Application of risk score analysis to low-coverage whole genome sequencing data for the noninvasive detection of trisomy 21, trisomy 18, and trisomy 13.

OBJECTIVES: Clinical performance of a low coverage, low cost, massively parallel sequencing (MPS)-based assay to stratify risk of trisomy 21, 18, and 13 pregnancies was determined. METHODS: The study included 1100 samples with birth outcome or karyotype results, comprising low-risk patients (84.2%) negative for risk indications from maternal age, serum screening, ultrasound, or family history, and high-risk patients (15.8%) with at least one of the aforementioned indications. Cell free DNA (cfDNA) was extracted from maternal plasma. Library preparation incorporated 96 index barcodes to enable sequencing on a HiSeq 2000 or 2500. Risk scores were calculated using chromosomal representation, fetal fraction, and maternal age at the estimated date of delivery. A risk score greater than or equal to 1 in 100 was used to stratify samples as high risk for trisomy 21, trisomy 18, or trisomy 13. RESULTS: Sensitivity and specificity were calculated based on risk group stratification. Trisomy 21, trisomy 18, and trisomy 13 were detected with greater than 99% sensitivity and 99.9% specificity. Fetal sex classification accuracy was 99.3%. CONCLUSIONS: We conclude that simplified MPS can be used to stratify the risk of pregnancies for trisomy 21, trisomy 18, and trisomy 13 and accurately determine fetal sex. © 2015 John Wiley & Sons, Ltd.

Circulating cell free DNA testing: are some test failures informative?

OBJECTIVE: The proportion of circulating cell free DNA derived from the feto-placental unit (fetal fraction or FF) correlates with test success and interpretation reliability. Some fetal disorders are associated with systematically lower FF, sometimes resulting in noninformative results. METHODS: We analyzed results from pregnancies tested in a nested case/control study derived from a cohort of 4664 high-risk pregnancies. Low FF was defined before and after adjusting for maternal weight and gestational age. RESULTS: Compared with euploid pregnancies, the median FF was significantly higher in Down syndrome pregnancies (ratio 1.17) and significantly lower in trisomy 18 and triploid pregnancies (ratios 0.71 and 0.19, respectively). Among 2157 pregnancies tested, 13 (0.6%) had FF <3.0% (all noninformative), including three trisomy 18 and three triploidy fetuses. After adjustment, 16 pregnancies (0.7%) had FF <0.3 multiples of the median (six informative), including one trisomy 18 and three triploidy fetuses. Modeled positive predictive values for low and high-risk populations were 7% and 30%, respectively. CONCLUSION: Among women with noninformative results attributable to low FF, trisomy 18 and/or triploidy risk are sufficiently high to warrant offering additional assessments (e.g. ultrasound). If the testing indication is ultrasound abnormality, amniocentesis and karyotype/microarray should be considered. © 2014 John Wiley & Sons, Ltd.

Maternal plasma cell-free DNA in the prediction of pre-eclampsia.

OBJECTIVES: To examine whether maternal plasma concentrations of total cell-free (cf)DNA and fetal fraction at 11-13 and 20-24 weeks' gestation in pregnancies that subsequently develop pre-eclampsia (PE) are different from those without this complication. METHODS: Total cfDNA and fetal fraction were measured in 20 cases of early PE requiring delivery at < 34 weeks, in 20 cases of late PE with delivery at ≥ 34 weeks and in 200 normotensive controls, at 11-13 and 20-24 weeks' gestation. Total cfDNA and fetal fraction measured at 11-13 weeks were converted to multiples of the median (MoM), corrected for maternal characteristics and gestational age. The distributions of total cfDNA and fetal fraction at 20-24 weeks were expressed as MoM of values at 11-13 weeks. The Mann-Whitney U-test was used to determine the significance of differences in the median values in each outcome group relative to that in the controls. RESULTS: In the early-PE group at 11-13 weeks, compared with controls, there was a significant increase in median total cfDNA (2104 genome equivalents (GE)/mL vs 1590 GE/mL) and a decrease in median fetal fraction (6.8% vs 8.7%). In the late-PE group at 20-24 weeks, compared with controls, there was a significant decrease in median fetal fraction (8.2% vs 9.6%). These significant differences between groups were not observed when the values were converted to MoM. CONCLUSION: Measurements of total cfDNA and fetal fraction in maternal plasma at 11-13 and 20-24 weeks are not predictive of PE.

Downregulation of RUNX3 and TES by hypermethylation in glioblastoma.

