Numbers of prenatal cell-free DNA screens performed: Results of a 2022 CAP exercise.

OBJECTIVE: Determine current analytical methods and number of cell-free (cf) DNA prenatal screening tests performed for common trisomies. METHODS: The College of American Pathologists 2022-B Noninvasive Prenatal Testing exercise was distributed in December 2022 to 93 participants in 22 countries. Supplemental questions included the number of tests performed in a recent month and the proportion of samples originating outside the United States (US). RESULTS: Eighty-three participants from three continents returned results; 74 (89%) were suitable for the analyses. Nine manufacturer/platform combinations were identified, most commonly Illumina/Nextseq (55%). The most common methodology was whole genome sequencing (76%). Annualized cfDNA tests were 2.80 million, with Asian, European and North American participants representing 10.6%, 6.5% and 82.9% of tests, respectively. When restricted to US in-country tests, the annualized rate was 2.18 million, with four of 20 participants testing 79.2%. Among 73 respondents, 63 (86%) were for-profit, eight (11%) were non-profit academic or government supported and the remaining two included hospital-based and private non-profit. Eighteen (25%) supported relevant academic training. CONCLUSION: In 2011, screening for common trisomies was based on serum/ultrasound markers with an estimated 2.96 million US pregnancies screened in 131 laboratories. In 2022, cfDNA-based screening was offered by 20 laboratories testing 2.18 million US pregnancies.

Prenatal serum screening for Down syndrome and neural tube defects in the United States: Changes in utilization patterns from 2012 to 2020.

OBJECTIVE: To compile current usage of serum-based prenatal screening for Down syndrome in the United States and compare it with results from a similar 2011/2012 survey. SETTING: The College of American Pathologists maternal screening proficiency testing survey includes a supplemental question on the first of three yearly distributions. METHODS: Information regarding tests offered and the monthly number of pregnancies tested for US-based laboratories were reviewed. Results were stratified by size of laboratory, tests offered, and pregnancies tested. Findings were compared to an earlier survey. RESULTS: Fifty-six laboratories reported they will have screened 1,131,336 pregnancies in 2020. Of these, 36% are screened by stand-alone first trimester testing, 48% by stand-alone second trimester testing, and 16% using tests that integrate results from both trimesters. Eighty percent of all serum screens were provided by the five laboratories that performed the most screens (at least 50,000). These five performed similar proportions of first or second trimester screens (42.2% and 41.8%, respectively). Compared to eight years earlier, there are now 54% fewer laboratories. Pregnancies screened using the first trimester, second trimester, and integrated protocols were lower by 27%, 69%, and 72%, respectively. The serum screening activity in the US showed a 62% decrease from 2012 levels. During 2012-2020, the number of cell-free DNA tests increased from negligible to 1,492,332. CONCLUSIONS: Maternal serum screening for common aneuploidies has changed significantly in eight years with fewer laboratories, a shift toward larger laboratories and a 2.5-fold reduction in pregnancies tested, likely due to the introduction of cell-free DNA screening.

Assessment of laboratories offering cell-free (cf) DNA screening for Down syndrome: results of the 2018 College of American Pathology External Educational Exercises.

PURPOSE: Summarize and interpret results from exercises distributed to laboratories offering cell-free (cf) DNA screening for Down syndrome. METHODS: The College of American Pathologists distributed three patient-derived plasma specimens twice in 2018. Sequencing platforms, test methods, results, and responses to supplemental questions were collected. Results were not graded but discrepancies were identified. RESULTS: Sixty-five laboratories from six continents enrolled; six provided no results. The most common methodology was shotgun/genome sequencing (39/56, 70%). Overall, 40% of the gestational or maternal age responses were incorrect but 45% of the errors were corrected by the next distribution. Fetal fractions from 54 responding laboratories generally agreed with the intended response. No genotyping errors occurred (40/40 for trisomy 21 and 226/226 for euploid challenges) but 10 additional tests failed (3.6%). All 213 fetal sex calls were correct. Participants reported their clinical text for a Down syndrome screen positive test; 39% were classified as inadequate or misleading. CONCLUSION: Patient-derived materials are suitable for all enrolled technologies/methodologies, but collecting material is challenging. Suggested clinical text includes the terms "screen positive" and "screen negative." Overall, laboratories performed well. Future efforts will focus on potential manufactured samples, clarifying results reporting and including additional chromosome abnormalities.

