF)

Cystic fibrosis is one of the most common autosomal recessive genetic disorders among Caucasians. It is characterised by mutations in the CFTR (Cystic Fibrosis Transmembrane Conductance regulator) gene. Mutations in the CFTR gene lead to changes in the characteristics of exocrine excretions. It affects the function of the chloride ion channel which is important in creating sweat, digestive juices and mucus. An absence of functional CFTR in the epithelial cell membrane leads to the production of sweat with a high salt content and mucus secretions with an abnormal viscosity (leading to stasis, obstruction and bronchial infection).

More than 2000 mutations have been reported with the most common mutation worldwide being a three base-pair deletion, deltaF508. This results in the omission of phenylalanine at position 508 of CFTR, leading to a combination of defective intracellular processing (which results in an absence of CFTR from the membrane) and defective channel function. 31 other mutations account for a further 20% of cases.

Indication for testing
  • Typical CF presentation
  • Atypical clinical presentation and/or borderline sweat test
  • Male infertility with CBAVD
  • Other CFTR related diseases in adults
  • Fetusus with bowel hyperechogenicity and/or loop dilation
  • Prenatal testing
  • CF carrier testing in individuals with a positive family history
  • Carrier testing for oocyte donors
Genetic testing

First option is testing for the most common F508del.

Second option is a CFTR screening assay for the common 33 pathogenic mutations (in individuals of European decent):

Delta F508 (76% White, 50% Coloured), 3120+1G→A (46% Black, 17% Coloured) and other 31 prevalent mutations (each less than 3%, 711+1G>T, 621+1G>, 1717-1G>, CFTRdele2,3(21kb) 3849+10kbC >T, 2789+5G>A, 1898+1G>A, G542X, G85E, Y1092X(C >A), G551D, R553X, 3659delC, N1303K, R560T, R117H, R1162X, L1077P, R117C, R1066C, L1065P, W1282X, R347H, R347P, I507del, T338I, I336K, 1677delTA, R334W, 3272-26A>G, 1078delT, 2183AA>G, 497, 515, 2184insA, 2143delT ,5T (9-13TG), 7T, 9T, 5T_9TG, 5T_10TG, 5T_11TG, 5T_12TG, 5T_13TG

Familial Hypercholesterolemia (FH)

Familial hypercholesterolemia (FH) is characterized by elevated cholesterol levels, specifically very high low-density-lipoprotein (LDL) levels in the blood and early cardiovascular disease. The LDL receptor protein normally removes LDL from the circulation. FH is an autosomal dominant disorder, which occurs in 1:500 people in most countries, but in 1:80 in the Afrikaner population in SA. Homozygous FH is much rarer, occurring in 1 in a million births and causes accelerated atherosclerosis in childhood. FH is caused mainly by mutations in the low-density lipoprotein receptor (LDLR) gene. Three founder mutations account for ~90% of FH cases among the Afrikaners in SA.

Familial defective apolipoprotein B100 (FDB) is due to a mutation in the apolipoprotein B (APOB) gene, that markedly reduces the affinity of the LDL receptor. FDB is characterised by moderately raised to high plasma cholesterol levels.

Indication for testing
  • Diagnostic testing of individuals affected with FH
  • Elevated levels of total cholesterol
  • Tendon xanthomata (TX) in patient
  • Family history of elevated cholesterol and heart disease
  • Family history of total cholesterol >7.5mmol/l
Genetic testing
  • Screening for three LDLR founder mutations, D227E, V429M and D175N.
  • Screening for the R3500Q mutation in the APOB gene is also performed.
Factor V Leiden (FV)

The Factor V Leiden (FV) mutation is the most common cause of inherited thrombophilia and accounts for over 90% of activated protein C resistance. FV has an incomplete autosomal dominant inheritance.

It results in an increased risk of venous thrombosis in heterozygous and homozygous individuals. It is associated with myocardial infarction, pulmonary embolism, deep venous thrombosis, preeclampsia, eclampsia, recurrent miscarriages and gall bladder dysfunction.