Glioblastoma, the most aggressive and least treatable form of malignant glioma, is the most common human brain tumor. Although many regions of allelic loss occur in glioblastomas, relatively few tumor suppressor genes have been found mutated at such loci. To address the possibility that epigenetic alterations are an alternative means of glioblastoma gene inactivation, we coupled pharmacological manipulation of methylation with gene profiling to identify potential methylation-regulated, tumor-related genes. Duplicates of three short-term cultured glioblastomas were exposed to 5 microM 5-aza-dC for 96 h followed by cRNA hybridization to an oligonucleotide microarray (Affymetrix U133A). We based candidate gene selection on bioinformatics, reverse transcription-polymerase chain reaction (RT-PCR), bisulfite sequencing, methylation-specific PCR and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Two genes identified in this manner, RUNX3 and Testin (TES), were subsequently shown to harbor frequent tumor-specific epigenetic alterations in primary glioblastomas. This overall approach therefore provides a powerful means to identify candidate tumor-suppressor genes for subsequent evaluation and may lead to the identification of genes whose epigenetic dysregulation is integral to glioblastoma tumorigenesis.

Lesbian families and family functioning: an overview.

OBJECTIVES: In the last 30 years a growing body of studies on lesbian parents and the development of children has been published. METHODS: Four computerized databases were identified studies for inclusion in this review of research on lesbian families, namely PsychInfo, Educational Resources Information Centre (ERIC), Medline, and the Social Sciences Citation Index. RESULTS: Forty-four empirical studies on lesbian families published between 1978 and 2003 were reviewed. In the research on lesbian families two phases were identified. To begin with, systematic studies on lesbian families focused on lesbian families with children who were born in a previous heterosexual relationship. More recently, studies included lesbian families whose children were born to the lesbian couple (planned lesbian families). In both phases, articles reporting results on children's development (such as sexual identity, emotional/behavioral development, social relationships and cognitive functioning), and parental functioning (such as mental psychological health and parenting skills). This paper presents and discusses major finding of the reviewed articles. CONCLUSION: Studies in both phases have emphasized that lesbian and heterosexual families are very much alike. However, it is the stigma of lesbianism that makes the family situation of lesbian families different. PRACTICE IMPLICATIONS: Healthcare workers should be informed about the similarities and differences between lesbian families and heterosexual families, and about the non-traditional family situation of planned lesbian families.

Microsatellites: perspectives and potentials of mass spectrometric analysis.

Mass spectrometry is a powerful analytical tool in biotechnology. The 'soft' ionization and desorption technologies matrix-assisted laser desorption/ionization and electrospray ionization have enabled mass spectrometric analysis of large biomolecules, such as proteins and nucleic acid amplification products, and paved the way for mass spectrometry to become a leading technology in current genomics and proteomics efforts. Large-scale analysis of single nucleotide polymorphisms by mass spectrometry has been commercially established. This article reviews applications of mass spectrometry for microsatellite analysis. Features and capabilities of the two most prominent techniques, matrix assisted laser desorption/ionization and electrospray-ionization mass spectrometry, are compared and their potential to address the limitations of conventional microsatellite analysis based on comparison of gel electrophoretic mobilities is explored.

Retention of imprinting of the human apoptosis-related gene TSSC3 in human brain tumors.

Genomic imprinting is the result of a gamete-specific modification leading to parental origin-specific gene expression in somatic cells of the offspring. Several embryonal tumors show loss of imprinting of genes clustered in human chromosome 11p15.5, an important tumor suppressor gene region, harboring several normally imprinted genes. TSSC3, a gene homologous to mouse TDAG51, implicated in Fas-mediated apoptosis, is also located in this region between hNAP2 and p57 (KIP2). TSSC3 is the first apoptosis-related gene found to be imprinted in placenta, liver and fetal tissues where it is expressed from the maternal allele in normal human development. This study investigated the imprinting status of TSSC3 in human normal, adult brain and in human neuroblastomas, medulloblastomas and glioblastomas. A polymorphism in exon 1 at position 54 was used to analyze the allelic expression of the TSSC3 gene by a primer oligo base extension (PROBE) assay using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). We found that the TSSC3 gene is not imprinted in human normal, adult brain and blood. In contrast, strong allelic bias resembling imprinting could be detected in most examined tumor specimens. The results demonstrate for the first time that the tumors under investigation are associated with a retention of imprinting of a potential growth inhibitory gene.

Application of nested PCR and mass spectrometry for DNA-based virus detection: HBV-DNA detected in the majority of isolated anti-HBc positive sera.