PLPHP deficiency: clinical, genetic, biochemical, and mechanistic insights.

Biallelic pathogenic variants in PLPBP (formerly called PROSC) have recently been shown to cause a novel form of vitamin B6-dependent epilepsy, the pathophysiological basis of which is poorly understood. When left untreated, the disease can progress to status epilepticus and death in infancy. Here we present 12 previously undescribed patients and six novel pathogenic variants in PLPBP. Suspected clinical diagnoses prior to identification of PLPBP variants included mitochondrial encephalopathy (two patients), folinic acid-responsive epilepsy (one patient) and a movement disorder compatible with AADC deficiency (one patient). The encoded protein, PLPHP is believed to be crucial for B6 homeostasis. We modelled the pathogenicity of the variants and developed a clinical severity scoring system. The most severe phenotypes were associated with variants leading to loss of function of PLPBP or significantly affecting protein stability/PLP-binding. To explore the pathophysiology of this disease further, we developed the first zebrafish model of PLPHP deficiency using CRISPR/Cas9. Our model recapitulates the disease, with plpbp-/- larvae showing behavioural, biochemical, and electrophysiological signs of seizure activity by 10 days post-fertilization and early death by 16 days post-fertilization. Treatment with pyridoxine significantly improved the epileptic phenotype and extended lifespan in plpbp-/- animals. Larvae had disruptions in amino acid metabolism as well as GABA and catecholamine biosynthesis, indicating impairment of PLP-dependent enzymatic activities. Using mass spectrometry, we observed significant B6 vitamer level changes in plpbp-/- zebrafish, patient fibroblasts and PLPHP-deficient HEK293 cells. Additional studies in human cells and yeast provide the first empirical evidence that PLPHP is localized in mitochondria and may play a role in mitochondrial metabolism. These models provide new insights into disease mechanisms and can serve as a platform for drug discovery.

Glycine decarboxylase deficiency-induced motor dysfunction in zebrafish is rescued by counterbalancing glycine synaptic level.

Glycine encephalopathy (GE), or nonketotic hyperglycinemia (NKH), is a rare recessive genetic disease caused by defective glycine cleavage and characterized by increased accumulation of glycine in all tissues. Here, based on new case reports of GLDC loss-of-function mutations in GE patients, we aimed to generate a zebrafish model of severe GE in order to unravel the molecular mechanism of the disease. Using CRISPR/Cas9, we knocked out the gldc gene and showed that gldc-/- fish recapitulate GE on a molecular level and present a motor phenotype reminiscent of severe GE symptoms. The molecular characterization of gldc-/- mutants showed a broad metabolic disturbance affecting amino acids and neurotransmitters other than glycine, with lactic acidosis at stages preceding death. Although a transient imbalance was found in cell proliferation in the brain of gldc-/- zebrafish, the main brain networks were not affected, thus suggesting that GE pathogenicity is mainly due to metabolic defects. We confirmed that the gldc-/- hypotonic phenotype is due to NMDA and glycine receptor overactivation, and demonstrated that gldc-/- larvae depict exacerbated hyperglycinemia at these synapses. Remarkably, we were able to rescue the motor dysfunction of gldc-/- larvae by counterbalancing pharmacologically or genetically the level of glycine at the synapse.

A novel method for quantitation of acylglycines in human dried blood spots by UPLC-tandem mass spectrometry.

