Single Nucleotide Polymorphism-Based Analysis of Cell-Free Fetal DNA in 3000 Cases from Germany and Austria.

BACKGROUND & PATIENT: Data from 3 008 patients, who underwent single-nucleotide-polymorphism (SNP)-based noninvasive prenatal testing (NIPT) are presented. METHOD: The PanoramaTM test (Natera, San Carlos, CA) was used to analyze cell-free fetal DNA from maternal blood for trisomies 21, 18, and 13, triploidy and sex-chromosome aneuploidies. RESULT: In 2 942 (97.8%) cases, a result was obtained. The average fetal fraction was 10.2%. A high-risk result for fetal aneuploidy was made for 65 (2.2%) cases. In 59 (90.8%) of these cases, invasive testing confirmed the aneuploidy. There were 6 false-positive cases. In the false-positive group, the fetal fraction was significantly lower. The overall positive predictive value was 90.8%. No false-negative cases were reported but many patients in this study have not delivered yet. Therefore, exact data cannot be given for potential false-negative cases. CONCLUSION: SNP-based NIPT is a reliable screening method for evaluating the risk of aneuploidies of chromosomes 21, 18 and 13. By using NIPT, the number of invasive procedures may be reduced significantly compared to maternal age and first-trimester screening.

Supernumerary small marker chromosome (SMC) and uniparental disomy 22 in a child with confined placental mosaicism of trisomy 22: trisomy rescue due to marker chromosome formation.

Trisomy rescue is one of various proposed mechanisms in formation of supernumerary small marker chromosomes (SMC) and uniparental disomy (UPD). In the present report a small de novo marker chromosome derived from chromosome 14 or 22 was diagnosed at prenatal diagnosis due to maternal age. Follow up investigations at birth revealed mosaicism 47,XX,+mar/46,XX. Using FISH, the marker was positive for the probe D14/22Z1, but negative for the probes midi 54 and D22Z4. Using three informative markers both chromosomes 22 were shown to be inherited from the mother (UPDmat). The results are consistent with nondisjunction at maternal meiosis I. The girl is 18 months old now and phenotypically normal. Cardiac and abdominal malformations were excluded by sonographic examinations. Motor and mental development is according to or ahead of developmental milestones (free walking with 10 months, first words at 12 months). The case confirms that maternal UPD 22 most likely is not associated with clinical abnormalities. According to FISH results, UPD 22, and 47,XX,+22 in the placenta, we conclude that the SMC was derived from alpha satellite sequences of chromosome 22. This case for the first time gives evidence that early postzygotic reduction of a chromosome to a small marker chromosome is a real existing mechanism to rescue a conceptus with trisomy.

A German Chlamydia trachomatis screening program employing semi-automated real-time PCR: results and perspectives.

BACKGROUND: Genital Chlamydia trachomatis infection is a worldwide public health burden. A screening program for C. trachomatis was therefore initiated by the public health insurers in Germany ("Gemeinsamer Bundesausschuss", GBA) in April 2008. OBJECTIVES: To estimate C. trachomatis prevalence from screening 115,766 asymptomatic females and 20,033 female patients with unspecific abdominal pain. STUDY DESIGN: Urine samples (pooled by five for the asymptomatic screening subjects) and cervical swabs were analyzed using semi-automated real-time PCR. Infection prevalence was determined separately in four categories of women, defined by health status (asymptomatic screening vs. non-screening with unspecified symptoms) and test material used. Comparative analyses were stratified by age and pregnancy status. RESULTS: Experimental evaluation of the assay used revealed a detection limit of 379 genome copies/ml urine. For pooled urine samples, the positive predictive value was 100% whereas the negative predictive value equaled 98.1%. The observed infection prevalence was higher for cervical swabs than for urine samples. Prevalence estimates also differed significantly between pregnant and non-pregnant adolescents (< or = 20 years), irrespective of the test material used (10.2% vs. 7.3% for cervical swabs, 10.9% vs. 6.1% for pooled urine samples). CONCLUSIONS: Our retrospective study, based upon a very large number of females from all parts of Germany, revealed a high infection prevalence in adolescents, particularly in pregnant adolescents, thereby justifying the screening directive of the German GBA.

A principle of quality assessment using a competitive polymerase chain reaction assay for the detection of Chlamydia trachomatis in cervical specimens.

The polymerase chain reaction (PCR)-based identification of Chlamydia trachomatis in clinical specimens should include a built-in control to assess the quality of the whole assay from DNA isolation to detection. For this purpose we established a competitive PCR assay with the following design. A 215 base-pair DNA fragment from a Chlamydia trachomatis plasmid sequence was amplified in a polymerase chain reaction. An internal control DNA was coamplified in the same reaction. The differentiation between the amplified C. trachomatis DNA and the internal control is based on hybridisation against two different probes using Enzymun Test DNA detection (Boehringer Mannheim). The internal control capture probe recognizes an additional 20 base-pair DNA sequence in the competitor DNA construct. Cervical swabs from 65 C. trachomatis positive patients were used. We examined the influence of different DNA isolation methods on the sensitivity of the assay. Detection of C. trachomatis from positive cervical swabs was compared using PCR and competitive PCR assays. The advantage of the competitive assay was a better assessment of reduced sensitivity arising from inhibitory effects or mistakes during the DNA preparation or amplification.

A competitive polymerase chain reaction assay for reliable identification of Bordetella pertussis in nasopharyngeal swabs.

In order to optimize the identification of clinically relevant quantities of Bordetella pertussis in nasopharyngeal swabs, an automated assay introducing competitive polymerase chain reaction was established. A 183 base pair DNA fragment from a repetitive region of the Bordetella pertussis genome was amplified in a polymerase chain reaction. An internal control DNA with nine base substitutions was coamplified in the same reaction. The differentiation between the amplified B. pertussis DNA and the internal control was based on hybridisation against two different probes using Enzymun Test DNA Detection (Boehringer Mannheim). Nasopharyngeal swabs from serologically positive patients, clinically diagnosed with whooping cough, serologically negative patients after contact with B. pertussis and a negative group were compared. The advantages of competitive PCR are a reduced risk of false-positive and false-negative results and the possibility to differentiate between the different PCR positive groups.

Identification of Bordetella pertussis in nasopharyngeal swabs using the polymerase chain reaction: evaluation of detection methods.

A 183 base pairs or 153 base pairs DNA fragment from a repetitive region of the Bordetella pertussis genome was amplified in a polymerase chain reaction. The sensitivities of three different detection methods (Enzymun Test, silver stained polyacrylamide gel, ethidium bromide stained agarose gel) after amplification by polymerase chain reaction showed that both a one-time polymerase chain reaction (35 cycles) with Enzymun testing as well as a nested polymerase chain reaction with either of the electrophoresis methods have high levels of sensitivity for detection of the infectious organism in nasopharyngeal swabs. Smears from 53 children with whooping cough and from 50 children without infections were analysed, using these methods. 51 patients with whooping cough gave positive test results, while 2 of the sick patients and all the control children gave negative results.