DNA preparations from three different groups of serum samples were examined for HBV-DNA via a nested polymerase chain reaction assay (lower detection limit: 10 viral genomes in 100 microliters serum): Group I consisted of 11 uninfected control sera, group II consisted of sera obtained from 11 HBV infected patients and group III consisted of 21 isolated anti-HBc positive samples. The 21 samples from group III were HBV-DNA negative according to a conventional non-nested PCR assay and hybridization with a 32P-labelled probe. Using nested PCR and mass spectrometry, HBV-DNA was detected in none of group I and in all of group II samples. In 11 out of 21 (52%) of the isolated anti-HBc positive sera from group III, HBV-DNA was detected. No correlation was observed between HBV-DNA positivity and anti-HBc titers. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry provided a fast, sensitive and non-radioactive assay for the detection of PCR products without the need for gel electrophoresis or hybridization with labelled probes.

Mothers' reports of infant crying and soothing in a multicultural population.

OBJECTIVES: To investigate the prevalence of infant crying and maternal soothing techniques in relation to ethnic origin and other sociodemographic variables. DESIGN: A questionnaire survey among mothers of 2-3 month old infants registered at six child health clinics in Amsterdam, the Netherlands. SUBJECTS: A questionnaire on sociodemographic characteristics and crying behaviour was completed for 1826 of 2180 (84%) infants invited with their parents to visit the child health clinics. A questionnaire on soothing techniques was also filled out at home for 1142 (63%) of these infants. RESULTS: Overall prevalences of "crying for three or more hours/24 hour day" "crying a lot", and "difficult to comfort" were 7.6%, 14.0%, and 10.3%, respectively. Problematic infant crying was reported by 20.3% of the mothers. Of these infants, only 14% met all three inclusion criteria. Problematic crying occurred less frequently among girls, second and later born children, Surinamese infants, and breast fed infants. Many mothers used soothing techniques that could affect their infant's health negatively. Shaking, slapping, and putting the baby to sleep in a prone position were more common among non-Dutch (especially Turkish) mothers than among Dutch mothers. Poorly educated mothers slapped their baby more often than highly educated mothers. CONCLUSIONS: Mothers' reports of infant crying and soothing varied sociodemographically. Much harm may be prevented by counselling parents (especially immigrants) on how and how not to respond to infant crying. Health education should start before the child's birth, because certain soothing techniques could be fatal, even when practised for the first time.

Combined amplification and sequencing in a single reaction using two DNA polymerases with differential incorporation rates for dideoxynucleotides.

We describe an approach, which combines the process of DNA amplification and sequence determination by using a pair of primers and two DNA polymerases with different incorporation rates for dideoxynucleotides. The process of target sequence amplification is carried out by the DNA polymerase with a low dideoxynucleotide incorporation rate while its polymerase counterpart with a high incorporation rate generates a sequence ladder. The needs for separate amplification via polymerase chain reaction (PCR) or cloning into plasmids including the respective purification steps therefore can be avoided. In addition, the use of dye terminator chemistry enables the simultaneous generation of forward and reverse sequence ladders, which can be separated based on the streptavidin-biotin system when one amplification primer is biotinylated.

Sensitivity and attachment: next steps for developmentalists.

This commentary focuses on rethinking the definition of sensitivity and addresses the issue of developmental change in sensitivity. Both topics will be discussed with regard to the clinical implications of attachment.

Recovery of nucleic acids from immobilized biotin-streptavidin complexes using ammonium hydroxide and applications in MALDI-TOF mass spectrometry.

The effects of ammonium hydroxide treatment of complexes consisting of biotinylated nucleic acids and immobilized streptavidin were investigated. It was found that incubation of such complexes with ammonium hydroxide at room temperature leads to denaturation of double-stranded DNA molecules, liberating only the complementary nonbiotinylated strand, whereas incubation at elevated temperatures leads to an efficient dissociation of biotin-streptavidin complexes. The introduced procedure is especially suitable as a purification and conditioning format prior to matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometric analysis of DNA from complex enzymatic reactions. This is demonstrated by analysis of polymerase chain reaction (PCR) and sequencing products.

Detection of hepatitis B virus DNA in serum samples via nested PCR and MALDI-TOF mass spectrometry.

In a blind study, nested polymerase chain reaction (PCR) was performed with control DNA and DNA preparations from serum samples of six patients. The detection limit was determined to be 100 molecules of template in 1 ml of serum. Hepatitis B virus (HBV) related products of nested PCR were purified by ultrafiltration and immobilisation on streptavidin coated magnetic beads. The immobilized PCR products were denatured from the beads and analyzed via matrix assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometry. The results of MALDI-TOF MS analysis were in agreement with the results obtained by polyacrylamide gel electrophoresis (PAGE) and with the data obtained by serological analysis. The detection strategy introduced here has a high potential for automation and represents a fast and reliable method of detection for HBV DNA in serum without the need for time consuming gel electrophoresis and labeling or hybridization procedures.