BACKGROUND: Several acylcarnitines used as primary markers on dried blood filter papers (DBS) for newborn screening lack specificity and contribute to a higher false positive rate. The analysis of urine acylglycines is useful in the diagnosis of inborn errors of metabolism (IEM) including medium chain acyl-CoA dehydrogenase deficiency (MCADD), isovaleric acidemia, and beta-ketothiolase deficiency (BKTD). Currently, no method for analyzing acylglycines from DBS has been published. METHODS: Acylglycines were extracted from two 3.2 mm DBS punches and butylated using Butanol-HCl. Ultra Performance Liquid Chromatography (UPLC-MS/MS) with run time of 10 min permits resolution and quantitation of 15 acylglycines; including several isobaric. Method development was completed. Reference intervals (n = 573) were established for four birth weight groups. Furthermore, samples from patients with a confirmed IEM (n = 11), and false positive screens (n = 78) were analyzed to validate the interpretation obtained from the newly established reference intervals. RESULTS: Calibration curves were linear from 0.005 to 25.0 µM. Ion suppression was evaluated as minimal (2 to 10%). Samples from known patients were used to validate the reference intervals. For C5OH-related disorders, tiglylglycine (TG), TG/acetylglycine (AG) ratio, 3methylcrotonylglycine (3MCG) and 3MCG/AG ratio increased specificity. Propionylglycine (PG) and PG/acetylglycine ratio were two discriminatory markers in the investigation of C3-related disorders. Hexanoylglycine (HG), octanoylglycine (OG), suberylglycine (SG), and the ratios HG/AG, OC/AG and SG/AG were excellent markers of MCADD deficiency. CONCLUSION: This method shows potential application as a second tier screen in order to reduce the false positive rate for a number of IEM targeted by newborn screening.

Pyridoxine-Dependent Epilepsy in Zebrafish Caused by Aldh7a1 Deficiency.

Pyridoxine-dependent epilepsy (PDE) is a rare disease characterized by mutations in the lysine degradation gene ALDH7A1 leading to recurrent neonatal seizures, which are uniquely alleviated by high doses of pyridoxine or pyridoxal 5'-phosphate (vitamin B6 vitamers). Despite treatment, neurodevelopmental disabilities are still observed in most PDE patients underlining the need for adjunct therapies. Over 60 years after the initial description of PDE, we report the first animal model for this disease: an aldh7a1-null zebrafish (Danio rerio) displaying deficient lysine metabolism and spontaneous and recurrent seizures in the larval stage (10 days postfertilization). Epileptiform electrographic activity was observed uniquely in mutants as a series of population bursts in tectal recordings. Remarkably, as is the case in human PDE, the seizures show an almost immediate sensitivity to pyridoxine and pyridoxal 5'-phosphate, with a resulting extension of the life span. Lysine supplementation aggravates the phenotype, inducing earlier seizure onset and death. By using mass spectrometry techniques, we further explored the metabolic effect of aldh7a1 knockout. Impaired lysine degradation with accumulation of PDE biomarkers, B6 deficiency, and low γ-aminobutyric acid levels were observed in the aldh7a1-/- larvae, which may play a significant role in the seizure phenotype and PDE pathogenesis. This novel model provides valuable insights into PDE pathophysiology; further research may offer new opportunities for drug discovery to control seizure activity and improve neurodevelopmental outcomes for PDE.

Comparison of clinical and biochemical markers of dehydration with the clinical dehydration scale in children: a case comparison trial.

BACKGROUND: The clinical dehydration scale (CDS) is a quick, easy-to-use tool with 4 clinical items and a score of 1-8 that serves to classify dehydration in children with gastroenteritis as no, some or moderate/severe dehydration. Studies validating the CDS (Friedman JN) with a comparison group remain elusive. We hypothesized that the CDS correlates with a wide spectrum of established markers of dehydration, making it an appropriate and easy-to-use clinical tool. METHODS: This study was designed as a prospective double-cohort trial in a single tertiary care center. Children with diarrhea and vomiting, who clinically required intravenous fluids for rehydration, were compared with minor trauma patients who required intravenous needling for conscious sedation. We compared the CDS with clinical and urinary markers (urinary electrolytes, proteins, ratios and fractional excretions) for dehydration in both groups using receiver operating characteristic (ROC) curves to determine the area under the curve (AUC). RESULTS: We enrolled 73 children (male = 36) in the dehydration group and 143 (male = 105) in the comparison group. Median age was 32 months (range 3-214) in the dehydration and 96 months (range 2.6-214 months, p < 0.0001) in the trauma group. Median CDS was 3 (range 0-8) within the dehydration group and 0 in the comparison group (p < 0.0001). The following parameters were statistically significant (p < 0.05) between the comparison group and the dehydrated group: difference in heart rate, diastolic blood pressure, urine sodium/potassium ratio, urine sodium, fractional sodium excretion, serum bicarbonate, and creatinine measurements. The best markers for dehydration were urine Na and serum bicarbonate (ROC AUC = 0.798 and 0.821, respectively). CDS was most closely correlated with serum bicarbonate (Pearson r = -0.3696, p = 0.002). CONCLUSION: Although serum bicarbonate is not the gold standard for dehydration, this study provides further evidence for the usefulness of the CDS as a dehydration marker in children. TRIAL REGISTRATION: Registered at ClinicalTrials.gov (NCT00462527) on April 18, 2007.

