A simple and effective approach for detecting maternal cell contamination in molecular prenatal diagnosis

Experience in prenatal genetic testing and reproductive decision-making for monogenic disorders from a single tertiary care genetics clinic in a low-middle income country

OBJECTIVES

Explore health-care seeking behaviour among couples with pregnancies at-risk of monogenic disorders and compare time duration for obtaining Prenatal Genetic Test (PGT) results based on (i) amniocentesis and Chorionic Villus Sampling (CVS) (ii) in-house testing and out-sourced testing. Report the spectrum of monogenic disorders in our cohort.

METHODS

Medical records of women consulting prenatal genetic counselling clinic at Aga Khan University Hospital, Karachi from December-2015 to March-2021 with history of miscarriage or a monogenic disorder in previous children were reviewed.

RESULTS

Forty-three pregnancies in 40 couples were evaluated, 37(93%) were consanguineous. Twenty-five (63%) couples consulted before and 15(37%) after conception. Thirty-one (71%) pregnancies underwent CVS at the mean gestational age of 13-weeks and 6-days ± 1-week and 3-days and amniocentesis at 16-weeks and 2-days ± 1-week and 4-days. PGT for 30 (70%) pregnancies was outsourced. The mean number of days for in-house PGT was 16.92 ± 7.80 days whereas for outsourced was 25.45 ± 7.7 days. Mean duration from procedure to PGT result was 20.55 days after CVS compared to 28.75 days after amniocentesis. Eight (18%) fetuses were homozygous for disease-causing variant for whom couples opted for termination of pregnancy (TOP). Twenty-six monogenetic disorders were identified in 40 families.

CONCLUSION

Proactive health-care seeking behaviour and TOP acceptance is present amongst couples who have experienced a genetic disorder.

Five Variable Number of Tandem Repeats Loci (D17S5, APOB, TPO Intron 10, IL-1α Intron 6, and CIAS1) in Thais and Application in the Prenatal Diagnostic Laboratory

Background: Prenatal diagnosis of genetic disease requires DNA analysis of fetal tissue of a responsible gene. Accurate diagnosis is useful for the appropriate management of pregnancy. However, maternal contamination of fetal specimens poses a high preanalytical risk of prenatal misdiagnosis. We have examined five variable number of tandem repeat (VNTR) polymorphisms for use in monitoring potential maternal contamination. Materials and Methods: A study was conducted to examine the heterozygosities of five VNTR loci including, D17S5, APOB, TPO intron 10, IL-1α intron 6, and CIAS1 in 200 unrelated Thai subjects and applied to the monitoring of maternal contamination in 22 families at risk of having fetuses with severe thalassemia. Results: The heterozygosities of D17S5, APOB, TPO intron 10, IL-1α intron 6, and CIAS1 VNTRs were 59.5, 19.5, 66.0, 35.5, and 42.0%, respectively. Therefore, the TPO intron 10 and D17S5 loci were chosen for prenatal diagnosis of thalassemia in 22 families. Analyses of these VNTRs demonstrated an increase of informative data from 59.1% provided by the routine D1S80 VNTR analysis to 90.9%. Conclusions: The VNTR diagnostic procedure described above is simple, cost-effective, rapid, and does not require the use of sophisticated instruments; it should prove useful in the prenatal diagnosis of thalassemia.

Preimplantation Genetic Testing for Spastic Paraplegia Type 3

INTRODUCTION

Spastic paraplegia type 3 (SPG3) is a common autosomal dominant neurogenetic disease, presenting during childhood with symptoms of mildly progressive spasticity and weakness of the lower limbs. SPG3 develops due to mutations of the ATL1 gene that encodes atlastin-1, a GTPase crucial for the function of dendrites of corticospinal neurons. Here we present a case of preimplantation genetic testing for SPG3.

PATIENT AND METHODS

A 30-year-old woman with clinical symptoms of autosomal dominant spastic paraplegia since her first year of life asked for genetic counselling. DNA sequencing revealed the existence of mutation c.715C>T (p. R239C) in the ATL1 gene, confirming the diagnosis of SPG3. The patient asked for preimplantation testing for SPG3 after in vitro fertilization. An allele-specific method of PCR amplification was created in order to distinguish the mutant and the normal allele in the patient and her mother who also had SPG3, while her normal father served as control. The same nested PCR approach was used for the preimplantation testing of 11 available embryos.