Indication for testing
  • History of recurrent venous thrombosis.
  • History of transient ischemic attacks or premature stroke.
  • Strong family history of venous thrombosis.
  • Females contemplating hormone therapy.
Genetic testing

DNA testing for the R506Q (1691G→A) mutation.

Fanconi Anemia (FA)

Fanconi anaemia (FA) is a chromosome instability syndrome with progressive bone marrow failure and an increased risk for cancers. Common manifestations include growth retardation, skin abnormalities (hyperpigmentation and café-au-lait spots), radial axis defects and less frequently, renal anomalies, hypogonadism, mental impairment, heart defects and diabetes mellitus. FA is seen most often in children, with a mean age of onset of 8 years. There is a 15,000-fold increased risk of MDS and AML in FA patients, with a mean age of developing a haematological malignancy at 13-15 years of age 2. FA is an autosomal recessive disorder and has a worldwide incidence of 1 in 300 000. South African Afrikaner, Black and Jewish FA patients have been shown to carry founder mutations in the FANCA (79%), FANCG (80%) and FANCC, respectively.

Indication for testing
  • Diagnostic testing for FA
  • Carrier and prenatal testing for individuals with a family history of FA
Genetic testing
  • FANCA screening for large deletions and 3398delA
  • FANCG screening for the 7-bp deletion, c.637_643delTACCGCC
  • FANCC screening for the splice site mutation, IVS4+4A>T

Acute Myeloid Leukemia (AML) in general has a poor prognosis. FLT3 (fms-like tyrosine kinase 3) is a receptor tyrosine kinase that is normally expressed on many cell types including hematologic stem cells. Assessment of the mutation status of the FLT3 receptor gene in karyotype normal AML is the most important prognostic indicator of disease outcome, which is often substantial, as many studies in AML have shown that the presence of FLT3 activating mutations portends a poor prognosis. For this reason FLT3 activation mutation testing is required to stratify disease and determine appropriate treatment options. This PCR assay targets regions of the FLT3 gene to identify internal tandem duplication (ITD) mutations and tyrosine kinase domain (TKD) mutations, such as the D835. Mutation of the FLT3 receptor, either by internal tandem duplication (ITD) of the juxtamembrane domain or by point mutation of the aspartic acid residue D835 in the activation loop of the kinase domain, causes constitutive activation of the FLT3 receptor.

FLT3 Internal Tandem Duplication (ITD)/length mutations are caused by duplication and insertion of a portion of the FLT3 gene that includes the region in and around the juxtamembrane (JM) region of the FLT3 gene. These mutations vary in both the location and the length of the inserted duplicated DNA sequence. ITD mutations result in constitutive autophosphorylation and activation of FLT3.

FLT3 Tyrosine Kinase Domain (TKD) mutations are caused by nucleic acid substitutions that result in a change in the amino acid sequence in this highly conserved catalytic center. TKD mutations, such as D835, result in constitutive autophosphorylation and activation of FLT3.

Mutations in nucleophosmin (NPM1) which almost always involve a 4-bp insertion (that varies) in a limited region of exon 12, causes aberrant cytoplasmic expression of nucleophosmin (NPMc+). A NPM1 mutation leads to a more favorouble prognosis in patients with AML which have a normal karyotype.

The clinical impact of NPM1 mutations is affected by the mutational status of the FLT3 gene. It has been proposed that combining the status of these two mutations allows for stratification into 3 prognostic groups: (1) Good prognosis FLT3-/NPM1+, (2) Intermediate prognosis FLT3-/NPM1- or FLT3+/NPM1+, (3) Poor prognosis FLT3+/NPM1-.

Indication for testing
  • Determine prognosis in patients with AML with a normal karyotype
  • Risk stratification and patient treatment
Genetic testing
  • DNA analysis of FLT3 ITD and D835 mutations and a 4bp insertion in exon 12 of NPM1.
Fragile X Syndrome

Fragile X syndrome, or Martin-Bell syndrome, is a syndrome of X-linked mental retardation. Boys with the syndrome may have large testicles (macroorchidism), prognathism, hypotonia and autism, and a characteristic but variable face with large ears, long face, high-arched palate, gynecomastia, and malocclusion. Additional abnormalities may include lordosis, heart defect, pectus excavatum, flat feet, shortening of the tubular bones of the hands, and joint laxity. Females who have one fragile chromosome and one normal X chromosome may range from normal to mild manifestations of fragile X syndrome.