The impact of maternal weight discrepancies on prenatal screening results for Down syndrome.

OBJECTIVE: This study aimed to assess the quantitative impact of maternal weight discrepancy on the screen result for Down syndrome when using Integrated Prenatal Screening and First Trimester Combined Screening. METHODS: The study population consisted of 78,165 women undergoing prenatal screening in Ontario, Canada, and 158 pregnancies affected with Down syndrome at one Ontario center. The study assessed quantitative alterations of the multiple of the median values of first and second-trimester serum markers and the risks of Down syndrome at a set of theoretical weight discrepancies. RESULTS: Weight discrepancies have the greatest impact on screening results when the initial risk is close to the risk cut-off. When the weight discrepancy is 5 lb or greater and the denominator of the initial risk is within 50 of the risk cut-off, the chance that a screen result will change from positive to negative or from negative to positive is 47-55% for women undertaking Integrated Prenatal Screening. This chance is 33-43% for women undertaking First Trimester Combined Screening. CONCLUSION: A weight discrepancy of five or more pounds has a significant impact on the risk of Down syndrome; correction of maternal weight would improve the accuracy of the screening test.

Cystatin C adaptation in the first month of life.

Je-Hyan Lee et al. have published a study on cystatin C concentrations in the first 30 days of life in 127 pre-term and 119 term neonates in this edition of Pediatric Nephrology, thereby closing a knowledge gap of detailed cystatin C concentrations beyond 72 h of life by day of life and by post-conceptional age. While the study objective has merit and a large number of measurements were included, there are some methodological limitations that bring the validity of the data into question as pure reference intervals for children up to 1 month of age, mostly because of the inclusion of patients that potentially could have an impaired glomerular filtration rate (GFR), for instance due to exposure to nephrotoxic drugs. We discuss the strengths and weaknesses of the study and outline an approach to definitely close this knowledge gap. We call for a worldwide collaboration to use Box-Cox transformations similar to the methodology used with growth charts to calculate age-independent z-scores and percentiles of neonatal and infant markers of GFR. This could also lead to better definitions of acute kidney injury in infants if GFR markers cross the percentiles based on post-conceptional or chronological age.

Standardized Procedural Practices of the Ontario Prenatal Screening Program for aneuploidies and open neural tube defects.

BACKGROUND/OBJECTIVES: The Ontario Prenatal Screening Program (OPSP) follows internationally recognized standardized procedures for laboratories and genetics clinics. However, it has been found that some procedures are subject to interpretation, so the current procedures are designed to facilitate a unified approach in the interpretation of literature recommendations. In Ontario, the OPSP offers multiple screening modalities with integrated prenatal screening (including both first and second trimester markers) being the most commonly chosen option. Other screening modalities include first trimester screening, second trimester quad screening, serum integrated screening, and NT-Quad. METHODS: The standardization was based on a literature review and on current practices in Ontario. RESULTS/DISCUSSION: The main finding of the review was a paucity of published data relating to the procedures and the decision-making processes involved in prenatal screening. The purpose of this publication is to provide the most up-to-date and pertinent information for clinical laboratory professionals involved with prenatal screening for Down syndrome, trisomy 18 and open neural tube defects.

Intraindividual variability of the modified Schwartz and novel CKiD GFR equations in pediatric renal transplant patients.