A strategy for rapid and efficient DNA sequencing by mass spectrometry.

Two methods of solid-phase Sanger DNA sequencing followed by detection with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry are demonstrated. In one method, sequencing ladders generated on an immobilized synthetic template were resolved up to the 63-mer including the primer. Detection sensitivity and resolution were sufficient for sequence analysis in the given range. This approach is particularly suitable for comparative (diagnostic) DNA sequencing. A second method that has the potential for high throughput de novo DNA sequencing is also presented; it uses immobilized duplex probes with five-base single-stranded overhangs to capture an unknown DNA template serving as primers for Sanger DNA sequencing. The power of mass spectrometry is demonstrated not only by its very high speed, but also by its ability to identify sequences that are not readable using gel electrophoresis.

Analysis of ligase chain reaction products via matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry.

A rapid and accurate detection of ligation products generated in ligase chain reactions (LCR) by using matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry (MALDI-TOF-MS) is reported. LCR with Pfu DNA ligase was performed with a wild-type template and a template carrying a single point mutation within the Escherichia coli lacI gene as a model system. Starting from about 1 fmol of template DNA the ligation product generated in the positive reactions was analyzed with HPLC and MALDI-TOF-MS, whereby the need of proper sample purification prior to mass spectrometric analysis was demonstrated. A purification procedure with a high potential for automation using streptavidin-coated magnetic particles and ultrafiltration was introduced. Plasmid DNA and short single-stranded oligonucleotides have been used as template. A point mutation could be discriminated from the wild-type template due to the absence or presence of ligation product. This approach allows the rapid-specific detection of template DNA in femtomole amounts and moreover can distinguish between sequence variations in DNA molecules down to point mutations without the need for labeling, gel electrophoresis, membrane transfer, or hybridization procedures.

Do first-year intervention effects endure? Follow-up during toddlerhood of a sample of Dutch irritable infants.

This study evaluated the enduring effectiveness of a skill-based training program to enhance maternal sensitivity between 6 and 9 months of age. 82 mothers and their toddlers were evaluated at 18 and 24 months, and 79 at 31/2 years on the bases of observations of free play, everyday interaction, problem solving, and peer interaction. Most of the significant behavioral changes noted in the second year pertain to attachment security, indices of maternal sensitivity across situations, and child cooperation. Some enduring effects on indices of sensitivity appear to be attachment-mediated. In the third year, results revealed direct enduring intervention effects on parental responsiveness and child cooperation. Attachment-mediated effects were evident for maternal assistance, child security, and positive peer contact. Attachment pattern also predicted differences in attractiveness of the focal child as an interactive partner.

A filtration method for plasmid isolation using microtiter filter plates.

A method for the simultaneous isolation of plasmid DNA from as many as 96 Escherichia coli clones in less than 2 h is described. It is based on a modified version of the alkaline lysis procedure originally described by Birnboim and Doly (Nucleic Acids Res. 7, 1513-1523, 1979). The handling of DNA samples is facilitated by the use of microtiter plates with membrane filter bottoms. All centrifugation steps are replaced by filtrations ("the filtration method"). The yield of plasmid DNA from 0.35 ml of an overnight culture is sufficient for restriction analysis of the plasmid clones. Up to 400 nucleotides' readable sequences could be obtained in cycle sequencing reactions with an unmodified sequencing protocol on an automated ABI sequencer.

The influence of temperament and mothering on attachment and exploration: an experimental manipulation of sensitive responsiveness among lower-class mothers with irritable infants.

6-month-old infants selected on irritability shortly after birth and their mothers were randomly assigned to 2 intervention and 2 control groups to test the hypothesis that enhancing maternal sensitive responsiveness will improve quality of mother-infant interaction, infant exploration, and attachment. The intervention lasted 3 months and ended when the child was 9 months of age. When infants were 9 months of age, intervention group mothers were significantly more responsive, stimulating, visually attentive, and controlling of their infant's behavior than control group mothers. Intervention infants had higher scores than control infants on sociability, self-soothing, and exploration, and they cried less. Quality of exploration also improved, with intervention infants engaged in cognitively sophisticated kinds of exploration more than control infants. At 12 months of age, significantly more intervention group dyads were securely attached than control group dyads.