RESULTS

The presence of the c.715C>T (p. R239C) mutation in the ATL1 gene was found in five embryos while six embryos carried normal alleles and were selected for IVF implantation. After three failed gestation attempts and one pregnancy ended by a spontaneous miscarriage in the first trimester due to a chromosomal abnormality, there was an achieved pregnancy with a totally normal embryo.

CONCLUSION

SPG3 may be degrading to a patient's quality of life; therefore, appropriate genetic counselling and preimplantation molecular testing may be provided as an option of prevention in offspring.

Incidence of haemoglobinopathies in Sicily: the impact of screening and prenatal diagnosis

BACKGROUND

Haemoglobinopathies are a major public health problem in Sicily: it was estimated a frequency of 1/245 couples are at risk of haemoglobinopathies. This paper reviews legislative actions, prevention activities, carrier screening, genetic counselling, foetal sampling and laboratory methodology analysis evolution reporting the results of 30 years of prevention actions to assess the efficiency of our preventative programme in the control of haemoglobinopathies in Sicily.

METHODS

This programme consisted principally of five phases: legislative actions, public awareness campaign, carrier screening, genetic counselling and prenatal diagnosis.

RESULTS

These programmes have been very effective, which we can see from a greater public awareness of thalassaemia and its prevention in the target population furthermore by a marked decline in the incidence of thalassaemia major and sickle cell anaemia from 1 in 245 live births in the absence of prevention to 1 in 2000, with a reduction in about 85%. The residual cases were because of a conscious choice by expecting parents in relation to improved life expectancy as well as improved quality of life of the affected patients.

CONCLUSION

The study suggests that public health authorities should act and invest in a similar programme for prevention of thalassaemia, as well as in relation to the increased survival of patients and the consequent organ complications.

A One-Step Real-Time PCR Assay for Rapid Prenatal Diagnosis of Sickle Cell Disease and Detection of Maternal Contamination

INTRODUCTION

Mutations at the codon 6 of the beta-globin gene (hemoglobin [Hb] S and HbC) can be routinely identified by various methods and prenatal diagnosis has been available to affected families for several years. However, the presence of maternal cells in fetal samples constitutes a serious potential source of prenatal misdiagnosis and most methods currently used to detect maternal contamination are based on the analysis of highly polymorphic loci. In addition, these methods are labor intensive and time consuming and risk carry-over contamination.

METHOD

We describe here a one-step method for mutation detection that uses fluorescent hybridization probes with melting curve analysis for both simultaneously prenatal diagnosis of sickle cell disease and potential maternal contamination.

RESULTS

Retrospective and prospective prenatal diagnosis studies (conducted in 20 and 50 cases, respectively), using both the regular procedure and real-time PCR assay show perfect concordant results. We show in addition, that as little as 5% maternal contamination can be detected and that genotype determinations are unambiguous.

Molecular basis and prenatal diagnosis of β-thalassemia among Balouch population in Iran

OBJECTIVE

To determine the molecular spectrum of β-thalassemia mutations among at-risk Balouch couples in Iran.

METHODS

Mutations' detection in DNAs extracted from the blood of partners of at-risk couples was characterized, and chorion villus sampling by amplification refractory mutation system and DNA sequencing was performed. Fetal diagnosis was also confirmed by linkage analysis.

RESULTS

Out of a total of 1234 at-risk Balouch couples referred to the center for prenatal diagnosis (PND) from June 2002 to June 2010, a high percentage of '67.4%' were from consanguineous marriages and 37.4% had between one and four affected children. The trend in referring gradually increased from 34 cases in 2002 to 357 cases in 2010. The astonishing finding was that, unlike most previous studies, only IVS 1-5 with an unusual frequency of 87.20% along with codon 8/9 (+G) with 4% constitutes about 91% of mutations. Altogether, 729 PNDs were made in 583 couples, 25% of whom had over one PND, and surprisingly five PNDs were made in the same woman within just 8 years.

CONCLUSION

Regarding the limited types of frequent mutations among Balouch population, it is hopefully believed that the incidence of β-thalassemia could be controlled by a correct diagnosis in the due time.