GFR in children can be obtained from a formula using SCr and height or various formulas including serum CysC. Recently, two new GFR formulas have been developed: (i) height and SCr-mSchwartz GFR and (ii) height, SCr, CysC, and serum urea (CKiD GFR). While these formulas proved to be accurate when compared to the gold standard, their use in children post-kidney Tx is yet to be assessed. A total of 1174 blood samples (urea, SCr and CysC) were analyzed from the post-Tx period in 24 Tx children (12 boys, median age = 8.6 yr) currently followed at our institution. CKiD GFR and mSchwartz GFR were compared using Bland-Altman analysis and the CV. The mSchwartz GFR overestimated the CKiD GFR (mean bias = 1.09 ± 0.14; 95% limits of agreements from 0.82 to 1.36). Median CV of CKiD GFR (10.3%) was significantly lower than that of mSchwartz GFR (15.0%), p = 0.04, and negatively correlated with the slope of GFR (r(2) = 0.34, p = 0.0026). In conclusion, CKiD GFR has a significantly lower intraindividual variation than mSchwartz GFR and may be better suited for longitudinal follow-up of patients post-Tx.

The impact of interlaboratory differences in cystatin C assay measurement on glomerular filtration rate estimation.

BACKGROUND AND OBJECTIVES: Cystatin C (CysC) is a promising marker of GFR. Several equations have been derived to estimate GFR from its serum concentration. Heterogeneity in the performance of these equations exists in validation studies even when the same CysC assay from the same manufacturer is utilized. This study was designed to examine the differences in CysC and GFR estimation (eGFR) using Siemens' nephelometric immunoassay and the Mayo Clinic equation. The ability of the eGFRs to predict measured GFR was also examined. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: Ninety-seven split samples were sent to laboratories at Children's Hospital of Eastern Ontario (CHEO) in Ottawa, Canada, and at the Mayo Clinic in Rochester, Minnesota. RESULTS: The mean CHEO CysC was 0.17 mg/L (10%) lower than the mean Mayo Clinic CysC. Using the Mayo Clinic equation, the mean eGFR difference was 7.2 ml/min per 1.73 m(2) (15%). Approximately 36% of the results agreed within 10%, while 13% were discordant by greater than 30%. Larger absolute differences in mean eGFR between the two laboratories were found in the subgroup with CysC less than 1.41 mg/L as compared with the subgroup greater than 1.41 mg/L (9.5 versus 5.0 ml/min per 1.73 m(2)). Correction of CHEO values to the Mayo Clinic did not improve GFR estimation. CONCLUSIONS: Significant differences in CysC measurement exist between laboratories using the same assay by the same manufacturer and these lead to clinically relevant differences in GFR estimation. This interlaboratory variability needs to be recognized when interpreting and comparing CysC and eGFR results.

Preliminary reference intervals for cystatin C and beta-trace protein in preterm and term neonates.

OBJECTIVE: To determine the reference intervals for serum cystatin C (CysC) and beta-trace protein (BTP) as markers of renal function in preterm and term neonates. DESIGN AND METHODS: Blood samples of 128 neonates (34% female) admitted to the NICU were analyzed to determine the levels of serum creatinine (enzymatically), CysC and BTP (nephelometric, Siemens Health Care). RESULTS: The reference intervals, categorized by age, were reported for the 128 neonates. Median (lower/upper limit) BTP were 1.85 (0.57/3.16) and 1.27 (0.51/2.07) mg/L on days 1 and 3. In keeping with maturation of renal function after birth, CysC and BTP fell from days one to day three after birth, whereas creatinine did not. CONCLUSION: Our data provides reference intervals for the levels of creatinine, CysC, and BTP in neonates on days 1 and 3 after birth and demonstrates that CysC and BTP reflect neonatal renal function, whereas creatinine reflects maternal renal function.

Diagnosis of glutaric aciduria type 1 by measuring 3-hydroxyglutaric acid in dried urine spots by liquid chromatography tandem mass spectrometry.