The syndrome is associated with the expansion of a single trinucleotide gene sequence (CGG) in the promoter region of the FMR1 gene on the X chromosome (Xq27.3), and results in a failure to express the FMR1 protein which is required for normal neural development. Expansion of the CGG repeating codon to such a degree results in a methylation of that portion of the DNA, effectively silencing the expression of the FMR1 protein. Mutation of the FMR1 gene leads to the transcriptional silencing of the fragile X-mental retardation protein, FMRP. In normal individuals, FMRP is believed to regulate a substantial population of mRNA. FMRP plays important roles in learning and memory, and also appears to be involved in development of axons, formation of synapses, and the wiring and development of neural circuits.

Indication for testing
  • Individuals suspected to be affected with Fragile X syndrome.
  • Carrier and prenatal testing of individuals with a family history of Fragile X syndrome.
Genetic testing
  • DNA analysis to determine the FMR1 CGG repeat length.
  • This assay is not able to detect point mutations or deletions within the FMR1 gene and provide no information on the methylation status of the FMR1 promoter.
Hereditary Hemochromatosis (HH)

Hemochromatosis is a common adult-onset condition that causes the body to absorb and store too much iron.

Primary hemochromatosis, is an autosomal recessive inherited disease.

Secondary hemochromatosis is caused by anemia, alcoholism and other disorders.

Hemochromatosis is characterised by an inappropriately high absorption of iron by the gastrointestinal mucosa, resulting in excessive storage of iron particularly in the liver, skin, pancreas, heart, joints and testes. The most common manifestation of tissue damage is liver cirrhosis with an increased risk of liver carcinoma and/or pancreas damage and diabetes.

Hemochromatosis type 1 (HFE 1) is linked to mutations in the HFE gene. The probability of developing HFE depends on the combination of inherited mutations. About 90% of patients with hemochromatosis bear a homozygous HFE C282Y mutation, while an additional 5% are compound heterozygotes with mutations HFE C282Y and HFE H63D.

Patients who are homozygous for the HFE H63D mutation develop a mild form of hemochromatosis only.

Heterozygous mutations of HFE H63D, S65C, C282Y and combined heterozygous mutations of HFE H63D and S65C without the collateral amino acid exchange at C282Y show no increased risk for hemochromatosis.

Indication for testing
  • Confirm clinical diagnosis of HH in individuals with abnormal biochemical findings of iron overload.
  • Screening family members of individuals with known HH.
Genetic testing
  • DNA analysis for three common mutations in the HFE gene: C282Y (c.845G→A), H63D (c.187C→G) and S65C (c.193A→T).
Huntington’s Disease (HD)

Huntington’s disease (HD) is a progressive neurodegenerative genetic disorder, which affects muscle co-ordination and leads to cognitive decline and dementia. HD is caused by a trinucleotide repeat expansion (CAG) in the Huntingtin (HTT) gene and follows an autosomal dominant inheritance pattern.

Physical symptoms of HD usually begin between 35 and 44 years of age. If symptoms begin before 20 years of age, it is considered juvenile HD. In these cases, the symptoms may progress faster and vary slightly. The exact way HD affects an individual varies and can differ even between members of the same family, but the symptoms progress predictably for most individuals.

Genetic testing can be performed at any stage, even before the onset of symptoms. Genetic counseling is available to inform and aid individuals considering testing.

Indication for testing
  • Diagnostic confirmation for HD in a symptomatic individual.
  • Presymptomatic testing for adults with a family history of HD.
  • It is strongly suggested that predictive testing not be offered to individuals until they are at least 18 years of age.
  • Prenatal testing is also available.
Genetic testing
  • DNA analysis to determine the number of CAG triplet repeat expansions in the HTT gene.