Prenatal Diagnosis of β-Thalassemia by Reverse Dot-Blot Hybridization in Southern China

Beta-thalassemia (thal) is the most common genetic disease and is widely distributed in southern China. Prenatal diagnosis is needed to prevent the birth of thalassemic offspring in couples at-risk. This can be performed in the first or second trimester of pregnancy by DNA analysis using polymerase chain reaction (PCR). As there are more than 30 mutations causing beta-thal in Chinese, the point mutation detection by reverse dot-blot for common mutations together with direct DNA sequencing was developed for prenatal diagnosis. Using reverse dot-blot, we were able to offer complete diagnosis in 315 (99.4%) of 317 pregnancies. Only two fetuses needed the DNA sequencing technique for diagnosis. Of the 319 at-risk fetuses, 82 (25.7%) were found to be normal, 143 (44.8%) to be heterozygous for beta-thal and 94 (29.5%) to be affected with beta-thal. Therefore, the combination of reverse dot-blot with direct DNA sequencing can perform prenatal diagnosis by DNA analysis in almost all cases at- risk of beta-thal in southern China.

Prenatal diagnosis and genetic counseling of a Chinese Alport syndrome kindred

Alport syndrome (AS) is a progressive renal disease characterized by hematuria and progressive renal failure. X-linked dominant AS (XLAS) is the major inheritance form, accounting for almost 80% of the cases, caused by mutations in COL4A5 gene. An accurate genetic diagnosis of AS is very important for genetic counseling and even prenatal diagnosis. In this study we detected mutation of COL4A5 by amplifying the entire coding sequence mRNA of peripheral blood lymphocytes using nested PCR in a Chinese XLAS family, and then performed the first prenatal diagnosis of AS in China. Mutation analysis of the fetus was performed on both cDNA-based level and DNA-based level of amniocytes. Fetus sex was determined by PCR amplification of SRY and karyotypes analysis. Maternal cell contamination was excluded by linkage analysis. There was a G-to-A substitution at position 4,271 in exon 46 of COL4A5 gene (c.G4271A) in the pregnant woman; this genetic variant has not been described previously and was a novel missense mutation. The fetus did not carry the same mutation as the mother. PCR amplification product of SRY and karyotypes analysis revealed a male fetus. Linkage analysis showed that there was no contamination of maternal cells in amniocytes.

Clinical consequences of an increasing trend of preferential use of cultured villi for molecular diagnosis by CVS

OBJECTIVE

To compare the use of uncultured versus cultured villus cells for DNA-based prenatal diagnosis.

METHODS

A retrospective review of molecular testing of chorionic villus sampling (CVS) cases from 1988-2007. Method of analysis, gestational age (GA) at CVS and at diagnosis, time from procedure to results, results of maternal contamination studies, and the laboratory employed were abstracted from patient charts. Trends in laboratory practices over time were analyzed.

RESULTS

Time from CVS to diagnosis was longer when cultured cells were used. Average GA at diagnosis was 14-6/7 weeks with cultured cells vs 13-0/7 weeks with uncultured villi (p < 0.001). Recently, laboratories are more frequently requiring cultured cells, resulting in significantly greater delays in time to diagnosis and GA at results.

CONCLUSIONS

'Direct' DNA extraction saves 2 weeks from CVS to results. More women are afforded the option of an earlier, safer pregnancy termination if uncultured villi are used for molecular diagnosis. Implementation of standardized DNA extraction protocols and sample-size requirements can optimize the use of uncultured villi for molecular prenatal diagnosis. Increased awareness of the importance of rapid results and the advantages of 'direct' DNA extraction from uncultured villi can lead to improvements that are of clinical significance for patients undergoing early prenatal diagnosis.

Testing for maternal cell contamination in prenatal samples: a comprehensive survey of current diagnostic practices in 35 molecular diagnostic laboratories

The potential presence of maternal cell contamination (MCC) in chorionic villus or amniotic fluid samples poses a serious preanalytical risk for prenatal misdiagnosis. The aim of this study was to identify current diagnostic practices in the absence of comprehensive practice guidelines. Thirty-five clinical molecular laboratories that conduct prenatal testing agreed to participate in a clinical practice survey. The survey included questions about sample requirements, test indications, assay type, test performance and limitations, criteria and management of uninformative test results, reporting, and billing. Sixty percent of participating laboratories performed testing on direct and cultured amniotic fluid, whereas forty percent tested cultured cells only. Most also accepted chorionic villus samples. Although MCC testing of fetal samples is recommended in guidelines by the American College of Medical Genetics, only 60% of surveyed laboratories performed it without exception. Commercially available assays were used by 75% of participating laboratories, and at least five identity markers were evaluated at 87% of the laboratories. The reported lower limit of MCC detection ranged from 1 to 20% but was not determined in all laboratories. MCC testing was performed in the majority of molecular diagnostic laboratories, but guidelines for standardization are needed to ensure optimal and accurate prenatal patient care.