Accumulation of glutaric acid (GA) and 3-hydroxyglutaric acid (3HGA) in body fluids is the biochemical hallmark of type 1 glutaric aciduria (GA1), a disorder characterized by acute striatal degeneration and a subsequent dystonia. To date, methods for quantification of 3HGA are mainly based on stable isotope dilution gas chromatography mass spectrometry (GC-MS) and require extensive sample preparation. Here we describe a simple liquid chromatography tandem MS (LC-MS/MS) method to quantify this important metabolite in dried urine spots (DUS). This method is based on derivatization with 4-[2-(N,N-dimethylamino)ethylaminosulfonyl]-7-(2-aminoethylamino)-2,1,3-benzoxadiazole (DAABD-AE). Derivatization was adopted to improve the chromatographic and mass spectrometric properties of the studied analytes. Derivatization was performed directly on a 3.2-mm disc of DUS as a sample without extraction. Sample mixture was heated at 60°C for 45 min, and 5 µl of the reaction solution was analyzed by LC-MS/MS. Reference ranges obtained were in excellent agreement with the literature. The method was applied retrospectively for the analysis of DUS samples from established low- and high-excreter GA1 patients as well as controls (n = 100). Comparison of results obtained versus those obtained by GC-MS was satisfactory (n = 14). In populations with a high risk of GA1, this approach will be useful as a primary screening method for high- or low-excreter variants. In these populations, however, DUS analysis should not be implemented before completing a parallel comparative study with the standard screening method (i.e., molecular testing). In addition, follow-up DUS GA and 3HGA testing of babies with elevated dried blood spot C5DC acylcarnitines will be useful as a first-tier diagnostic test, thus reducing the number of cases requiring enzymatic and molecular analyses to establish or refute the diagnosis of GA1.

Pediatric reference intervals for immunoglobulin G and its subclasses with Siemens immunonephelometric assays.

OBJECTIVE: To determine the pediatric reference intervals for the Dade Behring IgG subclass reagents. DESIGN AND METHODS: Blood samples of healthy children and adolescents were analyzed to determine the level of immunoglobulin G (IgG) and the IgG subclass using the reagents of Dade Behring Marburg GmbH. RESULTS: The reference intervals categorized by age were reported from a total of 436 samples. There was an excellent correlation between the total IgG and the sum of the IgG subclasses. CONCLUSIONS: Our data provide the missing pediatric reference intervals and enable the use of the Dade Behring nephelometric IgG subclass reagents in children and adolescents.

Measurement of plasma/serum acylcarnitines using tandem mass spectrometry.

Acylcarnitine analysis using tandem mass spectrometry has become a powerful tool in the investigation of pediatric patients presenting with clinical signs and symptoms suggestive of fatty acid oxidation defects. These signs are diverse and include failure to thrive, feeding difficulties, and cardiomyopathy. Because the signs and symptoms are nonspecific, the identification of acylcarnitines characteristic of these inherited diseases is necessary for diagnosis. We describe a method for the analysis of acylcarnitines in plasma or serum samples using electrospray ionization tandem mass spectrometry.

Development of a beta-trace protein based formula for estimation of glomerular filtration rate.

Beta-trace protein (BTP) is a novel marker of glomerular filtration rate (GFR). To date, no pediatric formula for calculating GFR based on BTP has been developed. We measured GFR, serum creatinine and BTP in 387 children who underwent 474 (99m)Tc-diethylene triamine pentaacetic acid renal scans. A BTP-based formula for estimating GFR was derived using stepwise linear regression analysis. A separate control group of 116 measurements in 99 children was used to validate the novel formula. A formula was also developed for each gender. The novel formula is: [formula: see text]. The Spearman rank correlation coefficient between the BTP-derived GFR estimate and the measured GFR was 0.80 [95% confidence interval (CI) 0.76-0.83], which is substantially better than that derived with the Schwartz formula (r = 0.70, 95% CI 0.65-0.74). The Bland-Altman analysis revealed a mean bias of 1.21% [standard deviation (SD) 28%] in the formula development dataset, which was virtually identical to the 1.03% mean bias (29.5% SD) in the validation group and no different from the Schwartz formula bias. The percentage of values within 10% (33.0 vs. 28.3%) and 30% deviation (76.8 vs. 72.6%) were better for BTP-based formula than for the Schwartz formula. Separate formulas according to gender did not perform better than that for the pediatric population. This BTP-based formula was found to estimate GFR with reasonable precision and provided improved accuracy over the Schwartz GFR formula.