The myeloproliferative disorders (MPD) are a group of haematological conditions where there is a primary disorder at the level of the multi-potent haematopoietic stem cells leading to increased production in one or more blood cell types.

Leukocytes from the majority of polycythemia vera (PV) patients and up to half of essential thrombocythemia (ET) patients and idiopathic myelofibrosis (IMF) patients have been found to carry the activation V617F mutation in the auto-inhibitory domain of the Janus Kinase 2 gene.

The V617F mutation also has been found in a minority of patients with other myeloid stem cell disorders, including chronic myelomonocytic leukemia (CMML) and myelodysplastic syndromes (MDS).

The common JAK2 mutation found is a single nucleotide substitution G>T at position 1849 resulting in a Valine to Phenylalanine substitution at codon 617 (V617F). This mutation renders the kinase constitutively active independent of ligand binding.

Identification of the JAK2 (V617F) mutation in myeloproliferative disorders (MPD) may be useful both to assist in identifying MPD and assessing patients for a viable targeted pharmacological treatment.

Indication for testing

Patients suspected to have PV, ET or IMF as well as CMML and MDS.

Genetic testing
  • DNA analysis for the V617F JAK2 mutation.
Leber Hereditary Optic Neuropathy

Leber hereditary optic neuropathy (LHON) causes optical nerve atrophy which can lead to bilateral visual loss. Males are more likely to be affected than females.

The G to A change at nucleotide position 11778 (m.11778G>A) from the mitochondrial ND4 gene is associated with LHON and it is transmitted by maternal inheritance.

Indication for testing
  • Individuals suspected to be affected with LHON.
  • Individuals with a family history of LHON.
Genetic testing
  • DNA analysis of the mitochondrial DNA mutation m.11778G>A.
Microdeletion Syndromes (MLPA)

Copy Number Variations (CNVs) are a prominent source of genetic variation in human DNA and play a role in a wide range of disorders. Microdeletion and microduplication syndromes are defined as a group of clinically recognisable disorders characterised by a small (< 5Mb) deletion or duplication of a chromosomal segment spanning multiple disease genes. The MLPA P245 Microdeletion syndromes-1 probemix has been developed to screen patients presenting with unexplained developmental delay and/or mental retardation for multiple microdeletion syndromes simultaneously. The probemix has a limited number of probes for specific chromosomal regions and will therefore not detect all possible causes of the syndromes included.

Indication for testing
  • Patients suspected to have one of the microdeletion/duplication syndromes
  • Patients with a family history of one of the syndromes
  • Prenatal testing can also be offered
Genetic testing
  • MLPA for the detection of copy number variations (CNVs) involved in developmental delay.

MPL is involved in megakaryocyte development and platelet production as well as hematopoietic stem cell homeostasis by encoding the thrombopoietin receptor which binds to thrombopoietin.

MPL mutations have been found to be present in 5-10% of JAK2/CALR unmutated ET and PMF cases.

MPL mutations may be present in a very low frequency in other myeloid malignancies (MDS, atypical CML or CMML). A positive result may not distinguish between ET and PMF or other myeloid neoplasms.

Indication for testing

Detection of MPL mutations is used for diagnosis and monitoring of patients with myeloproliferative neoplasms (MPN) and suggest either essential thrombocythemia (ET) or primary myelofibrosis (PMF) in a subset of cases in which JAK2 testing is negative.

Genetic testing
  • Mutation analysis testing for the W515L (TGG>TTG) and W515K (TGG>AAG) mutations in exon 10 of the MPL gene.

Lymphoplasmacytic lymphoma (LPL) is a distinct B-cell lymphoproliferative disorder primarlily characterized by bone marrow infiltration of lymphoplasmacytic cells. When LPL produces a serum monoclonal immunoglobulin of IgM class, it may be classified as Waldenstorms macroglobulinemia (WM). Based on the pathologic and phenotypic features of the tumour, it is difficult to differentiate between WM and similar B-cell tumors that may also have plasmacytic differentiation and/or secretion of IgM. Somatic mutations of MYD88 which is a key component of the Toll-like receptor signaling machinery is detected in about 90% of LPL. The somatic mutation may be observed less frequently in other small B-cell lymphomas such as marginal zone lymphoma (MZL), including nodal, splenic, or extranodal mucosa-associated lymphoid tissue (MALT). A somatic variant (T to C) at position 794 in MYD88 gene that results in an amino acid change from leucine to proline (L265P) to help distinguish this low-grade B-cell lymphoma from other B-cell lymphoma types.