Prenatal diagnosis of haemophilia A by chorionic villus sampling and cordocentesis: all India Institute of Medical Science experience

BACKGROUND AND OBJECTIVE

We looked at the two most commonly used methods for prenatal diagnosis, cordocentesis and chorionic villus sampling for prenatal diagnosis of haemophilia A in an Indian setting.

MATERIAL AND METHODS

The study sample included 16 families which reported to us for prenatal diagnosis of haemophilia A at All India Institute of Medical Science, New Delhi, India. Prenatal tests were done on chorionic villus samples or on cord blood (cordocentesis). Molecular work-up included the use of indirect mutation analysis in the form of linkage markers like CA-13, CA-22, Xba1 and Bcl1 as well as direct mutation analysis in the form of inversion 1 and 22 detection. Non-molecular work-up included primarily factor VIII assays.

RESULT

Chorionic villus sampling was performed in eight mothers. Of the other eight mothers, six underwent cord blood factor VIII assays because these had absence of family history and were negative for linkage and inversion 1 and 22. One patient had a female child and another had a fetus that showed congenital abnormalities.

CONCLUSION

We found that the choice of either technique, chorionic villus or cordocentesis, is not really an alternative, but rather dependent on the gestational age of presentation.

Prenatal diagnosis of β-thalassemia in Southern China

OBJECTIVE

To control the birth of thalassemic children in Southern China.

STUDY DESIGN

DNA-based diagnosis was offered on fetal tissues in pregnancies when beta-globin gene mutations were identifiable in both parents using polymerase chain reaction (PCR)-reverse dot blot (RDB) assay. An automated high-performance liquid chromatography (HPLC) system was used to analyze fetal hemoglobin in pregnancies when mutation was unidentified in at least one parent. Fetal samplings were collected by chorionic villi sampling (CVS) in the first trimester, and by amniocentesis or cordocentesis in the second trimester. Maternal contamination of fetal DNA was ruled out by short tandem repeats (STR) analysis.

RESULTS

Five hundered and forty-five fetuses of 540 at-risk pregnancies were performed prenatal diagnosis. Out of 540 fetuses tested by DNA analysis, 150 were found to be normal, 257 were carriers, whereas 133 were affected. Out of five fetuses diagnosed by HPLC, one fetus was affected and four were unaffected. Totally, 133 pregnancies with affected fetuses, except for one twin pregnancy, were voluntarily terminated, leading to a marked reduction of severe beta-thalassemia in this region.

CONCLUSIONS

Our prenatal diagnosis strategy proved to be highly effective. DNA- and HPLC-based testing could enable prenatal diagnosis of beta-thalassemia in all at-risk pregnancies.

Biochemical analysis of cultured chorionic villi for the prenatal diagnosis of peroxisomal disorders: biochemical thresholds and molecular sensitivity for maternal cell contamination detection

OBJECTIVES

The prenatal diagnosis of peroxisomal disorders is most often performed by biochemical analysis of cultured chorionic villus sample (CVS) or amniocytes. We aimed to (a) highlight the risk of maternal cell contamination (MCC) in biochemical prenatal diagnosis, (b) establish the threshold of these biochemical assays to MCC, and (c) document the sensitivity of PCR based genotyping of microsatellites for the detection of MCC in prenatal diagnosis of inborn errors by biochemical analysis.

METHODS

The threshold of each biochemical assay was assessed by co-cultivating fibroblasts from known affected and normal individuals. Genotypes for three polymorphic loci were determined by PCR and GeneScan analysis. The sensitivity of the molecular test was determined by DNA mixing experiments and isolation of DNA from co-cultivated fibroblasts.

RESULTS

MCC was detected in 2.5% of at risk CVS cultures (n = 79). Co-cultivation of defective and normal fibroblasts demonstrated that the peroxisomal biochemical assays were accurate at 25% contamination. Very low level DNA or cell contamination (1-5%) was detectable by genotyping, but an allele did not yield a definitive peak based on morphology until approximately 10% contamination. Furthermore, we demonstrated that other inborn errors of metabolism might be more susceptible to diagnostic error by low level MCC.

CONCLUSION

The sensitivity of the microsatellite analysis (> or =10%) is well within the threshold of peroxisomal biochemical assays. Although peroxisomal biochemical assays would not be predicted to introduce a false positive or negative result if MCC <10% were present but not recognised by molecular analysis, the same may not be true for other inborn errors of metabolism.