Indication for testing

Distinguishing lymphoplasmacytic lymphoma from other low-grade B-cell lymphoproliferative disorders which may be in the differential diagnosis.

Genetic testing
  • DNA analysis of the L265P mutation.
Prader-Willi Syndrome (PWS) and Angelman Syndrome (AS)

Prader-Willi syndrome (PWS) is a complex genetic condition that affects many parts of the body. In infancy, this condition is characterized by weak muscle tone (hypotonia), feeding difficulties, poor growth, and delayed development. Beginning in childhood, affected individuals develop an insatiable appetite, which leads to chronic overeating (hyperphagia) and obesity. Some people with Prader-Willi syndrome, particularly those with obesity, also develop type 2 diabetes. People with Prader-Willi syndrome typically have mild to moderate intellectual impairment and learning disabilities as well as behavioral problems.

Angelman syndrome (AS) is also a complex genetic disorder that primarily affects the nervous system. Characteristic features of this condition include delayed development, intellectual disability, severe speech impairment, and problems with movement and balance (ataxia).

PWS and AS are distinct neurogenetic disorders, however both usually caused by chromosomal deletions on chromosome 15q11 or by uniparental disomy (UPD). Normal individuals have one copy of the unmethylated paternal allele and one copy of the methylated maternal allele. Two methylated alleles from a maternal disomy will appear in the case of PWS or two unmethylated alleles from a paternal disomy will indicate AS.

Indication for testing
  • Diagnostic test for AS or PWS.
Genetic testing
  • Microdeletions in the AS/PWS critical region as well as methylation status of chromosome 15q11.
Prenatal Testing (QF-PCR)

Molecular techniques have been developed as a rapid prenatal diagnostic tool to aid clinicians in diagnosing the most common chromosome disorders (trisomies 21, 13, 18 and sex chromosome aneuploidies) within 3 working days. Commercial multiplex kits using the Quantitative Flourescent Polymerase Chain Reaction (QF-PCR) method are available and used on DNA from cells of fetal origin. Using PCR amplification, fluorescent dye labeled primers target highly polymorphic regions of DNA sequences, short tandem repeats (STRs) that are located on the chromosomes of interest. Autosomal markers are used to detect trisomies of chromosomes 13, 18 and 21. Additional markers on the sex chromosomes (X and Y) can detect the most common sex chromosome aneuploidies. The QF-PCR test is used as a preamble to full chromosome analysis but has been offered as a stand-alone test to women who are at a relatively lower risk for a chromosome abnormality in their current pregnancy. However, the test is specific and only the chromosomes in question will be investigated. This may mean that if an abnormality is present in any of the other autosomes, it will not be detected.

Indication for testing
  • Advanced maternal age.
  • Increased risk identified by maternal serum screening programs.
  • Fetal ultrasonography indicating increased risk.
  • Previous child with a chromosomal abnormality.
Genetic testing
  • Multiplex QF-PCR for specific STR’s on chromosomes 13, 18, 21 and X and Y.
Specific Mutation(s)
  • Trisomy 21 Down syndrome
  • Trisomy 18 Edwards syndrome
  • Trisomy 13 Patau syndrome
  • 47, XXY Klinefelter syndrome 
  • 45, X Turner syndrome
  • Risks increase exponentially with advancing maternal age
  • 1/7900 live births
  • 1/9500 live births
  • 1/600-800 live male births
  • 1/2500 live female births
Products of Conception (QF-PCR)

Molecular techniques have been developed as a rapid diagnostic tool to aid clinicians in diagnosing the most common chromosomal disorders involved in miscarriages (trisomies 13, 15, 16, 18, 21, 22 and sex chromosome aneuploidies as well as triploidy). Commercial multiplex kits using the Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR) methods are available and used on DNA from cells of fetal origin. Using PCR amplification, fluorescent dye labeled primers target highly polymorphic regions of DNA sequences, short tandem repeats (STRs) that are located on the chromosomes of interest. Autosomal markers are used to detect trisomies of chromosomes 13, 15, 16, 18, 21 and 22 as well as triploidy. Additional markers on the sex chromosomes (X and Y) can detect the most common sex chromosome aneuploidies. The QF-PCR test is used to replace full chromosome analysis as cell culture is often unsuccessful on products of conception. However, the test is specific and only the chromosomes in question will be investigated. This may mean that if an abnormality is present in any of the other autosomes, it will not be detected.

Indication for testing
  • Recurrent miscarriages
  • Previous child with a chromosomal abnormality
  • Any other abnormalities seen on ultrasound
Genetic testing
  • Multiplex QF-PCR for specific STR’s on chromosomes 13, 15, 16, 18, 21, 21 and X and Y.
  • If the QF-PCR is unsuccessful or uninformative FISH testing can also be conducted to detect aneuploidies of chromosomes 13, 18, 21 and the sex chromosomes.
Prothrombin (PT) G20210A

Prothrombin is a blood clotting protein, also called factor II that is needed to form fibrin. The prothrombin G20210A mutation is the second most common inherited thrombophilia after the factor V Leiden mutation. The mutation is inherited in an autosomal dominant manner.

The prothrombin G20210A mutation is associated with an increased risk of venous thromboembolism due to increased plasma prothrombin activity among carriers. In addition, there may be interactions with other risk factors for thrombosis, including pregnancy, the use of oral contraceptives, and immobilization.

Indication for testing
  • Individuals with clinically suspected thrombophilia.
  • History of venous thrombosis or pulmonary embolism, especially recurrent thrombosis.
  • Females contemplating hormone therapy.
Genetic testing
  • DNA analysis for the PT G20210A mutation.
Variegate Porphyria (VP)

Variegate porphyria (VP) is an autosomal dominant inherited disorder of haem metabolism. VP is associated with decreased protoporphyrinogen oxidase activity (PPO). The disorder is characterized by photosensitivity and a propensity to develop acute neuropsychiatric attacks with abdominal pain, vomiting, constipation, tachycardia, hypertension, psychiatric symptoms and, in the worst cases, quadriplegia.

The activity of this enzyme is reduced by 50 percent in most people with VP. In severe cases that begin early in life, the enzyme is almost completely inactive. Nongenetic factors such as certain drugs, stress, and others listed above can increase the demand for haem and the enzymes required to make haem. The combination of this increased demand and reduced activity of protoporphyrinogen oxidase disrupts haem production and allows byproducts of the process to accumulate in the liver, triggering an acute attack. The R59W mutation in the PPO gene is associated with VP and is seen as a founder mutation in Africa.

Indication for testing
  • Diagnostic testing for individuals affected by VP.
  • Testing of family members affected with VP.
Genetic testing
  • DNA analysis of the R59W mutation.
Y-Chromosome Deletion

Microdeletions in the Y chromosome have been found at a much higher rate in infertile men than in fertile men. Many of the deletions have been found in the azoospermia factor locus (AZF), at Yq11. Deletions in the AZFa, AZFb and AZFc/DAZ regions of the Y-chromosome occur in men with non-obstructive azoospermia and severe oligozoospermia. Sperm retrieval is ineffective for males with SCOS (Sertoli-cell-only syndrome) associated with AZFa and AZFb deletions, but has been achieved for males with AZFc deletions.

Indication for testing
  • Male infertility
Genetic testing

DNA testing is performed for key functional regions associated with Azoospermia Factor (AZF), namely the regions that flank AZFa and cover AZFb, AZFc, AZFd including DAZ, KAL-Y, SMCY and flanking loci for other key spermatogenesis-related genes (namely RBM1, DFFRY and DBY).